-- dump date 20140619_232924 -- class Genbank::misc_feature -- table misc_feature_note -- id note 338963000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 338963000002 DnaA N-terminal domain; Region: DnaA_N; pfam11638 338963000003 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 338963000004 Walker A motif; other site 338963000005 ATP binding site [chemical binding]; other site 338963000006 Walker B motif; other site 338963000007 arginine finger; other site 338963000008 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 338963000009 DnaA box-binding interface [nucleotide binding]; other site 338963000010 DNA polymerase III subunit beta; Validated; Region: PRK05643 338963000011 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 338963000012 putative DNA binding surface [nucleotide binding]; other site 338963000013 dimer interface [polypeptide binding]; other site 338963000014 beta-clamp/clamp loader binding surface; other site 338963000015 beta-clamp/translesion DNA polymerase binding surface; other site 338963000016 recombination protein F; Reviewed; Region: recF; PRK00064 338963000017 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963000018 Walker A/P-loop; other site 338963000019 ATP binding site [chemical binding]; other site 338963000020 Q-loop/lid; other site 338963000021 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963000022 ABC transporter signature motif; other site 338963000023 Walker B; other site 338963000024 D-loop; other site 338963000025 H-loop/switch region; other site 338963000026 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 338963000027 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 338963000028 Mg2+ binding site [ion binding]; other site 338963000029 G-X-G motif; other site 338963000030 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 338963000031 anchoring element; other site 338963000032 dimer interface [polypeptide binding]; other site 338963000033 ATP binding site [chemical binding]; other site 338963000034 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 338963000035 active site 338963000036 putative metal-binding site [ion binding]; other site 338963000037 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 338963000038 DNA gyrase subunit A; Validated; Region: PRK05560 338963000039 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 338963000040 CAP-like domain; other site 338963000041 active site 338963000042 primary dimer interface [polypeptide binding]; other site 338963000043 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 338963000044 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 338963000045 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 338963000046 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 338963000047 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 338963000048 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 338963000049 binding surface 338963000050 TPR motif; other site 338963000051 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 338963000052 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 338963000053 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 338963000054 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 338963000055 putative catalytic site [active] 338963000056 putative metal binding site [ion binding]; other site 338963000057 putative phosphate binding site [ion binding]; other site 338963000058 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 338963000059 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 338963000060 minor groove reading motif; other site 338963000061 helix-hairpin-helix signature motif; other site 338963000062 substrate binding pocket [chemical binding]; other site 338963000063 active site 338963000064 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 338963000065 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 338963000066 Transglycosylase; Region: Transgly; pfam00912 338963000067 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 338963000068 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 338963000069 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 338963000070 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963000071 homodimer interface [polypeptide binding]; other site 338963000072 catalytic residue [active] 338963000073 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 338963000074 Zn2+ binding site [ion binding]; other site 338963000075 Mg2+ binding site [ion binding]; other site 338963000076 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 338963000077 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 338963000078 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 338963000079 ATP synthase subunit C; Region: ATP-synt_C; cl00466 338963000080 Archease protein family (MTH1598/TM1083); Region: Archease; pfam01951 338963000081 Uncharacterized protein family UPF0027; Region: UPF0027; pfam01139 338963000082 hypothetical protein; Reviewed; Region: PRK09588 338963000083 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 338963000084 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 338963000085 putative NAD(P) binding site [chemical binding]; other site 338963000086 active site 338963000087 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 338963000088 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 338963000089 trimerization site [polypeptide binding]; other site 338963000090 active site 338963000091 Predicted membrane protein [Function unknown]; Region: COG2259 338963000092 Mpr1p, Pad1p N-terminal (MPN) domains; Region: MPN; cl13996 338963000093 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 338963000094 DEAD/DEAH box helicase; Region: DEAD; pfam00270 338963000095 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 338963000096 ADP-L-glycero-D-mannoheptose-6-epimerase; Provisional; Region: rfaD; PRK11150 338963000097 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 338963000098 NADP binding site [chemical binding]; other site 338963000099 homopentamer interface [polypeptide binding]; other site 338963000100 substrate binding site [chemical binding]; other site 338963000101 active site 338963000102 tellurite resistance protein TehB; Provisional; Region: PRK11207 338963000103 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 338963000104 S-adenosylmethionine binding site [chemical binding]; other site 338963000105 NRDE protein; Region: NRDE; pfam05742 338963000106 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 338963000107 Found in ATP-dependent protease La (LON); Region: LON; smart00464 338963000108 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 338963000109 Walker A motif; other site 338963000110 ATP binding site [chemical binding]; other site 338963000111 Walker B motif; other site 338963000112 arginine finger; other site 338963000113 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 338963000114 thiamine monophosphate kinase; Provisional; Region: PRK05731 338963000115 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 338963000116 ATP binding site [chemical binding]; other site 338963000117 dimerization interface [polypeptide binding]; other site 338963000118 HAMP domain; Region: HAMP; pfam00672 338963000119 dimerization interface [polypeptide binding]; other site 338963000120 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 338963000121 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 338963000122 dimer interface [polypeptide binding]; other site 338963000123 putative CheW interface [polypeptide binding]; other site 338963000124 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 338963000125 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 338963000126 putative binding surface; other site 338963000127 active site 338963000128 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 338963000129 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 338963000130 ATP binding site [chemical binding]; other site 338963000131 Mg2+ binding site [ion binding]; other site 338963000132 G-X-G motif; other site 338963000133 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 338963000134 Outer membrane lipoprotein-sorting protein [Cell envelope biogenesis, outer membrane]; Region: LolA; COG2834 338963000135 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 338963000136 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 338963000137 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 338963000138 ribosomal protein S12 methylthiotransferase RimO; Region: TIGR01125 338963000139 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 338963000140 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 338963000141 FeS/SAM binding site; other site 338963000142 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 338963000143 ApbE family; Region: ApbE; pfam02424 338963000144 NGN-insert domain found between N-terminal domain (D1) and C-terminal KOW domain (DIII) repeats of some N-Utilization Substance G (NusG) N-terminal (NGN); Region: NGN-insert_like; cd09910 338963000145 Heptaprenyl diphosphate synthase component I; Region: Hpre_diP_synt_I; pfam07456 338963000146 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 338963000147 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 338963000148 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963000149 Walker A/P-loop; other site 338963000150 ATP binding site [chemical binding]; other site 338963000151 Q-loop/lid; other site 338963000152 ABC transporter signature motif; other site 338963000153 Walker B; other site 338963000154 D-loop; other site 338963000155 H-loop/switch region; other site 338963000156 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 338963000157 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 338963000158 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963000159 Walker A/P-loop; other site 338963000160 ATP binding site [chemical binding]; other site 338963000161 Q-loop/lid; other site 338963000162 ABC transporter signature motif; other site 338963000163 Walker B; other site 338963000164 D-loop; other site 338963000165 H-loop/switch region; other site 338963000166 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963000167 Response regulator receiver domain; Region: Response_reg; pfam00072 338963000168 active site 338963000169 phosphorylation site [posttranslational modification] 338963000170 intermolecular recognition site; other site 338963000171 dimerization interface [polypeptide binding]; other site 338963000172 PilZ domain; Region: PilZ; cl01260 338963000173 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 338963000174 Na binding site [ion binding]; other site 338963000175 Prenyltransferase-like; Region: Prenyltrans_1; pfam13243 338963000176 Uncharacterized protein family (UPF0104); Region: UPF0104; pfam03706 338963000177 Uncharacterized protein family (UPF0104); Region: UPF0104; pfam03706 338963000178 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 338963000179 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 338963000180 Ligand binding site; other site 338963000181 Putative Catalytic site; other site 338963000182 DXD motif; other site 338963000183 Peptidase C1A subfamily (MEROPS database nomenclature); composed of cysteine peptidases (CPs) similar to papain, including the mammalian CPs (cathepsins B, C, F, H, L, K, O, S, V, X and W). Papain is an endopeptidase with specific substrate preferences; Region: Peptidase_C1A; cd02248 338963000184 active site 338963000185 S2 subsite; other site 338963000186 Uncharacterized protein with a C-terminal OMP (outer membrane protein) domain [Function unknown]; Region: COG4625 338963000187 Autotransporter beta-domain; Region: Autotransporter; smart00869 338963000188 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 338963000189 dimerization interface [polypeptide binding]; other site 338963000190 putative DNA binding site [nucleotide binding]; other site 338963000191 putative Zn2+ binding site [ion binding]; other site 338963000192 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 338963000193 Cysteine-rich domain; Region: CCG; pfam02754 338963000194 Cysteine-rich domain; Region: CCG; pfam02754 338963000195 Predicted permeases [General function prediction only]; Region: COG0701 338963000196 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 338963000197 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 338963000198 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 338963000199 catalytic residue [active] 338963000200 Fe-S cluster assembly protein NifU; Region: NifU_proper; TIGR02000 338963000201 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 338963000202 trimerization site [polypeptide binding]; other site 338963000203 active site 338963000204 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 338963000205 NifU-like domain; Region: NifU; cl00484 338963000206 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 338963000207 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 338963000208 dimer interface [polypeptide binding]; other site 338963000209 putative CheW interface [polypeptide binding]; other site 338963000210 Cache domain; Region: Cache_1; pfam02743 338963000211 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 338963000212 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 338963000213 putative active site [active] 338963000214 heme pocket [chemical binding]; other site 338963000215 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 338963000216 dimer interface [polypeptide binding]; other site 338963000217 phosphorylation site [posttranslational modification] 338963000218 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 338963000219 ATP binding site [chemical binding]; other site 338963000220 Mg2+ binding site [ion binding]; other site 338963000221 G-X-G motif; other site 338963000222 trehalose-6-phosphate phosphatase; Provisional; Region: PRK10187; cl17105 338963000223 Trehalose-phosphatase; Region: Trehalose_PPase; pfam02358 338963000224 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 338963000225 PAS domain; Region: PAS_9; pfam13426 338963000226 putative active site [active] 338963000227 heme pocket [chemical binding]; other site 338963000228 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 338963000229 LytTr DNA-binding domain; Region: LytTR; smart00850 338963000230 carbon-monoxide dehydrogenase, catalytic subunit; Region: CO_DH_cata; TIGR01702 338963000231 Carbon monoxide dehydrogenase (CODH) is found in acetogenic and methanogenic organisms and is responsible for the synthesis and breakdown of acetyl-CoA, respectively. CODH has two types of metal clusters, a cubane [Fe4-S4] center (B-cluster) similar to...; Region: CODH; cd01915 338963000232 ACS interaction site; other site 338963000233 CODH interaction site; other site 338963000234 cubane metal cluster (B-cluster) [ion binding]; other site 338963000235 Ni-Fe-S cluster (C-cluster) [ion binding]; other site 338963000236 CO dehydrogenase maturation factor [Cell division and chromosome partitioning]; Region: CooC; COG3640 338963000237 The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH). CODH from Rhodospirillum rubrum catalyzes the reversible...; Region: CooC; cd02034 338963000238 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 338963000239 4Fe-4S binding domain; Region: Fer4; cl02805 338963000240 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 338963000241 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 338963000242 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 338963000243 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 338963000244 cobalt transport protein CbiM; Validated; Region: PRK06265 338963000245 PDGLE domain; Region: PDGLE; pfam13190 338963000246 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 338963000247 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 338963000248 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 338963000249 TrkA-N domain; Region: TrkA_N; pfam02254 338963000250 TrkA-C domain; Region: TrkA_C; pfam02080 338963000251 TrkA-C domain; Region: TrkA_C; pfam02080 338963000252 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 338963000253 octanucleotide repeats; Pcar_R8001 338963000254 octanucleotide repeats; Pcar_R8002 338963000255 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 338963000256 Peptidase family U32; Region: Peptidase_U32; pfam01136 338963000257 Collagenase; Region: DUF3656; pfam12392 338963000258 Peptidase family U32; Region: Peptidase_U32; cl03113 338963000259 hypothetical protein; Reviewed; Region: PRK00024 338963000260 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 338963000261 MPN+ (JAMM) motif; other site 338963000262 Zinc-binding site [ion binding]; other site 338963000263 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 338963000264 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 338963000265 nucleophile elbow; other site 338963000266 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_9; cd04622 338963000267 Protein of unknown function (DUF3793); Region: DUF3793; pfam12672 338963000268 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 338963000269 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN_family; cd02803 338963000270 active site 338963000271 FMN binding site [chemical binding]; other site 338963000272 substrate binding site [chemical binding]; other site 338963000273 putative catalytic residue [active] 338963000274 Transcriptional regulator [Transcription]; Region: LysR; COG0583 338963000275 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 338963000276 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 338963000277 dimerization interface [polypeptide binding]; other site 338963000278 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 338963000279 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 338963000280 active site 338963000281 The THUMP domain is named after after thiouridine synthases, methylases and PSUSs; Region: THUMP; smart00981 338963000282 Transposase; Region: DEDD_Tnp_IS110; pfam01548 338963000283 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 338963000284 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 338963000285 Protein of unknown function (DUF1018); Region: DUF1018; pfam06252 338963000286 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 338963000287 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 338963000288 active site 1 [active] 338963000289 dimer interface [polypeptide binding]; other site 338963000290 hexamer interface [polypeptide binding]; other site 338963000291 active site 2 [active] 338963000292 Methyltransferase domain; Region: Methyltransf_23; pfam13489 338963000293 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 338963000294 S-adenosylmethionine binding site [chemical binding]; other site 338963000295 Methyltransferase domain; Region: Methyltransf_31; pfam13847 338963000296 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 338963000297 S-adenosylmethionine binding site [chemical binding]; other site 338963000298 DNA polymerase II large subunit; Provisional; Region: PRK14714 338963000299 DNA polymerase II large subunit; Provisional; Region: PRK14714 338963000300 Rubrerythrin [Energy production and conversion]; Region: COG1592 338963000301 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 338963000302 binuclear metal center [ion binding]; other site 338963000303 Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either...; Region: rubredoxin_like; cl00202 338963000304 iron binding site [ion binding]; other site 338963000305 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 338963000306 TrkA-N domain; Region: TrkA_N; pfam02254 338963000307 TrkA-C domain; Region: TrkA_C; pfam02080 338963000308 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 338963000309 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 338963000310 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 338963000311 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 338963000312 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 338963000313 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 338963000314 heptanucleotide repeats; Pcar_R7001 338963000315 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 338963000316 4-hydroxythreonine-4-phosphate dehydrogenase; Region: pdxA; TIGR00557 338963000317 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 338963000318 SurA N-terminal domain; Region: SurA_N; pfam09312 338963000319 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 338963000320 SurA N-terminal domain; Region: SurA_N_3; cl07813 338963000321 nitrogen fixation protein NifM; Region: nifM_nitrog; TIGR02933 338963000322 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 338963000323 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 338963000324 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; pfam02559 338963000325 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 338963000326 ATP binding site [chemical binding]; other site 338963000327 putative Mg++ binding site [ion binding]; other site 338963000328 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 338963000329 nucleotide binding region [chemical binding]; other site 338963000330 ATP-binding site [chemical binding]; other site 338963000331 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 338963000332 Quinolinate synthetase A protein; Region: NadA; pfam02445 338963000333 Sec-independent protein secretion pathway components [Intracellular trafficking and secretion]; Region: TatA; COG1826 338963000334 twin arginine translocase protein A; Provisional; Region: tatA; PRK00191 338963000335 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 338963000336 This domain is found in the extracellular portion of receptor-like proteins - such as serine/threonine kinases and adenylyl cyclases; Region: CHASE; smart01079 338963000337 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963000338 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963000339 metal binding site [ion binding]; metal-binding site 338963000340 active site 338963000341 I-site; other site 338963000342 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 338963000343 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963000344 Walker A/P-loop; other site 338963000345 ATP binding site [chemical binding]; other site 338963000346 Q-loop/lid; other site 338963000347 ABC transporter signature motif; other site 338963000348 Walker B; other site 338963000349 D-loop; other site 338963000350 H-loop/switch region; other site 338963000351 ABC-2 type transporter; Region: ABC2_membrane; cl17235 338963000352 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 338963000353 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 338963000354 active site 338963000355 excinuclease ABC subunit B; Provisional; Region: PRK05298 338963000356 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 338963000357 ATP binding site [chemical binding]; other site 338963000358 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 338963000359 nucleotide binding region [chemical binding]; other site 338963000360 ATP-binding site [chemical binding]; other site 338963000361 Ultra-violet resistance protein B; Region: UvrB; pfam12344 338963000362 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 338963000363 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 338963000364 active site 338963000365 HIGH motif; other site 338963000366 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 338963000367 KMSKS motif; other site 338963000368 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 338963000369 tRNA binding surface [nucleotide binding]; other site 338963000370 anticodon binding site; other site 338963000371 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 338963000372 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 338963000373 active site 338963000374 HIGH motif; other site 338963000375 nucleotide binding site [chemical binding]; other site 338963000376 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 338963000377 KMSKS motif; other site 338963000378 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 338963000379 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 338963000380 homotrimer interaction site [polypeptide binding]; other site 338963000381 zinc binding site [ion binding]; other site 338963000382 CDP-binding sites; other site 338963000383 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 338963000384 substrate binding site; other site 338963000385 dimer interface; other site 338963000386 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 338963000387 Tetratricopeptide repeat; Region: TPR_16; pfam13432 338963000388 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 338963000389 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 338963000390 putative ligand binding site [chemical binding]; other site 338963000391 chaperone protein DnaJ; Provisional; Region: PRK10767 338963000392 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 338963000393 HSP70 interaction site [polypeptide binding]; other site 338963000394 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 338963000395 substrate binding site [polypeptide binding]; other site 338963000396 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 338963000397 Zn binding sites [ion binding]; other site 338963000398 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 338963000399 dimer interface [polypeptide binding]; other site 338963000400 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 338963000401 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 338963000402 nucleotide binding site [chemical binding]; other site 338963000403 NEF interaction site [polypeptide binding]; other site 338963000404 SBD interface [polypeptide binding]; other site 338963000405 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 338963000406 GrpE; Region: GrpE; pfam01025 338963000407 dimer interface [polypeptide binding]; other site 338963000408 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 338963000409 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 338963000410 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 338963000411 Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]; Region: HemN; COG0635 338963000412 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 338963000413 FeS/SAM binding site; other site 338963000414 HemN C-terminal domain; Region: HemN_C; pfam06969 338963000415 Permease P (pink-eyed dilution). Mutations in the human melanosomal P gene were responsible for classic phenotype of oculocutaneous albinism type 2 (OCA2). Although the precise function of the P protein is unknown, it was predicted to regulate the...; Region: P_permease; cd01116 338963000416 Citrate transporter; Region: CitMHS; pfam03600 338963000417 transmembrane helices; other site 338963000418 Predicted amidohydrolase [General function prediction only]; Region: COG0388 338963000419 Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases); Region: nitrilase_5; cd07583 338963000420 putative active site [active] 338963000421 catalytic triad [active] 338963000422 putative dimer interface [polypeptide binding]; other site 338963000423 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 338963000424 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 338963000425 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 338963000426 Protein of unknown function (DUF3606); Region: DUF3606; pfam12244 338963000427 Bacterial SH3 domain; Region: SH3_3; pfam08239 338963000428 Mycoplasma pulmonis MnuA nuclease-like; Region: MnuA_DNase1-like; cd10283 338963000429 putative active site [active] 338963000430 putative catalytic site [active] 338963000431 putative Mg binding site IVb [ion binding]; other site 338963000432 putative phosphate binding site [ion binding]; other site 338963000433 putative DNA binding site [nucleotide binding]; other site 338963000434 putative Mg binding site IVa [ion binding]; other site 338963000435 Competence protein CoiA-like family; Region: CoiA; cl11541 338963000436 Homeodomain-like domain; Region: HTH_23; pfam13384 338963000437 Winged helix-turn helix; Region: HTH_29; pfam13551 338963000438 Integrase core domain; Region: rve; pfam00665 338963000439 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 338963000440 Integrase core domain; Region: rve_3; pfam13683 338963000441 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 338963000442 WYL domain; Region: WYL; pfam13280 338963000443 TniQ; Region: TniQ; pfam06527 338963000444 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 338963000445 AAA domain; Region: AAA_22; pfam13401 338963000446 Walker A motif; other site 338963000447 ATP binding site [chemical binding]; other site 338963000448 Walker B motif; other site 338963000449 arginine finger; other site 338963000450 Winged helix-turn helix; Region: HTH_29; pfam13551 338963000451 Integrase core domain; Region: rve; pfam00665 338963000452 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 338963000453 TnsA endonuclease N terminal; Region: Tn7_Tnp_TnsA_N; pfam08722 338963000454 TnsA endonuclease C terminal; Region: Tn7_Tnp_TnsA_C; pfam08721 338963000455 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 338963000456 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 338963000457 RHS protein; Region: RHS; pfam03527 338963000458 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 338963000459 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 338963000460 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 338963000461 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 338963000462 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 338963000463 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 338963000464 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 338963000465 Walker A motif; other site 338963000466 ATP binding site [chemical binding]; other site 338963000467 Walker B motif; other site 338963000468 Competence protein A; Region: Competence_A; pfam11104 338963000469 TPR repeat; Region: TPR_11; pfam13414 338963000470 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 338963000471 TPR motif; other site 338963000472 binding surface 338963000473 Tetratricopeptide repeat; Region: TPR_16; pfam13432 338963000474 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 338963000475 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 338963000476 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 338963000477 Type II cohesin domain, interaction partner of dockerin; Region: Type_II_cohesin; cd08547 338963000478 dockerin binding interface; other site 338963000479 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 338963000480 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 338963000481 ATP-dependent transcriptional regulator [Transcription]; Region: MalT; COG2909 338963000482 AAA ATPase domain; Region: AAA_16; pfam13191 338963000483 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 338963000484 trimer interface [polypeptide binding]; other site 338963000485 Haemagglutinin; Region: HIM; pfam05662 338963000486 YadA-like C-terminal region; Region: YadA; pfam03895 338963000487 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2268 338963000488 Band_7_flotillin: a subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. These two proteins are lipid raft-associated. Individual proteins of...; Region: Band_7_flotillin; cd03399 338963000489 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 338963000490 Phosphate transporter family; Region: PHO4; pfam01384 338963000491 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; COG1914 338963000492 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 338963000493 FOG: CBS domain [General function prediction only]; Region: COG0517 338963000494 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC; Region: CBS_pair_SpoIVFB_EriC_assoc2; cd04613 338963000495 conserved nucleotide sequence Moco-II; Pcar_R0090 338963000496 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 338963000497 Periplasmic binding protein TroA_e. 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_e; cd01142 338963000498 putative ligand binding residues [chemical binding]; other site 338963000499 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 338963000500 non-specific DNA binding site [nucleotide binding]; other site 338963000501 salt bridge; other site 338963000502 sequence-specific DNA binding site [nucleotide binding]; other site 338963000503 PBP superfamily domain; Region: PBP_like; pfam12727 338963000504 conserved nucleotide sequence Moco-II; Pcar_R0091 338963000505 Methyltransferase domain; Region: Methyltransf_31; pfam13847 338963000506 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 338963000507 S-adenosylmethionine binding site [chemical binding]; other site 338963000508 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 338963000509 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 338963000510 N-terminal plug; other site 338963000511 ligand-binding site [chemical binding]; other site 338963000512 FmdE, Molybdenum formylmethanofuran dehydrogenase operon; Region: FmdE; pfam02663 338963000513 Periplasmic binding protein TroA_e. 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_e; cd01142 338963000514 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 338963000515 putative ligand binding residues [chemical binding]; other site 338963000516 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 338963000517 ABC-ATPase subunit interface; other site 338963000518 dimer interface [polypeptide binding]; other site 338963000519 putative PBP binding regions; other site 338963000520 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 338963000521 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 338963000522 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 338963000523 Walker A/P-loop; other site 338963000524 ATP binding site [chemical binding]; other site 338963000525 Q-loop/lid; other site 338963000526 ABC transporter signature motif; other site 338963000527 Walker B; other site 338963000528 D-loop; other site 338963000529 H-loop/switch region; other site 338963000530 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]; Region: COG2191 338963000531 FmdE, Molybdenum formylmethanofuran dehydrogenase operon; Region: FmdE; pfam02663 338963000532 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 338963000533 S-adenosylmethionine binding site [chemical binding]; other site 338963000534 Radical SAM superfamily; Region: Radical_SAM; pfam04055 338963000535 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 338963000536 FeS/SAM binding site; other site 338963000537 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 338963000538 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 338963000539 NTPase; Region: NTPase_1; cl17478 338963000540 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 338963000541 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 338963000542 MarC family integral membrane protein; Region: MarC; pfam01914 338963000543 conserved nucleotide sequence; Pcar_R5011 338963000544 conserved nucleotide sequence fragment; Pcar_R5001 338963000545 conserved nucleotide sequence; Pcar_R5015 338963000546 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 338963000547 conserved nucleotide sequence; Pcar_R5006 338963000548 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 338963000549 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 338963000550 4Fe-4S binding domain; Region: Fer4_6; pfam12837 338963000551 Predicted flavin-nucleotide-binding protein [General function prediction only]; Region: COG3467 338963000552 ISPca4 3' sequence fragment; Pcar_R5089 338963000553 nicotinate phosphoribosyltransferase; Provisional; Region: PRK05321 338963000554 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 338963000555 active site 338963000556 Domain of unknown function (DUF1413); Region: DUF1413; pfam07205 338963000557 Probable metal-binding protein (DUF2387); Region: DUF2387; cl01410 338963000558 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 338963000559 Putative redox-active protein (C_GCAxxG_C_C); Region: C_GCAxxG_C_C; cl09920 338963000560 The Class III extradiol dioxygenase, 4,5-DOPA Dioxygenase, catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine; Region: 45_DOPA_Dioxygenase; cd07363 338963000561 putative active site [active] 338963000562 metal binding site [ion binding]; metal-binding site 338963000563 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 338963000564 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 338963000565 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 338963000566 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 338963000567 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 338963000568 protein binding site [polypeptide binding]; other site 338963000569 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 338963000570 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 338963000571 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 338963000572 GAF domain; Region: GAF; pfam01590 338963000573 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 338963000574 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 338963000575 Walker A motif; other site 338963000576 ATP binding site [chemical binding]; other site 338963000577 Walker B motif; other site 338963000578 arginine finger; other site 338963000579 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 338963000580 TrkA-N domain; Region: TrkA_N; pfam02254 338963000581 TrkA-C domain; Region: TrkA_C; pfam02080 338963000582 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 338963000583 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 338963000584 Putative exonuclease, RdgC; Region: RdgC; cl01122 338963000585 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 338963000586 putative active site pocket [active] 338963000587 dimerization interface [polypeptide binding]; other site 338963000588 putative catalytic residue [active] 338963000589 PAS domain; Region: PAS_9; pfam13426 338963000590 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 338963000591 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 338963000592 putative active site [active] 338963000593 heme pocket [chemical binding]; other site 338963000594 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 338963000595 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 338963000596 putative active site [active] 338963000597 heme pocket [chemical binding]; other site 338963000598 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 338963000599 dimer interface [polypeptide binding]; other site 338963000600 phosphorylation site [posttranslational modification] 338963000601 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 338963000602 ATP binding site [chemical binding]; other site 338963000603 Mg2+ binding site [ion binding]; other site 338963000604 G-X-G motif; other site 338963000605 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 338963000606 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963000607 active site 338963000608 phosphorylation site [posttranslational modification] 338963000609 intermolecular recognition site; other site 338963000610 dimerization interface [polypeptide binding]; other site 338963000611 Uncharacterized BCR, COG1636; Region: DUF208; pfam02677 338963000612 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 338963000613 dimerization interface [polypeptide binding]; other site 338963000614 putative DNA binding site [nucleotide binding]; other site 338963000615 putative Zn2+ binding site [ion binding]; other site 338963000616 Predicted permease; Region: DUF318; cl17795 338963000617 Predicted permease; Region: DUF318; cl17795 338963000618 Thioredoxin domain; Region: Thioredoxin_3; pfam13192 338963000619 S-adenosylmethionine synthetase; Provisional; Region: PRK04439 338963000620 Domain of unknown function (DUF1834); Region: DUF1834; cl02087 338963000621 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 338963000622 Family of unknown function (DUF490); Region: DUF490; pfam04357 338963000623 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 338963000624 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 338963000625 Surface antigen; Region: Bac_surface_Ag; pfam01103 338963000626 Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase] [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvB; COG0028 338963000627 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 338963000628 PYR/PP interface [polypeptide binding]; other site 338963000629 dimer interface [polypeptide binding]; other site 338963000630 TPP binding site [chemical binding]; other site 338963000631 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 338963000632 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cd00568 338963000633 TPP-binding site [chemical binding]; other site 338963000634 amino acid transporter; Region: 2A0306; TIGR00909 338963000635 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 338963000636 Uncharacterized subfamily of S-AdoMet dependent tetrapyrrole methylases; Region: TP_methylase_like; cd11724 338963000637 putative SAM binding site [chemical binding]; other site 338963000638 putative homodimer interface [polypeptide binding]; other site 338963000639 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 338963000640 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 338963000641 Moco binding site; other site 338963000642 Uncharacterized subfamily of S-AdoMet dependent tetrapyrrole methylases; Region: TP_methylase_like; cd11724 338963000643 putative SAM binding site [chemical binding]; other site 338963000644 putative homodimer interface [polypeptide binding]; other site 338963000645 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 338963000646 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 338963000647 N-terminal plug; other site 338963000648 ligand-binding site [chemical binding]; other site 338963000649 elongation factor G; Reviewed; Region: PRK13351 338963000650 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 338963000651 G1 box; other site 338963000652 putative GEF interaction site [polypeptide binding]; other site 338963000653 GTP/Mg2+ binding site [chemical binding]; other site 338963000654 Switch I region; other site 338963000655 G2 box; other site 338963000656 G3 box; other site 338963000657 Switch II region; other site 338963000658 G4 box; other site 338963000659 G5 box; other site 338963000660 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 338963000661 Elongation Factor G-like domain IV. This family includes the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria), ribosomal protection proteins that mediate tetracycline resistance and, an evolutionarily...; Region: EFG_like_IV; cd01680 338963000662 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 338963000663 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 338963000664 putative hydrolase; Provisional; Region: PRK02113 338963000665 multifunctional aminopeptidase A; Provisional; Region: PRK00913 338963000666 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 338963000667 interface (dimer of trimers) [polypeptide binding]; other site 338963000668 Substrate-binding/catalytic site; other site 338963000669 Zn-binding sites [ion binding]; other site 338963000670 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 338963000671 DNA-binding site [nucleotide binding]; DNA binding site 338963000672 RNA-binding motif; other site 338963000673 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: hisZ; PRK12292 338963000674 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 338963000675 dimer interface [polypeptide binding]; other site 338963000676 motif 1; other site 338963000677 active site 338963000678 motif 2; other site 338963000679 HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for...; Region: HGTP_anticodon; cl00266 338963000680 anticodon binding site; other site 338963000681 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 338963000682 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 338963000683 GDP-binding site [chemical binding]; other site 338963000684 ACT binding site; other site 338963000685 IMP binding site; other site 338963000686 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 338963000687 RNA/DNA hybrid binding site [nucleotide binding]; other site 338963000688 active site 338963000689 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 338963000690 NADH dehydrogenase subunit B; Validated; Region: PRK06411 338963000691 trifunctional NADH dehydrogenase I subunit B/C/D; Provisional; Region: PRK13292 338963000692 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; pfam00329 338963000693 NADH dehydrogenase subunit D; Validated; Region: PRK06075 338963000694 NADH dehydrogenase subunit E; Validated; Region: PRK07539 338963000695 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 338963000696 putative dimer interface [polypeptide binding]; other site 338963000697 [2Fe-2S] cluster binding site [ion binding]; other site 338963000698 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 338963000699 SLBB domain; Region: SLBB; pfam10531 338963000700 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 338963000701 NADH dehydrogenase subunit G; Validated; Region: PRK08166 338963000702 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 338963000703 catalytic loop [active] 338963000704 iron binding site [ion binding]; other site 338963000705 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 338963000706 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 338963000707 molybdopterin cofactor binding site; other site 338963000708 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex...; Region: MopB_CT_NDH-1_NuoG2-N7; cd02788 338963000709 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 338963000710 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 338963000711 4Fe-4S binding domain; Region: Fer4; cl02805 338963000712 4Fe-4S binding domain; Region: Fer4; pfam00037 338963000713 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 338963000714 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 338963000715 proton-translocating NADH-quinone oxidoreductase, chain L; Region: NDH_I_L; TIGR01974 338963000716 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 338963000717 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 338963000718 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 338963000719 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 338963000720 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 338963000721 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 338963000722 CoA binding domain; Region: CoA_binding_2; pfam13380 338963000723 conserved nucleotide sequence Moco-II; Pcar_R0092 338963000724 This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This...; Region: NifX_NifB; cl00252 338963000725 conserved nucleotide sequence; Pcar_R2001 338963000726 conserved nucleotide sequence Moco-II; Pcar_R0093 338963000727 MoeA_like. This domain is similar to a domain found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. There this domain is presumed to bind molybdopterin. The exact function of this subgroup is...; Region: MoeA_like; cd03522 338963000728 putative MPT binding site; other site 338963000729 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 338963000730 selenium-dependent molybdenum hydroxylase 1; Region: Se_dep_Molyb_1; TIGR03311 338963000731 catalytic loop [active] 338963000732 iron binding site [ion binding]; other site 338963000733 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 338963000734 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 338963000735 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 338963000736 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 338963000737 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 338963000738 Cysteine-rich domain; Region: CCG; pfam02754 338963000739 putative zinc finger/helix-turn-helix protein, YgiT family; Region: CxxCG_CxxCG_HTH; TIGR03830 338963000740 Methyltransferase domain; Region: Methyltransf_31; pfam13847 338963000741 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 338963000742 S-adenosylmethionine binding site [chemical binding]; other site 338963000743 Putative redox-active protein (C_GCAxxG_C_C); Region: C_GCAxxG_C_C; pfam09719 338963000744 Predicted Fe-S oxidoreductases [General function prediction only]; Region: COG1964 338963000745 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 338963000746 FeS/SAM binding site; other site 338963000747 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 338963000748 acyl-activating enzyme (AAE) consensus motif; other site 338963000749 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 338963000750 active site 338963000751 AMP binding site [chemical binding]; other site 338963000752 acyl-activating enzyme (AAE) consensus motif; other site 338963000753 CoA binding site [chemical binding]; other site 338963000754 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 338963000755 AMP binding site [chemical binding]; other site 338963000756 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 338963000757 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 338963000758 XdhC Rossmann domain; Region: XdhC_C; pfam13478 338963000759 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 338963000760 metal-binding site 338963000761 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 338963000762 Zn2+ binding site [ion binding]; other site 338963000763 Mg2+ binding site [ion binding]; other site 338963000764 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 338963000765 catalytic core [active] 338963000766 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 338963000767 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 338963000768 dimer interface [polypeptide binding]; other site 338963000769 conserved gate region; other site 338963000770 putative PBP binding loops; other site 338963000771 ABC-ATPase subunit interface; other site 338963000772 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963000773 putative bacteriocin export ABC transporter, lactococcin 972 group; Region: L_ocin_972_ABC; TIGR03608 338963000774 Walker A/P-loop; other site 338963000775 ATP binding site [chemical binding]; other site 338963000776 Q-loop/lid; other site 338963000777 ABC transporter signature motif; other site 338963000778 Walker B; other site 338963000779 D-loop; other site 338963000780 H-loop/switch region; other site 338963000781 Domain of unknown function (DUF364); Region: DUF364; pfam04016 338963000782 Protein of unknown function (DUF3343); Region: DUF3343; pfam11823 338963000783 Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS...; Region: SufS_like; cd06453 338963000784 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 338963000785 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 338963000786 catalytic residue [active] 338963000787 ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ModA; COG0725 338963000788 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 338963000789 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 338963000790 GSH binding site [chemical binding]; other site 338963000791 catalytic residues [active] 338963000792 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 338963000793 bifunctional homocysteine S-methyltransferase/5,10-methylenetetrahydrofolate reductase protein; Reviewed; Region: PRK08645 338963000794 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 338963000795 FAD binding site [chemical binding]; other site 338963000796 Coenzyme A pyrophosphatase (CoAse), a member of the Nudix hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes. The need of CoAses mainly arises under conditions of oxidative...; Region: CoAse; cd03426 338963000797 putative active site [active] 338963000798 putative CoA binding site [chemical binding]; other site 338963000799 nudix motif; other site 338963000800 metal binding site [ion binding]; metal-binding site 338963000801 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 338963000802 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 338963000803 substrate binding site [chemical binding]; other site 338963000804 hexamer interface [polypeptide binding]; other site 338963000805 metal binding site [ion binding]; metal-binding site 338963000806 16S rRNA methyltransferase B; Provisional; Region: PRK14902 338963000807 NusB family; Region: NusB; pfam01029 338963000808 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 338963000809 S-adenosylmethionine binding site [chemical binding]; other site 338963000810 Peptidase family M48; Region: Peptidase_M48; cl12018 338963000811 Protein of unknown function DUF116; Region: DUF116; pfam01976 338963000812 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 338963000813 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 338963000814 putative active site [active] 338963000815 substrate binding site [chemical binding]; other site 338963000816 putative cosubstrate binding site; other site 338963000817 catalytic site [active] 338963000818 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 338963000819 substrate binding site [chemical binding]; other site 338963000820 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 338963000821 active site 338963000822 catalytic residues [active] 338963000823 metal binding site [ion binding]; metal-binding site 338963000824 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 338963000825 CoA binding domain; Region: CoA_binding; smart00881 338963000826 CoA-ligase; Region: Ligase_CoA; pfam00549 338963000827 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 338963000828 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 338963000829 CoA-ligase; Region: Ligase_CoA; pfam00549 338963000830 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 338963000831 active site 338963000832 intersubunit interactions; other site 338963000833 catalytic residue [active] 338963000834 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor...; Region: Ribosomal_L24e_L24; cl00909 338963000835 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 338963000836 catalytic center binding site [active] 338963000837 ATP binding site [chemical binding]; other site 338963000838 Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria; Region: LPO; cd08176 338963000839 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 338963000840 dimer interface [polypeptide binding]; other site 338963000841 active site 338963000842 metal binding site [ion binding]; metal-binding site 338963000843 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD...; Region: ThiF_MoeB_HesA_family; cd00757 338963000844 hypothetical protein; Provisional; Region: PRK08328 338963000845 ATP binding site [chemical binding]; other site 338963000846 substrate interface [chemical binding]; other site 338963000847 ThiS family; Region: ThiS; pfam02597 338963000848 charged pocket; other site 338963000849 hydrophobic patch; other site 338963000850 Aldehyde:ferredoxin oxidoreductase [Energy production and conversion]; Region: COG2414 338963000851 Aldehyde ferredoxin oxidoreductase, N-terminal domain; Region: AFOR_N; pfam02730 338963000852 Aldehyde ferredoxin oxidoreductase, domains 2 & 3; Region: AFOR_C; pfam01314 338963000853 Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria; Region: LPO; cd08176 338963000854 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 338963000855 dimer interface [polypeptide binding]; other site 338963000856 active site 338963000857 metal binding site [ion binding]; metal-binding site 338963000858 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 338963000859 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 338963000860 dimer interface [polypeptide binding]; other site 338963000861 putative functional site; other site 338963000862 putative MPT binding site; other site 338963000863 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 338963000864 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 338963000865 active site 338963000866 NAD binding site [chemical binding]; other site 338963000867 metal binding site [ion binding]; metal-binding site 338963000868 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 338963000869 GAF domain; Region: GAF_3; pfam13492 338963000870 PAS fold; Region: PAS_4; pfam08448 338963000871 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 338963000872 dimer interface [polypeptide binding]; other site 338963000873 phosphorylation site [posttranslational modification] 338963000874 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 338963000875 ATP binding site [chemical binding]; other site 338963000876 Mg2+ binding site [ion binding]; other site 338963000877 G-X-G motif; other site 338963000878 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 338963000879 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963000880 active site 338963000881 phosphorylation site [posttranslational modification] 338963000882 intermolecular recognition site; other site 338963000883 dimerization interface [polypeptide binding]; other site 338963000884 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 338963000885 Walker A motif; other site 338963000886 ATP binding site [chemical binding]; other site 338963000887 Walker B motif; other site 338963000888 arginine finger; other site 338963000889 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 338963000890 electron transport complex RsxE subunit; Provisional; Region: PRK12405 338963000891 FMN-binding domain; Region: FMN_bind; cl01081 338963000892 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; pfam03116 338963000893 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 338963000894 SLBB domain; Region: SLBB; pfam10531 338963000895 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 338963000896 ferredoxin; Validated; Region: PRK07118 338963000897 Putative Fe-S cluster; Region: FeS; cl17515 338963000898 4Fe-4S binding domain; Region: Fer4; pfam00037 338963000899 electron transport complex protein RsxA; Provisional; Region: PRK05151 338963000900 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 338963000901 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 338963000902 inhibitor-cofactor binding pocket; inhibition site 338963000903 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963000904 catalytic residue [active] 338963000905 conserved nucleotide sequence; Pcar_R7201 338963000906 conserved nucleotide sequence; Pcar_R7202 338963000907 heptanucleotide repeats; Pcar_R7002 338963000908 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 338963000909 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 338963000910 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 338963000911 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 338963000912 FtsX-like permease family; Region: FtsX; pfam02687 338963000913 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 338963000914 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 338963000915 Walker A/P-loop; other site 338963000916 ATP binding site [chemical binding]; other site 338963000917 Q-loop/lid; other site 338963000918 ABC transporter signature motif; other site 338963000919 Walker B; other site 338963000920 D-loop; other site 338963000921 H-loop/switch region; other site 338963000922 macrolide transporter subunit MacA; Provisional; Region: PRK11578 338963000923 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 338963000924 HlyD family secretion protein; Region: HlyD_3; pfam13437 338963000925 cardiolipin synthase 2; Provisional; Region: PRK11263 338963000926 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 338963000927 putative active site [active] 338963000928 catalytic site [active] 338963000929 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 338963000930 putative active site [active] 338963000931 catalytic site [active] 338963000932 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 338963000933 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4399 338963000934 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4399 338963000935 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 338963000936 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 338963000937 Coenzyme A binding pocket [chemical binding]; other site 338963000938 Peptidase M20 acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE)-like; Region: M20_ArgE_DapE_like; cd08659 338963000939 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 338963000940 metal binding site [ion binding]; metal-binding site 338963000941 dimer interface [polypeptide binding]; other site 338963000942 glucose-1-phosphate thymidylylransferase, long form; Region: rmlA_long; TIGR01208 338963000943 NTP_transferases catalyze the transfer of nucleotides onto phosphosugars; Region: NTP_transferase; cd04181 338963000944 active site 338963000945 Substrate binding site; other site 338963000946 Mg++ binding site; other site 338963000947 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 338963000948 putative trimer interface [polypeptide binding]; other site 338963000949 putative CoA binding site [chemical binding]; other site 338963000950 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 338963000951 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat...; Region: Hsp33; cd00498 338963000952 dimerization interface [polypeptide binding]; other site 338963000953 domain crossover interface; other site 338963000954 redox-dependent activation switch; other site 338963000955 tRNA 2-selenouridine synthase; Region: tRNA_sel_U_synt; TIGR03167 338963000956 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 338963000957 active site residue [active] 338963000958 conserved nucleotide sequence; Pcar_R1001 338963000959 repeat; Pcar_R1101 338963000960 conserved nucleotide sequence; Pcar_R1002 338963000961 repeat; Pcar_R1102 338963000962 conserved nucleotide sequence; Pcar_R1003 338963000963 repeat; Pcar_R1103 338963000964 conserved nucleotide sequence; Pcar_R1004 338963000965 Domain of unknown function(DUF2779); Region: DUF2779; pfam11074 338963000966 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 338963000967 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 338963000968 conserved nucleotide sequence; Pcar_R5019 338963000969 conserved nucleotide sequence; Pcar_R5048 338963000970 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 338963000971 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 338963000972 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 338963000973 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 338963000974 HlyD family secretion protein; Region: HlyD_3; pfam13437 338963000975 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 338963000976 Protein export membrane protein; Region: SecD_SecF; cl14618 338963000977 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 338963000978 Sensory domain found in PocR; Region: PocR; pfam10114 338963000979 Predicted sensor domain [Signal transduction mechanisms / Transcription]; Region: PocR; COG4936 338963000980 PAS domain; Region: PAS; smart00091 338963000981 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 338963000982 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 338963000983 putative active site [active] 338963000984 heme pocket [chemical binding]; other site 338963000985 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 338963000986 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 338963000987 dimer interface [polypeptide binding]; other site 338963000988 phosphorylation site [posttranslational modification] 338963000989 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 338963000990 ATP binding site [chemical binding]; other site 338963000991 G-X-G motif; other site 338963000992 conserved nucleotide sequence; Pcar_R1005 338963000993 conserved nucleotide sequence; Pcar_R1006 338963000994 conserved nucleotide sequence; Pcar_R1007 338963000995 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; cl00399 338963000996 MoaE homodimer interface [polypeptide binding]; other site 338963000997 MoaD interaction [polypeptide binding]; other site 338963000998 active site residues [active] 338963000999 conserved nucleotide sequence; Pcar_R1104 338963001000 conserved nucleotide sequence; Pcar_R1008 338963001001 conserved nucleotide sequence; Pcar_R1105 338963001002 Protein of unknown function (DUF2726); Region: DUF2726; pfam10881 338963001003 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 338963001004 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 338963001005 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 338963001006 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 338963001007 conserved nucleotide sequence; Pcar_R1009 338963001008 conserved nucleotide sequence; Pcar_R1106 338963001009 Domain of unknown function (DUF3427); Region: DUF3427; pfam11907 338963001010 Bacillus subtilis YydB and related proteins, metallophosphatase domain; Region: MPP_YydB; cd07400 338963001011 Predicted phosphohydrolases [General function prediction only]; Region: Icc; COG1409 338963001012 putative active site [active] 338963001013 putative metal binding site [ion binding]; other site 338963001014 Predicted restriction endonuclease [Defense mechanisms]; Region: COG3440 338963001015 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 338963001016 active site 338963001017 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 338963001018 nucleotide binding site/active site [active] 338963001019 HIT family signature motif; other site 338963001020 catalytic residue [active] 338963001021 Uncharacterized conserved protein [Function unknown]; Region: COG0397 338963001022 hypothetical protein; Validated; Region: PRK00029 338963001023 PAS domain S-box; Region: sensory_box; TIGR00229 338963001024 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 338963001025 putative active site [active] 338963001026 heme pocket [chemical binding]; other site 338963001027 PAS domain; Region: PAS_9; pfam13426 338963001028 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 338963001029 putative active site [active] 338963001030 heme pocket [chemical binding]; other site 338963001031 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 338963001032 PAS fold; Region: PAS_3; pfam08447 338963001033 putative active site [active] 338963001034 heme pocket [chemical binding]; other site 338963001035 GAF domain; Region: GAF; pfam01590 338963001036 GAF domain; Region: GAF_2; pfam13185 338963001037 Sensory domain found in PocR; Region: PocR; pfam10114 338963001038 Predicted sensor domain [Signal transduction mechanisms / Transcription]; Region: PocR; COG4936 338963001039 PAS domain S-box; Region: sensory_box; TIGR00229 338963001040 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 338963001041 putative active site [active] 338963001042 heme pocket [chemical binding]; other site 338963001043 PAS domain S-box; Region: sensory_box; TIGR00229 338963001044 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 338963001045 putative active site [active] 338963001046 heme pocket [chemical binding]; other site 338963001047 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 338963001048 Histidine kinase; Region: HisKA_2; pfam07568 338963001049 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 338963001050 ATP binding site [chemical binding]; other site 338963001051 Mg2+ binding site [ion binding]; other site 338963001052 G-X-G motif; other site 338963001053 Protein of unknown function (DUF504); Region: DUF504; pfam04457 338963001054 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 338963001055 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 338963001056 SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response...; Region: SirA_like_N; cd03421 338963001057 selenium metabolism protein YedF; Region: selenium_YedF; TIGR03527 338963001058 CPxP motif; other site 338963001059 DsrE/DsrF-like family; Region: DrsE; pfam02635 338963001060 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 338963001061 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 338963001062 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 338963001063 catalytic residue [active] 338963001064 Protein of unknown function (DUF3343); Region: DUF3343; pfam11823 338963001065 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 338963001066 Mechanosensitive ion channel; Region: MS_channel; pfam00924 338963001067 Hemerythrin-like domain; Region: Hr-like; cd12108 338963001068 Fe binding site [ion binding]; other site 338963001069 AmmeMemoRadiSam system radical SAM enzyme; Region: AmmeMemoSam_rS; TIGR04337 338963001070 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 338963001071 FeS/SAM binding site; other site 338963001072 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 338963001073 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 338963001074 active site 338963001075 catalytic tetrad [active] 338963001076 conserved nucleotide sequence; Pcar_R1010 338963001077 conserved nucleotide sequence; Pcar_R1107 338963001078 conserved nucleotide sequence fragment; Pcar_R1011 338963001079 Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a...; Region: nucleoside_deaminase; cd01285 338963001080 nucleoside/Zn binding site; other site 338963001081 dimer interface [polypeptide binding]; other site 338963001082 catalytic motif [active] 338963001083 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 338963001084 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 338963001085 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963001086 active site 338963001087 phosphorylation site [posttranslational modification] 338963001088 intermolecular recognition site; other site 338963001089 dimerization interface [polypeptide binding]; other site 338963001090 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 338963001091 DNA binding site [nucleotide binding] 338963001092 nitrogenase molybdenum-iron cofactor biosynthesis protein NifE; Region: nifE; TIGR01283 338963001093 Nitrogenase_NifE_I: a subgroup of the NifE subunit of the NifEN complex: NifE forms an alpha2beta2 tetramer with NifN. NifE and NifN are structurally homologous to nitrogenase MoFe protein alpha and beta subunits respectively. NifEN participates in the...; Region: Nitrogenase_NifE_I; cd01968 338963001094 Nitrogenase_nifN1: A subgroup of the NifN subunit of the NifEN complex: NifN forms an alpha2beta2 tetramer with NifE. NifN and nifE are structurally homologous to nitrogenase MoFe protein beta and alpha subunits respectively. NifEN participates in the...; Region: Nitrogenase_NifN_1; cd01966 338963001095 Nitrogenase component 1 type Oxidoreductase; Region: Oxidored_nitro; pfam00148 338963001096 conserved nucleotide sequence; Pcar_R1012 338963001097 conserved nucleotide sequence; Pcar_R1013 338963001098 trimerization site [polypeptide binding]; other site 338963001099 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cl00528 338963001100 active site 338963001101 NifQ; Region: NifQ; pfam04891 338963001102 prenyltransferase; Reviewed; Region: ubiA; PRK12888 338963001103 UbiA prenyltransferase family; Region: UbiA; pfam01040 338963001104 conserved nucleotide sequence; Pcar_R1014 338963001105 conserved nucleotide sequence; Pcar_R1108 338963001106 conserved nucleotide sequence; Pcar_R1109 338963001107 conserved nucleotide sequence; Pcar_R1015 338963001108 aromatic acid decarboxylase; Validated; Region: PRK05920 338963001109 Flavoprotein; Region: Flavoprotein; pfam02441 338963001110 putative menaquinone biosynthesis protein, SCO4494 family; Region: mena_SCO4494; TIGR03700 338963001111 radical SAM enzyme, TIGR04100 family; Region: rSAM_pair_X 338963001112 menaquinone biosynthesis protein, SCO4550 family; Region: mena_SCO4550; TIGR03699 338963001113 conserved nucleotide sequence; Pcar_R1016 338963001114 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 338963001115 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 338963001116 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963001117 homodimer interface [polypeptide binding]; other site 338963001118 catalytic residue [active] 338963001119 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 338963001120 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 338963001121 minor groove reading motif; other site 338963001122 helix-hairpin-helix signature motif; other site 338963001123 substrate binding pocket [chemical binding]; other site 338963001124 active site 338963001125 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 338963001126 DNA glycosylase (MutY in bacteria and hMYH in humans) is responsible for repairing misread A*oxoG residues to C*G by removing the inappropriately paired adenine base from the DNA backbone. It belongs to the Nudix hydrolase superfamily and is important...; Region: DNA_Glycosylase_C; cd03431 338963001127 DNA binding and oxoG recognition site [nucleotide binding] 338963001128 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 338963001129 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 338963001130 catalytic site [active] 338963001131 putative active site [active] 338963001132 putative substrate binding site [chemical binding]; other site 338963001133 HRDC domain; Region: HRDC; pfam00570 338963001134 HRDC domain; Region: HRDC; pfam00570 338963001135 fumarate hydratase; Reviewed; Region: fumC; PRK00485 338963001136 Class II fumarases; Region: Fumarase_classII; cd01362 338963001137 active site 338963001138 tetramer interface [polypeptide binding]; other site 338963001139 HD domain; Region: HD_3; pfam13023 338963001140 seryl-tRNA synthetase; Provisional; Region: PRK05431 338963001141 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 338963001142 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 338963001143 dimer interface [polypeptide binding]; other site 338963001144 active site 338963001145 motif 1; other site 338963001146 motif 2; other site 338963001147 motif 3; other site 338963001148 Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a...; Region: nucleoside_deaminase; cd01285 338963001149 nucleoside/Zn binding site; other site 338963001150 dimer interface [polypeptide binding]; other site 338963001151 catalytic motif [active] 338963001152 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 338963001153 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 338963001154 ATP binding site [chemical binding]; other site 338963001155 Mg++ binding site [ion binding]; other site 338963001156 motif III; other site 338963001157 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 338963001158 nucleotide binding region [chemical binding]; other site 338963001159 ATP-binding site [chemical binding]; other site 338963001160 RNA recognition motif in Escherichia coli cold-shock DEAD box protein A (CsdA) and similar proteins; Region: RRM_EcCsdA_like; cd12499 338963001161 putative RNA binding site [nucleotide binding]; other site 338963001162 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 338963001163 (2R,3R)-2,3-butanediol dehydrogenase; Region: butanediol_DH_like; cd08233 338963001164 putative NAD(P) binding site [chemical binding]; other site 338963001165 catalytic Zn binding site [ion binding]; other site 338963001166 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 338963001167 dimer interface [polypeptide binding]; other site 338963001168 substrate binding site [chemical binding]; other site 338963001169 metal binding site [ion binding]; metal-binding site 338963001170 Uncharacterized ACR, COG1993; Region: DUF190; cl00872 338963001171 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; pfam13557 338963001172 palindrome; Pcar_R5078 338963001173 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 338963001174 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 338963001175 Walker A motif; other site 338963001176 ATP binding site [chemical binding]; other site 338963001177 Walker B motif; other site 338963001178 arginine finger; other site 338963001179 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 338963001180 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 338963001181 ThiC-associated domain; Region: ThiC-associated; pfam13667 338963001182 ThiC family; Region: ThiC; pfam01964 338963001183 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 338963001184 thiS-thiF/thiG interaction site; other site 338963001185 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 338963001186 ThiS interaction site; other site 338963001187 putative active site [active] 338963001188 tetramer interface [polypeptide binding]; other site 338963001189 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09240 338963001190 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 338963001191 FeS/SAM binding site; other site 338963001192 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 338963001193 Predicted inorganic polyphosphate/ATP-NAD kinase [General function prediction only]; Region: COG3199 338963001194 ATP-NAD kinase; Region: NAD_kinase; pfam01513 338963001195 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 338963001196 thiamine phosphate binding site [chemical binding]; other site 338963001197 active site 338963001198 pyrophosphate binding site [ion binding]; other site 338963001199 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 338963001200 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 338963001201 tetramer interface [polypeptide binding]; other site 338963001202 TPP-binding site [chemical binding]; other site 338963001203 heterodimer interface [polypeptide binding]; other site 338963001204 phosphorylation loop region [posttranslational modification] 338963001205 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 338963001206 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 338963001207 alpha subunit interface [polypeptide binding]; other site 338963001208 TPP binding site [chemical binding]; other site 338963001209 heterodimer interface [polypeptide binding]; other site 338963001210 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 338963001211 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 338963001212 E3 interaction surface; other site 338963001213 lipoyl attachment site [posttranslational modification]; other site 338963001214 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 338963001215 E3 interaction surface; other site 338963001216 lipoyl attachment site [posttranslational modification]; other site 338963001217 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 338963001218 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 338963001219 lipoyl synthase; Provisional; Region: PRK05481 338963001220 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 338963001221 FeS/SAM binding site; other site 338963001222 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 338963001223 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 338963001224 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 338963001225 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 338963001226 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 338963001227 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 338963001228 Nitroreductase family. Members of this family utilize FMN as a cofactor. This family is involved in the reduction of flavin or nitroaromatic compounds by using NAD(P)H as electron donor in a obligatory two-electron transfer. Nitrogenase is homodimer; Region: NADH_nitroreductase; cd02143 338963001229 putative FMN binding site [chemical binding]; other site 338963001230 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK08293 338963001231 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 338963001232 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 338963001233 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 338963001234 PGAP1-like protein; Region: PGAP1; pfam07819 338963001235 acyl-CoA esterase; Provisional; Region: PRK10673 338963001236 Predicted permeases [General function prediction only]; Region: COG0701 338963001237 squalene-hopene cyclase; Region: hopene_cyclase; TIGR01507 338963001238 Squalene cyclase (SQCY) domain subgroup 1; found in class II terpene cyclases that have an alpha 6 - alpha 6 barrel fold. Squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY) are integral membrane proteins that catalyze a cationic cyclization...; Region: SQCY_1; cd02892 338963001239 Active site cavity [active] 338963001240 catalytic acid [active] 338963001241 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: PspF; COG1221 338963001242 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 338963001243 Walker A motif; other site 338963001244 ATP binding site [chemical binding]; other site 338963001245 Walker B motif; other site 338963001246 arginine finger; other site 338963001247 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 338963001248 DNA-binding interface [nucleotide binding]; DNA binding site 338963001249 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 338963001250 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 338963001251 putative dimer interface [polypeptide binding]; other site 338963001252 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 338963001253 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 338963001254 putative dimer interface [polypeptide binding]; other site 338963001255 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 338963001256 Clp amino terminal domain; Region: Clp_N; pfam02861 338963001257 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 338963001258 Walker A motif; other site 338963001259 ATP binding site [chemical binding]; other site 338963001260 Walker B motif; other site 338963001261 arginine finger; other site 338963001262 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 338963001263 Walker A motif; other site 338963001264 ATP binding site [chemical binding]; other site 338963001265 Walker B motif; other site 338963001266 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 338963001267 heptanucleotide repeats; Pcar_R7003 338963001268 DNA-binding transcriptional regulator BaeR; Provisional; Region: PRK10710 338963001269 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963001270 active site 338963001271 phosphorylation site [posttranslational modification] 338963001272 intermolecular recognition site; other site 338963001273 dimerization interface [polypeptide binding]; other site 338963001274 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 338963001275 DNA binding site [nucleotide binding] 338963001276 signal transduction histidine-protein kinase BaeS; Provisional; Region: PRK10549 338963001277 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 338963001278 dimerization interface [polypeptide binding]; other site 338963001279 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 338963001280 dimer interface [polypeptide binding]; other site 338963001281 phosphorylation site [posttranslational modification] 338963001282 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 338963001283 ATP binding site [chemical binding]; other site 338963001284 Mg2+ binding site [ion binding]; other site 338963001285 G-X-G motif; other site 338963001286 methionine gamma-lyase; Validated; Region: PRK07049 338963001287 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 338963001288 dimer interface [polypeptide binding]; other site 338963001289 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 338963001290 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 338963001291 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 338963001292 HlyD family secretion protein; Region: HlyD_3; pfam13437 338963001293 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 338963001294 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 338963001295 Walker A/P-loop; other site 338963001296 ATP binding site [chemical binding]; other site 338963001297 Q-loop/lid; other site 338963001298 ABC transporter signature motif; other site 338963001299 Walker B; other site 338963001300 D-loop; other site 338963001301 H-loop/switch region; other site 338963001302 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 338963001303 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 338963001304 FtsX-like permease family; Region: FtsX; pfam02687 338963001305 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 338963001306 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 338963001307 ATP binding site [chemical binding]; other site 338963001308 Mg++ binding site [ion binding]; other site 338963001309 motif III; other site 338963001310 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 338963001311 nucleotide binding region [chemical binding]; other site 338963001312 ATP-binding site [chemical binding]; other site 338963001313 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 338963001314 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 338963001315 putative dimer interface [polypeptide binding]; other site 338963001316 zinc-ribbon domain; Region: zf-ribbon_3; cl11198 338963001317 Interferon-induced transmembrane protein; Region: CD225; pfam04505 338963001318 Protein of unknown function (DUF2752); Region: DUF2752; pfam10825 338963001319 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 338963001320 DNA-binding site [nucleotide binding]; DNA binding site 338963001321 RNA-binding motif; other site 338963001322 palindrome; Pcar_R5079 338963001323 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14965 338963001324 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 338963001325 Walker A motif; other site 338963001326 ATP binding site [chemical binding]; other site 338963001327 Walker B motif; other site 338963001328 arginine finger; other site 338963001329 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 338963001330 hypothetical protein; Validated; Region: PRK00153 338963001331 recombination protein RecR; Reviewed; Region: recR; PRK00076 338963001332 RecR protein; Region: RecR; pfam02132 338963001333 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 338963001334 putative active site [active] 338963001335 putative metal-binding site [ion binding]; other site 338963001336 tetramer interface [polypeptide binding]; other site 338963001337 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 338963001338 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 338963001339 dimer interface [polypeptide binding]; other site 338963001340 PYR/PP interface [polypeptide binding]; other site 338963001341 TPP binding site [chemical binding]; other site 338963001342 substrate binding site [chemical binding]; other site 338963001343 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 338963001344 Domain of unknown function; Region: EKR; pfam10371 338963001345 4Fe-4S binding domain; Region: Fer4_6; pfam12837 338963001346 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 338963001347 Thiamine pyrophosphate (TPP family), PFOR_PNO subfamily, TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This...; Region: TPP_PFOR_PNO; cd03377 338963001348 TPP-binding site [chemical binding]; other site 338963001349 dimer interface [polypeptide binding]; other site 338963001350 Roadblock/LC7 domain; Region: Robl_LC7; smart00960 338963001351 GTPase SAR1 and related small G proteins [General function prediction only]; Region: COG1100 338963001352 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 338963001353 G1 box; other site 338963001354 GTP/Mg2+ binding site [chemical binding]; other site 338963001355 G2 box; other site 338963001356 Switch I region; other site 338963001357 G3 box; other site 338963001358 Switch II region; other site 338963001359 G4 box; other site 338963001360 G5 box; other site 338963001361 TAT (twin-arginine translocation) pathway signal sequence; Region: TAT_signal; pfam10518 338963001362 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 338963001363 Peptidase M15; Region: Peptidase_M15_3; cl01194 338963001364 Competence protein A; Region: Competence_A; pfam11104 338963001365 Type IV pilus biogenesis; Region: Pilus_PilP; pfam11356 338963001366 Secretin N-terminal domain; Region: Secretin_N_2; pfam07655 338963001367 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 338963001368 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 338963001369 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 338963001370 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 338963001371 Walker A motif; other site 338963001372 ATP binding site [chemical binding]; other site 338963001373 Walker B motif; other site 338963001374 arginine finger; other site 338963001375 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 338963001376 binding surface 338963001377 TPR motif; other site 338963001378 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 338963001379 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 338963001380 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 338963001381 Walker A motif; other site 338963001382 ATP binding site [chemical binding]; other site 338963001383 Walker B motif; other site 338963001384 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 338963001385 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 338963001386 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 338963001387 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 338963001388 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 338963001389 PilX N-terminal; Region: PilX_N; pfam14341 338963001390 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 338963001391 calcium mediated ligand binding site; other site 338963001392 intermolecular salt bridges; other site 338963001393 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 338963001394 pyrroline-5-carboxylate reductase; Region: PLN02688 338963001395 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 338963001396 2-phosphoglycolate phosphatase, prokaryotic; Region: PGP_bact; TIGR01449 338963001397 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 338963001398 motif II; other site 338963001399 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 338963001400 Na2 binding site [ion binding]; other site 338963001401 putative substrate binding site 1 [chemical binding]; other site 338963001402 Na binding site 1 [ion binding]; other site 338963001403 putative substrate binding site 2 [chemical binding]; other site 338963001404 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 338963001405 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 338963001406 catalytic residue [active] 338963001407 Maf-like protein; Reviewed; Region: PRK00078 338963001408 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 338963001409 active site 338963001410 dimer interface [polypeptide binding]; other site 338963001411 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 338963001412 Glucose inhibited division protein A; Region: GIDA; pfam01134 338963001413 DNA topoisomerase I; Validated; Region: PRK06599 338963001414 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 338963001415 active site 338963001416 interdomain interaction site; other site 338963001417 putative metal-binding site [ion binding]; other site 338963001418 nucleotide binding site [chemical binding]; other site 338963001419 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 338963001420 domain I; other site 338963001421 DNA binding groove [nucleotide binding] 338963001422 phosphate binding site [ion binding]; other site 338963001423 domain II; other site 338963001424 domain III; other site 338963001425 nucleotide binding site [chemical binding]; other site 338963001426 catalytic site [active] 338963001427 domain IV; other site 338963001428 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 338963001429 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 338963001430 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 338963001431 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 338963001432 Protein of unknown function (DUF494); Region: DUF494; cl01103 338963001433 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 338963001434 DNA protecting protein DprA; Region: dprA; TIGR00732 338963001435 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 338963001436 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 338963001437 Tetratricopeptide repeat; Region: TPR_6; pfam13174 338963001438 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 338963001439 Peptidase family U32; Region: Peptidase_U32; pfam01136 338963001440 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 338963001441 phosphoprotein phosphatases of the metallophosphatase superfamily, metallophosphatase domain; Region: MPP_PPP_family; cd00144 338963001442 active site 338963001443 metal binding site [ion binding]; metal-binding site 338963001444 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 338963001445 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 338963001446 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 338963001447 dimer interface [polypeptide binding]; other site 338963001448 ADP-ribose binding site [chemical binding]; other site 338963001449 active site 338963001450 nudix motif; other site 338963001451 metal binding site [ion binding]; metal-binding site 338963001452 NADH pyrophosphatase; Reviewed; Region: nudC; PRK00241 338963001453 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 338963001454 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 338963001455 NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for...; Region: NADH_pyrophosphatase; cd03429 338963001456 putative NADH binding site [chemical binding]; other site 338963001457 putative active site [active] 338963001458 nudix motif; other site 338963001459 putative metal binding site [ion binding]; other site 338963001460 octanucleotide repeats; Pcar_R8003 338963001461 octanucleotide repeats; Pcar_R8004 338963001462 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 338963001463 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 338963001464 hexamer interface [polypeptide binding]; other site 338963001465 ligand binding site [chemical binding]; other site 338963001466 putative active site [active] 338963001467 NAD(P) binding site [chemical binding]; other site 338963001468 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK13581 338963001469 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 338963001470 ligand binding site [chemical binding]; other site 338963001471 NAD binding site [chemical binding]; other site 338963001472 dimerization interface [polypeptide binding]; other site 338963001473 catalytic site [active] 338963001474 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 338963001475 putative L-serine binding site [chemical binding]; other site 338963001476 SacI restriction endonuclease; Region: RE_SacI; pfam09566 338963001477 non-specific DNA binding site [nucleotide binding]; other site 338963001478 salt bridge; other site 338963001479 Cro/C1-type HTH DNA-binding domain; Region: HTH_26; pfam13443 338963001480 sequence-specific DNA binding site [nucleotide binding]; other site 338963001481 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 338963001482 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 338963001483 cofactor binding site; other site 338963001484 DNA binding site [nucleotide binding] 338963001485 substrate interaction site [chemical binding]; other site 338963001486 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 338963001487 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 338963001488 Rrf2 family protein; Region: rrf2_super; TIGR00738 338963001489 Transcriptional regulator; Region: Rrf2; pfam02082 338963001490 DsrE/DsrF-like family; Region: DrsE; pfam02635 338963001491 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 338963001492 haloacid dehalogenase-like hydrolase; Region: HAD; pfam12710 338963001493 Thioredoxin-like domain; Region: Thioredoxin_2; pfam13098 338963001494 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 338963001495 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 338963001496 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 338963001497 CoA-disulfide reductase; Region: CoA_CoA_reduc; TIGR03385 338963001498 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 338963001499 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 338963001500 Member of the Rhodanese Homology Domain superfamily. Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar...; Region: RHOD_Pyr_redox; cd01524 338963001501 active site residue [active] 338963001502 SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that...; Region: SirA_RHOD_Pry_redox; cd03420 338963001503 CPxP motif; other site 338963001504 DsrE/DsrF/DrsH-like family; Region: DrsE_2; pfam13686 338963001505 Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity; Region: Lysophospholipase_L1_like; cd01822 338963001506 active site 338963001507 catalytic triad [active] 338963001508 oxyanion hole [active] 338963001509 switch loop; other site 338963001510 ABC transporter ATPase component; Reviewed; Region: PRK11147 338963001511 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963001512 Walker A/P-loop; other site 338963001513 ATP binding site [chemical binding]; other site 338963001514 ABC transporter signature motif; other site 338963001515 Walker B; other site 338963001516 D-loop; other site 338963001517 H-loop/switch region; other site 338963001518 ABC transporter; Region: ABC_tran_2; pfam12848 338963001519 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 338963001520 conserved nucleotide sequence; Pcar_R7203 338963001521 Predicted membrane protein (DUF2238); Region: DUF2238; pfam09997 338963001522 Domain of Unknown Function with PDB structure (DUF3862); Region: DUF3862; pfam12978 338963001523 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 338963001524 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 338963001525 dinuclear metal binding motif [ion binding]; other site 338963001526 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 338963001527 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 338963001528 MoxR-like ATPases [General function prediction only]; Region: COG0714 338963001529 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3825 338963001530 Cache domain; Region: Cache_1; pfam02743 338963001531 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 338963001532 dimerization interface [polypeptide binding]; other site 338963001533 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 338963001534 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 338963001535 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 338963001536 dimer interface [polypeptide binding]; other site 338963001537 putative CheW interface [polypeptide binding]; other site 338963001538 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 338963001539 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 338963001540 WHG domain; Region: WHG; pfam13305 338963001541 squalene-hopene cyclase; Region: hopene_cyclase; TIGR01507 338963001542 Squalene cyclase (SQCY) domain subgroup 1; found in class II terpene cyclases that have an alpha 6 - alpha 6 barrel fold. Squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY) are integral membrane proteins that catalyze a cationic cyclization...; Region: SQCY_1; cd02892 338963001543 Active site cavity [active] 338963001544 catalytic acid [active] 338963001545 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 338963001546 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 338963001547 THF binding site; other site 338963001548 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 338963001549 substrate binding site [chemical binding]; other site 338963001550 THF binding site; other site 338963001551 zinc-binding site [ion binding]; other site 338963001552 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 338963001553 succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Validated; Region: PRK07570 338963001554 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 338963001555 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 338963001556 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07573 338963001557 L-aspartate oxidase; Provisional; Region: PRK06175 338963001558 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 338963001559 succinate dehydrogenase (or fumarate reductase) cytochrome b subunit, b558 family; Region: sdhC_b558_fam; TIGR02046 338963001560 Succinate:quinone oxidoreductase (SQR)-like Type B subfamily 2, transmembrane subunit; composed of proteins with similarity to the SQRs of Geobacter metallireducens and Corynebacterium glutamicum. SQR catalyzes the oxidation of succinate to fumarate...; Region: SQR_TypeB_2_TM; cd03498 338963001561 putative Iron-sulfur protein interface [polypeptide binding]; other site 338963001562 proximal heme binding site [chemical binding]; other site 338963001563 distal heme binding site [chemical binding]; other site 338963001564 putative dimer interface [polypeptide binding]; other site 338963001565 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 338963001566 Permease; Region: Permease; pfam02405 338963001567 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 338963001568 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 338963001569 Walker A/P-loop; other site 338963001570 ATP binding site [chemical binding]; other site 338963001571 Q-loop/lid; other site 338963001572 ABC transporter signature motif; other site 338963001573 Walker B; other site 338963001574 D-loop; other site 338963001575 H-loop/switch region; other site 338963001576 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 338963001577 mce related protein; Region: MCE; pfam02470 338963001578 VacJ like lipoprotein; Region: VacJ; cl01073 338963001579 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 338963001580 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 338963001581 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 338963001582 ligand binding site [chemical binding]; other site 338963001583 flexible hinge region; other site 338963001584 palindrome; Pcar_R5080 338963001585 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 338963001586 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 338963001587 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 338963001588 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 338963001589 N-terminal plug; other site 338963001590 ligand-binding site [chemical binding]; other site 338963001591 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 338963001592 MoaE interaction surface [polypeptide binding]; other site 338963001593 MoeB interaction surface [polypeptide binding]; other site 338963001594 thiocarboxylated glycine; other site 338963001595 Aldehyde ferredoxin oxidoreductase, N-terminal domain; Region: AFOR_N; smart00790 338963001596 Aldehyde ferredoxin oxidoreductase, domains 2 & 3; Region: AFOR_C; pfam01314 338963001597 Aerotolerance regulator N-terminal; Region: BatA; cl06567 338963001598 von Willebrand factor type A domain; Region: VWA_2; pfam13519 338963001599 metal ion-dependent adhesion site (MIDAS); other site 338963001600 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 338963001601 metal ion-dependent adhesion site (MIDAS); other site 338963001602 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 338963001603 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 338963001604 metal ion-dependent adhesion site (MIDAS); other site 338963001605 MoxR-like ATPases [General function prediction only]; Region: COG0714 338963001606 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 338963001607 Walker A motif; other site 338963001608 ATP binding site [chemical binding]; other site 338963001609 Walker B motif; other site 338963001610 arginine finger; other site 338963001611 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 338963001612 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 338963001613 ABC-ATPase subunit interface; other site 338963001614 dimer interface [polypeptide binding]; other site 338963001615 putative PBP binding regions; other site 338963001616 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 338963001617 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 338963001618 intersubunit interface [polypeptide binding]; other site 338963001619 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 338963001620 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 338963001621 Walker A/P-loop; other site 338963001622 ATP binding site [chemical binding]; other site 338963001623 Q-loop/lid; other site 338963001624 ABC transporter signature motif; other site 338963001625 Walker B; other site 338963001626 D-loop; other site 338963001627 H-loop/switch region; other site 338963001628 ethanolamine ammonia lyase large subunit; Provisional; Region: PRK15067 338963001629 Ethanolamine ammonia lyase large subunit (EutB); Region: EutB; pfam06751 338963001630 Ethanolamine ammonia-lyase light chain (EutC); Region: EutC; cl01762 338963001631 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 338963001632 Bacterial extracellular solute-binding protein; Region: SBP_bac_6; pfam13343 338963001633 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 338963001634 Precorrin-6x reductase [Coenzyme metabolism]; Region: CobK; COG2099 338963001635 Precorrin-6x reductase CbiJ/CobK; Region: CbiJ; pfam02571 338963001636 Precorrin-3B C(17)-methyltransferase (CobJ/CbiH); Region: Precorrin_3B_C17_MT; cd11646 338963001637 active site 338963001638 SAM binding site [chemical binding]; other site 338963001639 homodimer interface [polypeptide binding]; other site 338963001640 Cobalamin synthesis G N-terminal; Region: CbiG_N; pfam11760 338963001641 cobalamin biosynthesis protein CbiG; Provisional; Region: PRK07027 338963001642 Precorrin-4 C11-methyltransferase (CbiF/CobM); Region: Precorrin-4_C11-MT; cd11641 338963001643 active site 338963001644 SAM binding site [chemical binding]; other site 338963001645 homodimer interface [polypeptide binding]; other site 338963001646 conserved nucleotide sequence; Pcar_R7209 338963001647 conserved nucleotide sequence; Pcar_R7101 338963001648 heptanucleotide repeats; Pcar_R7004 338963001649 conserved nucleotide sequence; Pcar_R7102 338963001650 Precorrin-6Y methyltransferase, the cobalamin biosynthesis enzyme CbiE; Region: Precorrin-6Y-methylase; cd11644 338963001651 active site 338963001652 putative homodimer interface [polypeptide binding]; other site 338963001653 SAM binding site [chemical binding]; other site 338963001654 cobalt-precorrin-6A synthase; Reviewed; Region: cbiD; PRK00075 338963001655 Precorrin-2 C20-methyltransferase, also named CobI or CbiL; Region: Precorrin_2_C20_MT; cd11645 338963001656 active site 338963001657 SAM binding site [chemical binding]; other site 338963001658 homodimer interface [polypeptide binding]; other site 338963001659 conserved nucleotide sequence; Pcar_R7204 338963001660 conserved nucleotide sequence; Pcar_R7103 338963001661 heptanucleotide repeats; Pcar_R7005 338963001662 conserved nucleotide sequence; Pcar_R7104 338963001663 Uncharacterized protein conserved in archaea [Function unknown]; Region: COG3366 338963001664 Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), N-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the...; Region: CbiK_N; cd03412 338963001665 Cobalt chelatase (CbiK); Region: CbiK; pfam06180 338963001666 active site 338963001667 C-terminal domain interface [polypeptide binding]; other site 338963001668 Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), C-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the...; Region: CbiK_C; cd03413 338963001669 active site 338963001670 N-terminal domain interface [polypeptide binding]; other site 338963001671 conserved nucleotide sequence; Pcar_R7205 338963001672 conserved nucleotide sequence; Pcar_R7107 338963001673 peptide-modifying radical SAM enzyme CbpB; Region: rSAM_cobopep; TIGR04163 338963001674 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 338963001675 FeS/SAM binding site; other site 338963001676 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 338963001677 conserved nucleotide sequence; Pcar_R2002 338963001678 modified peptide precursor CbpA; Region: cobo_pep; TIGR04164 338963001679 conserved nucleotide sequence; Pcar_R1017 338963001680 cobalt-precorrin-8X methylmutase; Validated; Region: cbiC; cl00913 338963001681 Precorrin-8X methylmutase; Region: CbiC; pfam02570 338963001682 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 338963001683 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 338963001684 catalytic triad [active] 338963001685 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer; Region: CobA_CobO_BtuR; cd00561 338963001686 homodimer interface [polypeptide binding]; other site 338963001687 Walker A motif; other site 338963001688 ATP binding site [chemical binding]; other site 338963001689 hydroxycobalamin binding site [chemical binding]; other site 338963001690 Walker B motif; other site 338963001691 conserved nucleotide sequence; Pcar_R7206 338963001692 conserved nucleotide sequence; Pcar_R7105 338963001693 heptanucleotide repeats; Pcar_R7006 338963001694 conserved nucleotide sequence; Pcar_R7106 338963001695 CobD/Cbib protein; Region: CobD_Cbib; pfam03186 338963001696 L-threonine-O-3-phosphate decarboxylase; Region: L_thr_O3P_dcar; TIGR01140 338963001697 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 338963001698 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963001699 homodimer interface [polypeptide binding]; other site 338963001700 catalytic residue [active] 338963001701 cobyric acid synthase; Provisional; Region: PRK00784 338963001702 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 338963001703 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 338963001704 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 338963001705 catalytic triad [active] 338963001706 cobalamin synthase; Reviewed; Region: cobS; PRK00235 338963001707 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 338963001708 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 338963001709 active site pocket [active] 338963001710 putative dimer interface [polypeptide binding]; other site 338963001711 putative cataytic base [active] 338963001712 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a...; Region: CobU; cd00544 338963001713 homotrimer interface [polypeptide binding]; other site 338963001714 Walker A motif; other site 338963001715 GTP binding site [chemical binding]; other site 338963001716 Walker B motif; other site 338963001717 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 338963001718 catalytic core [active] 338963001719 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 338963001720 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 338963001721 active site 338963001722 SAM binding site [chemical binding]; other site 338963001723 homodimer interface [polypeptide binding]; other site 338963001724 ethanolamine ammonia lyase large subunit; Provisional; Region: PRK15067 338963001725 Ethanolamine ammonia lyase large subunit (EutB); Region: EutB; pfam06751 338963001726 Ethanolamine ammonia-lyase light chain (EutC); Region: EutC; cl01762 338963001727 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 338963001728 Bacterial extracellular solute-binding protein; Region: SBP_bac_6; pfam13343 338963001729 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 338963001730 B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the...; Region: radical_SAM_B12_BD; cd02068 338963001731 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 338963001732 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 338963001733 FeS/SAM binding site; other site 338963001734 Protein of unknown function (DUF4080); Region: DUF4080; pfam13311 338963001735 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 338963001736 Radical SAM superfamily; Region: Radical_SAM; pfam04055 338963001737 FeS/SAM binding site; other site 338963001738 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 338963001739 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 338963001740 dimerization interface [polypeptide binding]; other site 338963001741 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 338963001742 dimer interface [polypeptide binding]; other site 338963001743 phosphorylation site [posttranslational modification] 338963001744 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 338963001745 ATP binding site [chemical binding]; other site 338963001746 Mg2+ binding site [ion binding]; other site 338963001747 G-X-G motif; other site 338963001748 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963001749 response regulator GlrR; Provisional; Region: PRK15115 338963001750 active site 338963001751 phosphorylation site [posttranslational modification] 338963001752 intermolecular recognition site; other site 338963001753 dimerization interface [polypeptide binding]; other site 338963001754 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 338963001755 Walker A motif; other site 338963001756 ATP binding site [chemical binding]; other site 338963001757 Walker B motif; other site 338963001758 arginine finger; other site 338963001759 Bacterial SH3 domain homologues; Region: SH3b; smart00287 338963001760 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 338963001761 Cdc37 N terminal kinase binding; Region: CDC37_N; cl03951 338963001762 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 338963001763 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 338963001764 Nitroreductase family. Members of this family utilize FMN as a cofactor. This family is involved in the reduction of flavin or nitroaromatic compounds by using NAD(P)H as electron donor in a obligatory two-electron transfer. Nitrogenase is homodimer; Region: NADH_nitroreductase; cd02143 338963001765 putative FMN binding site [chemical binding]; other site 338963001766 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 338963001767 Amidase; Region: Amidase; pfam01425 338963001768 HipA-like N-terminal domain; Region: HipA_N; pfam07805 338963001769 HipA-like C-terminal domain; Region: HipA_C; pfam07804 338963001770 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 338963001771 non-specific DNA binding site [nucleotide binding]; other site 338963001772 salt bridge; other site 338963001773 sequence-specific DNA binding site [nucleotide binding]; other site 338963001774 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 338963001775 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 338963001776 Walker A motif; other site 338963001777 ATP binding site [chemical binding]; other site 338963001778 Walker B motif; other site 338963001779 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 338963001780 dimer interface [polypeptide binding]; other site 338963001781 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 338963001782 active site 338963001783 metal binding site [ion binding]; metal-binding site 338963001784 glutathione binding site [chemical binding]; other site 338963001785 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 338963001786 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 338963001787 Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial cardiolipin synthase; Region: PLDc_CLS_unchar2_1; cd09157 338963001788 putative active site [active] 338963001789 catalytic site [active] 338963001790 Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin synthase; Region: PLDc_CLS_unchar2_2; cd09163 338963001791 putative active site [active] 338963001792 catalytic site [active] 338963001793 heptanucleotide repeats; Pcar_R7007 338963001794 Hemerythrin; Region: Hemerythrin; cd12107 338963001795 Fe binding site [ion binding]; other site 338963001796 Nitroreductase-like family 3. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_3; cd02139 338963001797 putative FMN binding site [chemical binding]; other site 338963001798 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 338963001799 HSP70 interaction site [polypeptide binding]; other site 338963001800 Arsenate Reductase (ArsC) family, 15kD protein subfamily; composed of proteins of unknown function with similarity to thioredoxin-fold arsenic reductases, ArsC. It is encoded by an ORF present in a gene cluster associated with nitrogen fixation that also...; Region: ArsC_15kD; cd03033 338963001801 putative catalytic residues [active] 338963001802 Alkaline phosphatase [Inorganic ion transport and metabolism]; Region: PhoA; COG1785 338963001803 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cl15837 338963001804 dimer interface [polypeptide binding]; other site 338963001805 active site 338963001806 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963001807 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963001808 metal binding site [ion binding]; metal-binding site 338963001809 active site 338963001810 I-site; other site 338963001811 Methyltransferase domain; Region: Methyltransf_23; pfam13489 338963001812 Methyltransferase domain; Region: Methyltransf_11; pfam08241 338963001813 conserved nucleotide sequence; Pcar_R2003 338963001814 Ion transport protein; Region: Ion_trans; pfam00520 338963001815 Ion channel; Region: Ion_trans_2; pfam07885 338963001816 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 338963001817 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 338963001818 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 338963001819 PhnA protein; Region: PhnA; pfam03831 338963001820 PAS domain; Region: PAS_9; pfam13426 338963001821 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 338963001822 Legionella pneumophila major outer membrane protein precursor; Region: Legionella_OMP; pfam05150 338963001823 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3864 338963001824 Putative metallopeptidase domain; Region: DUF2201_N; pfam13203 338963001825 VWA-like domain (DUF2201); Region: DUF2201; pfam09967 338963001826 metal ion-dependent adhesion site (MIDAS); other site 338963001827 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 338963001828 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 338963001829 Walker A motif; other site 338963001830 ATP binding site [chemical binding]; other site 338963001831 Walker B motif; other site 338963001832 arginine finger; other site 338963001833 glucans biosynthesis protein; Provisional; Region: opgC; PRK03854 338963001834 Acyltransferase family; Region: Acyl_transf_3; pfam01757 338963001835 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 338963001836 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 338963001837 substrate binding pocket [chemical binding]; other site 338963001838 membrane-bound complex binding site; other site 338963001839 hinge residues; other site 338963001840 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 338963001841 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 338963001842 N-acetyl-D-glucosamine binding site [chemical binding]; other site 338963001843 catalytic residue [active] 338963001844 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 338963001845 Transposase; Region: DDE_Tnp_ISL3; pfam01610 338963001846 Protein of unknown function (DUF3423); Region: DUF3423; pfam11903 338963001847 Transposase domain (DUF772); Region: DUF772; pfam05598 338963001848 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 338963001849 conserved nucleotide sequence; Pcar_R5016 338963001850 Methyltransferase domain; Region: Methyltransf_31; pfam13847 338963001851 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 338963001852 S-adenosylmethionine binding site [chemical binding]; other site 338963001853 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 338963001854 conserved nucleotide sequence; Pcar_R5017 338963001855 conserved nucleotide sequence; Pcar_R5027 338963001856 Transposase; Region: DEDD_Tnp_IS110; pfam01548 338963001857 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 338963001858 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 338963001859 conserved nucleotide sequence; Pcar_R5030 338963001860 conserved nucleotide sequence; Pcar_R5031 338963001861 Transposase domain (DUF772); Region: DUF772; pfam05598 338963001862 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 338963001863 conserved nucleotide sequence; Pcar_R5050 338963001864 conserved nucleotide sequence; Pcar_R5023 338963001865 putative transposase OrfB; Reviewed; Region: PHA02517 338963001866 HTH-like domain; Region: HTH_21; pfam13276 338963001867 Integrase core domain; Region: rve; pfam00665 338963001868 Integrase core domain; Region: rve_3; pfam13683 338963001869 Transposase; Region: HTH_Tnp_1; cl17663 338963001870 Transposase; Region: DEDD_Tnp_IS110; pfam01548 338963001871 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 338963001872 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 338963001873 putative transposase OrfB; Reviewed; Region: PHA02517 338963001874 HTH-like domain; Region: HTH_21; pfam13276 338963001875 Integrase core domain; Region: rve; pfam00665 338963001876 Integrase core domain; Region: rve_3; pfam13683 338963001877 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 338963001878 Transposase; Region: HTH_Tnp_1; pfam01527 338963001879 conserved nucleotide sequence; Pcar_R5032 338963001880 conserved nucleotide sequence; Pcar_R5024 338963001881 conserved nucleotide sequence; Pcar_R5018 338963001882 conserved nucleotide sequence; Pcar_R5002 338963001883 integron integrase; Region: integrase_gron; TIGR02249 338963001884 IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and...; Region: INT_IntI; cd01193 338963001885 Int/Topo IB signature motif; other site 338963001886 penicillin-binding protein 1C; Region: PBP_1c; TIGR02073 338963001887 Transglycosylase; Region: Transgly; pfam00912 338963001888 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 338963001889 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 338963001890 octanucleotide repeats; Pcar_R8005 338963001891 octanucleotide repeats; Pcar_R8006 338963001892 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 338963001893 MG2 domain; Region: A2M_N; pfam01835 338963001894 protein structure with unknown function; Region: DUF4144; pfam13642 338963001895 Alpha-2-macroglobulin family; Region: A2M; pfam00207 338963001896 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 338963001897 surface patch; other site 338963001898 thioester region; other site 338963001899 specificity defining residues; other site 338963001900 Cache domain; Region: Cache_1; pfam02743 338963001901 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 338963001902 dimerization interface [polypeptide binding]; other site 338963001903 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 338963001904 dimer interface [polypeptide binding]; other site 338963001905 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 338963001906 putative CheW interface [polypeptide binding]; other site 338963001907 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 338963001908 putative CheA interaction surface; other site 338963001909 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 338963001910 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 338963001911 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 338963001912 ligand binding site [chemical binding]; other site 338963001913 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 338963001914 E3 Ubiquitin ligase; Region: GIDE; pfam12483 338963001915 elongation factor P; Provisional; Region: PRK14578 338963001916 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 338963001917 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 338963001918 RNA binding site [nucleotide binding]; other site 338963001919 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 338963001920 RNA binding site [nucleotide binding]; other site 338963001921 Predicted membrane protein [Function unknown]; Region: COG1584 338963001922 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 338963001923 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 338963001924 GIY-YIG motif/motif A; other site 338963001925 active site 338963001926 catalytic site [active] 338963001927 putative DNA binding site [nucleotide binding]; other site 338963001928 metal binding site [ion binding]; metal-binding site 338963001929 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 338963001930 4-alpha-glucanotransferase; Provisional; Region: PRK14508 338963001931 Uncharacterized protein At1g47420; Region: PLN02749 338963001932 Type I GTP cyclohydrolase folE2; Region: GCHY-1; pfam02649 338963001933 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 338963001934 propionate/acetate kinase; Provisional; Region: PRK12379 338963001935 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 338963001936 Cytochrome c; Region: Cytochrom_C; cl11414 338963001937 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 338963001938 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 338963001939 putative carbohydrate kinase; Provisional; Region: PRK10565 338963001940 YjeF-related protein N-terminus; Region: YjeF_N; pfam03853 338963001941 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 338963001942 putative substrate binding site [chemical binding]; other site 338963001943 putative ATP binding site [chemical binding]; other site 338963001944 Protein of unknown function (DUF1847); Region: DUF1847; pfam08901 338963001945 Predicted membrane protein (DUF2339); Region: DUF2339; pfam10101 338963001946 Protein of unknown function (DUF3795); Region: DUF3795; pfam12675 338963001947 Chemotaxis phosphatase CheX; Region: CheX; pfam13690 338963001948 Cache domain; Region: Cache_1; pfam02743 338963001949 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963001950 metal binding site [ion binding]; metal-binding site 338963001951 active site 338963001952 I-site; other site 338963001953 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 338963001954 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 338963001955 ATP binding site [chemical binding]; other site 338963001956 Mg++ binding site [ion binding]; other site 338963001957 motif III; other site 338963001958 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 338963001959 nucleotide binding region [chemical binding]; other site 338963001960 ATP-binding site [chemical binding]; other site 338963001961 cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E. coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these...; Region: cyclophilin_EcCYP_like; cd01920 338963001962 substrate binding site [chemical binding]; other site 338963001963 hypothetical protein; Provisional; Region: PRK10410 338963001964 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 338963001965 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 338963001966 tartrate dehydrogenase; Region: TTC; TIGR02089 338963001967 Transposase; Region: DEDD_Tnp_IS110; pfam01548 338963001968 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 338963001969 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 338963001970 Predicted amidohydrolase [General function prediction only]; Region: COG0388 338963001971 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 338963001972 active site 338963001973 catalytic triad [active] 338963001974 dimer interface [polypeptide binding]; other site 338963001975 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 338963001976 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 338963001977 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 338963001978 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963001979 active site 338963001980 phosphorylation site [posttranslational modification] 338963001981 intermolecular recognition site; other site 338963001982 dimerization interface [polypeptide binding]; other site 338963001983 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963001984 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963001985 metal binding site [ion binding]; metal-binding site 338963001986 active site 338963001987 I-site; other site 338963001988 Protein of unknown function (DUF4197); Region: DUF4197; pfam13852 338963001989 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 338963001990 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 338963001991 G1 box; other site 338963001992 putative GEF interaction site [polypeptide binding]; other site 338963001993 GTP/Mg2+ binding site [chemical binding]; other site 338963001994 Switch I region; other site 338963001995 G2 box; other site 338963001996 G3 box; other site 338963001997 Switch II region; other site 338963001998 G4 box; other site 338963001999 G5 box; other site 338963002000 RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the...; Region: RF3_II; cd03689 338963002001 Transcriptional regulator PadR-like family; Region: PadR; cl17335 338963002002 Predicted transcriptional regulators [Transcription]; Region: COG1695 338963002003 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 338963002004 dimerization interface [polypeptide binding]; other site 338963002005 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 338963002006 dimer interface [polypeptide binding]; other site 338963002007 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 338963002008 putative CheW interface [polypeptide binding]; other site 338963002009 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 338963002010 EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB...; Region: EcAsnRS_like_N; cd04318 338963002011 putative dimer interface [polypeptide binding]; other site 338963002012 putative anticodon binding site; other site 338963002013 Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as...; Region: AsxRS_core; cd00776 338963002014 homodimer interface [polypeptide binding]; other site 338963002015 motif 1; other site 338963002016 motif 2; other site 338963002017 active site 338963002018 motif 3; other site 338963002019 Domain of unknown function (DUF4177); Region: DUF4177; pfam13783 338963002020 conserved nucleotide sequence fragment; Pcar_R1018 338963002021 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 338963002022 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 338963002023 active site 338963002024 HIGH motif; other site 338963002025 dimer interface [polypeptide binding]; other site 338963002026 KMSKS motif; other site 338963002027 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 338963002028 Found in ATP-dependent protease La (LON); Region: LON; smart00464 338963002029 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 338963002030 Walker A motif; other site 338963002031 ATP binding site [chemical binding]; other site 338963002032 Walker B motif; other site 338963002033 arginine finger; other site 338963002034 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 338963002035 DNA polymerase I; Provisional; Region: PRK05755 338963002036 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 338963002037 active site 338963002038 metal binding site 1 [ion binding]; metal-binding site 338963002039 putative 5' ssDNA interaction site; other site 338963002040 metal binding site 3; metal-binding site 338963002041 metal binding site 2 [ion binding]; metal-binding site 338963002042 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 338963002043 putative DNA binding site [nucleotide binding]; other site 338963002044 putative metal binding site [ion binding]; other site 338963002045 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 338963002046 active site 338963002047 catalytic site [active] 338963002048 substrate binding site [chemical binding]; other site 338963002049 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 338963002050 active site 338963002051 DNA binding site [nucleotide binding] 338963002052 catalytic site [active] 338963002053 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 338963002054 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 338963002055 MgtE intracellular N domain; Region: MgtE_N; smart00924 338963002056 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 338963002057 Divalent cation transporter; Region: MgtE; pfam01769 338963002058 Recombination protein O N terminal; Region: RecO_N; pfam11967 338963002059 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 338963002060 Recombination protein O C terminal; Region: RecO_C; pfam02565 338963002061 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 338963002062 dimer interface [polypeptide binding]; other site 338963002063 motif 1; other site 338963002064 active site 338963002065 motif 2; other site 338963002066 motif 3; other site 338963002067 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 338963002068 pyruvate phosphate dikinase; Provisional; Region: PRK09279 338963002069 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 338963002070 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 338963002071 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 338963002072 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 338963002073 Endonuclease_V, a DNA repair enzyme that initiates repair of nitrosative deaminated purine bases; Region: Endonuclease_V; cd06559 338963002074 Active_site [active] 338963002075 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 338963002076 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 338963002077 Predicted membrane protein [Function unknown]; Region: COG2860 338963002078 UPF0126 domain; Region: UPF0126; pfam03458 338963002079 UPF0126 domain; Region: UPF0126; pfam03458 338963002080 conserved nucleotide sequence; Pcar_R3001 338963002081 Rhomboid family; Region: Rhomboid; pfam01694 338963002082 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 338963002083 transmembrane helices; other site 338963002084 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 338963002085 TrkA-C domain; Region: TrkA_C; pfam02080 338963002086 TrkA-C domain; Region: TrkA_C; pfam02080 338963002087 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 338963002088 heptanucleotide repeats; Pcar_R7008 338963002089 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 338963002090 thiamine phosphate binding site [chemical binding]; other site 338963002091 active site 338963002092 pyrophosphate binding site [ion binding]; other site 338963002093 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09240 338963002094 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 338963002095 FeS/SAM binding site; other site 338963002096 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 338963002097 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 338963002098 ThiS interaction site; other site 338963002099 putative active site [active] 338963002100 tetramer interface [polypeptide binding]; other site 338963002101 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 338963002102 thiS-thiF/thiG interaction site; other site 338963002103 ThiS-like ubiquitin; Region: ThiS-like; pfam14453 338963002104 thiamine biosynthesis protein ThiF; Provisional; Region: PRK08644 338963002105 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 338963002106 ATP binding site [chemical binding]; other site 338963002107 substrate interface [chemical binding]; other site 338963002108 Helix-turn-helix domain; Region: HTH_17; pfam12728 338963002109 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 338963002110 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 338963002111 YGGT family; Region: YGGT; pfam02325 338963002112 DivIVA protein; Region: DivIVA; pfam05103 338963002113 DivIVA domain; Region: DivI1A_domain; TIGR03544 338963002114 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 338963002115 rod shape-determining protein MreC; Provisional; Region: PRK13922 338963002116 Late embryogenesis abundant protein; Region: LEA_2; pfam03168 338963002117 Uncharacterized conserved protein [Function unknown]; Region: COG2006 338963002118 Domain of unknown function (DUF362); Region: DUF362; pfam04015 338963002119 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 338963002120 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 338963002121 Uncharacterized protein family UPF0047; Region: UPF0047; pfam01894 338963002122 Lipase (class 2); Region: Lipase_2; pfam01674 338963002123 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 338963002124 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 338963002125 active site 338963002126 Int/Topo IB signature motif; other site 338963002127 putative membrane-bound dehydrogenase domain; Region: Piru_Ver_Nterm; TIGR02604 338963002128 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 338963002129 Methyltransferase domain; Region: Methyltransf_24; pfam13578 338963002130 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 338963002131 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 338963002132 tetramer interface [polypeptide binding]; other site 338963002133 active site 338963002134 Mg2+/Mn2+ binding site [ion binding]; other site 338963002135 Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_like_3; cd12174 338963002136 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 338963002137 putative ligand binding site [chemical binding]; other site 338963002138 putative NAD binding site [chemical binding]; other site 338963002139 putative catalytic site [active] 338963002140 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 338963002141 NAD-dependent protein deacetylases, SIR2 family [Transcription]; Region: SIR2; COG0846 338963002142 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 338963002143 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 338963002144 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 338963002145 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 338963002146 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 338963002147 Uncharacterized conserved protein (DUF2249); Region: DUF2249; cl17719 338963002148 Response regulator receiver domain; Region: Response_reg; pfam00072 338963002149 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963002150 active site 338963002151 phosphorylation site [posttranslational modification] 338963002152 intermolecular recognition site; other site 338963002153 dimerization interface [polypeptide binding]; other site 338963002154 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 338963002155 GAF domain; Region: GAF_3; pfam13492 338963002156 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963002157 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963002158 metal binding site [ion binding]; metal-binding site 338963002159 active site 338963002160 I-site; other site 338963002161 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 338963002162 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 338963002163 TrkA-C domain; Region: TrkA_C; pfam02080 338963002164 TrkA-C domain; Region: TrkA_C; pfam02080 338963002165 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 338963002166 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 338963002167 Mechanosensitive ion channel; Region: MS_channel; pfam00924 338963002168 Putative zinc-finger; Region: zf-HC2; pfam13490 338963002169 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 338963002170 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 338963002171 transmembrane helices; other site 338963002172 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 338963002173 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 338963002174 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 338963002175 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 338963002176 Beta-Casp domain; Region: Beta-Casp; smart01027 338963002177 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 338963002178 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 338963002179 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 338963002180 dimer interface [polypeptide binding]; other site 338963002181 ssDNA binding site [nucleotide binding]; other site 338963002182 tetramer (dimer of dimers) interface [polypeptide binding]; other site 338963002183 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 338963002184 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 338963002185 putative acyl-acceptor binding pocket; other site 338963002186 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 338963002187 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 338963002188 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 338963002189 Bacitracin resistance protein BacA; Region: BacA; pfam02673 338963002190 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 338963002191 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 338963002192 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 338963002193 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 338963002194 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 338963002195 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 338963002196 Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form...; Region: Band_7_stomatin_like; cd03403 338963002197 YceG-like family; Region: YceG; pfam02618 338963002198 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 338963002199 dimerization interface [polypeptide binding]; other site 338963002200 membrane protein; Provisional; Region: PRK14393 338963002201 group II intron 5' sequence fragment; Pcar_R0096 338963002202 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 338963002203 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963002204 active site 338963002205 phosphorylation site [posttranslational modification] 338963002206 intermolecular recognition site; other site 338963002207 dimerization interface [polypeptide binding]; other site 338963002208 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 338963002209 DNA binding site [nucleotide binding] 338963002210 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 338963002211 dimerization interface [polypeptide binding]; other site 338963002212 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 338963002213 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 338963002214 putative active site [active] 338963002215 heme pocket [chemical binding]; other site 338963002216 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 338963002217 dimer interface [polypeptide binding]; other site 338963002218 phosphorylation site [posttranslational modification] 338963002219 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 338963002220 ATP binding site [chemical binding]; other site 338963002221 Mg2+ binding site [ion binding]; other site 338963002222 G-X-G motif; other site 338963002223 PBP superfamily domain; Region: PBP_like_2; cl17296 338963002224 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 338963002225 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4590 338963002226 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 338963002227 structural tetrad; other site 338963002228 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 338963002229 dimer interface [polypeptide binding]; other site 338963002230 conserved gate region; other site 338963002231 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 338963002232 putative PBP binding loops; other site 338963002233 ABC-ATPase subunit interface; other site 338963002234 ABC-type phosphate transport system, auxiliary component [Inorganic ion transport and metabolism]; Region: COG4985 338963002235 phosphate ABC transporter, permease protein PstA; Region: 3a0107s02c; TIGR00974 338963002236 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 338963002237 dimer interface [polypeptide binding]; other site 338963002238 conserved gate region; other site 338963002239 putative PBP binding loops; other site 338963002240 ABC-ATPase subunit interface; other site 338963002241 phosphate transporter ATP-binding protein; Provisional; Region: PRK14236 338963002242 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 338963002243 Walker A/P-loop; other site 338963002244 ATP binding site [chemical binding]; other site 338963002245 Q-loop/lid; other site 338963002246 ABC transporter signature motif; other site 338963002247 Walker B; other site 338963002248 D-loop; other site 338963002249 H-loop/switch region; other site 338963002250 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 338963002251 PhoU domain; Region: PhoU; pfam01895 338963002252 PhoU domain; Region: PhoU; pfam01895 338963002253 Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a...; Region: nucleoside_deaminase; cd01285 338963002254 nucleoside/Zn binding site; other site 338963002255 dimer interface [polypeptide binding]; other site 338963002256 catalytic motif [active] 338963002257 This domain contains a conserved N-terminal (F/Y)RG motif. It is functionally uncharacterised; Region: FRG; smart00901 338963002258 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; COG2005 338963002259 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 338963002260 Molybdopterin-binding protein [Coenzyme metabolism]; Region: MopI; COG3585 338963002261 Molybdopterin-binding protein [Coenzyme metabolism]; Region: MopI; COG3585 338963002262 PAS domain; Region: PAS_9; pfam13426 338963002263 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 338963002264 PAS domain; Region: PAS_9; pfam13426 338963002265 putative active site [active] 338963002266 heme pocket [chemical binding]; other site 338963002267 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963002268 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963002269 metal binding site [ion binding]; metal-binding site 338963002270 active site 338963002271 I-site; other site 338963002272 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 338963002273 PAS domain S-box; Region: sensory_box; TIGR00229 338963002274 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 338963002275 putative active site [active] 338963002276 heme pocket [chemical binding]; other site 338963002277 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 338963002278 DNA binding residues [nucleotide binding] 338963002279 Aldehyde ferredoxin oxidoreductase, N-terminal domain; Region: AFOR_N; pfam02730 338963002280 Aldehyde:ferredoxin oxidoreductase [Energy production and conversion]; Region: COG2414 338963002281 Aldehyde ferredoxin oxidoreductase, domains 2 & 3; Region: AFOR_C; pfam01314 338963002282 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 338963002283 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 338963002284 Domain of unknown function (DUF1956); Region: DUF1956; pfam09209 338963002285 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 338963002286 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 338963002287 HlyD family secretion protein; Region: HlyD_3; pfam13437 338963002288 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 338963002289 Protein export membrane protein; Region: SecD_SecF; cl14618 338963002290 four helix bundle suffix domain; Region: 4helix_suffix; TIGR04258 338963002291 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 338963002292 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 338963002293 Ligand Binding Site [chemical binding]; other site 338963002294 TIGR00269 family protein; Region: TIGR00269 338963002295 Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / Transcription]; Region: RsbU; COG2208 338963002296 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 338963002297 Predicted Zn-dependent peptidases, insulinase-like [General function prediction only]; Region: COG1026 338963002298 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 338963002299 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 338963002300 Peptidase M16C associated; Region: M16C_assoc; pfam08367 338963002301 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 338963002302 Helix-turn-helix domain; Region: HTH_17; pfam12728 338963002303 PBP superfamily domain; Region: PBP_like; pfam12727 338963002304 ABC-type tungstate transport system, permease component [Coenzyme metabolism]; Region: TupB; COG2998 338963002305 PBP superfamily domain; Region: PBP_like_2; pfam12849 338963002306 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 338963002307 Sulfate transporter family; Region: Sulfate_transp; pfam00916 338963002308 PAS domain S-box; Region: sensory_box; TIGR00229 338963002309 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 338963002310 putative active site [active] 338963002311 heme pocket [chemical binding]; other site 338963002312 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963002313 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963002314 metal binding site [ion binding]; metal-binding site 338963002315 active site 338963002316 I-site; other site 338963002317 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 338963002318 ferredoxin-NADP(+) reductase subunit alpha; Reviewed; Region: PRK06222 338963002319 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)...; Region: DHOD_e_trans_like1; cd06219 338963002320 FAD binding pocket [chemical binding]; other site 338963002321 FAD binding motif [chemical binding]; other site 338963002322 phosphate binding motif [ion binding]; other site 338963002323 beta-alpha-beta structure motif; other site 338963002324 NAD binding pocket [chemical binding]; other site 338963002325 Iron coordination center [ion binding]; other site 338963002326 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 338963002327 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 338963002328 aspartate aminotransferase; Provisional; Region: PRK05764 338963002329 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 338963002330 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963002331 homodimer interface [polypeptide binding]; other site 338963002332 catalytic residue [active] 338963002333 Ycf46; Provisional; Region: ycf46; CHL00195 338963002334 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 338963002335 Walker A motif; other site 338963002336 ATP binding site [chemical binding]; other site 338963002337 Walker B motif; other site 338963002338 arginine finger; other site 338963002339 prolyl-tRNA synthetase; Provisional; Region: PRK09194 338963002340 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 338963002341 dimer interface [polypeptide binding]; other site 338963002342 motif 1; other site 338963002343 active site 338963002344 motif 2; other site 338963002345 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 338963002346 putative deacylase active site [active] 338963002347 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 338963002348 active site 338963002349 motif 3; other site 338963002350 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 338963002351 anticodon binding site; other site 338963002352 Domain of unknown function (DUF4388); Region: DUF4388; pfam14332 338963002353 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 338963002354 active site 338963002355 dimer interface [polypeptide binding]; other site 338963002356 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 338963002357 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 338963002358 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 338963002359 elongation factor Tu; Reviewed; Region: PRK00049 338963002360 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 338963002361 G1 box; other site 338963002362 GEF interaction site [polypeptide binding]; other site 338963002363 GTP/Mg2+ binding site [chemical binding]; other site 338963002364 Switch I region; other site 338963002365 G2 box; other site 338963002366 G3 box; other site 338963002367 Switch II region; other site 338963002368 G4 box; other site 338963002369 G5 box; other site 338963002370 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 338963002371 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 338963002372 Antibiotic Binding Site [chemical binding]; other site 338963002373 50S ribosomal protein L33; Validated; Region: rpmG; PRK00504 338963002374 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 338963002375 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 338963002376 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 338963002377 putative homodimer interface [polypeptide binding]; other site 338963002378 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 338963002379 heterodimer interface [polypeptide binding]; other site 338963002380 homodimer interface [polypeptide binding]; other site 338963002381 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 338963002382 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 338963002383 23S rRNA interface [nucleotide binding]; other site 338963002384 L7/L12 interface [polypeptide binding]; other site 338963002385 putative thiostrepton binding site; other site 338963002386 L25 interface [polypeptide binding]; other site 338963002387 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 338963002388 mRNA/rRNA interface [nucleotide binding]; other site 338963002389 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 338963002390 23S rRNA interface [nucleotide binding]; other site 338963002391 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 338963002392 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 338963002393 L11 interface [polypeptide binding]; other site 338963002394 putative EF-Tu interaction site [polypeptide binding]; other site 338963002395 putative EF-G interaction site [polypeptide binding]; other site 338963002396 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 338963002397 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 338963002398 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 338963002399 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 338963002400 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 338963002401 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 338963002402 RPB3 interaction site [polypeptide binding]; other site 338963002403 RPB1 interaction site [polypeptide binding]; other site 338963002404 RPB11 interaction site [polypeptide binding]; other site 338963002405 RPB10 interaction site [polypeptide binding]; other site 338963002406 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 338963002407 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 338963002408 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 338963002409 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 338963002410 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 338963002411 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 338963002412 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 338963002413 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 338963002414 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 338963002415 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 338963002416 DNA binding site [nucleotide binding] 338963002417 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 338963002418 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 338963002419 S17 interaction site [polypeptide binding]; other site 338963002420 S8 interaction site; other site 338963002421 16S rRNA interaction site [nucleotide binding]; other site 338963002422 streptomycin interaction site [chemical binding]; other site 338963002423 23S rRNA interaction site [nucleotide binding]; other site 338963002424 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 338963002425 30S ribosomal protein S7; Validated; Region: PRK05302 338963002426 elongation factor G; Reviewed; Region: PRK00007 338963002427 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 338963002428 G1 box; other site 338963002429 putative GEF interaction site [polypeptide binding]; other site 338963002430 GTP/Mg2+ binding site [chemical binding]; other site 338963002431 Switch I region; other site 338963002432 G2 box; other site 338963002433 G3 box; other site 338963002434 Switch II region; other site 338963002435 G4 box; other site 338963002436 G5 box; other site 338963002437 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 338963002438 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 338963002439 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 338963002440 elongation factor Tu; Reviewed; Region: PRK00049 338963002441 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 338963002442 G1 box; other site 338963002443 GEF interaction site [polypeptide binding]; other site 338963002444 GTP/Mg2+ binding site [chemical binding]; other site 338963002445 Switch I region; other site 338963002446 G2 box; other site 338963002447 G3 box; other site 338963002448 Switch II region; other site 338963002449 G4 box; other site 338963002450 G5 box; other site 338963002451 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 338963002452 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 338963002453 Antibiotic Binding Site [chemical binding]; other site 338963002454 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 338963002455 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 338963002456 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 338963002457 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 338963002458 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 338963002459 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 338963002460 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 338963002461 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 338963002462 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 338963002463 putative translocon binding site; other site 338963002464 protein-rRNA interface [nucleotide binding]; other site 338963002465 ribosomal protein S3, bacterial type; Region: rpsC_bact; TIGR01009 338963002466 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 338963002467 G-X-X-G motif; other site 338963002468 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 338963002469 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 338963002470 23S rRNA interface [nucleotide binding]; other site 338963002471 5S rRNA interface [nucleotide binding]; other site 338963002472 putative antibiotic binding site [chemical binding]; other site 338963002473 L25 interface [polypeptide binding]; other site 338963002474 L27 interface [polypeptide binding]; other site 338963002475 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 338963002476 23S rRNA interface [nucleotide binding]; other site 338963002477 putative translocon interaction site; other site 338963002478 signal recognition particle (SRP54) interaction site; other site 338963002479 L23 interface [polypeptide binding]; other site 338963002480 trigger factor interaction site; other site 338963002481 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 338963002482 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 338963002483 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 338963002484 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 338963002485 RNA binding site [nucleotide binding]; other site 338963002486 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 338963002487 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 338963002488 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 338963002489 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08061 338963002490 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 338963002491 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 338963002492 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 338963002493 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 338963002494 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 338963002495 5S rRNA interface [nucleotide binding]; other site 338963002496 23S rRNA interface [nucleotide binding]; other site 338963002497 L5 interface [polypeptide binding]; other site 338963002498 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 338963002499 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 338963002500 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 338963002501 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that...; Region: Ribosomal_L30_like; cl00203 338963002502 23S rRNA binding site - archaea [nucleotide binding]; other site 338963002503 23S rRNA binding site - prokaryotes [nucleotide binding]; other site 338963002504 5S rRNA binding site - archaea; other site 338963002505 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 338963002506 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 338963002507 SecY translocase; Region: SecY; pfam00344 338963002508 adenylate kinase; Reviewed; Region: adk; PRK00279 338963002509 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 338963002510 AMP-binding site [chemical binding]; other site 338963002511 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 338963002512 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 338963002513 active site 338963002514 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 338963002515 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 338963002516 30S ribosomal protein S13; Region: bact_S13; TIGR03631 338963002517 30S ribosomal protein S11; Validated; Region: PRK05309 338963002518 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 338963002519 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 338963002520 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 338963002521 RNA binding surface [nucleotide binding]; other site 338963002522 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 338963002523 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 338963002524 alphaNTD homodimer interface [polypeptide binding]; other site 338963002525 alphaNTD - beta interaction site [polypeptide binding]; other site 338963002526 alphaNTD - beta' interaction site [polypeptide binding]; other site 338963002527 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 338963002528 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 338963002529 anthranilate synthase component I; Provisional; Region: PRK13565 338963002530 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 338963002531 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 338963002532 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 338963002533 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 338963002534 glutamine binding [chemical binding]; other site 338963002535 catalytic triad [active] 338963002536 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 338963002537 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 338963002538 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 338963002539 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 338963002540 active site 338963002541 ribulose/triose binding site [chemical binding]; other site 338963002542 phosphate binding site [ion binding]; other site 338963002543 substrate (anthranilate) binding pocket [chemical binding]; other site 338963002544 product (indole) binding pocket [chemical binding]; other site 338963002545 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 338963002546 active site 338963002547 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 338963002548 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 338963002549 ATP binding site [chemical binding]; other site 338963002550 Mg++ binding site [ion binding]; other site 338963002551 motif III; other site 338963002552 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 338963002553 nucleotide binding region [chemical binding]; other site 338963002554 ATP-binding site [chemical binding]; other site 338963002555 Family-5 Uracil-DNA glycosylases (UDG), found in thermophilic organisms; Region: UDG_F5_TTUDGB_like; cd10031 338963002556 Fe-S cluster binding site [ion binding]; other site 338963002557 DNA binding site [nucleotide binding] 338963002558 active site 338963002559 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 338963002560 RNA polymerases M/15 Kd subunit; Region: RNA_POL_M_15KD; cl02717 338963002561 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 338963002562 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 338963002563 LPS assembly outer membrane complex protein LptD; Provisional; Region: PRK03761 338963002564 Organic solvent tolerance protein; Region: OstA_C; pfam04453 338963002565 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 338963002566 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 338963002567 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 338963002568 Septum formation initiator; Region: DivIC; pfam04977 338963002569 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 338963002570 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 338963002571 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 338963002572 active site 338963002573 HIGH motif; other site 338963002574 KMSK motif region; other site 338963002575 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 338963002576 tRNA binding surface [nucleotide binding]; other site 338963002577 anticodon binding site; other site 338963002578 Sporulation related domain; Region: SPOR; pfam05036 338963002579 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; cl15377 338963002580 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 338963002581 Walker A motif; other site 338963002582 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 338963002583 This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of...; Region: MTH1175; cd00851 338963002584 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]; Region: COG1149 338963002585 This protein family's function is unkown. It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion; Region: Fer4_NifH_child; cd03110 338963002586 P loop nucleotide binding; other site 338963002587 switch II; other site 338963002588 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]; Region: COG1149 338963002589 This protein family's function is unkown. It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion; Region: Fer4_NifH_child; cd03110 338963002590 P loop nucleotide binding; other site 338963002591 switch II; other site 338963002592 This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of...; Region: MTH1175; cd00851 338963002593 Dinitrogenase iron-molybdenum cofactor; Region: Nitro_FeMo-Co; pfam02579 338963002594 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 338963002595 PAS domain; Region: PAS_9; pfam13426 338963002596 putative active site [active] 338963002597 heme pocket [chemical binding]; other site 338963002598 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 338963002599 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 338963002600 Walker A motif; other site 338963002601 ATP binding site [chemical binding]; other site 338963002602 Walker B motif; other site 338963002603 arginine finger; other site 338963002604 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 338963002605 dihydropyrimidine dehydrogenase subunit A; Provisional; Region: PRK11749 338963002606 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 338963002607 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 338963002608 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 338963002609 ferredoxin-NADP(+) reductase subunit alpha; Reviewed; Region: PRK06222 338963002610 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)...; Region: DHOD_e_trans_like1; cd06219 338963002611 FAD binding pocket [chemical binding]; other site 338963002612 FAD binding motif [chemical binding]; other site 338963002613 phosphate binding motif [ion binding]; other site 338963002614 beta-alpha-beta structure motif; other site 338963002615 NAD binding pocket [chemical binding]; other site 338963002616 Iron coordination center [ion binding]; other site 338963002617 HEAT repeats; Region: HEAT_2; pfam13646 338963002618 Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin; Region: ARM; cd00020 338963002619 protein binding surface [polypeptide binding]; other site 338963002620 HEAT repeats; Region: HEAT_2; pfam13646 338963002621 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 338963002622 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 338963002623 Zn2+ binding site [ion binding]; other site 338963002624 Mg2+ binding site [ion binding]; other site 338963002625 HEAT repeats; Region: HEAT_2; pfam13646 338963002626 HEAT repeats; Region: HEAT_2; pfam13646 338963002627 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 338963002628 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 338963002629 CoA-binding site [chemical binding]; other site 338963002630 ATP-binding [chemical binding]; other site 338963002631 Esterase/lipase [General function prediction only]; Region: COG1647 338963002632 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 338963002633 Transcriptional regulator [Transcription]; Region: IclR; COG1414 338963002634 Bacterial transcriptional regulator; Region: IclR; pfam01614 338963002635 Uncharacterized conserved protein [Function unknown]; Region: COG0585 338963002636 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 338963002637 Permutation of conserved domain; other site 338963002638 active site 338963002639 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 338963002640 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 338963002641 S-adenosylmethionine binding site [chemical binding]; other site 338963002642 3-deoxy-7-phosphoheptulonate synthase; Reviewed; Region: PRK08673 338963002643 phospho-2-dehydro-3-deoxyheptonate aldolase; Region: DAHP_synth_Bsub; TIGR01361 338963002644 phosphodiesterase YaeI; Provisional; Region: PRK11340 338963002645 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 338963002646 putative active site [active] 338963002647 putative metal binding site [ion binding]; other site 338963002648 primosome assembly protein PriA; Validated; Region: PRK05580 338963002649 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 338963002650 ATP binding site [chemical binding]; other site 338963002651 putative Mg++ binding site [ion binding]; other site 338963002652 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cl17351 338963002653 Predicted ornithine cyclodeaminase, mu-crystallin homolog [Amino acid transport and metabolism]; Region: COG2423 338963002654 ornithine cyclodeaminase; Validated; Region: PRK06823; cl17400 338963002655 Response regulator receiver domain; Region: Response_reg; pfam00072 338963002656 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963002657 active site 338963002658 phosphorylation site [posttranslational modification] 338963002659 intermolecular recognition site; other site 338963002660 dimerization interface [polypeptide binding]; other site 338963002661 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 338963002662 Nitrite and sulphite reductase 4Fe-4S domain; Region: NIR_SIR; pfam01077 338963002663 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 338963002664 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963002665 active site 338963002666 phosphorylation site [posttranslational modification] 338963002667 intermolecular recognition site; other site 338963002668 dimerization interface [polypeptide binding]; other site 338963002669 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 338963002670 DNA binding site [nucleotide binding] 338963002671 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 338963002672 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 338963002673 dimer interface [polypeptide binding]; other site 338963002674 phosphorylation site [posttranslational modification] 338963002675 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 338963002676 ATP binding site [chemical binding]; other site 338963002677 Mg2+ binding site [ion binding]; other site 338963002678 G-X-G motif; other site 338963002679 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 338963002680 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 338963002681 FMN binding site [chemical binding]; other site 338963002682 substrate binding site [chemical binding]; other site 338963002683 putative catalytic residue [active] 338963002684 putative heme d1 biosynthesis radical SAM protein NirJ2; Region: rSAM_NirJ2; TIGR04055 338963002685 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 338963002686 FeS/SAM binding site; other site 338963002687 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 338963002688 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 338963002689 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 338963002690 substrate binding site [chemical binding]; other site 338963002691 active site 338963002692 Ferrochelatase; Region: Ferrochelatase; pfam00762 338963002693 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 338963002694 C-terminal domain interface [polypeptide binding]; other site 338963002695 active site 338963002696 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 338963002697 active site 338963002698 N-terminal domain interface [polypeptide binding]; other site 338963002699 chaperone protein DnaJ; Provisional; Region: PRK14299 338963002700 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 338963002701 HSP70 interaction site [polypeptide binding]; other site 338963002702 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 338963002703 substrate binding site [polypeptide binding]; other site 338963002704 dimer interface [polypeptide binding]; other site 338963002705 protoporphyrinogen oxidase; Reviewed; Region: PRK11883 338963002706 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 338963002707 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 338963002708 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 338963002709 GTP/Mg2+ binding site [chemical binding]; other site 338963002710 G4 box; other site 338963002711 G5 box; other site 338963002712 G1 box; other site 338963002713 Switch I region; other site 338963002714 G2 box; other site 338963002715 G3 box; other site 338963002716 Switch II region; other site 338963002717 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 338963002718 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 338963002719 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 338963002720 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 338963002721 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 338963002722 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 338963002723 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 338963002724 dimer interface [polypeptide binding]; other site 338963002725 conserved gate region; other site 338963002726 putative PBP binding loops; other site 338963002727 ABC-ATPase subunit interface; other site 338963002728 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963002729 molybdenum ABC transporter, ATP-binding protein; Region: modC_ABC; TIGR02142 338963002730 Walker A/P-loop; other site 338963002731 ATP binding site [chemical binding]; other site 338963002732 Q-loop/lid; other site 338963002733 ABC transporter signature motif; other site 338963002734 Walker B; other site 338963002735 D-loop; other site 338963002736 H-loop/switch region; other site 338963002737 TOBE domain; Region: TOBE; cl01440 338963002738 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 338963002739 DNA-binding site [nucleotide binding]; DNA binding site 338963002740 RNA-binding motif; other site 338963002741 palindrome; Pcar_R5081 338963002742 SmpA / OmlA family; Region: SmpA_OmlA; cl17115 338963002743 Nucleoside 2-deoxyribosyltransferase; Region: Nuc_deoxyrib_tr; pfam05014 338963002744 Peptidase family M41; Region: Peptidase_M41; pfam01434 338963002745 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 338963002746 active site 338963002747 Domain of unknown function (DUF4213); Region: DUF4213; pfam13938 338963002748 Domain of unknown function (DUF364); Region: DUF364; pfam04016 338963002749 MarR family; Region: MarR; pfam01047 338963002750 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 338963002751 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 338963002752 putative substrate translocation pore; other site 338963002753 conserved nucleotide sequence; Pcar_R2004 338963002754 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 338963002755 YcfA-like protein; Region: YcfA; pfam07927 338963002756 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 338963002757 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 338963002758 HicB family; Region: HicB; pfam05534 338963002759 conserved nucleotide sequence; Pcar_R5052 338963002760 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 338963002761 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 338963002762 Walker A motif; other site 338963002763 ATP binding site [chemical binding]; other site 338963002764 Walker B motif; other site 338963002765 AAA domain; Region: AAA_30; pfam13604 338963002766 Protein of unknown function DUF262; Region: DUF262; pfam03235 338963002767 Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A; cl02626 338963002768 catalytic site [active] 338963002769 Helix-turn-helix domain; Region: HTH_38; pfam13936 338963002770 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 338963002771 MPN+ (JAMM) motif; other site 338963002772 Zinc-binding site [ion binding]; other site 338963002773 Protein of unknown function (DUF2787); Region: DUF2787; pfam10980 338963002774 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 338963002775 integrase; Provisional; Region: int; PHA02601 338963002776 active site 338963002777 DNA binding site [nucleotide binding] 338963002778 Int/Topo IB signature motif; other site 338963002779 conserved nucleotide sequence; Pcar_R5054 338963002780 'tRNA-Thr, fragment; Pcar_R0073' 338963002781 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 338963002782 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 338963002783 active site 338963002784 DNA binding site [nucleotide binding] 338963002785 Int/Topo IB signature motif; other site 338963002786 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 338963002787 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 338963002788 conserved nucleotide sequence; Pcar_R5055 338963002789 'tRNA-Thr, fragment; Pcar_R0074' 338963002790 Mechanosensitive ion channel; Region: MS_channel; pfam00924 338963002791 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 338963002792 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 338963002793 Domain of unknown function (DUF1956); Region: DUF1956; pfam09209 338963002794 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 338963002795 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 338963002796 HlyD family secretion protein; Region: HlyD_3; pfam13437 338963002797 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 338963002798 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 338963002799 Walker A/P-loop; other site 338963002800 ATP binding site [chemical binding]; other site 338963002801 Q-loop/lid; other site 338963002802 ABC transporter signature motif; other site 338963002803 Walker B; other site 338963002804 D-loop; other site 338963002805 H-loop/switch region; other site 338963002806 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 338963002807 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 338963002808 FtsX-like permease family; Region: FtsX; pfam02687 338963002809 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 338963002810 Sensory domain found in PocR; Region: PocR; pfam10114 338963002811 Predicted sensor domain [Signal transduction mechanisms / Transcription]; Region: PocR; COG4936 338963002812 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963002813 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963002814 metal binding site [ion binding]; metal-binding site 338963002815 active site 338963002816 I-site; other site 338963002817 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 338963002818 seryl-tRNA(sec) selenium transferase; Region: selA; TIGR00474 338963002819 Selenocysteine synthase N terminal; Region: Se-cys_synth_N; pfam12390 338963002820 Selenocysteine synthase [seryl-tRNASer selenium transferase] [Amino acid transport and metabolism]; Region: SelA; COG1921 338963002821 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 338963002822 catalytic residue [active] 338963002823 putative selenium metabolism protein, YedE family; Region: seleno_YedE; TIGR04112 338963002824 SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response...; Region: SirA_like_N; cd03421 338963002825 CPxP motif; other site 338963002826 selenium donor protein; Region: selD; TIGR00476 338963002827 Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The...; Region: SelD; cd02195 338963002828 dimerization interface [polypeptide binding]; other site 338963002829 putative ATP binding site [chemical binding]; other site 338963002830 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 338963002831 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; cl12060 338963002832 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; Region: PhosphMutase; cl17294 338963002833 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 338963002834 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 338963002835 active site 338963002836 nucleotide binding site [chemical binding]; other site 338963002837 HIGH motif; other site 338963002838 KMSKS motif; other site 338963002839 PBP superfamily domain; Region: PBP_like_2; cl17296 338963002840 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstC; COG0573 338963002841 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 338963002842 dimer interface [polypeptide binding]; other site 338963002843 conserved gate region; other site 338963002844 putative PBP binding loops; other site 338963002845 ABC-ATPase subunit interface; other site 338963002846 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 338963002847 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 338963002848 dimer interface [polypeptide binding]; other site 338963002849 conserved gate region; other site 338963002850 putative PBP binding loops; other site 338963002851 ABC-ATPase subunit interface; other site 338963002852 ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: PstB; COG1117 338963002853 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 338963002854 Walker A/P-loop; other site 338963002855 ATP binding site [chemical binding]; other site 338963002856 Q-loop/lid; other site 338963002857 ABC transporter signature motif; other site 338963002858 Walker B; other site 338963002859 D-loop; other site 338963002860 H-loop/switch region; other site 338963002861 Soluble P-type ATPase [General function prediction only]; Region: COG4087 338963002862 Transcriptional regulator [Transcription]; Region: LysR; COG0583 338963002863 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 338963002864 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 338963002865 putative dimerization interface [polypeptide binding]; other site 338963002866 selenocysteinyl-tRNA-specific translation factor; Provisional; Region: PRK10512 338963002867 SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; Region: SelB; cd04171 338963002868 G1 box; other site 338963002869 putative GEF interaction site [polypeptide binding]; other site 338963002870 GTP/Mg2+ binding site [chemical binding]; other site 338963002871 Switch I region; other site 338963002872 G2 box; other site 338963002873 G3 box; other site 338963002874 Switch II region; other site 338963002875 G4 box; other site 338963002876 G5 box; other site 338963002877 selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several...; Region: selB_II; cd03696 338963002878 This family represents the domain of elongation factor SelB, homologous to domain III of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements:...; Region: selB_III; cd04094 338963002879 Elongation factor SelB, winged helix; Region: SelB-wing_2; pfam09106 338963002880 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 338963002881 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 338963002882 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 338963002883 putative dimer interface [polypeptide binding]; other site 338963002884 [2Fe-2S] cluster binding site [ion binding]; other site 338963002885 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 338963002886 dimer interface [polypeptide binding]; other site 338963002887 [2Fe-2S] cluster binding site [ion binding]; other site 338963002888 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 338963002889 SLBB domain; Region: SLBB; pfam10531 338963002890 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 338963002891 Ferredoxin [Energy production and conversion]; Region: COG1146 338963002892 4Fe-4S binding domain; Region: Fer4; pfam00037 338963002893 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 338963002894 4Fe-4S binding domain; Region: Fer4; pfam00037 338963002895 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 338963002896 catalytic loop [active] 338963002897 iron binding site [ion binding]; other site 338963002898 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 338963002899 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 338963002900 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 338963002901 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 338963002902 Protein of unknown function DUF72; Region: DUF72; pfam01904 338963002903 hybrid cluster protein; Provisional; Region: PRK05290 338963002904 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 338963002905 ACS interaction site; other site 338963002906 CODH interaction site; other site 338963002907 Hybrid cluster protein (HCP), formerly known as prismane, is thought to play a role in nitrogen metabolism but its specific function is unknown. HCP has three structural domains, an N-terminal alpha-helical domain, and two similar domains comprising a...; Region: HCP; cd01914 338963002908 hybrid metal cluster; other site 338963002909 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 338963002910 Cation efflux family; Region: Cation_efflux; pfam01545 338963002911 Uncharacterized conserved protein [Function unknown]; Region: COG1433 338963002912 group II intron 5' sequence; Pcar_R0097 338963002913 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 338963002914 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 338963002915 putative active site [active] 338963002916 putative NTP binding site [chemical binding]; other site 338963002917 putative nucleic acid binding site [nucleotide binding]; other site 338963002918 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 338963002919 group II intron 3' sequence; Pcar_R0103 338963002920 Domain of unknown function (DUF4405); Region: DUF4405; pfam14358 338963002921 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 338963002922 TPR motif; other site 338963002923 binding surface 338963002924 TPR repeat; Region: TPR_11; pfam13414 338963002925 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 338963002926 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 338963002927 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 338963002928 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 338963002929 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 338963002930 Protein of unknown function (DUF3450); Region: DUF3450; pfam11932 338963002931 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 338963002932 Uncharacterized subfamily of S-AdoMet dependent tetrapyrrole methylases; Region: TP_methylase_like; cd11724 338963002933 putative SAM binding site [chemical binding]; other site 338963002934 putative homodimer interface [polypeptide binding]; other site 338963002935 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 338963002936 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 338963002937 N-terminal plug; other site 338963002938 ligand-binding site [chemical binding]; other site 338963002939 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 338963002940 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963002941 Walker A/P-loop; other site 338963002942 ATP binding site [chemical binding]; other site 338963002943 Q-loop/lid; other site 338963002944 ABC transporter signature motif; other site 338963002945 Walker B; other site 338963002946 D-loop; other site 338963002947 H-loop/switch region; other site 338963002948 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 338963002949 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 338963002950 dimer interface [polypeptide binding]; other site 338963002951 conserved gate region; other site 338963002952 putative PBP binding loops; other site 338963002953 ABC-ATPase subunit interface; other site 338963002954 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 338963002955 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 338963002956 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 338963002957 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 338963002958 S-adenosylmethionine binding site [chemical binding]; other site 338963002959 flavodoxin FldA; Validated; Region: PRK09267 338963002960 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 338963002961 S-adenosylmethionine binding site [chemical binding]; other site 338963002962 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 338963002963 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 338963002964 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 338963002965 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 338963002966 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 338963002967 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 338963002968 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 338963002969 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 338963002970 Pilus assembly protein, PilO; Region: PilO; cl01234 338963002971 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 338963002972 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 338963002973 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 338963002974 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 338963002975 ATP binding site [chemical binding]; other site 338963002976 Walker B motif; other site 338963002977 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 338963002978 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 338963002979 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 338963002980 Walker A motif; other site 338963002981 ATP binding site [chemical binding]; other site 338963002982 Walker B motif; other site 338963002983 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 338963002984 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 338963002985 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 338963002986 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 338963002987 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 338963002988 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 338963002989 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 338963002990 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 338963002991 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 338963002992 ligand binding site [chemical binding]; other site 338963002993 flexible hinge region; other site 338963002994 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 338963002995 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; cl01811 338963002996 Protein of unknown function (DUF3793); Region: DUF3793; pfam12672 338963002997 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 338963002998 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 338963002999 G1 box; other site 338963003000 GTP/Mg2+ binding site [chemical binding]; other site 338963003001 Switch I region; other site 338963003002 G2 box; other site 338963003003 G3 box; other site 338963003004 Switch II region; other site 338963003005 G4 box; other site 338963003006 G5 box; other site 338963003007 Nucleoside recognition; Region: Gate; pfam07670 338963003008 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 338963003009 Nucleoside recognition; Region: Gate; pfam07670 338963003010 Fe2+ transport system protein A [Inorganic ion transport and metabolism]; Region: FeoA; COG1918 338963003011 conserved nucleotide sequence; Pcar_R3002 338963003012 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional; Region: ribB; PRK03353 338963003013 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]; Region: RibB; COG0108 338963003014 conserved nucleotide sequence; Pcar_R5088 338963003015 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 338963003016 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 338963003017 active site 338963003018 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 338963003019 FeS/SAM binding site; other site 338963003020 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 338963003021 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 338963003022 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 338963003023 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 338963003024 carbon-monoxide dehydrogenase, catalytic subunit; Region: CO_DH_cata; TIGR01702 338963003025 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 338963003026 ACS interaction site; other site 338963003027 CODH interaction site; other site 338963003028 metal cluster binding site [ion binding]; other site 338963003029 Rrf2 family protein; Region: rrf2_super; TIGR00738 338963003030 Transcriptional regulator; Region: Rrf2; pfam02082 338963003031 K+-dependent Na+/Ca+ exchanger related-protein; Region: TIGR00367 338963003032 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 338963003033 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 338963003034 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 338963003035 Transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this domain superfamily was previously known as DUF156; Region: CsoR-like_DUF156; cd10148 338963003036 putative homodimer interface [polypeptide binding]; other site 338963003037 putative homotetramer interface [polypeptide binding]; other site 338963003038 putative allosteric switch controlling residues; other site 338963003039 putative metal binding site [ion binding]; other site 338963003040 putative homodimer-homodimer interface [polypeptide binding]; other site 338963003041 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 338963003042 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 338963003043 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 338963003044 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 338963003045 dimer interface [polypeptide binding]; other site 338963003046 conserved gate region; other site 338963003047 putative PBP binding loops; other site 338963003048 ABC-ATPase subunit interface; other site 338963003049 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 338963003050 dimer interface [polypeptide binding]; other site 338963003051 conserved gate region; other site 338963003052 putative PBP binding loops; other site 338963003053 ABC-ATPase subunit interface; other site 338963003054 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 338963003055 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 338963003056 Walker A/P-loop; other site 338963003057 ATP binding site [chemical binding]; other site 338963003058 Q-loop/lid; other site 338963003059 ABC transporter signature motif; other site 338963003060 Walker B; other site 338963003061 D-loop; other site 338963003062 H-loop/switch region; other site 338963003063 TOBE domain; Region: TOBE_2; pfam08402 338963003064 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; pfam00690 338963003065 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 338963003066 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 338963003067 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 338963003068 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 338963003069 motif II; other site 338963003070 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 338963003071 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 338963003072 active site 338963003073 NTP binding site [chemical binding]; other site 338963003074 metal binding triad [ion binding]; metal-binding site 338963003075 antibiotic binding site [chemical binding]; other site 338963003076 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 338963003077 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 338963003078 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 338963003079 ATP binding site [chemical binding]; other site 338963003080 putative Mg++ binding site [ion binding]; other site 338963003081 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; pfam08780 338963003082 Uncharacterized conserved protein [Function unknown]; Region: COG4715 338963003083 SWIM zinc finger; Region: SWIM; pfam04434 338963003084 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 338963003085 putative active site [active] 338963003086 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 338963003087 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 338963003088 Walker A motif; other site 338963003089 ATP binding site [chemical binding]; other site 338963003090 Walker B motif; other site 338963003091 arginine finger; other site 338963003092 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 338963003093 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 338963003094 acetoin reductases; Region: 23BDH; TIGR02415 338963003095 NAD(P) binding site [chemical binding]; other site 338963003096 active site 338963003097 conserved nucleotide sequence; Pcar_R2005 338963003098 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 338963003099 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 338963003100 FMN binding site [chemical binding]; other site 338963003101 active site 338963003102 catalytic residues [active] 338963003103 substrate binding site [chemical binding]; other site 338963003104 Protein of unknown function (DUF3820); Region: DUF3820; pfam12843 338963003105 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 338963003106 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 338963003107 Walker A/P-loop; other site 338963003108 ATP binding site [chemical binding]; other site 338963003109 Q-loop/lid; other site 338963003110 ABC transporter signature motif; other site 338963003111 Walker B; other site 338963003112 D-loop; other site 338963003113 H-loop/switch region; other site 338963003114 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 338963003115 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 338963003116 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 338963003117 Walker A/P-loop; other site 338963003118 ATP binding site [chemical binding]; other site 338963003119 Q-loop/lid; other site 338963003120 ABC transporter signature motif; other site 338963003121 Walker B; other site 338963003122 D-loop; other site 338963003123 H-loop/switch region; other site 338963003124 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 338963003125 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 338963003126 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 338963003127 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 338963003128 S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression; Region: S1_Tex; cd05685 338963003129 RNA binding site [nucleotide binding]; other site 338963003130 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 338963003131 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 338963003132 active site 338963003133 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 338963003134 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 338963003135 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963003136 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963003137 metal binding site [ion binding]; metal-binding site 338963003138 active site 338963003139 I-site; other site 338963003140 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 338963003141 dimerization interface [polypeptide binding]; other site 338963003142 putative DNA binding site [nucleotide binding]; other site 338963003143 putative Zn2+ binding site [ion binding]; other site 338963003144 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 338963003145 active site residue [active] 338963003146 conserved nucleotide sequence; Pcar_R5056 338963003147 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 338963003148 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 338963003149 putative dimer interface [polypeptide binding]; other site 338963003150 [2Fe-2S] cluster binding site [ion binding]; other site 338963003151 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 338963003152 dimer interface [polypeptide binding]; other site 338963003153 [2Fe-2S] cluster binding site [ion binding]; other site 338963003154 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 338963003155 SLBB domain; Region: SLBB; pfam10531 338963003156 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 338963003157 Homeodomain-like domain; Region: HTH_23; pfam13384 338963003158 Winged helix-turn helix; Region: HTH_29; pfam13551 338963003159 Integrase core domain; Region: rve; pfam00665 338963003160 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 338963003161 Integrase core domain; Region: rve_3; pfam13683 338963003162 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; pfam13557 338963003163 LysE type translocator; Region: LysE; cl00565 338963003164 Conserved hypothetical protein (Lin0512_fam); Region: Lin0512_fam; pfam09585 338963003165 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 338963003166 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 338963003167 putative active site [active] 338963003168 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 338963003169 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 338963003170 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 338963003171 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 338963003172 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 338963003173 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 338963003174 ABC transporter substrate binding protein; Region: ABC_sub_bind; cl17301 338963003175 PAS fold; Region: PAS_4; pfam08448 338963003176 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 338963003177 putative active site [active] 338963003178 heme pocket [chemical binding]; other site 338963003179 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 338963003180 PAS domain; Region: PAS_9; pfam13426 338963003181 putative active site [active] 338963003182 heme pocket [chemical binding]; other site 338963003183 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963003184 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963003185 metal binding site [ion binding]; metal-binding site 338963003186 active site 338963003187 I-site; other site 338963003188 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 338963003189 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 338963003190 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 338963003191 Walker A/P-loop; other site 338963003192 ATP binding site [chemical binding]; other site 338963003193 Q-loop/lid; other site 338963003194 ABC transporter signature motif; other site 338963003195 Walker B; other site 338963003196 D-loop; other site 338963003197 H-loop/switch region; other site 338963003198 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 338963003199 dimer interface [polypeptide binding]; other site 338963003200 conserved gate region; other site 338963003201 ABC-ATPase subunit interface; other site 338963003202 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; cl00614 338963003203 AAK_UMPK-MosAB: This CD includes the alpha and beta subunits of the Mo storage protein (MosA and MosB) which are related to uridine monophosphate kinase (UMPK) enzymes that catalyze the phosphorylation of UMP by ATP, yielding UDP, and playing a key role...; Region: AAK_UMPK-MosAB; cd04255 338963003204 putative nucleotide binding site [chemical binding]; other site 338963003205 putative substrate binding site [chemical binding]; other site 338963003206 Protein of unknown function (DUF4125); Region: DUF4125; pfam13526 338963003207 Domain of unknown function (DUF4037); Region: DUF4037; pfam13228 338963003208 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 338963003209 binding surface 338963003210 TPR motif; other site 338963003211 Tetratricopeptide repeat; Region: TPR_12; pfam13424 338963003212 Tetratricopeptide repeat; Region: TPR_12; pfam13424 338963003213 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 338963003214 PAS domain; Region: PAS_9; pfam13426 338963003215 putative active site [active] 338963003216 heme pocket [chemical binding]; other site 338963003217 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963003218 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963003219 metal binding site [ion binding]; metal-binding site 338963003220 active site 338963003221 I-site; other site 338963003222 glycyl radical enzyme, PFL2/glycerol dehydratase family; Region: PFL2-3; TIGR01774 338963003223 Pyruvate formate lyase 2 and related enzymes; Region: PFL2_DhaB_BssA; cd01677 338963003224 dimer interface [polypeptide binding]; other site 338963003225 active site 338963003226 glycine loop; other site 338963003227 Domain of unknown function (DUF4104); Region: DUF4104; pfam13372 338963003228 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cl17270 338963003229 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 338963003230 active site 338963003231 substrate binding site [chemical binding]; other site 338963003232 ATP binding site [chemical binding]; other site 338963003233 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 338963003234 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 338963003235 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 338963003236 Multidrug resistance efflux transporter; Region: EmrE; pfam13536 338963003237 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 338963003238 EamA-like transporter family; Region: EamA; cl17759 338963003239 heptanucleotide repeats; Pcar_R7009 338963003240 glycyl-radical enzyme activating protein family; Region: PFLE_PFLC; TIGR02494 338963003241 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 338963003242 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 338963003243 conserved nucleotide sequence; Pcar_R0094 338963003244 ATP synthase CF0 B' subunit; Validated; Region: atpG; CHL00118 338963003245 F0F1 ATP synthase subunit B; Validated; Region: PRK07352 338963003246 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 338963003247 F0F1 ATP synthase subunit delta; Provisional; Region: PRK13429 338963003248 F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]; Region: AtpH; cl17210 338963003249 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 338963003250 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 338963003251 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 338963003252 beta subunit interaction interface [polypeptide binding]; other site 338963003253 Walker A motif; other site 338963003254 ATP binding site [chemical binding]; other site 338963003255 Walker B motif; other site 338963003256 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 338963003257 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 338963003258 core domain interface [polypeptide binding]; other site 338963003259 delta subunit interface [polypeptide binding]; other site 338963003260 epsilon subunit interface [polypeptide binding]; other site 338963003261 octanucleotide repeats; Pcar_R8007 338963003262 octanucleotide repeats; Pcar_R8008 338963003263 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 338963003264 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 338963003265 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 338963003266 alpha subunit interaction interface [polypeptide binding]; other site 338963003267 Walker A motif; other site 338963003268 ATP binding site [chemical binding]; other site 338963003269 Walker B motif; other site 338963003270 inhibitor binding site; inhibition site 338963003271 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 338963003272 F0F1 ATP synthase subunit epsilon; Provisional; Region: atpC; PRK13446 338963003273 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 338963003274 gamma subunit interface [polypeptide binding]; other site 338963003275 epsilon subunit interface [polypeptide binding]; other site 338963003276 LBP interface [polypeptide binding]; other site 338963003277 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 338963003278 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 338963003279 ATP synthase subunit C; Region: ATP-synt_C; cl00466 338963003280 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 338963003281 Predicted transcriptional regulator [Transcription]; Region: COG2378 338963003282 WYL domain; Region: WYL; pfam13280 338963003283 helicase Cas3; Provisional; Region: PRK09694 338963003284 CRISPR/Cas system-associated protein Cas3'' Region: Cas3''_I; cd09641 338963003285 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 338963003286 CRISPR/Cas system-associated protein Cse1; Region: Cse1_I-E; cd09729 338963003287 CRISPR/Cas system-associated protein Cse2; Region: Cse2_I-E; cd09731 338963003288 CT1975-like protein; Region: Cas_CT1975; pfam09344 338963003289 CRISPR-associated protein (Cas_Cas5); Region: Cas_Cas5d; pfam09704 338963003290 CRISPR/Cas system-associated RAMP superfamily protein Cas5; Region: Cas5_I-E; cd09645 338963003291 This domain forms an anti-parallel beta strand structure with flanking alpha helical regions; Region: CRISPR_assoc; smart01101 338963003292 PemK-like protein; Region: PemK; pfam02452 338963003293 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]; Region: NikR; COG0864 338963003294 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-E; cd09719 338963003295 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I-E; cd09648 338963003296 conserved nucleotide sequence; Pcar_R5058 338963003297 conserved nucleotide sequence; Pcar_R5059 338963003298 Cache domain; Region: Cache_1; pfam02743 338963003299 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 338963003300 dimerization interface [polypeptide binding]; other site 338963003301 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 338963003302 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 338963003303 dimer interface [polypeptide binding]; other site 338963003304 putative CheW interface [polypeptide binding]; other site 338963003305 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 338963003306 dimer interface [polypeptide binding]; other site 338963003307 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 338963003308 putative CheW interface [polypeptide binding]; other site 338963003309 Predicted transcriptional regulators [Transcription]; Region: COG1695 338963003310 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 338963003311 Multidrug resistance efflux transporter; Region: EmrE; pfam13536 338963003312 EamA-like transporter family; Region: EamA; cl17759 338963003313 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 338963003314 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and...; Region: PLPDE_IV; cd00449 338963003315 homodimer interface [polypeptide binding]; other site 338963003316 substrate-cofactor binding pocket; other site 338963003317 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963003318 catalytic residue [active] 338963003319 Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]; Region: TrpE; COG0147 338963003320 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 338963003321 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 338963003322 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 338963003323 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963003324 active site 338963003325 phosphorylation site [posttranslational modification] 338963003326 intermolecular recognition site; other site 338963003327 dimerization interface [polypeptide binding]; other site 338963003328 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 338963003329 DNA binding residues [nucleotide binding] 338963003330 dimerization interface [polypeptide binding]; other site 338963003331 Sensory domain found in PocR; Region: PocR; pfam10114 338963003332 Predicted sensor domain [Signal transduction mechanisms / Transcription]; Region: PocR; COG4936 338963003333 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 338963003334 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 338963003335 putative active site [active] 338963003336 heme pocket [chemical binding]; other site 338963003337 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 338963003338 dimer interface [polypeptide binding]; other site 338963003339 phosphorylation site [posttranslational modification] 338963003340 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 338963003341 ATP binding site [chemical binding]; other site 338963003342 Mg2+ binding site [ion binding]; other site 338963003343 G-X-G motif; other site 338963003344 conserved nucleotide sequence; Pcar_R5020 338963003345 camphor resistance protein CrcB; Provisional; Region: PRK14222 338963003346 PII-like signaling protein [Signal transduction mechanisms]; Region: COG1993 338963003347 conserved nucleotide sequence; Pcar_R5033 338963003348 EthD domain; Region: EthD; cl17553 338963003349 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 338963003350 conserved nucleotide sequence; Pcar_R5034 338963003351 Domain of unknown function (DUF4372); Region: DUF4372; pfam14294 338963003352 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 338963003353 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 338963003354 conserved nucleotide sequence; Pcar_R5035 338963003355 AAA domain; Region: AAA_31; pfam13614 338963003356 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 338963003357 P-loop; other site 338963003358 Magnesium ion binding site [ion binding]; other site 338963003359 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 338963003360 Magnesium ion binding site [ion binding]; other site 338963003361 Nucleoid-associated protein [General function prediction only]; Region: COG3081 338963003362 37-kD nucleoid-associated bacterial protein; Region: NA37; pfam04245 338963003363 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 338963003364 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 338963003365 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 338963003366 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 338963003367 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 338963003368 Ligand Binding Site [chemical binding]; other site 338963003369 TilS substrate C-terminal domain; Region: TilS_C; smart00977 338963003370 FtsH Extracellular; Region: FtsH_ext; pfam06480 338963003371 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 338963003372 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 338963003373 Walker A motif; other site 338963003374 ATP binding site [chemical binding]; other site 338963003375 Walker B motif; other site 338963003376 arginine finger; other site 338963003377 Peptidase family M41; Region: Peptidase_M41; pfam01434 338963003378 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 338963003379 dihydropteroate synthase; Region: DHPS; TIGR01496 338963003380 substrate binding pocket [chemical binding]; other site 338963003381 dimer interface [polypeptide binding]; other site 338963003382 inhibitor binding site; inhibition site 338963003383 Uncharacterized conserved protein [Function unknown]; Region: COG1624 338963003384 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 338963003385 YbbR-like protein; Region: YbbR; pfam07949 338963003386 YbbR-like protein; Region: YbbR; pfam07949 338963003387 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14314 338963003388 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 338963003389 active site 338963003390 substrate binding site [chemical binding]; other site 338963003391 metal binding site [ion binding]; metal-binding site 338963003392 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 338963003393 active site 338963003394 hydrophilic channel; other site 338963003395 dimerization interface [polypeptide binding]; other site 338963003396 catalytic residues [active] 338963003397 active site lid [active] 338963003398 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 338963003399 FOG: CBS domain [General function prediction only]; Region: COG0517 338963003400 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the BON (bacterial OsmY and nodulation domain) domain. BON is a putative phospholipid-binding domain found in a family of osmotic shock protection...; Region: CBS_pair_BON_assoc; cd04586 338963003401 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 338963003402 aspartate kinase; Reviewed; Region: PRK06635 338963003403 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 338963003404 putative nucleotide binding site [chemical binding]; other site 338963003405 putative catalytic residues [active] 338963003406 putative Mg ion binding site [ion binding]; other site 338963003407 putative aspartate binding site [chemical binding]; other site 338963003408 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 338963003409 putative allosteric regulatory site; other site 338963003410 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 338963003411 putative allosteric regulatory residue; other site 338963003412 putative alpha-isopropylmalate/homocitrate synthase family transferase; Provisional; Region: PRK12344 338963003413 Desulfobacterium autotrophicum LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA3; cd07941 338963003414 active site 338963003415 catalytic residues [active] 338963003416 metal binding site [ion binding]; metal-binding site 338963003417 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 338963003418 comEA protein; Region: comE; TIGR01259 338963003419 Protein of unknown function (DUF983); Region: DUF983; cl02211 338963003420 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 338963003421 Mechanosensitive ion channel; Region: MS_channel; pfam00924 338963003422 Response regulator receiver domain; Region: Response_reg; pfam00072 338963003423 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963003424 active site 338963003425 phosphorylation site [posttranslational modification] 338963003426 intermolecular recognition site; other site 338963003427 dimerization interface [polypeptide binding]; other site 338963003428 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963003429 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963003430 metal binding site [ion binding]; metal-binding site 338963003431 active site 338963003432 I-site; other site 338963003433 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 338963003434 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 338963003435 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 338963003436 dimerization interface [polypeptide binding]; other site 338963003437 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 338963003438 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 338963003439 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 338963003440 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 338963003441 ATP binding site [chemical binding]; other site 338963003442 Mg2+ binding site [ion binding]; other site 338963003443 G-X-G motif; other site 338963003444 ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: PhnD; COG3221 338963003445 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 338963003446 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 338963003447 membrane-bound complex binding site; other site 338963003448 hinge residues; other site 338963003449 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 338963003450 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 338963003451 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 338963003452 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 338963003453 putative active site; other site 338963003454 catalytic triad [active] 338963003455 putative dimer interface [polypeptide binding]; other site 338963003456 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 338963003457 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957; cl01113 338963003458 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 338963003459 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 338963003460 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 338963003461 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 338963003462 active site 338963003463 AAA domain; Region: AAA_32; pfam13654 338963003464 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 338963003465 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 338963003466 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 338963003467 Nitrogen regulatory protein P-II; Region: P-II; smart00938 338963003468 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 338963003469 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 338963003470 Etoposide-induced protein 2.4 (EI24); Region: EI24; cl01126 338963003471 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1; Region: FBPase; cd00354 338963003472 AMP binding site [chemical binding]; other site 338963003473 metal binding site [ion binding]; metal-binding site 338963003474 active site 338963003475 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 338963003476 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 338963003477 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Reviewed; Region: PRK11867 338963003478 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 338963003479 TPP-binding site [chemical binding]; other site 338963003480 2-oxoglutarate ferredoxin oxidoreductase subunit alpha; Validated; Region: PRK08659 338963003481 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 338963003482 dimer interface [polypeptide binding]; other site 338963003483 PYR/PP interface [polypeptide binding]; other site 338963003484 TPP binding site [chemical binding]; other site 338963003485 substrate binding site [chemical binding]; other site 338963003486 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 338963003487 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 338963003488 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 338963003489 oxalate/formate antiporter family transporter; Region: 2A0111; TIGR00890 338963003490 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 338963003491 putative substrate translocation pore; other site 338963003492 AIR carboxylase; Region: AIRC; pfam00731 338963003493 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 338963003494 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 338963003495 dimer interface [polypeptide binding]; other site 338963003496 PYR/PP interface [polypeptide binding]; other site 338963003497 TPP binding site [chemical binding]; other site 338963003498 substrate binding site [chemical binding]; other site 338963003499 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 338963003500 Domain of unknown function; Region: EKR; pfam10371 338963003501 4Fe-4S binding domain; Region: Fer4_6; pfam12837 338963003502 4Fe-4S binding domain; Region: Fer4; pfam00037 338963003503 Thiamine pyrophosphate (TPP family), PFOR_PNO subfamily, TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This...; Region: TPP_PFOR_PNO; cd03377 338963003504 TPP-binding site [chemical binding]; other site 338963003505 dimer interface [polypeptide binding]; other site 338963003506 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 338963003507 dimerization interface [polypeptide binding]; other site 338963003508 putative Zn2+ binding site [ion binding]; other site 338963003509 putative DNA binding site [nucleotide binding]; other site 338963003510 malate dehydrogenase; Reviewed; Region: PRK06223 338963003511 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 338963003512 NAD(P) binding site [chemical binding]; other site 338963003513 dimer interface [polypeptide binding]; other site 338963003514 tetramer (dimer of dimers) interface [polypeptide binding]; other site 338963003515 substrate binding site [chemical binding]; other site 338963003516 isocitrate dehydrogenase; Validated; Region: PRK07362 338963003517 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 338963003518 Domain of unknown function (DUF4398); Region: DUF4398; pfam14346 338963003519 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 338963003520 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 338963003521 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 338963003522 dimer interface [polypeptide binding]; other site 338963003523 anticodon binding site; other site 338963003524 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 338963003525 homodimer interface [polypeptide binding]; other site 338963003526 motif 1; other site 338963003527 active site 338963003528 motif 2; other site 338963003529 GAD domain; Region: GAD; pfam02938 338963003530 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 338963003531 motif 3; other site 338963003532 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 338963003533 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 338963003534 dimer interface [polypeptide binding]; other site 338963003535 motif 1; other site 338963003536 active site 338963003537 motif 2; other site 338963003538 motif 3; other site 338963003539 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 338963003540 anticodon binding site; other site 338963003541 Response regulator receiver domain; Region: Response_reg; pfam00072 338963003542 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963003543 active site 338963003544 phosphorylation site [posttranslational modification] 338963003545 intermolecular recognition site; other site 338963003546 dimerization interface [polypeptide binding]; other site 338963003547 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963003548 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963003549 metal binding site [ion binding]; metal-binding site 338963003550 active site 338963003551 I-site; other site 338963003552 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 338963003553 Competence protein; Region: Competence; pfam03772 338963003554 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 338963003555 HDOD domain; Region: HDOD; pfam08668 338963003556 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 338963003557 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 338963003558 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 338963003559 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 338963003560 rod shape-determining protein MreC; Provisional; Region: PRK13922 338963003561 rod shape-determining protein MreC; Region: MreC; pfam04085 338963003562 rod shape-determining protein MreB; Provisional; Region: PRK13927 338963003563 MreB and similar proteins; Region: MreB_like; cd10225 338963003564 nucleotide binding site [chemical binding]; other site 338963003565 Mg binding site [ion binding]; other site 338963003566 putative protofilament interaction site [polypeptide binding]; other site 338963003567 RodZ interaction site [polypeptide binding]; other site 338963003568 periplasmic folding chaperone; Provisional; Region: PRK10788 338963003569 SurA N-terminal domain; Region: SurA_N_3; cl07813 338963003570 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 338963003571 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 338963003572 ATP binding site [chemical binding]; other site 338963003573 active site 338963003574 substrate binding site [chemical binding]; other site 338963003575 heptanucleotide repeats; Pcar_R7010 338963003576 palindrome; Pcar_R5082 338963003577 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 338963003578 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 338963003579 ATP-grasp domain; Region: ATP-grasp; pfam02222 338963003580 Glyoxalase-like domain; Region: Glyoxalase_2; pfam12681 338963003581 Cupin superfamily (DUF985); Region: Cupin_5; pfam06172 338963003582 response regulator PleD; Reviewed; Region: pleD; PRK09581 338963003583 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963003584 active site 338963003585 phosphorylation site [posttranslational modification] 338963003586 intermolecular recognition site; other site 338963003587 dimerization interface [polypeptide binding]; other site 338963003588 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 338963003589 putative active site [active] 338963003590 heme pocket [chemical binding]; other site 338963003591 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963003592 metal binding site [ion binding]; metal-binding site 338963003593 active site 338963003594 I-site; other site 338963003595 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 338963003596 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 338963003597 HAMP domain; Region: HAMP; pfam00672 338963003598 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 338963003599 dimer interface [polypeptide binding]; other site 338963003600 phosphorylation site [posttranslational modification] 338963003601 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 338963003602 ATP binding site [chemical binding]; other site 338963003603 Mg2+ binding site [ion binding]; other site 338963003604 G-X-G motif; other site 338963003605 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963003606 Response regulator receiver domain; Region: Response_reg; pfam00072 338963003607 active site 338963003608 phosphorylation site [posttranslational modification] 338963003609 intermolecular recognition site; other site 338963003610 dimerization interface [polypeptide binding]; other site 338963003611 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 338963003612 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963003613 active site 338963003614 phosphorylation site [posttranslational modification] 338963003615 intermolecular recognition site; other site 338963003616 dimerization interface [polypeptide binding]; other site 338963003617 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 338963003618 putative binding surface; other site 338963003619 active site 338963003620 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 338963003621 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 338963003622 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 338963003623 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 338963003624 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 338963003625 RNA binding surface [nucleotide binding]; other site 338963003626 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 338963003627 S-AdoMet dependent tetrapyrrole methylases; Region: TP_methylase; cl00304 338963003628 active site 338963003629 homodimer interface [polypeptide binding]; other site 338963003630 SAM binding site [chemical binding]; other site 338963003631 DNA repair exonuclease [DNA replication, recombination, and repair]; Region: SbcD; COG0420 338963003632 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 338963003633 active site 338963003634 metal binding site [ion binding]; metal-binding site 338963003635 DNA binding site [nucleotide binding] 338963003636 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963003637 AAA domain; Region: AAA_23; pfam13476 338963003638 Walker A/P-loop; other site 338963003639 ATP binding site [chemical binding]; other site 338963003640 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963003641 Walker B; other site 338963003642 D-loop; other site 338963003643 H-loop/switch region; other site 338963003644 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 338963003645 nucleotide binding site/active site [active] 338963003646 HIT family signature motif; other site 338963003647 catalytic residue [active] 338963003648 DnaK suppressor protein [Signal transduction mechanisms]; Region: DksA; COG1734 338963003649 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 338963003650 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 338963003651 Zn2+ binding site [ion binding]; other site 338963003652 Mg2+ binding site [ion binding]; other site 338963003653 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 338963003654 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 338963003655 Uncharacterized conserved protein [Function unknown]; Region: COG0432 338963003656 Methyltransferase domain; Region: Methyltransf_31; pfam13847 338963003657 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 338963003658 S-adenosylmethionine binding site [chemical binding]; other site 338963003659 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 338963003660 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 338963003661 putative RNA binding site [nucleotide binding]; other site 338963003662 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 338963003663 cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E. coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these...; Region: cyclophilin_EcCYP_like; cd01920 338963003664 substrate binding site [chemical binding]; other site 338963003665 4Fe-4S binding domain; Region: Fer4_5; pfam12801 338963003666 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 338963003667 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 338963003668 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 338963003669 conserved nucleotide sequence fragment; Pcar_R7210 338963003670 nicotinate phosphoribosyltransferase; Validated; Region: PRK09243 338963003671 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 338963003672 active site 338963003673 This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS)...; Region: YbaK_deacylase; cd00002 338963003674 putative deacylase active site [active] 338963003675 Rhomboid family; Region: Rhomboid; pfam01694 338963003676 putative succinate semialdehyde dehydrogenase; Provisional; Region: PRK13968 338963003677 Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 1-like; Region: ALDH_SSADH1_GabD1; cd07100 338963003678 NAD(P) binding site [chemical binding]; other site 338963003679 catalytic residues [active] 338963003680 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 338963003681 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 338963003682 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 338963003683 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 338963003684 Uncharacterized homolog of PrgY (pheromone shutdown protein) [Function unknown]; Region: COG1916 338963003685 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 338963003686 dimerization interface [polypeptide binding]; other site 338963003687 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 338963003688 PAS fold; Region: PAS_3; pfam08447 338963003689 putative active site [active] 338963003690 heme pocket [chemical binding]; other site 338963003691 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963003692 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963003693 metal binding site [ion binding]; metal-binding site 338963003694 active site 338963003695 I-site; other site 338963003696 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 338963003697 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 338963003698 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 338963003699 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 338963003700 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 338963003701 short chain dehydrogenase; Provisional; Region: PRK06172 338963003702 classical (c) SDRs; Region: SDR_c; cd05233 338963003703 NAD(P) binding site [chemical binding]; other site 338963003704 active site 338963003705 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 338963003706 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 338963003707 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 338963003708 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; cl07055 338963003709 DnaA box-binding interface [nucleotide binding]; other site 338963003710 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 338963003711 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 338963003712 dimer interface [polypeptide binding]; other site 338963003713 active site 338963003714 metal binding site [ion binding]; metal-binding site 338963003715 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 338963003716 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 338963003717 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 338963003718 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN_family; cd02803 338963003719 active site 338963003720 FMN binding site [chemical binding]; other site 338963003721 substrate binding site [chemical binding]; other site 338963003722 putative catalytic residue [active] 338963003723 Predicted transcriptional regulators [Transcription]; Region: COG1733 338963003724 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 338963003725 dimerization interface [polypeptide binding]; other site 338963003726 putative DNA binding site [nucleotide binding]; other site 338963003727 putative Zn2+ binding site [ion binding]; other site 338963003728 Transcriptional regulator [Transcription]; Region: LysR; COG0583 338963003729 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 338963003730 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 338963003731 dimerization interface [polypeptide binding]; other site 338963003732 Membrane transport protein; Region: Mem_trans; cl09117 338963003733 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 338963003734 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 338963003735 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 338963003736 Virulence protein [General function prediction only]; Region: COG3943 338963003737 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 338963003738 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 338963003739 non-specific DNA binding site [nucleotide binding]; other site 338963003740 salt bridge; other site 338963003741 sequence-specific DNA binding site [nucleotide binding]; other site 338963003742 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 338963003743 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 338963003744 dimer interface [polypeptide binding]; other site 338963003745 active site 338963003746 metal binding site [ion binding]; metal-binding site 338963003747 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 338963003748 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 338963003749 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 338963003750 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 338963003751 active site 338963003752 catalytic tetrad [active] 338963003753 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 338963003754 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 338963003755 HlyD family secretion protein; Region: HlyD_3; pfam13437 338963003756 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 338963003757 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 338963003758 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 338963003759 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 338963003760 putative substrate translocation pore; other site 338963003761 recombination factor protein RarA/unknown domain fusion protein; Reviewed; Region: PRK13341 338963003762 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 338963003763 Walker A motif; other site 338963003764 ATP binding site [chemical binding]; other site 338963003765 Walker B motif; other site 338963003766 arginine finger; other site 338963003767 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 338963003768 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 338963003769 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 338963003770 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 338963003771 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 338963003772 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 338963003773 Response regulator receiver domain; Region: Response_reg; pfam00072 338963003774 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963003775 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963003776 metal binding site [ion binding]; metal-binding site 338963003777 active site 338963003778 I-site; other site 338963003779 heptanucleotide repeats; Pcar_R7011 338963003780 PilZ domain; Region: PilZ; pfam07238 338963003781 PilZ domain; Region: PilZ; pfam07238 338963003782 Flagellar protein FliS; Region: FliS; cl00654 338963003783 Flagellar capping protein [Cell motility and secretion]; Region: FliD; COG1345 338963003784 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 338963003785 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 338963003786 FlaG protein; Region: FlaG; pfam03646 338963003787 flagellin; Provisional; Region: PRK12802 338963003788 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 338963003789 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 338963003790 flagellin; Provisional; Region: PRK12802 338963003791 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 338963003792 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 338963003793 N-terminal catalytic domain of alpha-galactosidase; glycoside hydrolase family 57 (GH57); Region: GH57N_PfGalA_like; cd10794 338963003794 putative active site [active] 338963003795 catalytic site [active] 338963003796 Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis]; Region: Fmt; COG0223 338963003797 Formyl transferase catalytic core domain found in a group of proteins with unknown functions; Region: FMT_core_like_4; cd08651 338963003798 putative active site [active] 338963003799 putative substrate binding site [chemical binding]; other site 338963003800 putative cosubstrate binding site; other site 338963003801 catalytic site [active] 338963003802 C-terminal subdomain of the formyltransferase domain on ArnA, which modifies lipid A with 4-amino-4-deoxy-l-arabinose; Region: Arna_FMT_C; cd08702 338963003803 active site 338963003804 Uncharacterized proteins, LmbE homologs [Function unknown]; Region: COG2120 338963003805 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis]; Region: RimK; COG0189 338963003806 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 338963003807 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 338963003808 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 338963003809 NAD(P) binding site [chemical binding]; other site 338963003810 active site 338963003811 Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase] [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvB; COG0028 338963003812 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 338963003813 PYR/PP interface [polypeptide binding]; other site 338963003814 dimer interface [polypeptide binding]; other site 338963003815 TPP binding site [chemical binding]; other site 338963003816 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 338963003817 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 338963003818 TPP-binding site [chemical binding]; other site 338963003819 dimer interface [polypeptide binding]; other site 338963003820 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 338963003821 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 338963003822 active site 338963003823 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 338963003824 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 338963003825 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 338963003826 Radical SAM superfamily; Region: Radical_SAM; pfam04055 338963003827 FeS/SAM binding site; other site 338963003828 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 338963003829 Fe-S oxidoreductase [Energy production and conversion]; Region: COG1032 338963003830 B12 binding domain; Region: B12-binding; pfam02310 338963003831 B12 binding site [chemical binding]; other site 338963003832 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 338963003833 FeS/SAM binding site; other site 338963003834 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 338963003835 binding surface 338963003836 Tetratricopeptide repeat; Region: TPR_16; pfam13432 338963003837 TPR motif; other site 338963003838 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 338963003839 FeS/SAM binding site; other site 338963003840 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 338963003841 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 338963003842 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 338963003843 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 338963003844 NAD(P) binding site [chemical binding]; other site 338963003845 active site 338963003846 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; cl17405 338963003847 lipopolysaccharide biosynthesis protein RfbH; Provisional; Region: PRK15407 338963003848 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 338963003849 inhibitor-cofactor binding pocket; inhibition site 338963003850 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963003851 catalytic residue [active] 338963003852 CDP-glucose 4,6-dehydratase; Region: CDP_4_6_dhtase; TIGR02622 338963003853 CDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: CDP_GD_SDR_e; cd05252 338963003854 NAD binding site [chemical binding]; other site 338963003855 homotetramer interface [polypeptide binding]; other site 338963003856 homodimer interface [polypeptide binding]; other site 338963003857 substrate binding site [chemical binding]; other site 338963003858 active site 338963003859 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 338963003860 G1P_cytidylyltransferase catalyzes the production of CDP-D-Glucose; Region: G1P_cytidylyltransferase; cd02524 338963003861 substrate binding site; other site 338963003862 B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the...; Region: radical_SAM_B12_BD; cd02068 338963003863 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 338963003864 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 338963003865 FeS/SAM binding site; other site 338963003866 Methyltransferase domain; Region: Methyltransf_31; pfam13847 338963003867 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 338963003868 S-adenosylmethionine binding site [chemical binding]; other site 338963003869 pseudaminic acid biosynthesis-associated protein PseG; Region: PseG; TIGR03590 338963003870 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 338963003871 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 338963003872 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 338963003873 active site 338963003874 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 338963003875 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 338963003876 active site 338963003877 catalytic tetrad [active] 338963003878 gluconate 5-dehydrogenase; Provisional; Region: PRK08213 338963003879 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 338963003880 NAD(P) binding site [chemical binding]; other site 338963003881 active site 338963003882 NeuB family; Region: NeuB; pfam03102 338963003883 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 338963003884 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 338963003885 inhibitor-cofactor binding pocket; inhibition site 338963003886 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963003887 catalytic residue [active] 338963003888 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 338963003889 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 338963003890 NAD(P) binding site [chemical binding]; other site 338963003891 homodimer interface [polypeptide binding]; other site 338963003892 substrate binding site [chemical binding]; other site 338963003893 active site 338963003894 Protein of unknown function DUF115; Region: MAF_flag10; pfam01973 338963003895 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 338963003896 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 338963003897 binding surface 338963003898 TPR motif; other site 338963003899 Protein of unknown function DUF115; Region: MAF_flag10; pfam01973 338963003900 flagellar assembly protein FliW; Provisional; Region: PRK13285 338963003901 Global regulator protein family; Region: CsrA; pfam02599 338963003902 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 338963003903 flagellar hook-associated protein FlgL; Validated; Region: flgL; PRK07701 338963003904 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 338963003905 conserved nucleotide sequence; Pcar_R2006 338963003906 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK07739 338963003907 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 338963003908 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 338963003909 flagellar biosynthesis anti-sigma factor FlgM; Region: FlgM_jcvi; TIGR03824 338963003910 Rod binding protein; Region: Rod-binding; pfam10135 338963003911 heptanucleotide repeats; Pcar_R7012 338963003912 heptanucleotide repeats; Pcar_R7013 338963003913 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 338963003914 Flagellar P-ring protein; Region: FlgI; pfam02119 338963003915 heptanucleotide repeats; Pcar_R7014 338963003916 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 338963003917 Flagellar L-ring protein; Region: FlgH; pfam02107 338963003918 SAF-like; Region: SAF_2; pfam13144 338963003919 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 338963003920 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 338963003921 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 338963003922 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 338963003923 flagellar hook-basal body protein; Region: FlgEFG_subfam; TIGR03506 338963003924 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 338963003925 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 338963003926 Predicted transcriptional regulator [General function prediction only]; Region: COG2522 338963003927 RNA polymerase sigma factor, FliA/WhiG family; Region: FliA_WhiG; TIGR02479 338963003928 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 338963003929 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 338963003930 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 338963003931 DNA binding residues [nucleotide binding] 338963003932 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 338963003933 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 338963003934 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 338963003935 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 338963003936 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 338963003937 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 338963003938 FHIPEP family; Region: FHIPEP; pfam00771 338963003939 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 338963003940 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 338963003941 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 338963003942 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 338963003943 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 338963003944 flagellar biosynthetic protein FliO; Region: FliO_TIGR; TIGR03500 338963003945 flagellar motor switch protein FliN; Region: fliN; TIGR02480 338963003946 Flagellar motor switch protein [Cell motility and secretion]; Region: FliM; COG1868 338963003947 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 338963003948 Flagellar basal body-associated protein FliL; Region: FliL; pfam03748 338963003949 flagellar motor protein MotS; Reviewed; Region: PRK06925 338963003950 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 338963003951 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 338963003952 ligand binding site [chemical binding]; other site 338963003953 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 338963003954 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 338963003955 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 338963003956 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 338963003957 dimer interface [polypeptide binding]; other site 338963003958 decamer (pentamer of dimers) interface [polypeptide binding]; other site 338963003959 catalytic triad [active] 338963003960 peroxidatic and resolving cysteines [active] 338963003961 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963003962 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963003963 metal binding site [ion binding]; metal-binding site 338963003964 active site 338963003965 I-site; other site 338963003966 group II intron 5' sequence fragment; Pcar_R0098 338963003967 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 338963003968 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 338963003969 dimer interface [polypeptide binding]; other site 338963003970 active site 338963003971 heme binding site [chemical binding]; other site 338963003972 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 338963003973 Autotransporter beta-domain; Region: Autotransporter; smart00869 338963003974 Response regulator receiver domain; Region: Response_reg; pfam00072 338963003975 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963003976 active site 338963003977 phosphorylation site [posttranslational modification] 338963003978 intermolecular recognition site; other site 338963003979 dimerization interface [polypeptide binding]; other site 338963003980 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 338963003981 GAF domain; Region: GAF_3; pfam13492 338963003982 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963003983 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963003984 metal binding site [ion binding]; metal-binding site 338963003985 active site 338963003986 I-site; other site 338963003987 HEAT repeats; Region: HEAT_2; pfam13646 338963003988 HEAT repeats; Region: HEAT_2; pfam13646 338963003989 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 338963003990 Zn2+ binding site [ion binding]; other site 338963003991 Mg2+ binding site [ion binding]; other site 338963003992 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 338963003993 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 338963003994 ligand binding site [chemical binding]; other site 338963003995 flexible hinge region; other site 338963003996 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 338963003997 Double zinc ribbon; Region: DZR; pfam12773 338963003998 Adenylyl- / guanylyl cyclase, catalytic domain; Region: CYCc; smart00044 338963003999 cyclase homology domain; Region: CHD; cd07302 338963004000 nucleotidyl binding site; other site 338963004001 metal binding site [ion binding]; metal-binding site 338963004002 dimer interface [polypeptide binding]; other site 338963004003 Predicted ATPase [General function prediction only]; Region: COG3899 338963004004 AAA ATPase domain; Region: AAA_16; pfam13191 338963004005 FOG: TPR repeat [General function prediction only]; Region: NrfG; COG0457 338963004006 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 338963004007 TPR motif; other site 338963004008 binding surface 338963004009 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 338963004010 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 338963004011 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 338963004012 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 338963004013 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 338963004014 Protein of unknown function (DUF3766); Region: DUF3766; cl11797 338963004015 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 338963004016 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 338963004017 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 338963004018 Uncharacterized conserved protein [Function unknown]; Region: COG3334 338963004019 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 338963004020 Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they...; Region: ATPase_flagellum-secretory_path_III; cd01136 338963004021 Walker A motif/ATP binding site; other site 338963004022 Walker B motif; other site 338963004023 Flagellar biosynthesis/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FliH; COG1317 338963004024 Flagellar assembly protein FliH; Region: FliH; pfam02108 338963004025 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 338963004026 FliG C-terminal domain; Region: FliG_C; pfam01706 338963004027 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 338963004028 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 338963004029 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 338963004030 Flagellar hook-basal body complex protein FliE; Region: FliE; pfam02049 338963004031 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 338963004032 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 338963004033 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 338963004034 flagellar basal-body rod protein FlgB; Region: FlgB; TIGR01396 338963004035 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 338963004036 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 338963004037 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 338963004038 putative binding surface; other site 338963004039 active site 338963004040 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 338963004041 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 338963004042 putative binding surface; other site 338963004043 active site 338963004044 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 338963004045 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 338963004046 ATP binding site [chemical binding]; other site 338963004047 Mg2+ binding site [ion binding]; other site 338963004048 G-X-G motif; other site 338963004049 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 338963004050 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 338963004051 putative CheA interaction surface; other site 338963004052 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 338963004053 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 338963004054 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 338963004055 S-adenosylmethionine binding site [chemical binding]; other site 338963004056 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 338963004057 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963004058 active site 338963004059 phosphorylation site [posttranslational modification] 338963004060 intermolecular recognition site; other site 338963004061 dimerization interface [polypeptide binding]; other site 338963004062 CheB methylesterase; Region: CheB_methylest; pfam01339 338963004063 CheD chemotactic sensory transduction; Region: CheD; cl00810 338963004064 HDOD domain; Region: HDOD; pfam08668 338963004065 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 338963004066 Zn2+ binding site [ion binding]; other site 338963004067 Mg2+ binding site [ion binding]; other site 338963004068 Response regulator receiver domain; Region: Response_reg; pfam00072 338963004069 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963004070 active site 338963004071 phosphorylation site [posttranslational modification] 338963004072 intermolecular recognition site; other site 338963004073 dimerization interface [polypeptide binding]; other site 338963004074 Response regulator receiver domain; Region: Response_reg; pfam00072 338963004075 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963004076 active site 338963004077 phosphorylation site [posttranslational modification] 338963004078 intermolecular recognition site; other site 338963004079 dimerization interface [polypeptide binding]; other site 338963004080 Predicted inhibitor of MCP methylation, homolog of CheC [Cell motility and secretion]; Region: COG1406 338963004081 Chemotaxis phosphatase CheX; Region: CheX; pfam13690 338963004082 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 338963004083 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963004084 active site 338963004085 phosphorylation site [posttranslational modification] 338963004086 intermolecular recognition site; other site 338963004087 dimerization interface [polypeptide binding]; other site 338963004088 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 338963004089 Walker A motif; other site 338963004090 ATP binding site [chemical binding]; other site 338963004091 Walker B motif; other site 338963004092 arginine finger; other site 338963004093 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 338963004094 AmmeMemoRadiSam system protein A; Region: AmmeMemoSam_A; TIGR04335 338963004095 AMMECR1; Region: AMMECR1; pfam01871 338963004096 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 338963004097 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 338963004098 G1 box; other site 338963004099 putative GEF interaction site [polypeptide binding]; other site 338963004100 GTP/Mg2+ binding site [chemical binding]; other site 338963004101 Switch I region; other site 338963004102 G2 box; other site 338963004103 G3 box; other site 338963004104 Switch II region; other site 338963004105 G4 box; other site 338963004106 G5 box; other site 338963004107 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 338963004108 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 338963004109 Peptidase family M48; Region: Peptidase_M48; pfam01435 338963004110 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 338963004111 binding surface 338963004112 TPR motif; other site 338963004113 TPR repeat; Region: TPR_11; pfam13414 338963004114 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 338963004115 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 338963004116 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 338963004117 FeS/SAM binding site; other site 338963004118 TRAM domain; Region: TRAM; pfam01938 338963004119 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; Region: PHP_HisPPase; cd07432 338963004120 active site 338963004121 hypothetical protein; Provisional; Region: PRK06361 338963004122 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 338963004123 M42 Peptidase, Endoglucanases; Region: M42_Frv; cd05656 338963004124 oligomer interface [polypeptide binding]; other site 338963004125 active site 338963004126 metal binding site [ion binding]; metal-binding site 338963004127 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 338963004128 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 338963004129 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 338963004130 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 338963004131 active site 338963004132 GMP synthase; Reviewed; Region: guaA; PRK00074 338963004133 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 338963004134 AMP/PPi binding site [chemical binding]; other site 338963004135 candidate oxyanion hole; other site 338963004136 catalytic triad [active] 338963004137 potential glutamine specificity residues [chemical binding]; other site 338963004138 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 338963004139 ATP Binding subdomain [chemical binding]; other site 338963004140 Ligand Binding sites [chemical binding]; other site 338963004141 Dimerization subdomain; other site 338963004142 Predicted transcriptional regulator [Transcription]; Region: COG2378 338963004143 HTH domain; Region: HTH_11; pfam08279 338963004144 WYL domain; Region: WYL; pfam13280 338963004145 Maf-like protein; Region: Maf; pfam02545 338963004146 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 338963004147 active site 338963004148 dimer interface [polypeptide binding]; other site 338963004149 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 338963004150 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; Region: PHP_PolIIIA_DnaE3; cd12113 338963004151 active site 338963004152 PHP Thumb interface [polypeptide binding]; other site 338963004153 metal binding site [ion binding]; metal-binding site 338963004154 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 338963004155 generic binding surface II; other site 338963004156 generic binding surface I; other site 338963004157 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 338963004158 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 338963004159 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 338963004160 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 338963004161 Sporulation related domain; Region: SPOR; pfam05036 338963004162 HDOD domain; Region: HDOD; pfam08668 338963004163 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963004164 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963004165 metal binding site [ion binding]; metal-binding site 338963004166 active site 338963004167 I-site; other site 338963004168 glycerate kinase; Region: TIGR00045 338963004169 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 338963004170 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 338963004171 FtsH Extracellular; Region: FtsH_ext; pfam06480 338963004172 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 338963004173 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 338963004174 Walker A motif; other site 338963004175 ATP binding site [chemical binding]; other site 338963004176 Walker B motif; other site 338963004177 arginine finger; other site 338963004178 Peptidase family M41; Region: Peptidase_M41; pfam01434 338963004179 palindrome; Pcar_R5083 338963004180 enolase; Provisional; Region: eno; PRK00077 338963004181 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 338963004182 dimer interface [polypeptide binding]; other site 338963004183 metal binding site [ion binding]; metal-binding site 338963004184 substrate binding pocket [chemical binding]; other site 338963004185 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 338963004186 PhoH-like protein; Region: PhoH; pfam02562 338963004187 Predicted membrane-associated HD superfamily hydrolase [General function prediction only]; Region: COG1480 338963004188 7TM receptor with intracellular HD hydrolase; Region: 7TM-7TMR_HD; pfam07698 338963004189 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 338963004190 Zn2+ binding site [ion binding]; other site 338963004191 Mg2+ binding site [ion binding]; other site 338963004192 Uncharacterized protein family UPF0054; Region: UPF0054; pfam02130 338963004193 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; pfam01219 338963004194 PAP2_like proteins, diacylglycerol_kinase like sub-family. In some prokaryotes, PAP2_like phosphatase domains appear fused to E. coli DAGK-like trans-membrane diacylglycerol kinase domains. The cellular function of these architectures remains to be...; Region: PAP2_diacylglycerolkinase; cd03383 338963004195 active site 338963004196 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 338963004197 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 338963004198 Transporter associated domain; Region: CorC_HlyC; smart01091 338963004199 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 338963004200 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 338963004201 putative active site [active] 338963004202 catalytic triad [active] 338963004203 putative dimer interface [polypeptide binding]; other site 338963004204 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 338963004205 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 338963004206 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 338963004207 NAD(P) binding site [chemical binding]; other site 338963004208 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 338963004209 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate family; Region: PorD_KorD; TIGR02179 338963004210 4Fe-4S binding domain; Region: Fer4; pfam00037 338963004211 pyruvate ferredoxin oxidoreductase subunit alpha; Reviewed; Region: porA; PRK08367 338963004212 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 338963004213 dimer interface [polypeptide binding]; other site 338963004214 PYR/PP interface [polypeptide binding]; other site 338963004215 TPP binding site [chemical binding]; other site 338963004216 substrate binding site [chemical binding]; other site 338963004217 pyruvate ferredoxin oxidoreductase subunit beta; Provisional; Region: PRK11865 338963004218 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 338963004219 TPP-binding site [chemical binding]; other site 338963004220 acyl-CoA synthetase; Provisional; Region: PRK12583 338963004221 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 338963004222 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_2; cd05917 338963004223 acyl-activating enzyme (AAE) consensus motif; other site 338963004224 putative AMP binding site [chemical binding]; other site 338963004225 putative active site [active] 338963004226 putative CoA binding site [chemical binding]; other site 338963004227 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 338963004228 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 338963004229 acyl-activating enzyme (AAE) consensus motif; other site 338963004230 AMP binding site [chemical binding]; other site 338963004231 active site 338963004232 CoA binding site [chemical binding]; other site 338963004233 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 338963004234 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 338963004235 non-specific DNA binding site [nucleotide binding]; other site 338963004236 salt bridge; other site 338963004237 sequence-specific DNA binding site [nucleotide binding]; other site 338963004238 Cupin domain; Region: Cupin_2; pfam07883 338963004239 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 338963004240 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 338963004241 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963004242 catalytic residue [active] 338963004243 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 338963004244 EamA-like transporter family; Region: EamA; pfam00892 338963004245 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 338963004246 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 338963004247 putative catalytic cysteine [active] 338963004248 peptide chain release factor 2; Validated; Region: prfB; PRK00578 338963004249 This domain is found in peptide chain release factors; Region: PCRF; smart00937 338963004250 RF-1 domain; Region: RF-1; pfam00472 338963004251 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 338963004252 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 338963004253 dimer interface [polypeptide binding]; other site 338963004254 putative anticodon binding site; other site 338963004255 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 338963004256 motif 1; other site 338963004257 active site 338963004258 motif 2; other site 338963004259 motif 3; other site 338963004260 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 338963004261 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 338963004262 FtsX-like permease family; Region: FtsX; pfam02687 338963004263 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 338963004264 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 338963004265 Walker A/P-loop; other site 338963004266 ATP binding site [chemical binding]; other site 338963004267 Q-loop/lid; other site 338963004268 ABC transporter signature motif; other site 338963004269 Walker B; other site 338963004270 D-loop; other site 338963004271 H-loop/switch region; other site 338963004272 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 338963004273 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 338963004274 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 338963004275 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 338963004276 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 338963004277 Surface antigen; Region: Bac_surface_Ag; pfam01103 338963004278 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 338963004279 periplasmic chaperone; Provisional; Region: PRK10780 338963004280 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 338963004281 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 338963004282 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 338963004283 trimer interface [polypeptide binding]; other site 338963004284 active site 338963004285 UDP-GlcNAc binding site [chemical binding]; other site 338963004286 lipid binding site [chemical binding]; lipid-binding site 338963004287 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 338963004288 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 338963004289 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 338963004290 active site 338963004291 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 338963004292 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 338963004293 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 338963004294 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 338963004295 inhibitor-cofactor binding pocket; inhibition site 338963004296 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963004297 catalytic residue [active] 338963004298 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 338963004299 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 338963004300 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 338963004301 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 338963004302 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 338963004303 Walker A/P-loop; other site 338963004304 ATP binding site [chemical binding]; other site 338963004305 Q-loop/lid; other site 338963004306 ABC transporter signature motif; other site 338963004307 Walker B; other site 338963004308 D-loop; other site 338963004309 H-loop/switch region; other site 338963004310 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 338963004311 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 338963004312 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 338963004313 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 338963004314 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; pfam02606 338963004315 Uncharacterized conserved protein [Function unknown]; Region: COG2835 338963004316 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 338963004317 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 338963004318 putative active site [active] 338963004319 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 338963004320 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 338963004321 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 338963004322 putative active site [active] 338963004323 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 338963004324 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 338963004325 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 338963004326 active site 338963004327 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 338963004328 active site 338963004329 ATP binding site [chemical binding]; other site 338963004330 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 338963004331 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 338963004332 dimer interface [polypeptide binding]; other site 338963004333 active site 338963004334 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 338963004335 Ligand binding site; other site 338963004336 Putative Catalytic site; other site 338963004337 DXD motif; other site 338963004338 Lipid A Biosynthesis N-terminal domain; Region: LAB_N; cl01627 338963004339 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 338963004340 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 338963004341 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 338963004342 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 338963004343 lipopolysaccharide core heptose(I) kinase RfaP; Provisional; Region: PRK15123 338963004344 NeuB family; Region: NeuB; pfam03102 338963004345 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 338963004346 ligand binding site; other site 338963004347 tetramer interface; other site 338963004348 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 338963004349 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 338963004350 active site 338963004351 motif I; other site 338963004352 motif II; other site 338963004353 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 338963004354 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 338963004355 Substrate binding site; other site 338963004356 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 338963004357 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 338963004358 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 338963004359 putative ribose interaction site [chemical binding]; other site 338963004360 putative ADP binding site [chemical binding]; other site 338963004361 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 338963004362 active site 338963004363 nucleotide binding site [chemical binding]; other site 338963004364 HIGH motif; other site 338963004365 KMSKS motif; other site 338963004366 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 338963004367 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 338963004368 active site 338963004369 motif I; other site 338963004370 motif II; other site 338963004371 hypothetical protein; Provisional; Region: PRK11820 338963004372 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 338963004373 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 338963004374 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 338963004375 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 338963004376 catalytic site [active] 338963004377 G-X2-G-X-G-K; other site 338963004378 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 338963004379 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 338963004380 HD domain; Region: HD_4; pfam13328 338963004381 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 338963004382 synthetase active site [active] 338963004383 NTP binding site [chemical binding]; other site 338963004384 metal binding site [ion binding]; metal-binding site 338963004385 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 338963004386 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 338963004387 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 338963004388 homotrimer interaction site [polypeptide binding]; other site 338963004389 putative active site [active] 338963004390 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 338963004391 Protein of unknown function (DUF523); Region: DUF523; pfam04463 338963004392 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 338963004393 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 338963004394 active site 338963004395 substrate binding site [chemical binding]; other site 338963004396 cosubstrate binding site; other site 338963004397 catalytic site [active] 338963004398 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 338963004399 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 338963004400 dimerization interface [polypeptide binding]; other site 338963004401 putative ATP binding site [chemical binding]; other site 338963004402 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 338963004403 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 338963004404 Coenzyme A binding pocket [chemical binding]; other site 338963004405 dihydroorotate dehydrogenase electron transfer subunit; Reviewed; Region: PRK00054 338963004406 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to...; Region: DHOD_e_trans; cd06218 338963004407 FAD binding pocket [chemical binding]; other site 338963004408 FAD binding motif [chemical binding]; other site 338963004409 phosphate binding motif [ion binding]; other site 338963004410 beta-alpha-beta structure motif; other site 338963004411 NAD binding pocket [chemical binding]; other site 338963004412 Iron coordination center [ion binding]; other site 338963004413 dihydroorotate dehydrogenase (subfamily 1) family protein; Region: pyrD_sub1_fam; TIGR01037 338963004414 Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. 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...; Region: DHOD_1B_like; cd04740 338963004415 heterodimer interface [polypeptide binding]; other site 338963004416 active site 338963004417 FMN binding site [chemical binding]; other site 338963004418 homodimer interface [polypeptide binding]; other site 338963004419 substrate binding site [chemical binding]; other site 338963004420 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 338963004421 DHH family; Region: DHH; pfam01368 338963004422 FOG: CBS domain [General function prediction only]; Region: COG0517 338963004423 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with an upstream DHH domain which performs a phosphoesterase function and a downstream polyA polymerase domain. CBS is a small domain originally...; Region: CBS_pair_DHH_polyA_Pol_assoc; cd04595 338963004424 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 338963004425 active site 338963004426 NTP binding site [chemical binding]; other site 338963004427 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 338963004428 metal binding triad [ion binding]; metal-binding site 338963004429 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 338963004430 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 338963004431 Peptidase family M50; Region: Peptidase_M50; pfam02163 338963004432 active site 338963004433 putative substrate binding region [chemical binding]; other site 338963004434 segregation and condensation protein A; Reviewed; Region: scpA; PRK00104 338963004435 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 338963004436 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 338963004437 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 338963004438 RNA binding surface [nucleotide binding]; other site 338963004439 Pseudouridine synthases, RsuA subfamily; Region: PseudoU_synth_RsuA_like; cd02870 338963004440 active site 338963004441 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 338963004442 TPR motif; other site 338963004443 binding surface 338963004444 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 338963004445 TPR motif; other site 338963004446 Tetratricopeptide repeat; Region: TPR_12; pfam13424 338963004447 binding surface 338963004448 Tetratricopeptide repeat; Region: TPR_12; pfam13424 338963004449 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 338963004450 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 338963004451 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 338963004452 ATP binding site [chemical binding]; other site 338963004453 Mg2+ binding site [ion binding]; other site 338963004454 G-X-G motif; other site 338963004455 MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is...; Region: MutL_Trans; cd00782 338963004456 ATP binding site [chemical binding]; other site 338963004457 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 338963004458 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 338963004459 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 338963004460 bacterial Hfq-like; Region: Hfq; cd01716 338963004461 hexamer interface [polypeptide binding]; other site 338963004462 Sm1 motif; other site 338963004463 RNA binding site [nucleotide binding]; other site 338963004464 Sm2 motif; other site 338963004465 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 338963004466 Tetratricopeptide repeat; Region: TPR_12; pfam13424 338963004467 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 338963004468 binding surface 338963004469 TPR motif; other site 338963004470 TPR repeat; Region: TPR_11; pfam13414 338963004471 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 338963004472 binding surface 338963004473 TPR motif; other site 338963004474 TPR repeat; Region: TPR_11; pfam13414 338963004475 Flagellin N-methylase; Region: FliB; cl00497 338963004476 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 338963004477 This PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily and is found in both archaea and bacteria. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible...; Region: PGM_like2; cd05800 338963004478 active site 338963004479 substrate binding site [chemical binding]; other site 338963004480 metal binding site [ion binding]; metal-binding site 338963004481 EVE domain; Region: EVE; cl00728 338963004482 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 338963004483 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 338963004484 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB; cd01045 338963004485 diiron binding motif [ion binding]; other site 338963004486 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB; cd01045 338963004487 Uncharacterized conserved protein [Function unknown]; Region: COG1633 338963004488 diiron binding motif [ion binding]; other site 338963004489 group II intron 5' sequence; Pcar_R0099 338963004490 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 338963004491 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 338963004492 putative active site [active] 338963004493 putative NTP binding site [chemical binding]; other site 338963004494 putative nucleic acid binding site [nucleotide binding]; other site 338963004495 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 338963004496 Rossmann-like domain; Region: Rossmann-like; pfam10727 338963004497 Domain of unknown function (DUF2520); Region: DUF2520; pfam10728 338963004498 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 338963004499 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 338963004500 ACT domain-containing protein [General function prediction only]; Region: COG4747 338963004501 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains; Region: ACT_Bt0572_1; cd04908 338963004502 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 338963004503 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 338963004504 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 338963004505 acyl-activating enzyme (AAE) consensus motif; other site 338963004506 AMP binding site [chemical binding]; other site 338963004507 active site 338963004508 CoA binding site [chemical binding]; other site 338963004509 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 338963004510 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 338963004511 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 338963004512 N-acetyl-D-glucosamine binding site [chemical binding]; other site 338963004513 catalytic residue [active] 338963004514 L-aspartate oxidase; Provisional; Region: PRK09077 338963004515 L-aspartate oxidase; Provisional; Region: PRK06175 338963004516 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 338963004517 Chorismate mutase type II; Region: CM_2; pfam01817 338963004518 3-deoxy-7-phosphoheptulonate synthase; Reviewed; Region: PRK08673 338963004519 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 338963004520 active site 338963004521 amidophosphoribosyltransferase; Provisional; Region: PRK09123 338963004522 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 338963004523 active site 338963004524 tetramer interface [polypeptide binding]; other site 338963004525 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 338963004526 active site 338963004527 CobB/CobQ-like glutamine amidotransferase domain; Region: GATase_5; pfam13507 338963004528 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 338963004529 conserved cys residue [active] 338963004530 Phosphoribosylformylglycinamidine (FGAM) synthase; Region: PurS; cl00789 338963004531 Phosphoribosylformylglycinamidine (FGAM) synthase, synthetase domain [Nucleotide transport and metabolism]; Region: PurL; COG0046 338963004532 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 338963004533 dimerization interface [polypeptide binding]; other site 338963004534 ATP binding site [chemical binding]; other site 338963004535 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 338963004536 dimerization interface [polypeptide binding]; other site 338963004537 ATP binding site [chemical binding]; other site 338963004538 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 338963004539 glyceraldehyde-3-phosphate dehydrogenase; Validated; Region: PRK07729 338963004540 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 338963004541 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 338963004542 Phosphoglycerate kinase; Region: PGK; pfam00162 338963004543 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 338963004544 substrate binding site [chemical binding]; other site 338963004545 hinge regions; other site 338963004546 ADP binding site [chemical binding]; other site 338963004547 catalytic site [active] 338963004548 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 338963004549 triosephosphate isomerase; Provisional; Region: PRK14567 338963004550 substrate binding site [chemical binding]; other site 338963004551 dimer interface [polypeptide binding]; other site 338963004552 catalytic triad [active] 338963004553 Preprotein translocase SecG subunit; Region: SecG; pfam03840 338963004554 group II intron 5' sequence; Pcar_R0100 338963004555 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 338963004556 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 338963004557 putative active site [active] 338963004558 putative NTP binding site [chemical binding]; other site 338963004559 putative nucleic acid binding site [nucleotide binding]; other site 338963004560 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 338963004561 group II intron 3' sequence; Pcar_R0104 338963004562 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 338963004563 dimerization interface [polypeptide binding]; other site 338963004564 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 338963004565 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 338963004566 dimer interface [polypeptide binding]; other site 338963004567 putative CheW interface [polypeptide binding]; other site 338963004568 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; cl01811 338963004569 Protein of unknown function (DUF1255); Region: DUF1255; pfam06865 338963004570 Predicted membrane protein (DUF2157); Region: DUF2157; pfam09925 338963004571 conserved nucleotide sequence; Pcar_R5036 338963004572 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 338963004573 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963004574 active site 338963004575 phosphorylation site [posttranslational modification] 338963004576 intermolecular recognition site; other site 338963004577 dimerization interface [polypeptide binding]; other site 338963004578 FOG: CBS domain [General function prediction only]; Region: COG0517 338963004579 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_24; cd04637 338963004580 Response regulator receiver domain; Region: Response_reg; pfam00072 338963004581 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963004582 active site 338963004583 phosphorylation site [posttranslational modification] 338963004584 intermolecular recognition site; other site 338963004585 dimerization interface [polypeptide binding]; other site 338963004586 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 338963004587 PAS fold; Region: PAS_3; pfam08447 338963004588 putative active site [active] 338963004589 heme pocket [chemical binding]; other site 338963004590 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 338963004591 GAF domain; Region: GAF_2; pfam13185 338963004592 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 338963004593 putative active site [active] 338963004594 heme pocket [chemical binding]; other site 338963004595 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 338963004596 PAS fold; Region: PAS_3; pfam08447 338963004597 putative active site [active] 338963004598 heme pocket [chemical binding]; other site 338963004599 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 338963004600 PAS domain; Region: PAS_9; pfam13426 338963004601 putative active site [active] 338963004602 heme pocket [chemical binding]; other site 338963004603 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963004604 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963004605 metal binding site [ion binding]; metal-binding site 338963004606 active site 338963004607 I-site; other site 338963004608 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 338963004609 conserved nucleotide sequence; Pcar_R5060 338963004610 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; pfam03747 338963004611 DoxX-like family; Region: DoxX_2; pfam13564 338963004612 putative UV damage endonuclease; Provisional; Region: uvsE; PRK02308 338963004613 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 338963004614 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 338963004615 Transposase; Region: HTH_Tnp_1; pfam01527 338963004616 putative transposase OrfB; Reviewed; Region: PHA02517 338963004617 HTH-like domain; Region: HTH_21; pfam13276 338963004618 Integrase core domain; Region: rve; pfam00665 338963004619 Integrase core domain; Region: rve_2; pfam13333 338963004620 SOUL heme-binding protein; Region: SOUL; pfam04832 338963004621 putative transposase OrfB; Reviewed; Region: PHA02517 338963004622 HTH-like domain; Region: HTH_21; pfam13276 338963004623 Integrase core domain; Region: rve; pfam00665 338963004624 Integrase core domain; Region: rve_3; pfam13683 338963004625 Transposase; Region: HTH_Tnp_1; cl17663 338963004626 conserved nucleotide sequence; Pcar_R5039 338963004627 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 338963004628 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 338963004629 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 338963004630 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 338963004631 Soluble P-type ATPase [General function prediction only]; Region: COG4087 338963004632 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 338963004633 conserved nucleotide sequence; Pcar_R5061 338963004634 conserved nucleotide sequence; Pcar_R5040 338963004635 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 338963004636 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 338963004637 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 338963004638 dimerization interface [polypeptide binding]; other site 338963004639 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 338963004640 dimer interface [polypeptide binding]; other site 338963004641 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 338963004642 putative CheW interface [polypeptide binding]; other site 338963004643 Yhdh and yhfp-like putative quinone oxidoreductases; Region: MDR_yhdh_yhfp; cd05280 338963004644 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 338963004645 NADP binding site [chemical binding]; other site 338963004646 dimer interface [polypeptide binding]; other site 338963004647 Macro domain, Poa1p_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 ADP-ribose...; Region: Macro_Poa1p_like; cd02901 338963004648 ADP-ribose binding site [chemical binding]; other site 338963004649 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 338963004650 FAD binding domain; Region: FAD_binding_4; pfam01565 338963004651 Berberine and berberine like; Region: BBE; pfam08031 338963004652 heptanucleotide repeats; Pcar_R7015 338963004653 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 338963004654 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 338963004655 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 338963004656 ABC transporter; Region: ABC_tran_2; pfam12848 338963004657 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 338963004658 Entericidin EcnA/B family; Region: Entericidin; pfam08085 338963004659 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; pfam04828 338963004660 ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; Region: ACT_UUR-ACR-like; cd04873 338963004661 ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; Region: ACT_UUR-ACR-like; cd04873 338963004662 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 338963004663 metal binding triad; other site 338963004664 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 338963004665 oxidoreductase; Validated; Region: PRK05717 338963004666 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 338963004667 NAD(P) binding site [chemical binding]; other site 338963004668 active site 338963004669 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 338963004670 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 338963004671 ATP-grasp domain; Region: ATP-grasp_4; cl17255 338963004672 Radical SAM superfamily; Region: Radical_SAM; pfam04055 338963004673 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 338963004674 FeS/SAM binding site; other site 338963004675 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 338963004676 Sporulation related domain; Region: SPOR; pfam05036 338963004677 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 338963004678 NlpC/P60 family; Region: NLPC_P60; pfam00877 338963004679 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 338963004680 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 338963004681 dimerization interface [polypeptide binding]; other site 338963004682 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 338963004683 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 338963004684 dimer interface [polypeptide binding]; other site 338963004685 putative CheW interface [polypeptide binding]; other site 338963004686 group II intron 5' sequence; Pcar_R0101 338963004687 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 338963004688 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 338963004689 putative active site [active] 338963004690 putative NTP binding site [chemical binding]; other site 338963004691 putative nucleic acid binding site [nucleotide binding]; other site 338963004692 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 338963004693 group II intron 3' sequence; Pcar_R0105 338963004694 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 338963004695 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 338963004696 active site 338963004697 metal binding site [ion binding]; metal-binding site 338963004698 DNA binding site [nucleotide binding] 338963004699 heptanucleotide repeats; Pcar_R7016 338963004700 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 338963004701 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963004702 Walker A/P-loop; other site 338963004703 ATP binding site [chemical binding]; other site 338963004704 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963004705 ABC transporter signature motif; other site 338963004706 Walker B; other site 338963004707 D-loop; other site 338963004708 H-loop/switch region; other site 338963004709 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 338963004710 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 338963004711 integron integrase; Region: integrase_gron; TIGR02249 338963004712 IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and...; Region: INT_IntI; cd01193 338963004713 Int/Topo IB signature motif; other site 338963004714 conserved nucleotide sequence; Pcar_R5003 338963004715 Homeodomain-like domain; Region: HTH_23; pfam13384 338963004716 Winged helix-turn helix; Region: HTH_29; pfam13551 338963004717 Integrase core domain; Region: rve; pfam00665 338963004718 Integrase core domain; Region: rve_3; pfam13683 338963004719 putative transposase OrfB; Reviewed; Region: PHA02517 338963004720 HTH-like domain; Region: HTH_21; pfam13276 338963004721 Integrase core domain; Region: rve; pfam00665 338963004722 Integrase core domain; Region: rve_3; pfam13683 338963004723 Transposase; Region: HTH_Tnp_1; cl17663 338963004724 Transposase domain (DUF772); Region: DUF772; pfam05598 338963004725 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 338963004726 Transposase; Region: DEDD_Tnp_IS110; pfam01548 338963004727 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 338963004728 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 338963004729 conserved nucleotide sequence; Pcar_R5028 338963004730 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4339 338963004731 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 338963004732 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 338963004733 Coenzyme A binding pocket [chemical binding]; other site 338963004734 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 338963004735 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 338963004736 motif II; other site 338963004737 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 338963004738 active site residue [active] 338963004739 pH-dependent sodium/proton antiporter; Reviewed; Region: nhaA; PRK09560 338963004740 conserved nucleotide sequence; Pcar_R0079 338963004741 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 338963004742 substrate binding site [chemical binding]; other site 338963004743 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 338963004744 S-adenosylmethionine binding site [chemical binding]; other site 338963004745 Peptidase family M48; Region: Peptidase_M48; pfam01435 338963004746 putative metalloenzyme radical SAM/SPASM domain maturase; Region: rSAM_Geo_metal; TIGR04311 338963004747 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 338963004748 FeS/SAM binding site; other site 338963004749 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 338963004750 Gram-negative porin; Region: Porin_4; pfam13609 338963004751 glycyl-radical enzyme activating protein family; Region: PFLE_PFLC; TIGR02494 338963004752 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 338963004753 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 338963004754 FeS/SAM binding site; other site 338963004755 glycyl radical enzyme, PFL2/glycerol dehydratase family; Region: PFL2-3; TIGR01774 338963004756 Pyruvate formate lyase 2 and related enzymes; Region: PFL2_DhaB_BssA; cd01677 338963004757 dimer interface [polypeptide binding]; other site 338963004758 active site 338963004759 glycine loop; other site 338963004760 Sensory domain found in PocR; Region: PocR; pfam10114 338963004761 Predicted sensor domain [Signal transduction mechanisms / Transcription]; Region: PocR; COG4936 338963004762 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 338963004763 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 338963004764 putative active site [active] 338963004765 heme pocket [chemical binding]; other site 338963004766 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 338963004767 dimer interface [polypeptide binding]; other site 338963004768 phosphorylation site [posttranslational modification] 338963004769 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 338963004770 ATP binding site [chemical binding]; other site 338963004771 Mg2+ binding site [ion binding]; other site 338963004772 G-X-G motif; other site 338963004773 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 338963004774 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963004775 active site 338963004776 phosphorylation site [posttranslational modification] 338963004777 intermolecular recognition site; other site 338963004778 dimerization interface [polypeptide binding]; other site 338963004779 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 338963004780 DNA binding residues [nucleotide binding] 338963004781 dimerization interface [polypeptide binding]; other site 338963004782 lysine-2,3-aminomutase; Region: lys_2_3_AblA; TIGR03820 338963004783 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 338963004784 FeS/SAM binding site; other site 338963004785 Lysine-2,3-aminomutase; Region: LAM_C; pfam12544 338963004786 putative beta-lysine N-acetyltransferase; Region: GNAT_ablB; TIGR03827 338963004787 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 338963004788 Coenzyme A binding pocket [chemical binding]; other site 338963004789 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 338963004790 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 338963004791 dimerization interface [polypeptide binding]; other site 338963004792 active site 338963004793 metal binding site [ion binding]; metal-binding site 338963004794 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 338963004795 dsRNA binding site [nucleotide binding]; other site 338963004796 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 338963004797 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 338963004798 FeS/SAM binding site; other site 338963004799 GTPase Era; Reviewed; Region: era; PRK00089 338963004800 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 338963004801 G1 box; other site 338963004802 GTP/Mg2+ binding site [chemical binding]; other site 338963004803 Switch I region; other site 338963004804 G2 box; other site 338963004805 Switch II region; other site 338963004806 G3 box; other site 338963004807 G4 box; other site 338963004808 G5 box; other site 338963004809 KH domain; Region: KH_2; pfam07650 338963004810 GTP-binding protein Der; Reviewed; Region: PRK00093 338963004811 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 338963004812 G1 box; other site 338963004813 GTP/Mg2+ binding site [chemical binding]; other site 338963004814 Switch I region; other site 338963004815 G2 box; other site 338963004816 Switch II region; other site 338963004817 G3 box; other site 338963004818 G4 box; other site 338963004819 G5 box; other site 338963004820 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 338963004821 G1 box; other site 338963004822 GTP/Mg2+ binding site [chemical binding]; other site 338963004823 Switch I region; other site 338963004824 G2 box; other site 338963004825 G3 box; other site 338963004826 Switch II region; other site 338963004827 G4 box; other site 338963004828 G5 box; other site 338963004829 Domain of unknown function (DUF4388); Region: DUF4388; pfam14332 338963004830 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963004831 active site 338963004832 phosphorylation site [posttranslational modification] 338963004833 intermolecular recognition site; other site 338963004834 dimerization interface [polypeptide binding]; other site 338963004835 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 338963004836 putative binding surface; other site 338963004837 active site 338963004838 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 338963004839 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 338963004840 ATP binding site [chemical binding]; other site 338963004841 Mg2+ binding site [ion binding]; other site 338963004842 G-X-G motif; other site 338963004843 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 338963004844 CheW-like domain; Region: CheW; pfam01584 338963004845 Response regulator receiver domain; Region: Response_reg; pfam00072 338963004846 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963004847 active site 338963004848 phosphorylation site [posttranslational modification] 338963004849 intermolecular recognition site; other site 338963004850 dimerization interface [polypeptide binding]; other site 338963004851 GAF domain; Region: GAF_2; pfam13185 338963004852 GAF domain; Region: GAF_3; pfam13492 338963004853 Response regulator receiver domain; Region: Response_reg; pfam00072 338963004854 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963004855 active site 338963004856 phosphorylation site [posttranslational modification] 338963004857 intermolecular recognition site; other site 338963004858 dimerization interface [polypeptide binding]; other site 338963004859 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 338963004860 rRNA binding site [nucleotide binding]; other site 338963004861 predicted 30S ribosome binding site; other site 338963004862 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 338963004863 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 338963004864 HIGH motif; other site 338963004865 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 338963004866 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 338963004867 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 338963004868 active site 338963004869 KMSKS motif; other site 338963004870 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 338963004871 tRNA binding surface [nucleotide binding]; other site 338963004872 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 338963004873 Lipopolysaccharide-assembly; Region: LptE; pfam04390 338963004874 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 338963004875 DNA polymerase III, delta subunit; Region: holA; TIGR01128 338963004876 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 338963004877 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 338963004878 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 338963004879 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 338963004880 TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and...; Region: TGS_ThrRS_N; cd01667 338963004881 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 338963004882 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 338963004883 active site 338963004884 dimer interface [polypeptide binding]; other site 338963004885 motif 1; other site 338963004886 motif 2; other site 338963004887 motif 3; other site 338963004888 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 338963004889 anticodon binding site; other site 338963004890 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 338963004891 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 338963004892 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 338963004893 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 338963004894 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 338963004895 23S rRNA binding site [nucleotide binding]; other site 338963004896 L21 binding site [polypeptide binding]; other site 338963004897 L13 binding site [polypeptide binding]; other site 338963004898 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 338963004899 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 338963004900 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 338963004901 dimer interface [polypeptide binding]; other site 338963004902 motif 1; other site 338963004903 active site 338963004904 motif 2; other site 338963004905 motif 3; other site 338963004906 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 338963004907 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 338963004908 putative tRNA-binding site [nucleotide binding]; other site 338963004909 B3/4 domain; Region: B3_4; pfam03483 338963004910 tRNA synthetase B5 domain; Region: B5; smart00874 338963004911 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 338963004912 dimer interface [polypeptide binding]; other site 338963004913 motif 1; other site 338963004914 motif 3; other site 338963004915 motif 2; other site 338963004916 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 338963004917 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 338963004918 IHF dimer interface [polypeptide binding]; other site 338963004919 IHF - DNA interface [nucleotide binding]; other site 338963004920 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 338963004921 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 338963004922 DNA binding residues [nucleotide binding] 338963004923 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 338963004924 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 338963004925 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 338963004926 S-adenosylmethionine binding site [chemical binding]; other site 338963004927 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 338963004928 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 338963004929 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 338963004930 Peptidase family M23; Region: Peptidase_M23; pfam01551 338963004931 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 338963004932 RNA polymerase sigma factor RpoS; Region: rpoS_proteo; TIGR02394 338963004933 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 338963004934 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 338963004935 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 338963004936 DNA binding residues [nucleotide binding] 338963004937 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 338963004938 active site 338963004939 conserved nucleotide sequence; Pcar_R3003 338963004940 conserved nucleotide sequence; Pcar_R3004 338963004941 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 338963004942 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs; Region: NTP-PPase_MazG_Nterm; cd11528 338963004943 homodimer interface [polypeptide binding]; other site 338963004944 metal binding site [ion binding]; metal-binding site 338963004945 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs' Region: NTP-PPase_MazG_Cterm; cd11529 338963004946 homodimer interface [polypeptide binding]; other site 338963004947 active site 338963004948 putative chemical substrate binding site [chemical binding]; other site 338963004949 metal binding site [ion binding]; metal-binding site 338963004950 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 338963004951 50S ribosomal protein L32; Reviewed; Region: rpmF; PRK12286 338963004952 putative phosphate acyltransferase; Provisional; Region: PRK05331 338963004953 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 338963004954 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 338963004955 dimer interface [polypeptide binding]; other site 338963004956 active site 338963004957 CoA binding pocket [chemical binding]; other site 338963004958 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 338963004959 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 338963004960 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 338963004961 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 338963004962 NAD(P) binding site [chemical binding]; other site 338963004963 homotetramer interface [polypeptide binding]; other site 338963004964 homodimer interface [polypeptide binding]; other site 338963004965 active site 338963004966 acyl carrier protein; Provisional; Region: acpP; PRK00982 338963004967 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 338963004968 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 338963004969 dimer interface [polypeptide binding]; other site 338963004970 active site 338963004971 Ribose/Galactose Isomerase; Region: LacAB_rpiB; pfam02502 338963004972 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 338963004973 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 338963004974 dimer interface [polypeptide binding]; other site 338963004975 active site 338963004976 glycine-pyridoxal phosphate binding site [chemical binding]; other site 338963004977 folate binding site [chemical binding]; other site 338963004978 Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the...; Region: deoxycytidylate_deaminase; cd01286 338963004979 catalytic motif [active] 338963004980 Zn binding site [ion binding]; other site 338963004981 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 338963004982 ATP cone domain; Region: ATP-cone; pfam03477 338963004983 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 338963004984 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 338963004985 catalytic motif [active] 338963004986 Zn binding site [ion binding]; other site 338963004987 RibD C-terminal domain; Region: RibD_C; cl17279 338963004988 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 338963004989 Lumazine binding domain; Region: Lum_binding; pfam00677 338963004990 Lumazine binding domain; Region: Lum_binding; pfam00677 338963004991 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 338963004992 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 338963004993 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 338963004994 dimerization interface [polypeptide binding]; other site 338963004995 active site 338963004996 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 338963004997 homopentamer interface [polypeptide binding]; other site 338963004998 active site 338963004999 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 338963005000 putative RNA binding site [nucleotide binding]; other site 338963005001 Cytosol aminopeptidase family, N-terminal domain; Region: Peptidase_M17_N; pfam02789 338963005002 homoserine dehydrogenase; Provisional; Region: PRK06349 338963005003 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 338963005004 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 338963005005 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 338963005006 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 338963005007 OAH/OAS sulfhydrylase; Region: OAH_OAS_sulfhy; TIGR01326 338963005008 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 338963005009 homodimer interface [polypeptide binding]; other site 338963005010 substrate-cofactor binding pocket; other site 338963005011 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963005012 catalytic residue [active] 338963005013 Fibronectin-binding protein A N-terminus (FbpA); Region: FbpA; pfam05833 338963005014 Domain of unknown function (DUF814); Region: DUF814; pfam05670 338963005015 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 338963005016 IHF dimer interface [polypeptide binding]; other site 338963005017 IHF - DNA interface [nucleotide binding]; other site 338963005018 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 338963005019 non-specific DNA binding site [nucleotide binding]; other site 338963005020 salt bridge; other site 338963005021 sequence-specific DNA binding site [nucleotide binding]; other site 338963005022 Cupin domain; Region: Cupin_2; pfam07883 338963005023 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 338963005024 sequence-specific DNA binding site [nucleotide binding]; other site 338963005025 salt bridge; other site 338963005026 Cupin domain; Region: Cupin_2; pfam07883 338963005027 biotin synthase; Region: bioB; TIGR00433 338963005028 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 338963005029 FeS/SAM binding site; other site 338963005030 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 338963005031 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 338963005032 AAA domain; Region: AAA_26; pfam13500 338963005033 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 338963005034 adenosylmethionine-8-amino-7-oxononanoate transaminase; Region: bioA; TIGR00508 338963005035 inhibitor-cofactor binding pocket; inhibition site 338963005036 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963005037 catalytic residue [active] 338963005038 Nicotinamidase/pyrazinamidase (PZase). Nicotinamidase, a ubiquitous enzyme in prokaryotes, converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD). The same enzyme is...; Region: nicotinamidase; cd01011 338963005039 Isochorismatase family; Region: Isochorismatase; pfam00857 338963005040 catalytic triad [active] 338963005041 metal binding site [ion binding]; metal-binding site 338963005042 conserved cis-peptide bond; other site 338963005043 hopene-associated glycosyltransferase HpnB; Region: HpnB; TIGR03469 338963005044 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 338963005045 active site 338963005046 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 338963005047 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 338963005048 tyrosine kinase; Provisional; Region: PRK11519 338963005049 Chain length determinant protein; Region: Wzz; cl15801 338963005050 G-rich domain on putative tyrosine kinase; Region: GNVR; pfam13807 338963005051 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 338963005052 Capsular polysaccharide biosynthesis protein [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: CapC; COG4464 338963005053 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 338963005054 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 338963005055 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 338963005056 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 338963005057 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 338963005058 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 338963005059 putative NAD(P) binding site [chemical binding]; other site 338963005060 active site 338963005061 putative substrate binding site [chemical binding]; other site 338963005062 HPP family; Region: HPP; pfam04982 338963005063 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 338963005064 Zn2+ binding site [ion binding]; other site 338963005065 Mg2+ binding site [ion binding]; other site 338963005066 octanucleotide repeats; Pcar_R8009 338963005067 octanucleotide repeats; Pcar_R8010 338963005068 Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Energy production and conversion]; Region: DsrA; COG2221 338963005069 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 338963005070 Nitrite and sulphite reductase 4Fe-4S domain; Region: NIR_SIR; pfam01077 338963005071 Uncharacterized protein family UPF0547; Region: UPF0547; pfam10571 338963005072 conserved nucleotide sequence; Pcar_R5062 338963005073 conserved nucleotide sequence; Pcar_R5064 338963005074 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 338963005075 conserved nucleotide sequence; Pcar_R5065 338963005076 Suppression of tumorigenicity 7; Region: ST7; cd11557 338963005077 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 338963005078 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 338963005079 Peptidase family M23; Region: Peptidase_M23; pfam01551 338963005080 Protein of unknown function (DUF3592); Region: DUF3592; pfam12158 338963005081 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 338963005082 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 338963005083 dimer interface [polypeptide binding]; other site 338963005084 active site 338963005085 metal binding site [ion binding]; metal-binding site 338963005086 glutathione binding site [chemical binding]; other site 338963005087 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 338963005088 Zn2+ binding site [ion binding]; other site 338963005089 Mg2+ binding site [ion binding]; other site 338963005090 translation initiation factor Sui1; Validated; Region: PRK06824 338963005091 Homologs of eIF1/SUI1 including Escherichia coli YciH; Region: YciH_like; cd11567 338963005092 putative rRNA binding site [nucleotide binding]; other site 338963005093 'conserved nucleotide sequence, repeat-containing, fragment; Pcar_R6001' 338963005094 'conserved nucleotide sequence, repeat-containing, fragment; Pcar_R6002' 338963005095 'conserved nucleotide sequence, repeat-containing, fragment; Pcar_R6003' 338963005096 GxxExxY protein; Region: GxxExxY; TIGR04256 338963005097 'conserved nucleotide sequence, repeat-containing, fragment; Pcar_R6004' 338963005098 'conserved nucleotide sequence, repeat-containing, fragment; Pcar_R6005' 338963005099 'conserved nucleotide sequence, repeat-containing, fragment; Pcar_R6006' 338963005100 'conserved nucleotide sequence, repeat-containing; Pcar_R6007' 338963005101 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 338963005102 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 338963005103 active site 338963005104 dimer interface [polypeptide binding]; other site 338963005105 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 338963005106 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 338963005107 active site 338963005108 FMN binding site [chemical binding]; other site 338963005109 substrate binding site [chemical binding]; other site 338963005110 3Fe-4S cluster binding site [ion binding]; other site 338963005111 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 338963005112 domain interface; other site 338963005113 conserved nucleotide sequence; Pcar_R2007 338963005114 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 338963005115 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 338963005116 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 338963005117 catalytic motif [active] 338963005118 Catalytic residue [active] 338963005119 Protein of unknown function (DUF429); Region: DUF429; pfam04250 338963005120 dihydrolipoamide dehydrogenase; Validated; Region: PRK06292 338963005121 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 338963005122 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 338963005123 Predicted membrane protein [Function unknown]; Region: COG3174 338963005124 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 338963005125 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 338963005126 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 338963005127 Beta-Casp domain; Region: Beta-Casp; smart01027 338963005128 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 338963005129 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 338963005130 This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins. WecA is an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate (Und-P) GlcNAc-1-phosphate transferase that catalyzes the formation of a phosphodiester bond...; Region: GT_WecA_like; cd06853 338963005131 Mg++ binding site [ion binding]; other site 338963005132 putative catalytic motif [active] 338963005133 substrate binding site [chemical binding]; other site 338963005134 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 338963005135 Sel1-like repeats; Region: SEL1; smart00671 338963005136 Sel1-like repeats; Region: SEL1; smart00671 338963005137 Sel1-like repeats; Region: SEL1; smart00671 338963005138 Sel1-like repeats; Region: SEL1; smart00671 338963005139 Sel1-like repeats; Region: SEL1; smart00671 338963005140 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 338963005141 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 338963005142 ligand binding site [chemical binding]; other site 338963005143 flexible hinge region; other site 338963005144 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 338963005145 putative switch regulator; other site 338963005146 non-specific DNA interactions [nucleotide binding]; other site 338963005147 DNA binding site [nucleotide binding] 338963005148 sequence specific DNA binding site [nucleotide binding]; other site 338963005149 putative cAMP binding site [chemical binding]; other site 338963005150 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 338963005151 active site 338963005152 Protein of unknown function (DUF2845); Region: DUF2845; pfam11006 338963005153 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK12461 338963005154 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 338963005155 active site 338963005156 Uncharacterized Candidatus kuenenia aldehyde dehydrogenase AldH (CAJ73105)-like; Region: ALDH_AldH-CAJ73105; cd07131 338963005157 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 338963005158 NAD binding site [chemical binding]; other site 338963005159 catalytic residues [active] 338963005160 Predicted GTPase [General function prediction only]; Region: COG2403 338963005161 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 338963005162 Uncharacterized protein containing a ferredoxin domain [Function unknown]; Region: COG4739 338963005163 Uncharacterized protein containing a ferredoxin domain (DUF2148); Region: DUF2148; pfam09918 338963005164 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 338963005165 nudix motif; other site 338963005166 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 338963005167 Nitrogen regulatory protein P-II; Region: P-II; smart00938 338963005168 glutamine synthetase, type I; Region: GlnA; TIGR00653 338963005169 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 338963005170 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 338963005171 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 338963005172 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 338963005173 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963005174 catalytic residue [active] 338963005175 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 338963005176 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 338963005177 active site 338963005178 metal binding site [ion binding]; metal-binding site 338963005179 homotetramer interface [polypeptide binding]; other site 338963005180 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 338963005181 nucleotide binding site/active site [active] 338963005182 HIT family signature motif; other site 338963005183 catalytic residue [active] 338963005184 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 338963005185 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 338963005186 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 338963005187 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 338963005188 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 338963005189 nucleotide binding site [chemical binding]; other site 338963005190 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 338963005191 phosphofructokinase; Region: PFK_mixed; TIGR02483 338963005192 active site 338963005193 ADP/pyrophosphate binding site [chemical binding]; other site 338963005194 dimerization interface [polypeptide binding]; other site 338963005195 allosteric effector site; other site 338963005196 fructose-1,6-bisphosphate binding site; other site 338963005197 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 338963005198 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 338963005199 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 338963005200 MutS domain I; Region: MutS_I; pfam01624 338963005201 MutS domain II; Region: MutS_II; pfam05188 338963005202 MutS domain III; Region: MutS_III; pfam05192 338963005203 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 338963005204 Walker A/P-loop; other site 338963005205 ATP binding site [chemical binding]; other site 338963005206 Q-loop/lid; other site 338963005207 ABC transporter signature motif; other site 338963005208 Walker B; other site 338963005209 D-loop; other site 338963005210 H-loop/switch region; other site 338963005211 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 338963005212 AMIN domain; Region: AMIN; pfam11741 338963005213 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 338963005214 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 338963005215 active site 338963005216 metal binding site [ion binding]; metal-binding site 338963005217 PII uridylyl-transferase; Provisional; Region: PRK05092 338963005218 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 338963005219 metal binding triad; other site 338963005220 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 338963005221 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_UUR-like_1; cd04900 338963005222 C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_ACR-UUR-like_2; cd04899 338963005223 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 338963005224 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 338963005225 active site 338963005226 Int/Topo IB signature motif; other site 338963005227 cofactor-independent phosphoglycerate mutase; Provisional; Region: PRK04200 338963005228 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; Region: PhosphMutase; cl17294 338963005229 Calx-beta domain; Region: Calx-beta; cl02522 338963005230 Calx-beta domain; Region: Calx-beta; cl02522 338963005231 Domains in Na-Ca exchangers and integrin-beta4; Region: Calx_beta; smart00237 338963005232 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 338963005233 Domains in Na-Ca exchangers and integrin-beta4; Region: Calx_beta; smart00237 338963005234 Pectate lyase; Region: Pec_lyase_C; cl01593 338963005235 Pectate lyase; Region: Pec_lyase_C; cl01593 338963005236 Bacterial sugar transferase; Region: Bac_transf; pfam02397 338963005237 carbamoyl phosphate synthase-like protein; Provisional; Region: PRK12767 338963005238 ATP-grasp domain; Region: ATP-grasp_4; cl17255 338963005239 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 338963005240 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 338963005241 active site 338963005242 metal binding site [ion binding]; metal-binding site 338963005243 homotetramer interface [polypeptide binding]; other site 338963005244 This family is most closely related to the GT1 family of glycosyltransferases. cap1E in Streptococcus pneumoniae is required for the synthesis of type 1 capsular polysaccharides; Region: GT1_cap1E_like; cd03808 338963005245 putative ADP-binding pocket [chemical binding]; other site 338963005246 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 338963005247 This family is most closely related to the GT1 family of glycosyltransferases. WbnK in Shigella dysenteriae has been shown to be involved in the type 7 O-antigen biosynthesis; Region: GT1_WbnK_like; cd03807 338963005248 sugar transferase, PEP-CTERM/EpsH1 system associated; Region: stp2; TIGR03088 338963005249 putative ADP-binding pocket [chemical binding]; other site 338963005250 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 338963005251 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 338963005252 inhibitor-cofactor binding pocket; inhibition site 338963005253 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963005254 catalytic residue [active] 338963005255 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 338963005256 Wzx, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_Wzx_like; cd13128 338963005257 conserved nucleotide sequence; Pcar_R2008 338963005258 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 338963005259 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 338963005260 putative ADP-binding pocket [chemical binding]; other site 338963005261 This family is most closely related to the GT1 family of glycosyltransferases. cap1E in Streptococcus pneumoniae is required for the synthesis of type 1 capsular polysaccharides; Region: GT1_cap1E_like; cd03808 338963005262 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 338963005263 putative ADP-binding pocket [chemical binding]; other site 338963005264 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 338963005265 Bacterial sugar transferase; Region: Bac_transf; pfam02397 338963005266 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 338963005267 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 338963005268 inhibitor-cofactor binding pocket; inhibition site 338963005269 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963005270 catalytic residue [active] 338963005271 Bacterial sugar transferase; Region: Bac_transf; pfam02397 338963005272 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 338963005273 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 338963005274 dimer interface [polypeptide binding]; other site 338963005275 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963005276 catalytic residue [active] 338963005277 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 338963005278 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 338963005279 NAD(P) binding site [chemical binding]; other site 338963005280 homodimer interface [polypeptide binding]; other site 338963005281 substrate binding site [chemical binding]; other site 338963005282 active site 338963005283 Uncharacterized protein conserved in bacteria (DUF2320); Region: DUF2320; pfam10082 338963005284 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 338963005285 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 338963005286 SLBB domain; Region: SLBB; pfam10531 338963005287 SLBB domain; Region: SLBB; pfam10531 338963005288 exopolysaccharide transport protein family; Region: eps_transp_fam; TIGR01005 338963005289 Chain length determinant protein; Region: Wzz; pfam02706 338963005290 G-rich domain on putative tyrosine kinase; Region: GNVR; pfam13807 338963005291 Chain length determinant protein; Region: Wzz; cl15801 338963005292 Capsular polysaccharide biosynthesis protein [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: CapC; COG4464 338963005293 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 338963005294 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 338963005295 TPR motif; other site 338963005296 binding surface 338963005297 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 338963005298 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 338963005299 active site 338963005300 ADP/pyrophosphate binding site [chemical binding]; other site 338963005301 dimerization interface [polypeptide binding]; other site 338963005302 allosteric effector site; other site 338963005303 fructose-1,6-bisphosphate binding site; other site 338963005304 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 338963005305 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 338963005306 2-ketoisovalerate ferredoxin reductase; Validated; Region: PRK07119 338963005307 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 338963005308 dimer interface [polypeptide binding]; other site 338963005309 PYR/PP interface [polypeptide binding]; other site 338963005310 TPP binding site [chemical binding]; other site 338963005311 substrate binding site [chemical binding]; other site 338963005312 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, beta subunit [Energy production and conversion]; Region: PorB; COG1013 338963005313 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 338963005314 TPP-binding site [chemical binding]; other site 338963005315 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 338963005316 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 338963005317 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 338963005318 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 338963005319 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 338963005320 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 338963005321 TRAM domain; Region: TRAM; cl01282 338963005322 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 338963005323 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 338963005324 S-adenosylmethionine binding site [chemical binding]; other site 338963005325 Sm and related proteins; Region: Sm_like; cl00259 338963005326 ribosome maturation protein RimP; Reviewed; Region: PRK00092 338963005327 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 338963005328 putative oligomer interface [polypeptide binding]; other site 338963005329 putative RNA binding site [nucleotide binding]; other site 338963005330 NusA N-terminal domain; Region: NusA_N; pfam08529 338963005331 transcription elongation factor NusA; Provisional; Region: nusA; PRK12327 338963005332 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 338963005333 RNA binding site [nucleotide binding]; other site 338963005334 homodimer interface [polypeptide binding]; other site 338963005335 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 338963005336 G-X-X-G motif; other site 338963005337 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 338963005338 G-X-X-G motif; other site 338963005339 hypothetical protein; Provisional; Region: PRK09190 338963005340 Protein of unknown function (DUF448); Region: DUF448; pfam04296 338963005341 putative RNA binding cleft [nucleotide binding]; other site 338963005342 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; Region: Ribosomal_L7Ae; cl00600 338963005343 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 338963005344 translation initiation factor IF-2; Region: IF-2; TIGR00487 338963005345 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 338963005346 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 338963005347 G1 box; other site 338963005348 putative GEF interaction site [polypeptide binding]; other site 338963005349 GTP/Mg2+ binding site [chemical binding]; other site 338963005350 Switch I region; other site 338963005351 G2 box; other site 338963005352 G3 box; other site 338963005353 Switch II region; other site 338963005354 G4 box; other site 338963005355 G5 box; other site 338963005356 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 338963005357 Translation-initiation factor 2; Region: IF-2; pfam11987 338963005358 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 338963005359 Protein of unknown function (DUF503); Region: DUF503; pfam04456 338963005360 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 338963005361 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 338963005362 DHH family; Region: DHH; pfam01368 338963005363 tRNA pseudouridine(55) synthase; Region: TruB; TIGR00431 338963005364 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 338963005365 RNA binding site [nucleotide binding]; other site 338963005366 active site 338963005367 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 338963005368 16S/18S rRNA binding site [nucleotide binding]; other site 338963005369 S13e-L30e interaction site [polypeptide binding]; other site 338963005370 25S rRNA binding site [nucleotide binding]; other site 338963005371 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 338963005372 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 338963005373 RNase E interface [polypeptide binding]; other site 338963005374 trimer interface [polypeptide binding]; other site 338963005375 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 338963005376 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 338963005377 RNase E interface [polypeptide binding]; other site 338963005378 trimer interface [polypeptide binding]; other site 338963005379 active site 338963005380 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 338963005381 putative nucleic acid binding region [nucleotide binding]; other site 338963005382 G-X-X-G motif; other site 338963005383 S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA; Region: S1_PNPase; cd04472 338963005384 RNA binding site [nucleotide binding]; other site 338963005385 domain interface; other site 338963005386 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 338963005387 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 338963005388 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 338963005389 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 338963005390 trimer interface [polypeptide binding]; other site 338963005391 active site 338963005392 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 338963005393 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 338963005394 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 338963005395 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 338963005396 PhoU domain; Region: PhoU; pfam01895 338963005397 PhoU domain; Region: PhoU; pfam01895 338963005398 exopolyphosphatase; Region: exo_poly_only; TIGR03706 338963005399 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 338963005400 indolepyruvate ferredoxin oxidoreductase, alpha subunit; Region: IOR_alpha; TIGR03336 338963005401 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 338963005402 dimer interface [polypeptide binding]; other site 338963005403 PYR/PP interface [polypeptide binding]; other site 338963005404 TPP binding site [chemical binding]; other site 338963005405 substrate binding site [chemical binding]; other site 338963005406 Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as...; Region: TPP_IOR_alpha; cd02008 338963005407 TPP-binding site; other site 338963005408 indolepyruvate oxidoreductase subunit beta; Reviewed; Region: PRK06853 338963005409 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 338963005410 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 338963005411 phenylacetate-CoA ligase; Region: PA_CoA_ligase; TIGR02155 338963005412 acyl-activating enzyme (AAE) consensus motif; other site 338963005413 AMP binding site [chemical binding]; other site 338963005414 active site 338963005415 CoA binding site [chemical binding]; other site 338963005416 ACT domain-containing protein [General function prediction only]; Region: COG4747 338963005417 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains; Region: ACT_Bt0572_1; cd04908 338963005418 C-terminal ACT domain of a novel protein composed of just two ACT domains; Region: ACT_Bt0572_2; cd04882 338963005419 conserved nucleotide sequence; Pcar_R5053 338963005420 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 338963005421 aspartate aminotransferase; Provisional; Region: PRK05764 338963005422 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 338963005423 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963005424 homodimer interface [polypeptide binding]; other site 338963005425 catalytic residue [active] 338963005426 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963005427 daunorubicin resistance ABC transporter ATP-binding subunit; Region: drrA; TIGR01188 338963005428 Walker A/P-loop; other site 338963005429 ATP binding site [chemical binding]; other site 338963005430 Q-loop/lid; other site 338963005431 ABC transporter signature motif; other site 338963005432 Walker B; other site 338963005433 D-loop; other site 338963005434 H-loop/switch region; other site 338963005435 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 338963005436 ABC-2 type transporter; Region: ABC2_membrane; cl17235 338963005437 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 338963005438 Sodium Bile acid symporter family; Region: SBF; cl17470 338963005439 CoA-disulfide reductase; Region: CoA_CoA_reduc; TIGR03385 338963005440 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 338963005441 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 338963005442 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 338963005443 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 338963005444 active site residue [active] 338963005445 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 338963005446 PAS domain; Region: PAS_9; pfam13426 338963005447 putative active site [active] 338963005448 heme pocket [chemical binding]; other site 338963005449 phage shock protein operon transcriptional activator; Provisional; Region: pspF; PRK11608 338963005450 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 338963005451 Walker A motif; other site 338963005452 ATP binding site [chemical binding]; other site 338963005453 Walker B motif; other site 338963005454 arginine finger; other site 338963005455 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 338963005456 Uncharacterized conserved protein [Function unknown]; Region: COG1433 338963005457 Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits...; Region: Prefoldin; cl09111 338963005458 This putative domain contains a quite highly conserved sequence of CGGC in its central region; Region: CGGC; smart01078 338963005459 This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of...; Region: MTH1175; cd00851 338963005460 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]; Region: COG1149 338963005461 This protein family's function is unkown. It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion; Region: Fer4_NifH_child; cd03110 338963005462 switch II; other site 338963005463 Fe-S oxidoreductases [Energy production and conversion]; Region: COG0731 338963005464 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 338963005465 FeS/SAM binding site; other site 338963005466 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 338963005467 S-adenosylmethionine binding site [chemical binding]; other site 338963005468 This protein family's function is unkown. It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion; Region: Fer4_NifH_child; cd03110 338963005469 Ferredoxin [Energy production and conversion]; Region: COG1146 338963005470 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 338963005471 switch II; other site 338963005472 Metal-dependent hydrolases of the beta-lactamase superfamily II [General function prediction only]; Region: COG1237 338963005473 antiporter inner membrane protein; Provisional; Region: PRK11670 338963005474 Domain of unknown function DUF59; Region: DUF59; pfam01883 338963005475 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 338963005476 Walker A motif; other site 338963005477 Ubiquitin-like proteins; Region: UBQ; cl00155 338963005478 charged pocket; other site 338963005479 hydrophobic patch; other site 338963005480 Protein of unknown function (DUF2899); Region: DUF2899; pfam11449 338963005481 redox-sensing transcriptional repressor Rex; Provisional; Region: PRK05472 338963005482 CoA binding domain; Region: CoA_binding; pfam02629 338963005483 Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria; Region: LPO; cd08176 338963005484 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 338963005485 dimer interface [polypeptide binding]; other site 338963005486 active site 338963005487 metal binding site [ion binding]; metal-binding site 338963005488 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 338963005489 DNA binding residues [nucleotide binding] 338963005490 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 338963005491 dimer interface [polypeptide binding]; other site 338963005492 copper binding site [ion binding]; other site 338963005493 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 338963005494 metal-binding site [ion binding] 338963005495 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 338963005496 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 338963005497 metal-binding site [ion binding] 338963005498 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 338963005499 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 338963005500 motif II; other site 338963005501 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 338963005502 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 338963005503 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 338963005504 putative dimerization interface [polypeptide binding]; other site 338963005505 Conserved hypothetical protein 698; Region: Cons_hypoth698; cl01075 338963005506 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 338963005507 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 338963005508 DNA-binding site [nucleotide binding]; DNA binding site 338963005509 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 338963005510 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963005511 homodimer interface [polypeptide binding]; other site 338963005512 catalytic residue [active] 338963005513 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 338963005514 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 338963005515 Walker A motif; other site 338963005516 ATP binding site [chemical binding]; other site 338963005517 Walker B motif; other site 338963005518 arginine finger; other site 338963005519 Putative metallopeptidase domain; Region: DUF2201_N; pfam13203 338963005520 VWA-like domain (DUF2201); Region: DUF2201; pfam09967 338963005521 metal ion-dependent adhesion site (MIDAS); other site 338963005522 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 338963005523 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 338963005524 putative dimer interface [polypeptide binding]; other site 338963005525 [2Fe-2S] cluster binding site [ion binding]; other site 338963005526 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 338963005527 dimer interface [polypeptide binding]; other site 338963005528 [2Fe-2S] cluster binding site [ion binding]; other site 338963005529 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 338963005530 SLBB domain; Region: SLBB; pfam10531 338963005531 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 338963005532 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 338963005533 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 338963005534 bidirectional hydrogenase complex protein HoxU; Validated; Region: PRK07569 338963005535 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 338963005536 catalytic loop [active] 338963005537 iron binding site [ion binding]; other site 338963005538 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 338963005539 [FeFe] hydrogenase, group A; Region: FeFe_hydrog_A; TIGR02512 338963005540 4Fe-4S binding domain; Region: Fer4; pfam00037 338963005541 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 338963005542 Iron hydrogenase small subunit; Region: Fe_hyd_SSU; pfam02256 338963005543 palindrome; Pcar_R5084 338963005544 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 338963005545 Cysteine-rich domain; Region: CCG; pfam02754 338963005546 Cysteine-rich domain; Region: CCG; pfam02754 338963005547 biotin synthase; Provisional; Region: PRK07094 338963005548 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 338963005549 FeS/SAM binding site; other site 338963005550 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 338963005551 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 338963005552 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 338963005553 ssDNA binding site; other site 338963005554 generic binding surface II; other site 338963005555 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 338963005556 ATP binding site [chemical binding]; other site 338963005557 putative Mg++ binding site [ion binding]; other site 338963005558 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 338963005559 nucleotide binding region [chemical binding]; other site 338963005560 ATP-binding site [chemical binding]; other site 338963005561 hybrid cluster protein-associated redox disulfide domain; Region: prismane_assoc; TIGR03980 338963005562 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 338963005563 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 338963005564 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 338963005565 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 338963005566 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 338963005567 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 338963005568 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 338963005569 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 338963005570 ATP-grasp domain; Region: ATP-grasp_4; cl17255 338963005571 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 338963005572 IMP binding site; other site 338963005573 dimer interface [polypeptide binding]; other site 338963005574 interdomain contacts; other site 338963005575 partial ornithine binding site; other site 338963005576 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 338963005577 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 338963005578 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 338963005579 catalytic site [active] 338963005580 subunit interface [polypeptide binding]; other site 338963005581 dihydroorotase; Validated; Region: pyrC; PRK09357 338963005582 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 338963005583 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 338963005584 active site 338963005585 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 338963005586 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 338963005587 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 338963005588 Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase [Nucleotide transport and metabolism]; Region: PyrR; COG2065 338963005589 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 338963005590 active site 338963005591 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 338963005592 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 338963005593 Catalytic site [active] 338963005594 GTP-binding protein LepA; Provisional; Region: PRK05433 338963005595 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 338963005596 G1 box; other site 338963005597 putative GEF interaction site [polypeptide binding]; other site 338963005598 GTP/Mg2+ binding site [chemical binding]; other site 338963005599 Switch I region; other site 338963005600 G2 box; other site 338963005601 G3 box; other site 338963005602 Switch II region; other site 338963005603 G4 box; other site 338963005604 G5 box; other site 338963005605 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 338963005606 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 338963005607 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 338963005608 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 338963005609 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 338963005610 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 338963005611 acyl-activating enzyme (AAE) consensus motif; other site 338963005612 putative AMP binding site [chemical binding]; other site 338963005613 putative active site [active] 338963005614 putative CoA binding site [chemical binding]; other site 338963005615 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cd00400 338963005616 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 338963005617 Cl- selectivity filter; other site 338963005618 Cl- binding residues [ion binding]; other site 338963005619 pore gating glutamate residue; other site 338963005620 dimer interface [polypeptide binding]; other site 338963005621 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC; Region: CBS_pair_SpoIVFB_EriC_assoc2; cd04613 338963005622 FOG: CBS domain [General function prediction only]; Region: COG0517 338963005623 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 338963005624 CoenzymeA binding site [chemical binding]; other site 338963005625 subunit interaction site [polypeptide binding]; other site 338963005626 PHB binding site; other site 338963005627 TM2 domain; Region: TM2; cl00984 338963005628 TM2 domain; Region: TM2; cl00984 338963005629 RmuC family; Region: RmuC; pfam02646 338963005630 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cl00514 338963005631 FMN binding site [chemical binding]; other site 338963005632 dimer interface [polypeptide binding]; other site 338963005633 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cl00514 338963005634 FMN binding site [chemical binding]; other site 338963005635 dimer interface [polypeptide binding]; other site 338963005636 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_u2; cd11539 338963005637 metal binding site [ion binding]; metal-binding site 338963005638 [FeFe] hydrogenase H-cluster maturation GTPase HydF; Region: GTP_HydF; TIGR03918 338963005639 E. coli Ras-like protein (Era)-like GTPase; Region: Era_like; cd00880 338963005640 G1 box; other site 338963005641 GTP/Mg2+ binding site [chemical binding]; other site 338963005642 Switch I region; other site 338963005643 G2 box; other site 338963005644 Switch II region; other site 338963005645 G3 box; other site 338963005646 G4 box; other site 338963005647 G5 box; other site 338963005648 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 338963005649 Aspartase; Region: Aspartase; cd01357 338963005650 active sites [active] 338963005651 tetramer interface [polypeptide binding]; other site 338963005652 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09613 338963005653 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 338963005654 FeS/SAM binding site; other site 338963005655 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 338963005656 biotin synthase; Provisional; Region: PRK07094 338963005657 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 338963005658 FeS/SAM binding site; other site 338963005659 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 338963005660 bidirectional hydrogenase complex protein HoxU; Validated; Region: PRK07569 338963005661 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 338963005662 catalytic loop [active] 338963005663 iron binding site [ion binding]; other site 338963005664 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 338963005665 [FeFe] hydrogenase, group A; Region: FeFe_hydrog_A; TIGR02512 338963005666 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 338963005667 Iron hydrogenase small subunit; Region: Fe_hyd_SSU; pfam02256 338963005668 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 338963005669 SLBB domain; Region: SLBB; pfam10531 338963005670 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 338963005671 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 338963005672 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 338963005673 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 338963005674 dimer interface [polypeptide binding]; other site 338963005675 [2Fe-2S] cluster binding site [ion binding]; other site 338963005676 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 338963005677 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 338963005678 putative dimer interface [polypeptide binding]; other site 338963005679 [2Fe-2S] cluster binding site [ion binding]; other site 338963005680 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; pfam01985 338963005681 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 338963005682 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 338963005683 Zn2+ binding site [ion binding]; other site 338963005684 Mg2+ binding site [ion binding]; other site 338963005685 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 338963005686 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 338963005687 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 338963005688 S-adenosylmethionine binding site [chemical binding]; other site 338963005689 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 338963005690 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 338963005691 active site 338963005692 (T/H)XGH motif; other site 338963005693 Creatinine amidohydrolase; Region: Creatininase; pfam02633 338963005694 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 338963005695 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 338963005696 FeS/SAM binding site; other site 338963005697 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 338963005698 active site 338963005699 Domain of unknown function (DUF329); Region: DUF329; pfam03884 338963005700 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 338963005701 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 338963005702 active site 338963005703 NTP binding site [chemical binding]; other site 338963005704 metal binding triad [ion binding]; metal-binding site 338963005705 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 338963005706 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 338963005707 Aminotransferase class I and II; Region: Aminotran_1_2; pfam00155 338963005708 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963005709 homodimer interface [polypeptide binding]; other site 338963005710 catalytic residue [active] 338963005711 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 338963005712 Class I histone deacetylase AcuC (Acetoin utilization protein)-like enzymes; Region: HDAC_AcuC_like; cd09994 338963005713 active site 338963005714 Zn binding site [ion binding]; other site 338963005715 aminopeptidase N; Provisional; Region: pepN; PRK14015 338963005716 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 338963005717 active site 338963005718 Zn binding site [ion binding]; other site 338963005719 conserved nucleotide sequence; Pcar_R2009 338963005720 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 338963005721 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 338963005722 HIGH motif; other site 338963005723 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 338963005724 active site 338963005725 KMSKS motif; other site 338963005726 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 338963005727 putative ligand binding pocket/active site [active] 338963005728 putative metal binding site [ion binding]; other site 338963005729 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 338963005730 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 338963005731 Thrombospondin type 3 repeat; Region: TSP_3; pfam02412 338963005732 carboxy-terminal protease; Provisional; Region: PRK11186 338963005733 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 338963005734 protein binding site [polypeptide binding]; other site 338963005735 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 338963005736 Catalytic dyad [active] 338963005737 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 338963005738 putative manganese-dependent inorganic pyrophosphatase; Provisional; Region: PRK14869 338963005739 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with a DRTGG domain upstream. The function of the DRTGG domain, named after its conserved residues, is unknown. CBS is a small domain originally...; Region: CBS_pair_DRTGG_assoc2; cd04597 338963005740 DRTGG domain; Region: DRTGG; pfam07085 338963005741 DHHA2 domain; Region: DHHA2; pfam02833 338963005742 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 338963005743 dimerization interface [polypeptide binding]; other site 338963005744 putative DNA binding site [nucleotide binding]; other site 338963005745 putative Zn2+ binding site [ion binding]; other site 338963005746 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 338963005747 PUA domain; Region: PUA; cl00607 338963005748 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 338963005749 putative RNA binding site [nucleotide binding]; other site 338963005750 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 338963005751 S-adenosylmethionine binding site [chemical binding]; other site 338963005752 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 338963005753 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 338963005754 pimelyl-[acyl-carrier protein] methyl ester esterase; Region: bioH; TIGR01738 338963005755 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 338963005756 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS); Region: KBL_like; cd06454 338963005757 substrate-cofactor binding pocket; other site 338963005758 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963005759 catalytic residue [active] 338963005760 6-carboxyhexanoate--CoA ligase; Provisional; Region: PRK01322 338963005761 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 338963005762 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 338963005763 TPP-binding site; other site 338963005764 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 338963005765 PYR/PP interface [polypeptide binding]; other site 338963005766 dimer interface [polypeptide binding]; other site 338963005767 TPP binding site [chemical binding]; other site 338963005768 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 338963005769 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 338963005770 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 338963005771 substrate binding pocket [chemical binding]; other site 338963005772 chain length determination region; other site 338963005773 substrate-Mg2+ binding site; other site 338963005774 catalytic residues [active] 338963005775 aspartate-rich region 1; other site 338963005776 active site lid residues [active] 338963005777 aspartate-rich region 2; other site 338963005778 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 338963005779 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 338963005780 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 338963005781 generic binding surface II; other site 338963005782 generic binding surface I; other site 338963005783 AAA domain; Region: AAA_31; pfam13614 338963005784 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 338963005785 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 338963005786 Magnesium ion binding site [ion binding]; other site 338963005787 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 338963005788 NodB motif; other site 338963005789 putative active site [active] 338963005790 putative catalytic site [active] 338963005791 Zn binding site [ion binding]; other site 338963005792 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 338963005793 C-terminal peptidase (prc); Region: prc; TIGR00225 338963005794 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 338963005795 protein binding site [polypeptide binding]; other site 338963005796 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 338963005797 Catalytic dyad [active] 338963005798 conserved nucleotide sequence; Pcar_R3005 338963005799 conserved nucleotide sequence; Pcar_R3006 338963005800 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 338963005801 Peptidase family M23; Region: Peptidase_M23; pfam01551 338963005802 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 338963005803 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 338963005804 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 338963005805 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963005806 Walker A/P-loop; other site 338963005807 ATP binding site [chemical binding]; other site 338963005808 Q-loop/lid; other site 338963005809 ABC transporter signature motif; other site 338963005810 Walker B; other site 338963005811 D-loop; other site 338963005812 H-loop/switch region; other site 338963005813 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 338963005814 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 338963005815 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 338963005816 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 338963005817 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 338963005818 TPR repeat; Region: TPR_11; pfam13414 338963005819 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 338963005820 binding surface 338963005821 TPR motif; other site 338963005822 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 338963005823 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 338963005824 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 338963005825 Cohesin domain, interaction parter of dockerin; Region: cohesin_like; cd08546 338963005826 dockerin binding interface; other site 338963005827 Tfp pilus assembly protein, ATPase PilM [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilM; COG4972 338963005828 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 338963005829 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 338963005830 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 338963005831 Walker A motif; other site 338963005832 ATP binding site [chemical binding]; other site 338963005833 Walker B motif; other site 338963005834 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 338963005835 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 338963005836 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 338963005837 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 338963005838 IHF dimer interface [polypeptide binding]; other site 338963005839 IHF - DNA interface [nucleotide binding]; other site 338963005840 Found in ATP-dependent protease La (LON); Region: LON; smart00464 338963005841 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 338963005842 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 338963005843 Walker A motif; other site 338963005844 ATP binding site [chemical binding]; other site 338963005845 Walker B motif; other site 338963005846 arginine finger; other site 338963005847 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 338963005848 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 338963005849 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 338963005850 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 338963005851 Walker A motif; other site 338963005852 ATP binding site [chemical binding]; other site 338963005853 Walker B motif; other site 338963005854 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 338963005855 Clp protease; Region: CLP_protease; pfam00574 338963005856 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 338963005857 oligomer interface [polypeptide binding]; other site 338963005858 active site residues [active] 338963005859 trigger factor; Region: tig; TIGR00115 338963005860 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 338963005861 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 338963005862 thymidylate kinase; Validated; Region: tmk; PRK00698 338963005863 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 338963005864 TMP-binding site; other site 338963005865 ATP-binding site [chemical binding]; other site 338963005866 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 338963005867 DNA polymerase III subunit delta'; Validated; Region: PRK08058 338963005868 Walker A motif; other site 338963005869 ATP binding site [chemical binding]; other site 338963005870 Walker B motif; other site 338963005871 arginine finger; other site 338963005872 DNA polymerase III, delta subunit, C terminal; Region: DNApol3-delta_C; pfam09115 338963005873 Uncharacterized homolog of PSP1 [Function unknown]; Region: COG1774 338963005874 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 338963005875 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 338963005876 active site 338963005877 HIGH motif; other site 338963005878 KMSKS motif; other site 338963005879 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 338963005880 tRNA binding surface [nucleotide binding]; other site 338963005881 anticodon binding site; other site 338963005882 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 338963005883 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 338963005884 active site 338963005885 radical SAM protein, TatD family-associated; Region: tatD_link_rSAM; TIGR04038 338963005886 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 338963005887 FeS/SAM binding site; other site 338963005888 PilZ domain; Region: PilZ; cl01260 338963005889 Protein of unknown function (DUF3135); Region: DUF3135; pfam11333 338963005890 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 338963005891 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 338963005892 dimer interface [polypeptide binding]; other site 338963005893 active site 338963005894 metal binding site [ion binding]; metal-binding site 338963005895 Rhodococcus ruber 6-oxolauric acid dehydrogenase-like; Region: ALDH_CddD_SSP0762; cd07138 338963005896 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 338963005897 NAD binding site [chemical binding]; other site 338963005898 catalytic residues [active] 338963005899 Ferredoxin [Energy production and conversion]; Region: COG1146 338963005900 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 338963005901 putative adenylate-forming enzyme; Region: aden_form_hyp; TIGR02304 338963005902 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 338963005903 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like3; cd05668 338963005904 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 338963005905 metal binding site [ion binding]; metal-binding site 338963005906 putative dimer interface [polypeptide binding]; other site 338963005907 conserved nucleotide sequence; Pcar_R2010 338963005908 Protein of unknown function (DUF4242); Region: DUF4242; pfam14026 338963005909 Domain of unknown function (DUF4186); Region: DUF4186; pfam13811 338963005910 Part of AAA domain; Region: AAA_19; pfam13245 338963005911 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 338963005912 Family description; Region: UvrD_C_2; pfam13538 338963005913 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 338963005914 probable DNA repair protein; Region: TIGR03623 338963005915 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 338963005916 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 338963005917 dimer interface [polypeptide binding]; other site 338963005918 Uncharacterized conserved protein [Function unknown]; Region: COG3350 338963005919 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 338963005920 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 338963005921 Soluble P-type ATPase [General function prediction only]; Region: COG4087 338963005922 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 338963005923 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 338963005924 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 338963005925 HlyD family secretion protein; Region: HlyD_3; pfam13437 338963005926 octanucleotide repeats; Pcar_R8011 338963005927 octanucleotide repeats; Pcar_R8012 338963005928 Outer membrane efflux protein; Region: OEP; pfam02321 338963005929 Outer membrane efflux protein; Region: OEP; pfam02321 338963005930 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 338963005931 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 338963005932 dimer interface [polypeptide binding]; other site 338963005933 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963005934 catalytic residue [active] 338963005935 OAH/OAS sulfhydrylase; Region: OAH_OAS_sulfhy; TIGR01326 338963005936 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 338963005937 homodimer interface [polypeptide binding]; other site 338963005938 substrate-cofactor binding pocket; other site 338963005939 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963005940 catalytic residue [active] 338963005941 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD...; Region: ThiF_MoeB_HesA_family; cd00757 338963005942 thiazole biosynthesis adenylyltransferase ThiF, E. coli subfamily; Region: adenyl_thiF; TIGR02356 338963005943 ATP binding site [chemical binding]; other site 338963005944 substrate interface [chemical binding]; other site 338963005945 ThiS family; Region: ThiS; pfam02597 338963005946 charged pocket; other site 338963005947 hydrophobic patch; other site 338963005948 biotin synthase; Provisional; Region: PRK07094 338963005949 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 338963005950 FeS/SAM binding site; other site 338963005951 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 338963005952 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 338963005953 Sulfatase; Region: Sulfatase; cl17466 338963005954 putative metal dependent hydrolase; Provisional; Region: PRK11598 338963005955 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 338963005956 Sulfatase; Region: Sulfatase; pfam00884 338963005957 conserved nucleotide sequence; Pcar_R0095 338963005958 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 338963005959 HAMP domain; Region: HAMP; pfam00672 338963005960 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 338963005961 dimer interface [polypeptide binding]; other site 338963005962 phosphorylation site [posttranslational modification] 338963005963 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 338963005964 ATP binding site [chemical binding]; other site 338963005965 Mg2+ binding site [ion binding]; other site 338963005966 G-X-G motif; other site 338963005967 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 338963005968 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963005969 active site 338963005970 phosphorylation site [posttranslational modification] 338963005971 intermolecular recognition site; other site 338963005972 dimerization interface [polypeptide binding]; other site 338963005973 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 338963005974 DNA binding site [nucleotide binding] 338963005975 Quinolinate synthetase A protein; Region: NadA; pfam02445 338963005976 Protein of unknown function (DUF3343); Region: DUF3343; pfam11823 338963005977 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 338963005978 Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS...; Region: SufS_like; cd06453 338963005979 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 338963005980 catalytic residue [active] 338963005981 Transcriptional regulator; Region: Rrf2; cl17282 338963005982 Rrf2 family protein; Region: rrf2_super; TIGR00738 338963005983 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 338963005984 alpha-glucan phosphorylases; Region: more_P_ylases; TIGR02094 338963005985 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 338963005986 FAD binding site [chemical binding]; other site 338963005987 Predicted oxidoreductases of the aldo/keto reductase family [General function prediction only]; Region: COG1453 338963005988 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 338963005989 active site 338963005990 catalytic tetrad [active] 338963005991 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 338963005992 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 338963005993 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 338963005994 Walker A motif; other site 338963005995 ATP binding site [chemical binding]; other site 338963005996 Walker B motif; other site 338963005997 arginine finger; other site 338963005998 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 338963005999 conserved palindrome; Pcar_R5066 338963006000 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 338963006001 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963006002 Walker A/P-loop; other site 338963006003 ATP binding site [chemical binding]; other site 338963006004 Q-loop/lid; other site 338963006005 ABC transporter signature motif; other site 338963006006 Walker B; other site 338963006007 D-loop; other site 338963006008 H-loop/switch region; other site 338963006009 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 338963006010 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 338963006011 dimer interface [polypeptide binding]; other site 338963006012 conserved gate region; other site 338963006013 putative PBP binding loops; other site 338963006014 ABC-ATPase subunit interface; other site 338963006015 Domain of unknown function (DUF4213); Region: DUF4213; pfam13938 338963006016 Domain of unknown function (DUF364); Region: DUF364; pfam04016 338963006017 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 338963006018 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 338963006019 heptanucleotide repeats; Pcar_R7017 338963006020 LexA repressor; Validated; Region: PRK00215 338963006021 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 338963006022 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 338963006023 Catalytic site [active] 338963006024 octanucleotide repeats; Pcar_R8013 338963006025 octanucleotide repeats; Pcar_R8014 338963006026 conserved nucleotide sequence; Pcar_R4001 338963006027 octanucleotide repeats; Pcar_R8015 338963006028 octanucleotide repeats; Pcar_R8016 338963006029 octanucleotide repeats; Pcar_R8017 338963006030 octanucleotide repeats; Pcar_R8018 338963006031 DNA polymerase IV; Validated; Region: PRK01810 338963006032 Y-family of DNA polymerases; Region: PolY; cd00424 338963006033 active site 338963006034 DNA binding site [nucleotide binding] 338963006035 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 338963006036 heptanucleotide repeats; Pcar_R7018 338963006037 heptanucleotide repeats; Pcar_R7019 338963006038 DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]; Region: DnaE; COG0587 338963006039 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 338963006040 active site 338963006041 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 338963006042 generic binding surface I; other site 338963006043 generic binding surface II; other site 338963006044 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 338963006045 Ca2+ binding site [ion binding]; other site 338963006046 Predicted membrane protein [Function unknown]; Region: COG2246 338963006047 GtrA-like protein; Region: GtrA; pfam04138 338963006048 Flp/Fap pilin component; Region: Flp_Fap; cl01585 338963006049 Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]; Region: CpaB; COG3745 338963006050 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 338963006051 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 338963006052 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 338963006053 BON domain; Region: BON; pfam04972 338963006054 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 338963006055 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 338963006056 TadE-like protein; Region: TadE; pfam07811 338963006057 Putative Tad-like Flp pilus-assembly; Region: Tad_C; pfam09977 338963006058 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963006059 active site 338963006060 dimerization interface [polypeptide binding]; other site 338963006061 AAA domain; Region: AAA_31; pfam13614 338963006062 This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains...; Region: CpaE_like; cd03111 338963006063 This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains...; Region: CpaE_like; cd03111 338963006064 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 338963006065 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 338963006066 ATP binding site [chemical binding]; other site 338963006067 Walker A motif; other site 338963006068 hexamer interface [polypeptide binding]; other site 338963006069 Walker B motif; other site 338963006070 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 338963006071 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 338963006072 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 338963006073 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 338963006074 FOG: TPR repeat [General function prediction only]; Region: NrfG; COG0457 338963006075 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 338963006076 binding surface 338963006077 TPR motif; other site 338963006078 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 338963006079 binding surface 338963006080 TPR motif; other site 338963006081 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 338963006082 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 338963006083 ATP binding site [chemical binding]; other site 338963006084 Methyltransferase domain; Region: Methyltransf_23; pfam13489 338963006085 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 338963006086 DPG_synthase is involved in protein N-linked glycosylation; Region: DPG_synthase; cd04188 338963006087 Ligand binding site; other site 338963006088 Ligand binding site; other site 338963006089 Ligand binding site; other site 338963006090 Putative Catalytic site; other site 338963006091 DXD motif; other site 338963006092 PAP2_like proteins, Aur1_like subfamily. Yeast Aur1p or Ipc1p is necessary for the addition of inositol phosphate to ceramide, an essential step in yeast sphingolipid synthesis, and is the target of several antifungal compounds such as aureobasidin; Region: PAP2_Aur1_like; cd03386 338963006093 active site 338963006094 60S ribosomal protein L37a; Provisional; Region: PTZ00255; cl00875 338963006095 conserved nucleotide sequence; Pcar_R2011 338963006096 heat shock protein 90; Provisional; Region: PRK05218 338963006097 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 338963006098 ATP binding site [chemical binding]; other site 338963006099 Mg2+ binding site [ion binding]; other site 338963006100 G-X-G motif; other site 338963006101 conserved nucleotide sequence; Pcar_R1019 338963006102 Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]; Region: COG1331 338963006103 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 338963006104 catalytic residues [active] 338963006105 octanucleotide repeats; Pcar_R8019 338963006106 octanucleotide repeats; Pcar_R8020 338963006107 octanucleotide repeats; Pcar_R8021 338963006108 conserved nucleotide sequence; Pcar_R8101 338963006109 octanucleotide repeats; Pcar_R8022 338963006110 octanucleotide repeats; Pcar_R8023 338963006111 conserved nucleotide sequence; Pcar_R8102 338963006112 octanucleotide repeats; Pcar_R8024 338963006113 phosphoenolpyruvate carboxykinase; Provisional; Region: PRK04210 338963006114 active site 338963006115 metal-binding site [ion binding] 338963006116 nucleotide-binding site [chemical binding]; other site 338963006117 conserved nucleotide sequence; Pcar_R7207 338963006118 precorrin-3B synthase; Region: CobG; TIGR02435 338963006119 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 338963006120 sulfate adenylyltransferase subunit 1; Provisional; Region: cysN; PRK05124 338963006121 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 338963006122 CysD dimerization site [polypeptide binding]; other site 338963006123 G1 box; other site 338963006124 putative GEF interaction site [polypeptide binding]; other site 338963006125 GTP/Mg2+ binding site [chemical binding]; other site 338963006126 Switch I region; other site 338963006127 G2 box; other site 338963006128 G3 box; other site 338963006129 Switch II region; other site 338963006130 G4 box; other site 338963006131 G5 box; other site 338963006132 CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NodQ_II; cd03695 338963006133 TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NoDQ_III; cd04095 338963006134 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 338963006135 active site 338963006136 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 338963006137 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 338963006138 Active Sites [active] 338963006139 conserved nucleotide sequence; Pcar_R4002 338963006140 conserved nucleotide sequence; Pcar_R4003 338963006141 conserved nucleotide sequence fragment; Pcar_R4004 338963006142 octanucleotide repeats; Pcar_R8025 338963006143 octanucleotide repeats; Pcar_R8026 338963006144 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 338963006145 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 338963006146 Active Sites [active] 338963006147 Predicted membrane protein (DUF2061); Region: DUF2061; pfam09834 338963006148 octanucleotide repeats; Pcar_R8027 338963006149 octanucleotide repeats; Pcar_R8028 338963006150 octanucleotide repeats; Pcar_R8029 338963006151 octanucleotide repeats; Pcar_R8030 338963006152 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 338963006153 Low molecular weight phosphatase family; Region: LMWPc; cd00115 338963006154 active site 338963006155 conserved nucleotide sequence; Pcar_R1020 338963006156 heptanucleotide repeats; Pcar_R7020 338963006157 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 338963006158 VacJ like lipoprotein; Region: VacJ; cl01073 338963006159 conserved nucleotide sequence fragment; Pcar_R4005 338963006160 octanucleotide repeats; Pcar_R8031 338963006161 conserved nucleotide sequence; Pcar_R8103 338963006162 octanucleotide repeats; Pcar_R8032 338963006163 octanucleotide repeats; Pcar_R8033 338963006164 conserved nucleotide sequence; Pcar_R8104 338963006165 octanucleotide repeats; Pcar_R8034 338963006166 Shikimate kinase [Amino acid transport and metabolism]; Region: AroK; COG0703 338963006167 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 338963006168 ADP binding site [chemical binding]; other site 338963006169 magnesium binding site [ion binding]; other site 338963006170 putative shikimate binding site; other site 338963006171 octanucleotide repeats; Pcar_R8035 338963006172 octanucleotide repeats; Pcar_R8036 338963006173 conserved nucleotide sequence fragment; Pcar_R4006 338963006174 Cytotoxic translational repressor of toxin-antitoxin stability system [Translation, ribosomal structure and biogenesis / Cell division and chromosome partitioning]; Region: RelE; COG2026 338963006175 octanucleotide repeats; Pcar_R8037 338963006176 octanucleotide repeats; Pcar_R8038 338963006177 conserved nucleotide sequence; Pcar_R4007 338963006178 conserved nucleotide sequence; Pcar_R4008 338963006179 conserved nucleotide sequence; Pcar_R4009 338963006180 conserved nucleotide sequence; Pcar_R4010 338963006181 conserved nucleotide sequence; Pcar_R4011 338963006182 conserved nucleotide sequence; Pcar_R4012 338963006183 octanucleotide repeats; Pcar_R8039 338963006184 conserved nucleotide sequence; Pcar_R8105 338963006185 octanucleotide repeats; Pcar_R8040 338963006186 phosphomannomutase CpsG; Provisional; Region: PRK15414 338963006187 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 338963006188 active site 338963006189 substrate binding site [chemical binding]; other site 338963006190 metal binding site [ion binding]; metal-binding site 338963006191 hypothetical protein; Reviewed; Region: PRK12275 338963006192 four helix bundle protein; Region: TIGR02436 338963006193 heptanucleotide repeats; Pcar_R7021 338963006194 Homeodomain-like domain; Region: HTH_23; pfam13384 338963006195 Winged helix-turn helix; Region: HTH_29; pfam13551 338963006196 Integrase core domain; Region: rve; pfam00665 338963006197 Integrase core domain; Region: rve_3; pfam13683 338963006198 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 338963006199 active site 338963006200 NTP binding site [chemical binding]; other site 338963006201 metal binding triad [ion binding]; metal-binding site 338963006202 antibiotic binding site [chemical binding]; other site 338963006203 Bacterial dnaA protein helix-turn-helix domain; Region: Bac_DnaA_C; smart00760 338963006204 DnaA box-binding interface [nucleotide binding]; other site 338963006205 conserved nucleotide sequence; Pcar_R5042 338963006206 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 338963006207 non-specific DNA binding site [nucleotide binding]; other site 338963006208 salt bridge; other site 338963006209 sequence-specific DNA binding site [nucleotide binding]; other site 338963006210 conserved nucleotide sequence; Pcar_R5043 338963006211 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 338963006212 Transposase; Region: DDE_Tnp_ISL3; pfam01610 338963006213 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 338963006214 Plasmid stabilisation system protein; Region: Plasmid_stabil; pfam05016 338963006215 conserved nucleotide sequence; Pcar_R5044 338963006216 Transposase IS200 like; Region: Y1_Tnp; cl00848 338963006217 Bacterial dnaA protein helix-turn-helix domain; Region: Bac_DnaA_C; smart00760 338963006218 DnaA box-binding interface [nucleotide binding]; other site 338963006219 conserved nucleotide sequence; Pcar_R4013 338963006220 octanucleotide repeats; Pcar_R8041 338963006221 conserved nucleotide sequence; Pcar_R8106 338963006222 octanucleotide repeats; Pcar_R8042 338963006223 phosphomannomutase CpsG; Provisional; Region: PRK15414 338963006224 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 338963006225 active site 338963006226 substrate binding site [chemical binding]; other site 338963006227 metal binding site [ion binding]; metal-binding site 338963006228 hypothetical protein; Reviewed; Region: PRK12275 338963006229 four helix bundle protein; Region: TIGR02436 338963006230 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 338963006231 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 338963006232 Substrate binding site; other site 338963006233 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 338963006234 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 338963006235 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 338963006236 active site 338963006237 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 338963006238 Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the...; Region: LbH_MAT_like; cd04647 338963006239 trimer interface [polypeptide binding]; other site 338963006240 active site 338963006241 substrate binding site [chemical binding]; other site 338963006242 CoA binding site [chemical binding]; other site 338963006243 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 338963006244 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 338963006245 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 338963006246 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 338963006247 Polysaccharide pyruvyl transferase family protein [Cell wall/membrane/envelope biogenesis]; Region: WcaK; COG2327 338963006248 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; pfam04230 338963006249 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; cl09156 338963006250 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 338963006251 Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the...; Region: LbH_MAT_like; cd04647 338963006252 trimer interface [polypeptide binding]; other site 338963006253 active site 338963006254 substrate binding site [chemical binding]; other site 338963006255 CoA binding site [chemical binding]; other site 338963006256 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 338963006257 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 338963006258 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 338963006259 UDP-glucose 4-epimerase; Region: PLN02240 338963006260 NAD binding site [chemical binding]; other site 338963006261 homodimer interface [polypeptide binding]; other site 338963006262 active site 338963006263 substrate binding site [chemical binding]; other site 338963006264 conserved nucleotide sequence fragment; Pcar_R4014 338963006265 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 338963006266 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 338963006267 glutaminase active site [active] 338963006268 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 338963006269 dimer interface [polypeptide binding]; other site 338963006270 active site 338963006271 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 338963006272 dimer interface [polypeptide binding]; other site 338963006273 active site 338963006274 conserved nucleotide sequence fragment; Pcar_R4015 338963006275 conserved nucleotide sequence; Pcar_R4016 338963006276 conserved nucleotide sequence fragment; Pcar_R4017 338963006277 conserved nucleotide sequence; Pcar_R4018 338963006278 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 338963006279 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 338963006280 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 338963006281 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 338963006282 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 338963006283 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 338963006284 NAD binding site [chemical binding]; other site 338963006285 homodimer interface [polypeptide binding]; other site 338963006286 active site 338963006287 substrate binding site [chemical binding]; other site 338963006288 octanucleotide repeats; Pcar_R8043 338963006289 octanucleotide repeats; Pcar_R8044 338963006290 octanucleotide repeats; Pcar_R8045 338963006291 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK07111 338963006292 Stage III sporulation protein AF (Spore_III_AF); Region: Spore_III_AF; cl17562 338963006293 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4924 338963006294 Uncharacterized protein conserved in bacteria N-term (DUF3322); Region: DUF3322; pfam11795 338963006295 Uncharacterized protein conserved in bacteria C-term(DUF2220); Region: DUF2220; pfam09983 338963006296 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4913 338963006297 P-loop containing region of AAA domain; Region: AAA_29; pfam13555 338963006298 Putative exonuclease SbcCD, C subunit; Region: SbcCD_C; pfam13558 338963006299 Domain of unknown function (DUF4194); Region: DUF4194; pfam13835 338963006300 Protein of unknown function (DUF3375); Region: DUF3375; pfam11855 338963006301 Fic family protein [Function unknown]; Region: COG3177 338963006302 phage baseplate assembly protein V; Region: phage_P2_V; TIGR01644 338963006303 Bacteriophage Mu Gp45 protein; Region: Phage_Mu_Gp45; cl15410 338963006304 Mu-like prophage tail protein gpP [General function prediction only]; Region: COG4379 338963006305 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 338963006306 Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_36K_type; cd07022 338963006307 tandem repeat interface [polypeptide binding]; other site 338963006308 oligomer interface [polypeptide binding]; other site 338963006309 active site residues [active] 338963006310 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 338963006311 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 338963006312 integrase; Provisional; Region: PRK09692 338963006313 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 338963006314 active site 338963006315 Int/Topo IB signature motif; other site 338963006316 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 338963006317 SmpB-tmRNA interface; other site 338963006318 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 338963006319 Uncharacterized conserved protein [Function unknown]; Region: COG2928 338963006320 Cytosine deaminase and related metal-dependent hydrolases [Nucleotide transport and metabolism / General function prediction only]; Region: SsnA; COG0402 338963006321 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 338963006322 active site 338963006323 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 338963006324 tetramerization interface [polypeptide binding]; other site 338963006325 active site 338963006326 Pantoate-beta-alanine ligase; Region: PanC; cd00560 338963006327 pantoate--beta-alanine ligase; Region: panC; TIGR00018 338963006328 active site 338963006329 ATP-binding site [chemical binding]; other site 338963006330 pantoate-binding site; other site 338963006331 HXXH motif; other site 338963006332 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 338963006333 oligomerization interface [polypeptide binding]; other site 338963006334 active site 338963006335 metal binding site [ion binding]; metal-binding site 338963006336 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 338963006337 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 338963006338 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 338963006339 dimer interface [polypeptide binding]; other site 338963006340 [2Fe-2S] cluster binding site [ion binding]; other site 338963006341 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 338963006342 [FeFe] hydrogenase, group A; Region: FeFe_hydrog_A; TIGR02512 338963006343 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 338963006344 Putative Fe-S cluster; Region: FeS; cl17515 338963006345 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 338963006346 PAS fold; Region: PAS_4; pfam08448 338963006347 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 338963006348 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 338963006349 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 338963006350 Radical SAM superfamily; Region: Radical_SAM; pfam04055 338963006351 FeS/SAM binding site; other site 338963006352 Formate/nitrite transporter; Region: Form_Nir_trans; pfam01226 338963006353 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 338963006354 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 338963006355 GTP binding site; other site 338963006356 formate dehydrogenase accessory protein; Reviewed; Region: PRK00724 338963006357 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 338963006358 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 338963006359 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 338963006360 catalytic residue [active] 338963006361 Gamma carbonic anhydrases (CA): Carbonic anhydrases are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism, involving the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed...; Region: LbH_gamma_CA; cd00710 338963006362 trimer interface [polypeptide binding]; other site 338963006363 active site 338963006364 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 338963006365 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 338963006366 catalytic loop [active] 338963006367 iron binding site [ion binding]; other site 338963006368 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 338963006369 4Fe-4S binding domain; Region: Fer4; pfam00037 338963006370 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_Formate-Dh-H; cd02753 338963006371 [4Fe-4S] binding site [ion binding]; other site 338963006372 molybdopterin cofactor binding site; other site 338963006373 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_CT_Formate-Dh_H; cd02790 338963006374 molybdopterin cofactor binding site; other site 338963006375 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 338963006376 SLBB domain; Region: SLBB; pfam10531 338963006377 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 338963006378 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 338963006379 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 338963006380 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 338963006381 dimer interface [polypeptide binding]; other site 338963006382 [2Fe-2S] cluster binding site [ion binding]; other site 338963006383 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 338963006384 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 338963006385 putative dimer interface [polypeptide binding]; other site 338963006386 [2Fe-2S] cluster binding site [ion binding]; other site 338963006387 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 338963006388 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 338963006389 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; pfam09835 338963006390 UGMP family protein; Validated; Region: PRK09604 338963006391 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 338963006392 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 338963006393 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 338963006394 putative active site [active] 338963006395 PhoH-like protein; Region: PhoH; pfam02562 338963006396 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK08665 338963006397 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 338963006398 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 338963006399 active site 338963006400 dimer interface [polypeptide binding]; other site 338963006401 effector binding site; other site 338963006402 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 338963006403 TSCPD domain; Region: TSCPD; pfam12637 338963006404 hypothetical protein; Provisional; Region: PRK05170 338963006405 Permeases of the major facilitator superfamily [General function prediction only]; Region: COG2270 338963006406 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 338963006407 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 338963006408 Glycerophosphodiester phosphodiesterase domain of Streptomyces coelicolor cytoplasmic phosphodiesterases UgpQ2 and similar proteins; Region: GDPD_cytoplasmic_ScUgpQ2_like; cd08561 338963006409 putative active site [active] 338963006410 catalytic site [active] 338963006411 putative metal binding site [ion binding]; other site 338963006412 Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either...; Region: rubredoxin_like; cl00202 338963006413 iron binding site [ion binding]; other site 338963006414 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 338963006415 MiaB-like tRNA modifying enzyme; Region: MiaB-like-C; TIGR01579 338963006416 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 338963006417 FeS/SAM binding site; other site 338963006418 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 338963006419 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 338963006420 Ligand Binding Site [chemical binding]; other site 338963006421 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 338963006422 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 338963006423 trimerization site [polypeptide binding]; other site 338963006424 active site 338963006425 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 338963006426 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 338963006427 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 338963006428 catalytic residue [active] 338963006429 Transcriptional regulator; Region: Rrf2; cl17282 338963006430 Rrf2 family protein; Region: rrf2_super; TIGR00738 338963006431 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 338963006432 serine O-acetyltransferase; Region: cysE; TIGR01172 338963006433 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 338963006434 trimer interface [polypeptide binding]; other site 338963006435 active site 338963006436 substrate binding site [chemical binding]; other site 338963006437 CoA binding site [chemical binding]; other site 338963006438 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 338963006439 active site 338963006440 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 338963006441 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 338963006442 DNA binding site [nucleotide binding] 338963006443 catalytic residue [active] 338963006444 H2TH interface [polypeptide binding]; other site 338963006445 putative catalytic residues [active] 338963006446 turnover-facilitating residue; other site 338963006447 intercalation triad [nucleotide binding]; other site 338963006448 8OG recognition residue [nucleotide binding]; other site 338963006449 putative reading head residues; other site 338963006450 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 338963006451 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 338963006452 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 338963006453 Na2 binding site [ion binding]; other site 338963006454 putative substrate binding site 1 [chemical binding]; other site 338963006455 Na binding site 1 [ion binding]; other site 338963006456 putative substrate binding site 2 [chemical binding]; other site 338963006457 conserved nucleotide sequence; Pcar_R2012 338963006458 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 338963006459 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 338963006460 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 338963006461 dimer interface [polypeptide binding]; other site 338963006462 conserved gate region; other site 338963006463 putative PBP binding loops; other site 338963006464 ABC-ATPase subunit interface; other site 338963006465 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 338963006466 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 338963006467 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 338963006468 dimer interface [polypeptide binding]; other site 338963006469 conserved gate region; other site 338963006470 putative PBP binding loops; other site 338963006471 ABC-ATPase subunit interface; other site 338963006472 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 338963006473 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 338963006474 peptide binding site [polypeptide binding]; other site 338963006475 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 338963006476 TPR motif; other site 338963006477 binding surface 338963006478 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 338963006479 TPR motif; other site 338963006480 binding surface 338963006481 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 338963006482 binding surface 338963006483 TPR motif; other site 338963006484 TPR repeat; Region: TPR_11; pfam13414 338963006485 Tetratricopeptide repeat; Region: TPR_12; pfam13424 338963006486 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 338963006487 TPR motif; other site 338963006488 binding surface 338963006489 TPR repeat; Region: TPR_11; pfam13414 338963006490 TPR repeat; Region: TPR_11; pfam13414 338963006491 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 338963006492 binding surface 338963006493 TPR motif; other site 338963006494 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2187 338963006495 AAA domain; Region: AAA_33; pfam13671 338963006496 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 338963006497 active site 338963006498 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 338963006499 anti sigma factor interaction site; other site 338963006500 regulatory phosphorylation site [posttranslational modification]; other site 338963006501 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 338963006502 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 338963006503 Mg2+ binding site [ion binding]; other site 338963006504 G-X-G motif; other site 338963006505 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 338963006506 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 338963006507 motif II; other site 338963006508 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 338963006509 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 338963006510 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 338963006511 RNA binding surface [nucleotide binding]; other site 338963006512 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 338963006513 active site 338963006514 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 338963006515 active site 2 [active] 338963006516 active site 1 [active] 338963006517 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 338963006518 IHF dimer interface [polypeptide binding]; other site 338963006519 IHF - DNA interface [nucleotide binding]; other site 338963006520 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 338963006521 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 338963006522 tandem repeat interface [polypeptide binding]; other site 338963006523 oligomer interface [polypeptide binding]; other site 338963006524 active site residues [active] 338963006525 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 338963006526 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 338963006527 RNA binding site [nucleotide binding]; other site 338963006528 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 338963006529 RNA binding site [nucleotide binding]; other site 338963006530 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 338963006531 RNA binding site [nucleotide binding]; other site 338963006532 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 338963006533 RNA binding site [nucleotide binding]; other site 338963006534 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 338963006535 RNA binding site [nucleotide binding]; other site 338963006536 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 338963006537 RNA binding site [nucleotide binding]; other site 338963006538 LytB protein; Region: LYTB; cl00507 338963006539 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 338963006540 cytidylate kinase; Provisional; Region: cmk; PRK00023 338963006541 Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor; Region: CMPK; cd02020 338963006542 CMP-binding site; other site 338963006543 The sites determining sugar specificity; other site 338963006544 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 338963006545 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 338963006546 hinge; other site 338963006547 active site 338963006548 cyclohexadienyl dehydrogenase; Validated; Region: PRK07502 338963006549 prephenate dehydrogenase; Validated; Region: PRK08507 338963006550 Chorismate mutase type II; Region: CM_2; pfam01817 338963006551 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 338963006552 Prephenate dehydratase; Region: PDT; pfam00800 338963006553 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 338963006554 putative L-Phe binding site [chemical binding]; other site 338963006555 aspartate aminotransferase; Provisional; Region: PRK06836 338963006556 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 338963006557 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963006558 homodimer interface [polypeptide binding]; other site 338963006559 catalytic residue [active] 338963006560 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic...; Region: PRX_like1; cd02969 338963006561 putative catalytic residue [active] 338963006562 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 338963006563 DHH family; Region: DHH; pfam01368 338963006564 DHHA1 domain; Region: DHHA1; pfam02272 338963006565 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 338963006566 Protein export membrane protein; Region: SecD_SecF; pfam02355 338963006567 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 338963006568 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 338963006569 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 338963006570 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 338963006571 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 338963006572 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 338963006573 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 338963006574 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; pfam09838 338963006575 uncharacterized radical SAM protein YgiQ; Region: SAM_YgiQ; TIGR03904 338963006576 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 338963006577 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 338963006578 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 338963006579 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 338963006580 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 338963006581 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 338963006582 23S rRNA interface [nucleotide binding]; other site 338963006583 L3 interface [polypeptide binding]; other site 338963006584 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 338963006585 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 338963006586 dimerization interface 3.5A [polypeptide binding]; other site 338963006587 active site 338963006588 Cobalt transport protein; Region: CbiQ; cl00463 338963006589 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 338963006590 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 338963006591 tartrate dehydrogenase; Region: TTC; TIGR02089 338963006592 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 338963006593 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 338963006594 3-isopropylmalate dehydratase small subunit; Reviewed; Region: leuD; PRK00439 338963006595 substrate binding site [chemical binding]; other site 338963006596 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 338963006597 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 338963006598 substrate binding site [chemical binding]; other site 338963006599 ligand binding site [chemical binding]; other site 338963006600 2-isopropylmalate synthase; Validated; Region: PRK00915 338963006601 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 338963006602 active site 338963006603 catalytic residues [active] 338963006604 metal binding site [ion binding]; metal-binding site 338963006605 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 338963006606 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 338963006607 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 338963006608 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 338963006609 putative valine binding site [chemical binding]; other site 338963006610 dimer interface [polypeptide binding]; other site 338963006611 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 338963006612 acetolactate synthase 3 catalytic subunit; Reviewed; Region: PRK06048 338963006613 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 338963006614 PYR/PP interface [polypeptide binding]; other site 338963006615 dimer interface [polypeptide binding]; other site 338963006616 TPP binding site [chemical binding]; other site 338963006617 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 338963006618 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 338963006619 TPP-binding site [chemical binding]; other site 338963006620 dimer interface [polypeptide binding]; other site 338963006621 dihydroxy-acid dehydratase; Provisional; Region: PRK00911 338963006622 6-phosphogluconate dehydratase; Region: edd; TIGR01196 338963006623 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 338963006624 Glycoprotease family; Region: Peptidase_M22; pfam00814 338963006625 RIP metalloprotease RseP; Region: TIGR00054 338963006626 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 338963006627 active site 338963006628 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 338963006629 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 338963006630 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 338963006631 putative substrate binding region [chemical binding]; other site 338963006632 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 338963006633 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 338963006634 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 338963006635 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 338963006636 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 338963006637 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 338963006638 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 338963006639 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 338963006640 catalytic residue [active] 338963006641 putative FPP diphosphate binding site; other site 338963006642 putative FPP binding hydrophobic cleft; other site 338963006643 dimer interface [polypeptide binding]; other site 338963006644 putative IPP diphosphate binding site; other site 338963006645 ribosome recycling factor; Reviewed; Region: frr; PRK00083 338963006646 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 338963006647 hinge region; other site 338963006648 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 338963006649 putative nucleotide binding site [chemical binding]; other site 338963006650 uridine monophosphate binding site [chemical binding]; other site 338963006651 homohexameric interface [polypeptide binding]; other site 338963006652 elongation factor Ts; Provisional; Region: tsf; PRK09377 338963006653 UBA/TS-N domain; Region: UBA; pfam00627 338963006654 Elongation factor TS; Region: EF_TS; pfam00889 338963006655 Elongation factor TS; Region: EF_TS; pfam00889 338963006656 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 338963006657 rRNA interaction site [nucleotide binding]; other site 338963006658 S8 interaction site; other site 338963006659 putative laminin-1 binding site; other site 338963006660 Predicted permeases [General function prediction only]; Region: COG0795 338963006661 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 338963006662 Predicted permeases [General function prediction only]; Region: COG0795 338963006663 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 338963006664 Adenosylhomocysteinase; Provisional; Region: PTZ00075 338963006665 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 338963006666 homotetramer interface [polypeptide binding]; other site 338963006667 ligand binding site [chemical binding]; other site 338963006668 catalytic site [active] 338963006669 NAD binding site [chemical binding]; other site 338963006670 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 338963006671 dimerization interface [polypeptide binding]; other site 338963006672 putative DNA binding site [nucleotide binding]; other site 338963006673 putative Zn2+ binding site [ion binding]; other site 338963006674 Methyltransferase domain; Region: Methyltransf_23; pfam13489 338963006675 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 338963006676 S-adenosylmethionine binding site [chemical binding]; other site 338963006677 GT_2_like_a represents a glycosyltransferase family-2 subfamily with unknown function; Region: GT_2_like_a; cd02522 338963006678 transferase 2, rSAM/selenodomain-associated; Region: glyco_like_mftF; TIGR04283 338963006679 Probable Catalytic site; other site 338963006680 S-adenosylmethionine synthetase; Validated; Region: PRK05250 338963006681 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 338963006682 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 338963006683 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 338963006684 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 338963006685 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 338963006686 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 338963006687 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 338963006688 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 338963006689 dimerization domain swap beta strand [polypeptide binding]; other site 338963006690 regulatory protein interface [polypeptide binding]; other site 338963006691 active site 338963006692 regulatory phosphorylation site [posttranslational modification]; other site 338963006693 PTS system mannose/fructose/sorbose family IID component; Region: EIID-AGA; pfam03613 338963006694 PTS system sorbose-specific iic component; Region: EII-Sor; cl01506 338963006695 PTS system sorbose subfamily IIB component; Region: PTSIIB_sorb; pfam03830 338963006696 active site 338963006697 phosphorylation site [posttranslational modification] 338963006698 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_man; cd00006 338963006699 active pocket/dimerization site; other site 338963006700 active site 338963006701 phosphorylation site [posttranslational modification] 338963006702 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 338963006703 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 338963006704 active site 338963006705 phosphorylation site [posttranslational modification] 338963006706 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 338963006707 30S subunit binding site; other site 338963006708 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 338963006709 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 338963006710 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 338963006711 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 338963006712 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 338963006713 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 338963006714 Walker A/P-loop; other site 338963006715 ATP binding site [chemical binding]; other site 338963006716 Q-loop/lid; other site 338963006717 ABC transporter signature motif; other site 338963006718 Walker B; other site 338963006719 D-loop; other site 338963006720 H-loop/switch region; other site 338963006721 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 338963006722 OstA-like protein; Region: OstA; pfam03968 338963006723 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 338963006724 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 338963006725 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 338963006726 active site 338963006727 motif I; other site 338963006728 motif II; other site 338963006729 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 338963006730 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 338963006731 putative active site [active] 338963006732 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 338963006733 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 338963006734 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 338963006735 CTP synthetase; Validated; Region: pyrG; PRK05380 338963006736 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 338963006737 Catalytic site [active] 338963006738 active site 338963006739 UTP binding site [chemical binding]; other site 338963006740 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 338963006741 active site 338963006742 putative oxyanion hole; other site 338963006743 catalytic triad [active] 338963006744 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 338963006745 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 338963006746 Ligand binding site; other site 338963006747 oligomer interface; other site 338963006748 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 338963006749 Uncharacterized conserved protein [Function unknown]; Region: COG5276 338963006750 LVIVD repeat; Region: LVIVD; pfam08309 338963006751 Uncharacterized conserved protein [Function unknown]; Region: COG5276 338963006752 LVIVD repeat; Region: LVIVD; pfam08309 338963006753 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 338963006754 dimerization interface [polypeptide binding]; other site 338963006755 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 338963006756 dimer interface [polypeptide binding]; other site 338963006757 phosphorylation site [posttranslational modification] 338963006758 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 338963006759 ATP binding site [chemical binding]; other site 338963006760 Mg2+ binding site [ion binding]; other site 338963006761 G-X-G motif; other site 338963006762 Response regulator receiver domain; Region: Response_reg; pfam00072 338963006763 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963006764 active site 338963006765 phosphorylation site [posttranslational modification] 338963006766 intermolecular recognition site; other site 338963006767 dimerization interface [polypeptide binding]; other site 338963006768 Mn-dependent transcriptional regulator [Transcription]; Region: TroR; COG1321 338963006769 Iron dependent repressor, metal binding and dimerisation domain; Region: Fe_dep_repr_C; pfam02742 338963006770 FeoA domain; Region: FeoA; pfam04023 338963006771 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 338963006772 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 338963006773 G1 box; other site 338963006774 GTP/Mg2+ binding site [chemical binding]; other site 338963006775 Switch I region; other site 338963006776 G2 box; other site 338963006777 G3 box; other site 338963006778 Switch II region; other site 338963006779 G4 box; other site 338963006780 G5 box; other site 338963006781 Nucleoside recognition; Region: Gate; pfam07670 338963006782 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 338963006783 Nucleoside recognition; Region: Gate; pfam07670 338963006784 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 338963006785 metal binding site 2 [ion binding]; metal-binding site 338963006786 putative DNA binding helix; other site 338963006787 metal binding site 1 [ion binding]; metal-binding site 338963006788 dimer interface [polypeptide binding]; other site 338963006789 structural Zn2+ binding site [ion binding]; other site 338963006790 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 338963006791 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; pfam02683 338963006792 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 338963006793 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 338963006794 catalytic residues [active] 338963006795 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 338963006796 CoenzymeA binding site [chemical binding]; other site 338963006797 subunit interaction site [polypeptide binding]; other site 338963006798 PHB binding site; other site 338963006799 Predicted permeases [General function prediction only]; Region: COG0679 338963006800 pyruvate carboxylase; Reviewed; Region: PRK12999 338963006801 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 338963006802 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 338963006803 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 338963006804 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 338963006805 active site 338963006806 catalytic residues [active] 338963006807 metal binding site [ion binding]; metal-binding site 338963006808 homodimer binding site [polypeptide binding]; other site 338963006809 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 338963006810 carboxyltransferase (CT) interaction site; other site 338963006811 biotinylation site [posttranslational modification]; other site 338963006812 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 338963006813 Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form...; Region: Band_7_stomatin_like; cd03403 338963006814 Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]; Region: NfeD; COG1030 338963006815 Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Region: Clp_protease_NfeD_1; cd07020 338963006816 dimer interface [polypeptide binding]; other site 338963006817 active site residues [active] 338963006818 NfeD-like C-terminal, partner-binding; Region: NfeD; pfam01957 338963006819 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 338963006820 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963006821 active site 338963006822 phosphorylation site [posttranslational modification] 338963006823 intermolecular recognition site; other site 338963006824 dimerization interface [polypeptide binding]; other site 338963006825 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 338963006826 Walker A motif; other site 338963006827 ATP binding site [chemical binding]; other site 338963006828 Walker B motif; other site 338963006829 arginine finger; other site 338963006830 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 338963006831 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 338963006832 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 338963006833 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 338963006834 A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity...; Region: APP_MetAP; cd01066 338963006835 active site 338963006836 AMP-binding domain protein; Validated; Region: PRK08315 338963006837 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 338963006838 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_2; cd05917 338963006839 acyl-activating enzyme (AAE) consensus motif; other site 338963006840 putative AMP binding site [chemical binding]; other site 338963006841 putative active site [active] 338963006842 putative CoA binding site [chemical binding]; other site 338963006843 Response regulator receiver domain; Region: Response_reg; pfam00072 338963006844 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963006845 active site 338963006846 phosphorylation site [posttranslational modification] 338963006847 intermolecular recognition site; other site 338963006848 dimerization interface [polypeptide binding]; other site 338963006849 PilZ domain; Region: PilZ; cl01260 338963006850 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 338963006851 MgtC family; Region: MgtC; pfam02308 338963006852 MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea; Region: MogA_MoaB; cd00886 338963006853 MPT binding site; other site 338963006854 trimer interface [polypeptide binding]; other site 338963006855 MOSC domain; Region: MOSC; pfam03473 338963006856 Elongation factor G (EF-G) family; Region: EF-G_bact; cd04170 338963006857 elongation factor G; Reviewed; Region: PRK12740 338963006858 G1 box; other site 338963006859 putative GEF interaction site [polypeptide binding]; other site 338963006860 GTP/Mg2+ binding site [chemical binding]; other site 338963006861 Switch I region; other site 338963006862 G2 box; other site 338963006863 G3 box; other site 338963006864 Switch II region; other site 338963006865 G4 box; other site 338963006866 G5 box; other site 338963006867 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 338963006868 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 338963006869 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 338963006870 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 338963006871 nucleotide binding site [chemical binding]; other site 338963006872 Type III pantothenate kinase; Region: Pan_kinase; cl17198 338963006873 Biotin operon repressor [Transcription]; Region: BirA; COG1654 338963006874 biotin--protein ligase; Provisional; Region: PRK08330 338963006875 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 338963006876 Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]; Region: NadC; COG0157 338963006877 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 338963006878 dimerization interface [polypeptide binding]; other site 338963006879 active site 338963006880 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 338963006881 ligand binding site [chemical binding]; other site 338963006882 Uncharacterized conserved protein [Function unknown]; Region: COG2014 338963006883 Domain of unknown function (DUF4213); Region: DUF4213; pfam13938 338963006884 Domain of unknown function (DUF364); Region: DUF364; pfam04016 338963006885 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 338963006886 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 338963006887 putative active site [active] 338963006888 putative metal binding site [ion binding]; other site 338963006889 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 338963006890 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 338963006891 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 338963006892 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 338963006893 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 338963006894 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 338963006895 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 338963006896 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 338963006897 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 338963006898 Walker A motif; other site 338963006899 ATP binding site [chemical binding]; other site 338963006900 Walker B motif; other site 338963006901 arginine finger; other site 338963006902 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 338963006903 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 338963006904 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 338963006905 substrate binding pocket [chemical binding]; other site 338963006906 chain length determination region; other site 338963006907 substrate-Mg2+ binding site; other site 338963006908 catalytic residues [active] 338963006909 aspartate-rich region 1; other site 338963006910 active site lid residues [active] 338963006911 aspartate-rich region 2; other site 338963006912 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 338963006913 HSP70 interaction site [polypeptide binding]; other site 338963006914 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 338963006915 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 338963006916 dimerization interface [polypeptide binding]; other site 338963006917 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 338963006918 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 338963006919 dimer interface [polypeptide binding]; other site 338963006920 putative CheW interface [polypeptide binding]; other site 338963006921 Fibrinogen alpha/beta chain family; Region: Fib_alpha; pfam08702 338963006922 ribonuclease Z; Provisional; Region: PRK02126 338963006923 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 338963006924 active site clefts [active] 338963006925 zinc binding site [ion binding]; other site 338963006926 dimer interface [polypeptide binding]; other site 338963006927 phosphoglucomutase; Validated; Region: PRK07564 338963006928 This bacterial PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl...; Region: PGM_like3; cd05801 338963006929 active site 338963006930 substrate binding site [chemical binding]; other site 338963006931 metal binding site [ion binding]; metal-binding site 338963006932 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 338963006933 Coenzyme A binding pocket [chemical binding]; other site 338963006934 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 338963006935 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 338963006936 ATP binding site [chemical binding]; other site 338963006937 Mg2+ binding site [ion binding]; other site 338963006938 G-X-G motif; other site 338963006939 type I citrate synthase; Reviewed; Region: PRK09569 338963006940 citrate (Si)-synthase, eukaryotic; Region: cit_synth_euk; TIGR01793 338963006941 oxalacetate binding site [chemical binding]; other site 338963006942 citrylCoA binding site [chemical binding]; other site 338963006943 coenzyme A binding site [chemical binding]; other site 338963006944 catalytic triad [active] 338963006945 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 338963006946 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 338963006947 FMN binding site [chemical binding]; other site 338963006948 active site 338963006949 catalytic residues [active] 338963006950 substrate binding site [chemical binding]; other site 338963006951 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 338963006952 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 338963006953 putative active site [active] 338963006954 heme pocket [chemical binding]; other site 338963006955 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 338963006956 phosphorylation site [posttranslational modification] 338963006957 dimer interface [polypeptide binding]; other site 338963006958 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 338963006959 ATP binding site [chemical binding]; other site 338963006960 G-X-G motif; other site 338963006961 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 338963006962 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963006963 active site 338963006964 phosphorylation site [posttranslational modification] 338963006965 intermolecular recognition site; other site 338963006966 dimerization interface [polypeptide binding]; other site 338963006967 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 338963006968 Walker A motif; other site 338963006969 ATP binding site [chemical binding]; other site 338963006970 Walker B motif; other site 338963006971 arginine finger; other site 338963006972 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 338963006973 replicative DNA helicase; Region: DnaB; TIGR00665 338963006974 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 338963006975 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 338963006976 Walker A motif; other site 338963006977 ATP binding site [chemical binding]; other site 338963006978 Walker B motif; other site 338963006979 DNA binding loops [nucleotide binding] 338963006980 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 338963006981 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 338963006982 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 338963006983 Predicted membrane protein (DUF2232); Region: DUF2232; pfam09991 338963006984 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 338963006985 Ribosomal protein S6; Region: Ribosomal_S6; pfam01250 338963006986 GTP-binding protein YchF; Reviewed; Region: PRK09601 338963006987 YchF GTPase; Region: YchF; cd01900 338963006988 G1 box; other site 338963006989 GTP/Mg2+ binding site [chemical binding]; other site 338963006990 Switch I region; other site 338963006991 G2 box; other site 338963006992 Switch II region; other site 338963006993 G3 box; other site 338963006994 G4 box; other site 338963006995 G5 box; other site 338963006996 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 338963006997 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 338963006998 Inorganic H+ pyrophosphatase; Region: H_PPase; pfam03030 338963006999 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 338963007000 putative active site [active] 338963007001 catalytic residue [active] 338963007002 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 338963007003 ribosomal protein L25, Ctc-form; Region: ctc_TL5; TIGR00731 338963007004 5S rRNA interface [nucleotide binding]; other site 338963007005 CTC domain interface [polypeptide binding]; other site 338963007006 L16 interface [polypeptide binding]; other site 338963007007 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 338963007008 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 338963007009 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 338963007010 active site 338963007011 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK14614 338963007012 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 338963007013 Walker A motif; other site 338963007014 ATP binding site [chemical binding]; other site 338963007015 Walker B motif; other site 338963007016 arginine finger; other site 338963007017 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG0390 338963007018 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 338963007019 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963007020 Walker A/P-loop; other site 338963007021 ATP binding site [chemical binding]; other site 338963007022 Q-loop/lid; other site 338963007023 ABC transporter signature motif; other site 338963007024 Walker B; other site 338963007025 D-loop; other site 338963007026 H-loop/switch region; other site 338963007027 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 338963007028 Fe-S cluster binding site [ion binding]; other site 338963007029 active site 338963007030 Zinc dependent phospholipase C; Region: Zn_dep_PLPC; pfam00882 338963007031 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 338963007032 Flavoprotein; Region: Flavoprotein; pfam02441 338963007033 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 338963007034 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 338963007035 3'-5' exoribonuclease YhaM; Provisional; Region: PRK13480 338963007036 YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is...; Region: YhaM_OBF_like; cd04492 338963007037 generic binding surface I; other site 338963007038 generic binding surface II; other site 338963007039 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 338963007040 Zn2+ binding site [ion binding]; other site 338963007041 Mg2+ binding site [ion binding]; other site 338963007042 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 338963007043 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 338963007044 Response regulator receiver domain; Region: Response_reg; pfam00072 338963007045 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963007046 active site 338963007047 phosphorylation site [posttranslational modification] 338963007048 intermolecular recognition site; other site 338963007049 dimerization interface [polypeptide binding]; other site 338963007050 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 338963007051 dimer interface [polypeptide binding]; other site 338963007052 phosphorylation site [posttranslational modification] 338963007053 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 338963007054 ATP binding site [chemical binding]; other site 338963007055 Mg2+ binding site [ion binding]; other site 338963007056 G-X-G motif; other site 338963007057 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 338963007058 Ligand Binding Site [chemical binding]; other site 338963007059 Response regulator receiver domain; Region: Response_reg; pfam00072 338963007060 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963007061 active site 338963007062 phosphorylation site [posttranslational modification] 338963007063 intermolecular recognition site; other site 338963007064 dimerization interface [polypeptide binding]; other site 338963007065 purine nucleoside phosphorylase; Provisional; Region: PRK08202 338963007066 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 338963007067 non-specific DNA binding site [nucleotide binding]; other site 338963007068 salt bridge; other site 338963007069 sequence-specific DNA binding site [nucleotide binding]; other site 338963007070 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 338963007071 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 338963007072 binding surface 338963007073 TPR motif; other site 338963007074 TPR repeat; Region: TPR_11; pfam13414 338963007075 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 338963007076 binding surface 338963007077 TPR motif; other site 338963007078 TPR repeat; Region: TPR_11; pfam13414 338963007079 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 338963007080 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14463 338963007081 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 338963007082 FeS/SAM binding site; other site 338963007083 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 338963007084 active site 338963007085 multimer interface [polypeptide binding]; other site 338963007086 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 338963007087 PAS fold; Region: PAS_3; pfam08447 338963007088 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 338963007089 putative active site [active] 338963007090 heme pocket [chemical binding]; other site 338963007091 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 338963007092 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 338963007093 putative active site [active] 338963007094 heme pocket [chemical binding]; other site 338963007095 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 338963007096 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 338963007097 putative active site [active] 338963007098 heme pocket [chemical binding]; other site 338963007099 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 338963007100 dimer interface [polypeptide binding]; other site 338963007101 phosphorylation site [posttranslational modification] 338963007102 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 338963007103 ATP binding site [chemical binding]; other site 338963007104 Mg2+ binding site [ion binding]; other site 338963007105 G-X-G motif; other site 338963007106 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 338963007107 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 338963007108 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 338963007109 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 338963007110 active site 338963007111 dimerization interface [polypeptide binding]; other site 338963007112 ribonuclease PH; Reviewed; Region: rph; PRK00173 338963007113 Ribonuclease PH; Region: RNase_PH_bact; cd11362 338963007114 hexamer interface [polypeptide binding]; other site 338963007115 active site 338963007116 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 338963007117 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 338963007118 active site 338963007119 metal binding site [ion binding]; metal-binding site 338963007120 DHH family; Region: DHH; pfam01368 338963007121 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 338963007122 TPR repeat; Region: TPR_11; pfam13414 338963007123 TPR repeat; Region: TPR_11; pfam13414 338963007124 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 338963007125 binding surface 338963007126 TPR motif; other site 338963007127 TPR repeat; Region: TPR_11; pfam13414 338963007128 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 338963007129 binding surface 338963007130 TPR motif; other site 338963007131 TPR repeat; Region: TPR_11; pfam13414 338963007132 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 338963007133 binding surface 338963007134 TPR motif; other site 338963007135 Domain of unknown function (DUF3524); Region: DUF3524; pfam12038 338963007136 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 338963007137 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 338963007138 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 338963007139 putative ADP-ribose binding site [chemical binding]; other site 338963007140 putative active site [active] 338963007141 Domain of unknown function (DUF4388); Region: DUF4388; pfam14332 338963007142 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 338963007143 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 338963007144 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 338963007145 ABC transporter; Region: ABC_tran_2; pfam12848 338963007146 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 338963007147 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 338963007148 S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and...; Region: S1_RNase_E; cd04453 338963007149 homodimer interface [polypeptide binding]; other site 338963007150 oligonucleotide binding site [chemical binding]; other site 338963007151 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 338963007152 Smr domain; Region: Smr; pfam01713 338963007153 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 338963007154 binding surface 338963007155 TPR motif; other site 338963007156 TPR repeat; Region: TPR_11; pfam13414 338963007157 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 338963007158 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 338963007159 N-acetyl-D-glucosamine binding site [chemical binding]; other site 338963007160 catalytic residue [active] 338963007161 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 338963007162 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 338963007163 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 338963007164 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 338963007165 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 338963007166 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 338963007167 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 338963007168 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 338963007169 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 338963007170 HflX GTPase family; Region: HflX; cd01878 338963007171 G1 box; other site 338963007172 GTP/Mg2+ binding site [chemical binding]; other site 338963007173 Switch I region; other site 338963007174 G2 box; other site 338963007175 G3 box; other site 338963007176 Switch II region; other site 338963007177 G4 box; other site 338963007178 G5 box; other site 338963007179 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 338963007180 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 338963007181 NAD binding site [chemical binding]; other site 338963007182 homotetramer interface [polypeptide binding]; other site 338963007183 homodimer interface [polypeptide binding]; other site 338963007184 substrate binding site [chemical binding]; other site 338963007185 active site 338963007186 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 338963007187 Response regulator receiver domain; Region: Response_reg; pfam00072 338963007188 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963007189 active site 338963007190 phosphorylation site [posttranslational modification] 338963007191 intermolecular recognition site; other site 338963007192 dimerization interface [polypeptide binding]; other site 338963007193 PAS domain; Region: PAS_9; pfam13426 338963007194 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 338963007195 putative active site [active] 338963007196 heme pocket [chemical binding]; other site 338963007197 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963007198 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963007199 metal binding site [ion binding]; metal-binding site 338963007200 active site 338963007201 I-site; other site 338963007202 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 338963007203 NAD(P)H:flavin oxidoreductase-like family 1. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes; Region: NADPH_oxidoreductase_1; cd02150 338963007204 putative FMN binding site [chemical binding]; other site 338963007205 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 338963007206 S-adenosylmethionine binding site [chemical binding]; other site 338963007207 Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones]; Region: PflA; COG1180 338963007208 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 338963007209 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 338963007210 intersubunit interface [polypeptide binding]; other site 338963007211 flavoprotein, HI0933 family; Region: TIGR00275 338963007212 DEAD-like helicases superfamily; Region: DEXDc; smart00487 338963007213 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 338963007214 ATP binding site [chemical binding]; other site 338963007215 putative Mg++ binding site [ion binding]; other site 338963007216 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 338963007217 nucleotide binding region [chemical binding]; other site 338963007218 ATP-binding site [chemical binding]; other site 338963007219 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 338963007220 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 338963007221 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 338963007222 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 338963007223 Protein of unknown function DUF58; Region: DUF58; pfam01882 338963007224 MoxR-like ATPases [General function prediction only]; Region: COG0714 338963007225 ATPase family associated with various cellular activities (AAA); Region: AAA_3; pfam07726 338963007226 Walker A motif; other site 338963007227 ATP binding site [chemical binding]; other site 338963007228 Walker B motif; other site 338963007229 arginine finger; other site 338963007230 Flagellar hook-associated protein [Cell motility and secretion]; Region: FlgK; COG1256 338963007231 Spore Coat Protein U domain; Region: SCPU; pfam05229 338963007232 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 338963007233 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 338963007234 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 338963007235 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 338963007236 Spore Coat Protein U domain; Region: SCPU; cl02253 338963007237 chain length determinant protein tyrosine kinase EpsG; Region: EpsG; TIGR03029 338963007238 bacteriophage N4 adsorption protein B; Provisional; Region: nfrB; PRK15489 338963007239 Protein of unknown function (DUF456); Region: DUF456; pfam04306 338963007240 Protein of unknown function (DUF2959); Region: DUF2959; pfam11172 338963007241 Predicted membrane protein [Function unknown]; Region: COG2261 338963007242 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 338963007243 Histone deacetylase class IV also known as histone deacetylase 11; Region: HDAC_classIV; cd09993 338963007244 putative active site [active] 338963007245 Zn binding site [ion binding]; other site 338963007246 short chain dehydrogenase; Validated; Region: PRK08264 338963007247 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 338963007248 NAD(P) binding site [chemical binding]; other site 338963007249 active site 338963007250 acetoin reductases; Region: 23BDH; TIGR02415 338963007251 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 338963007252 NAD(P) binding site [chemical binding]; other site 338963007253 active site 338963007254 conserved nucleotide sequence; Pcar_R2013 338963007255 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 338963007256 dimerization domain [polypeptide binding]; other site 338963007257 dimer interface [polypeptide binding]; other site 338963007258 catalytic residues [active] 338963007259 octanucleotide repeats; Pcar_R8046 338963007260 Predicted membrane protein [Function unknown]; Region: COG1971 338963007261 Domain of unknown function DUF; Region: DUF204; pfam02659 338963007262 Domain of unknown function DUF; Region: DUF204; pfam02659 338963007263 octanucleotide repeats; Pcar_R8047 338963007264 Repair protein; Region: Repair_PSII; pfam04536 338963007265 octanucleotide repeats; Pcar_R8048 338963007266 octanucleotide repeats; Pcar_R8049 338963007267 23S rRNA m(2)G2445 methyltransferase; Provisional; Region: rlmL; PRK11783 338963007268 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 338963007269 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 338963007270 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 338963007271 S-adenosylmethionine binding site [chemical binding]; other site 338963007272 octanucleotide repeats; Pcar_R8050 338963007273 octanucleotide repeats; Pcar_R8051 338963007274 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 338963007275 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 338963007276 transmembrane helices; other site 338963007277 MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea; Region: MogA_MoaB; cd00886 338963007278 MPT binding site; other site 338963007279 trimer interface [polypeptide binding]; other site 338963007280 PAS fold; Region: PAS_4; pfam08448 338963007281 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 338963007282 putative active site [active] 338963007283 heme pocket [chemical binding]; other site 338963007284 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963007285 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963007286 metal binding site [ion binding]; metal-binding site 338963007287 active site 338963007288 I-site; other site 338963007289 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 338963007290 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 338963007291 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 338963007292 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 338963007293 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 338963007294 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 338963007295 hopanoid biosynthesis associated radical SAM protein HpnH; Region: HpnH; TIGR03470 338963007296 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 338963007297 FeS/SAM binding site; other site 338963007298 Domain of unknown function (DUF3463); Region: DUF3463; pfam11946 338963007299 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 338963007300 hopanoid biosynthesis associated RND transporter like protein HpnN; Region: HpnN; TIGR03480 338963007301 Ornithine/acetylornithine aminotransferase [Amino acid transport and metabolism]; Region: ArgD; COG4992 338963007302 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 338963007303 inhibitor-cofactor binding pocket; inhibition site 338963007304 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963007305 catalytic residue [active] 338963007306 molybdate ABC transporter periplasmic substrate-binding protein; Provisional; Region: PRK04168 338963007307 tungstate ABC transporter binding protein WtpA; Region: tungstate_WtpA; TIGR03730 338963007308 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 338963007309 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 338963007310 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963007311 Walker A/P-loop; other site 338963007312 ATP binding site [chemical binding]; other site 338963007313 Q-loop/lid; other site 338963007314 ABC transporter signature motif; other site 338963007315 Walker B; other site 338963007316 D-loop; other site 338963007317 H-loop/switch region; other site 338963007318 TOBE domain; Region: TOBE_2; pfam08402 338963007319 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 338963007320 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 338963007321 dimer interface [polypeptide binding]; other site 338963007322 conserved gate region; other site 338963007323 putative PBP binding loops; other site 338963007324 ABC-ATPase subunit interface; other site 338963007325 molybdate ABC transporter periplasmic substrate-binding protein; Provisional; Region: PRK04168 338963007326 tungstate ABC transporter binding protein WtpA; Region: tungstate_WtpA; TIGR03730 338963007327 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 338963007328 homodimer interaction site [polypeptide binding]; other site 338963007329 cofactor binding site; other site 338963007330 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 338963007331 Predicted Fe-S oxidoreductases [General function prediction only]; Region: COG0535 338963007332 FeS/SAM binding site; other site 338963007333 Methyltransferase domain; Region: Methyltransf_31; pfam13847 338963007334 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 338963007335 S-adenosylmethionine binding site [chemical binding]; other site 338963007336 Uncharacterized conserved protein [Function unknown]; Region: COG0398 338963007337 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 338963007338 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 338963007339 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963007340 active site 338963007341 phosphorylation site [posttranslational modification] 338963007342 intermolecular recognition site; other site 338963007343 dimerization interface [polypeptide binding]; other site 338963007344 ANTAR domain; Region: ANTAR; pfam03861 338963007345 Dinitrogenase reductase ADP-ribosyltransferase (DRAT); Region: DRAT; pfam07357 338963007346 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; cl00614 338963007347 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 338963007348 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 338963007349 non-specific DNA binding site [nucleotide binding]; other site 338963007350 salt bridge; other site 338963007351 sequence-specific DNA binding site [nucleotide binding]; other site 338963007352 Cupin domain; Region: Cupin_2; pfam07883 338963007353 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 338963007354 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 338963007355 conserved nucleotide sequence; Pcar_R1021 338963007356 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 338963007357 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 338963007358 dimer interface [polypeptide binding]; other site 338963007359 active site 338963007360 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 338963007361 catalytic residues [active] 338963007362 substrate binding site [chemical binding]; other site 338963007363 arginine decarboxylase; Provisional; Region: PRK05354 338963007364 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 338963007365 dimer interface [polypeptide binding]; other site 338963007366 active site 338963007367 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 338963007368 catalytic residues [active] 338963007369 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 338963007370 NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the...; Region: NifH; cd02040 338963007371 nitrogenase iron protein; Region: nifH; TIGR01287 338963007372 Nucleotide-binding sites [chemical binding]; other site 338963007373 Walker A motif; other site 338963007374 Switch I region of nucleotide binding site; other site 338963007375 Fe4S4 binding sites [ion binding]; other site 338963007376 Switch II region of nucleotide binding site; other site 338963007377 nitrogenase molybdenum-iron cofactor biosynthesis protein NifE; Region: nifE; TIGR01283 338963007378 Nitrogenase_MoFe_alpha_II: Nitrogenase MoFe protein, beta subunit. A group of proteins similar to the alpha subunit of the MoFe protein of the molybdenum (Mo-) nitrogenase. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to...; Region: Nitrogenase_MoFe_alpha; cd01976 338963007379 MoFe protein alpha/beta subunit interactions; other site 338963007380 Alpha subunit P cluster binding residues; other site 338963007381 FeMoco binding residues [chemical binding]; other site 338963007382 MoFe protein alpha subunit/Fe protein contacts; other site 338963007383 MoFe protein dimer/ dimer interactions; other site 338963007384 nitrogenase molybdenum-iron protein beta chain; Region: nifK; TIGR01286 338963007385 Nitrogenase_MoFe_beta: Nitrogenase MoFe protein, beta subunit. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to ammonia. The Molybdenum (Mo-) nitrogenase is the most widespread and best characterized of these systems; Region: Nitrogenase_MoFe_beta; cd01974 338963007386 MoFe protein beta/alpha subunit interactions; other site 338963007387 Beta subunit P cluster binding residues; other site 338963007388 MoFe protein beta subunit/Fe protein contacts; other site 338963007389 MoFe protein dimer/ dimer interactions; other site 338963007390 NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein...; Region: NifX; cd00853 338963007391 ferredoxin III, nif-specific; Region: fdxN_nitrog; TIGR02936 338963007392 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 338963007393 This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This...; Region: NifX_NifB; cl00252 338963007394 Domain of unknown function (DUF1858); Region: DUF1858; cl14817 338963007395 Bacterial extracellular solute-binding protein; Region: SBP_bac_6; pfam13343 338963007396 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 338963007397 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 338963007398 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963007399 Walker A/P-loop; other site 338963007400 ATP binding site [chemical binding]; other site 338963007401 Q-loop/lid; other site 338963007402 ABC transporter signature motif; other site 338963007403 Walker B; other site 338963007404 D-loop; other site 338963007405 H-loop/switch region; other site 338963007406 heptanucleotide repeats; Pcar_R7022 338963007407 Radical SAM superfamily; Region: Radical_SAM; pfam04055 338963007408 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 338963007409 FeS/SAM binding site; other site 338963007410 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 338963007411 putative PBP binding loops; other site 338963007412 ABC-ATPase subunit interface; other site 338963007413 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963007414 molybdenum ABC transporter, ATP-binding protein; Region: modC_ABC; TIGR02142 338963007415 Walker A/P-loop; other site 338963007416 ATP binding site [chemical binding]; other site 338963007417 Q-loop/lid; other site 338963007418 ABC transporter signature motif; other site 338963007419 Walker B; other site 338963007420 D-loop; other site 338963007421 H-loop/switch region; other site 338963007422 TOBE domain; Region: TOBE; cl01440 338963007423 trans-homoaconitate synthase; Reviewed; Region: aksA; PRK11858 338963007424 Streptomyces rubellomurinus FrbC and related proteins, catalytic TIM barrel domain; Region: DRE_TIM_NifV; cd07939 338963007425 active site 338963007426 catalytic residues [active] 338963007427 metal binding site [ion binding]; metal-binding site 338963007428 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB; cd01045 338963007429 diiron binding motif [ion binding]; other site 338963007430 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 338963007431 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 338963007432 Coenzyme A binding pocket [chemical binding]; other site 338963007433 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 338963007434 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 338963007435 putative active site [active] 338963007436 catalytic site [active] 338963007437 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 338963007438 putative active site [active] 338963007439 catalytic site [active] 338963007440 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 338963007441 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 338963007442 acyl-activating enzyme (AAE) consensus motif; other site 338963007443 AMP binding site [chemical binding]; other site 338963007444 active site 338963007445 CoA binding site [chemical binding]; other site 338963007446 indolepyruvate oxidoreductase subunit B; Reviewed; Region: PRK06274 338963007447 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 338963007448 indolepyruvate ferredoxin oxidoreductase, alpha subunit; Region: IOR_alpha; TIGR03336 338963007449 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 338963007450 dimer interface [polypeptide binding]; other site 338963007451 PYR/PP interface [polypeptide binding]; other site 338963007452 TPP binding site [chemical binding]; other site 338963007453 substrate binding site [chemical binding]; other site 338963007454 Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as...; Region: TPP_IOR_alpha; cd02008 338963007455 TPP-binding site; other site 338963007456 4Fe-4S binding domain; Region: Fer4; pfam00037 338963007457 ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein; Region: ACT_1ZPV; cd04872 338963007458 Uncharacterized proteins with similarity to Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL_like_DUF711; cd08025 338963007459 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 338963007460 'tRNA-Leu, fragment; Pcar_R0085' 338963007461 Fic family protein [Function unknown]; Region: COG3177 338963007462 Fic/DOC family N-terminal; Region: Fic_N; pfam13784 338963007463 Fic/DOC family; Region: Fic; pfam02661 338963007464 S25 ribosomal protein; Region: Ribosomal_S25; cl02050 338963007465 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 338963007466 Transposase; Region: HTH_Tnp_1; cl17663 338963007467 Menaquinone biosynthesis; Region: VitK2_biosynth; pfam02621 338963007468 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 338963007469 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 338963007470 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 338963007471 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 338963007472 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 338963007473 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 338963007474 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 338963007475 carboxyltransferase (CT) interaction site; other site 338963007476 biotinylation site [posttranslational modification]; other site 338963007477 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 338963007478 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 338963007479 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 338963007480 active site 338963007481 Roadblock/LC7 domain; Region: Robl_LC7; cl00886 338963007482 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 338963007483 binding surface 338963007484 TPR motif; other site 338963007485 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 338963007486 active site 338963007487 dimer interface [polypeptide binding]; other site 338963007488 metal binding site [ion binding]; metal-binding site 338963007489 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 338963007490 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 338963007491 Tetramer interface [polypeptide binding]; other site 338963007492 active site 338963007493 FMN-binding site [chemical binding]; other site 338963007494 AMIN domain; Region: AMIN; pfam11741 338963007495 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 338963007496 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 338963007497 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 338963007498 Pilus assembly protein, PilP; Region: PilP; pfam04351 338963007499 Pilus assembly protein, PilO; Region: PilO; pfam04350 338963007500 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 338963007501 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 338963007502 Cell division protein FtsA; Region: FtsA; cl17206 338963007503 Competence protein A; Region: Competence_A; pfam11104 338963007504 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 338963007505 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 338963007506 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 338963007507 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 338963007508 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 338963007509 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 338963007510 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 338963007511 Walker A/P-loop; other site 338963007512 ATP binding site [chemical binding]; other site 338963007513 Q-loop/lid; other site 338963007514 ABC transporter signature motif; other site 338963007515 Walker B; other site 338963007516 D-loop; other site 338963007517 H-loop/switch region; other site 338963007518 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 338963007519 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 338963007520 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963007521 active site 338963007522 phosphorylation site [posttranslational modification] 338963007523 intermolecular recognition site; other site 338963007524 dimerization interface [polypeptide binding]; other site 338963007525 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 338963007526 Walker A motif; other site 338963007527 ATP binding site [chemical binding]; other site 338963007528 Walker B motif; other site 338963007529 arginine finger; other site 338963007530 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 338963007531 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 338963007532 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 338963007533 putative active site [active] 338963007534 heme pocket [chemical binding]; other site 338963007535 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 338963007536 phosphorylation site [posttranslational modification] 338963007537 dimer interface [polypeptide binding]; other site 338963007538 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 338963007539 ATP binding site [chemical binding]; other site 338963007540 Mg2+ binding site [ion binding]; other site 338963007541 G-X-G motif; other site 338963007542 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 338963007543 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 338963007544 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 338963007545 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 338963007546 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 338963007547 Walker A motif; other site 338963007548 ATP binding site [chemical binding]; other site 338963007549 Walker B motif; other site 338963007550 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 338963007551 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 338963007552 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 338963007553 Walker A motif; other site 338963007554 ATP binding site [chemical binding]; other site 338963007555 Walker B motif; other site 338963007556 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 338963007557 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 338963007558 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 338963007559 shikimate binding site; other site 338963007560 NAD(P) binding site [chemical binding]; other site 338963007561 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 338963007562 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 338963007563 active site 338963007564 Riboflavin kinase; Region: Flavokinase; smart00904 338963007565 ribonuclease R; Region: RNase_R; TIGR02063 338963007566 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 338963007567 RNB domain; Region: RNB; pfam00773 338963007568 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase...; Region: S1_RNase_R; cd04471 338963007569 RNA binding site [nucleotide binding]; other site 338963007570 Uncharacterized conserved protein [Function unknown]; Region: COG4198 338963007571 Protein of unknown function (DUF1015); Region: DUF1015; pfam06245 338963007572 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 338963007573 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 338963007574 PA14 domain; Region: PA14; cl08459 338963007575 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 338963007576 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 338963007577 Tfp pilus assembly protein PilX [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilX; COG4726 338963007578 PilX N-terminal; Region: PilX_N; pfam14341 338963007579 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 338963007580 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 338963007581 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 338963007582 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 338963007583 Type II transport protein GspH; Region: GspH; pfam12019 338963007584 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 338963007585 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963007586 active site 338963007587 phosphorylation site [posttranslational modification] 338963007588 intermolecular recognition site; other site 338963007589 dimerization interface [polypeptide binding]; other site 338963007590 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 338963007591 Walker A motif; other site 338963007592 ATP binding site [chemical binding]; other site 338963007593 Walker B motif; other site 338963007594 arginine finger; other site 338963007595 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 338963007596 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 338963007597 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 338963007598 dimerization interface [polypeptide binding]; other site 338963007599 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 338963007600 dimer interface [polypeptide binding]; other site 338963007601 phosphorylation site [posttranslational modification] 338963007602 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 338963007603 ATP binding site [chemical binding]; other site 338963007604 Mg2+ binding site [ion binding]; other site 338963007605 G-X-G motif; other site 338963007606 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 338963007607 putative substrate translocation pore; other site 338963007608 Major Facilitator Superfamily; Region: MFS_1; pfam07690 338963007609 heptanucleotide repeats; Pcar_R7023 338963007610 Uncharacterized conserved protein [Function unknown]; Region: COG1915 338963007611 Saccharopine dehydrogenase N-terminal domain; Region: SDH_N_domain; cd12144 338963007612 homodimer interface [polypeptide binding]; other site 338963007613 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 338963007614 Zn2+ binding site [ion binding]; other site 338963007615 Mg2+ binding site [ion binding]; other site 338963007616 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 338963007617 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 338963007618 substrate binding site [chemical binding]; other site 338963007619 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 338963007620 substrate binding site [chemical binding]; other site 338963007621 ligand binding site [chemical binding]; other site 338963007622 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 338963007623 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 338963007624 ligand binding site [chemical binding]; other site 338963007625 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 338963007626 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 338963007627 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 338963007628 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 338963007629 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 338963007630 GatB domain; Region: GatB_Yqey; smart00845 338963007631 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Region: COG0182; cl00348 338963007632 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 338963007633 Glutamine synthetase adenylyltransferase [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms]; Region: GlnE; COG1391 338963007634 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 338963007635 metal binding triad; other site 338963007636 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 338963007637 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 338963007638 metal binding triad; other site 338963007639 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 338963007640 Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor...; Region: IPT; cl15674 338963007641 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 338963007642 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 338963007643 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 338963007644 ABC transporter; Region: ABC_tran_2; pfam12848 338963007645 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 338963007646 Shikimate kinase [Amino acid transport and metabolism]; Region: AroK; COG0703 338963007647 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 338963007648 ADP binding site [chemical binding]; other site 338963007649 magnesium binding site [ion binding]; other site 338963007650 putative shikimate binding site; other site 338963007651 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 338963007652 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN_family; cd02803 338963007653 active site 338963007654 FMN binding site [chemical binding]; other site 338963007655 substrate binding site [chemical binding]; other site 338963007656 putative catalytic residue [active] 338963007657 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 338963007658 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 338963007659 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 338963007660 Transcriptional regulator [Transcription]; Region: LysR; COG0583 338963007661 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 338963007662 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 338963007663 dimerization interface [polypeptide binding]; other site 338963007664 Dehydroquinase class II; Region: DHquinase_II; pfam01220 338963007665 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 338963007666 trimer interface [polypeptide binding]; other site 338963007667 active site 338963007668 dimer interface [polypeptide binding]; other site 338963007669 Homeodomain-like domain; Region: HTH_23; pfam13384 338963007670 Winged helix-turn helix; Region: HTH_29; pfam13551 338963007671 Integrase core domain; Region: rve; pfam00665 338963007672 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 338963007673 Integrase core domain; Region: rve_3; pfam13683 338963007674 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 338963007675 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 338963007676 NAD(P) binding site [chemical binding]; other site 338963007677 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 338963007678 Major Facilitator Superfamily; Region: MFS_1; pfam07690 338963007679 putative substrate translocation pore; other site 338963007680 Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Region: HTH_MerR-like; cd00592 338963007681 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 338963007682 DNA binding residues [nucleotide binding] 338963007683 dimer interface [polypeptide binding]; other site 338963007684 Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Region: HTH_MerR-like; cd00592 338963007685 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 338963007686 DNA binding residues [nucleotide binding] 338963007687 dimer interface [polypeptide binding]; other site 338963007688 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 338963007689 putative substrate translocation pore; other site 338963007690 Major Facilitator Superfamily; Region: MFS_1; pfam07690 338963007691 Family description; Region: VCBS; pfam13517 338963007692 3-dehydroquinate dehydratase [Amino acid transport and metabolism]; Region: AroD; COG0710 338963007693 Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase); Region: DHQase_I; cd00502 338963007694 active site 338963007695 catalytic residue [active] 338963007696 dimer interface [polypeptide binding]; other site 338963007697 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 338963007698 Major Facilitator Superfamily; Region: MFS_1; pfam07690 338963007699 putative substrate translocation pore; other site 338963007700 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 338963007701 Shikimate 5-dehydrogenase [Amino acid transport and metabolism]; Region: AroE; COG0169 338963007702 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 338963007703 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 338963007704 shikimate binding site; other site 338963007705 NAD(P) binding site [chemical binding]; other site 338963007706 conserved nucleotide sequence; Pcar_R5021 338963007707 mycofactocin system FadH/OYE family oxidoreductase 2; Region: mycofact_OYE_2; TIGR03997 338963007708 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN_family; cd02803 338963007709 active site 338963007710 FMN binding site [chemical binding]; other site 338963007711 substrate binding site [chemical binding]; other site 338963007712 putative catalytic residue [active] 338963007713 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 338963007714 Homeodomain-like domain; Region: HTH_23; pfam13384 338963007715 Winged helix-turn helix; Region: HTH_29; pfam13551 338963007716 Integrase core domain; Region: rve; pfam00665 338963007717 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 338963007718 Integrase core domain; Region: rve_3; pfam13683 338963007719 radical SAM family uncharacterized protein; Region: rSAM_fuse_unch; TIGR03960 338963007720 cell division protein FtsZ; Validated; Region: PRK09330 338963007721 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 338963007722 nucleotide binding site [chemical binding]; other site 338963007723 SulA interaction site; other site 338963007724 cell division protein FtsA; Region: ftsA; TIGR01174 338963007725 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 338963007726 nucleotide binding site [chemical binding]; other site 338963007727 SHS2 domain inserted in FTSA; Region: SHS2_FTSA; pfam02491 338963007728 Cell division protein FtsA; Region: FtsA; pfam14450 338963007729 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 338963007730 Cell division protein FtsQ; Region: FtsQ; pfam03799 338963007731 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 338963007732 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 338963007733 ATP-grasp domain; Region: ATP-grasp_4; cl17255 338963007734 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 338963007735 FAD binding domain; Region: FAD_binding_4; pfam01565 338963007736 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 338963007737 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 338963007738 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 338963007739 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 338963007740 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 338963007741 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 338963007742 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 338963007743 homodimer interface [polypeptide binding]; other site 338963007744 active site 338963007745 cell division protein FtsW; Region: ftsW; TIGR02614 338963007746 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK14106 338963007747 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 338963007748 NAD(P) binding pocket [chemical binding]; other site 338963007749 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 338963007750 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 338963007751 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 338963007752 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 338963007753 Mg++ binding site [ion binding]; other site 338963007754 putative catalytic motif [active] 338963007755 putative substrate binding site [chemical binding]; other site 338963007756 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 338963007757 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 338963007758 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 338963007759 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 338963007760 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 338963007761 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 338963007762 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 338963007763 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 338963007764 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 338963007765 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 338963007766 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 338963007767 PASTA domain of PBP2x-like proteins, second repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by...; Region: PASTA_Pbp2x-like_2; cd06575 338963007768 Cell division protein FtsL; Region: FtsL; cl11433 338963007769 MraW methylase family; Region: Methyltransf_5; cl17771 338963007770 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 338963007771 cell division protein MraZ; Reviewed; Region: PRK00326 338963007772 MraZ protein; Region: MraZ; pfam02381 338963007773 MraZ protein; Region: MraZ; pfam02381 338963007774 Domain of unknown function DUF21; Region: DUF21; pfam01595 338963007775 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 338963007776 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 338963007777 Transporter associated domain; Region: CorC_HlyC; smart01091 338963007778 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 338963007779 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 338963007780 nucleotide binding pocket [chemical binding]; other site 338963007781 K-X-D-G motif; other site 338963007782 catalytic site [active] 338963007783 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 338963007784 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 338963007785 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 338963007786 Dimer interface [polypeptide binding]; other site 338963007787 BRCT sequence motif; other site 338963007788 Acylphosphatase; Region: Acylphosphatase; pfam00708 338963007789 Predicted methyltransferases [General function prediction only]; Region: COG0313 338963007790 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 338963007791 putative SAM binding site [chemical binding]; other site 338963007792 putative homodimer interface [polypeptide binding]; other site 338963007793 NAD synthetase; Reviewed; Region: nadE; PRK02628 338963007794 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 338963007795 multimer interface [polypeptide binding]; other site 338963007796 active site 338963007797 catalytic triad [active] 338963007798 protein interface 1 [polypeptide binding]; other site 338963007799 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 338963007800 homodimer interface [polypeptide binding]; other site 338963007801 NAD binding pocket [chemical binding]; other site 338963007802 ATP binding pocket [chemical binding]; other site 338963007803 Mg binding site [ion binding]; other site 338963007804 active-site loop [active] 338963007805 hypothetical protein; Reviewed; Region: PRK12497 338963007806 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 338963007807 RNA/DNA hybrid binding site [nucleotide binding]; other site 338963007808 active site 338963007809 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 338963007810 SAM-dependent RNA methyltransferase; Region: Methyltrn_RNA_4; pfam09936 338963007811 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 338963007812 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 338963007813 RimM N-terminal domain; Region: RimM; pfam01782 338963007814 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837 338963007815 hypothetical protein; Provisional; Region: PRK00468 338963007816 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 338963007817 signal recognition particle protein; Provisional; Region: PRK10867 338963007818 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 338963007819 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 338963007820 P loop; other site 338963007821 GTP binding site [chemical binding]; other site 338963007822 Signal peptide binding domain; Region: SRP_SPB; pfam02978 338963007823 Protein of unknown function (DUF721); Region: DUF721; pfam05258 338963007824 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 338963007825 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 338963007826 S-adenosylmethionine binding site [chemical binding]; other site 338963007827 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 338963007828 ResB-like family; Region: ResB; pfam05140 338963007829 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 338963007830 AIR carboxylase; Region: AIRC; pfam00731 338963007831 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 338963007832 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 338963007833 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 338963007834 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 338963007835 heptanucleotide repeats; Pcar_R7024 338963007836 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 338963007837 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 338963007838 purine monophosphate binding site [chemical binding]; other site 338963007839 dimer interface [polypeptide binding]; other site 338963007840 putative catalytic residues [active] 338963007841 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 338963007842 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 338963007843 Uncharacterized metal-binding protein [General function prediction only]; Region: COG3894 338963007844 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 338963007845 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 338963007846 active site 338963007847 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 338963007848 dimer interface [polypeptide binding]; other site 338963007849 substrate binding site [chemical binding]; other site 338963007850 catalytic residues [active] 338963007851 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 338963007852 thiamine phosphate binding site [chemical binding]; other site 338963007853 active site 338963007854 pyrophosphate binding site [ion binding]; other site 338963007855 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of...; Region: HMPP_kinase; cd01169 338963007856 dimer interface [polypeptide binding]; other site 338963007857 substrate binding site [chemical binding]; other site 338963007858 ATP binding site [chemical binding]; other site 338963007859 thiamine biosynthesis protein ThiC; Provisional; Region: PRK13352 338963007860 thiamine biosynthesis protein ThiC; Region: thiC; TIGR00190 338963007861 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 338963007862 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 338963007863 DNA-binding site [nucleotide binding]; DNA binding site 338963007864 The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain; Region: UTRA; smart00866 338963007865 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 338963007866 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 338963007867 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963007868 catalytic residue [active] 338963007869 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 338963007870 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 338963007871 substrate binding site [chemical binding]; other site 338963007872 active site 338963007873 catalytic residues [active] 338963007874 heterodimer interface [polypeptide binding]; other site 338963007875 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 338963007876 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 338963007877 motif II; other site 338963007878 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 338963007879 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 338963007880 HlyD family secretion protein; Region: HlyD_3; pfam13437 338963007881 multidrug efflux protein; Reviewed; Region: PRK09579 338963007882 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 338963007883 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 338963007884 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 338963007885 multidrug efflux protein; Reviewed; Region: PRK01766 338963007886 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 338963007887 cation binding site [ion binding]; other site 338963007888 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 338963007889 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 338963007890 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963007891 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963007892 metal binding site [ion binding]; metal-binding site 338963007893 active site 338963007894 I-site; other site 338963007895 Homeodomain-like domain; Region: HTH_23; pfam13384 338963007896 Winged helix-turn helix; Region: HTH_29; pfam13551 338963007897 Integrase core domain; Region: rve; pfam00665 338963007898 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 338963007899 Integrase core domain; Region: rve_3; pfam13683 338963007900 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 338963007901 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 338963007902 NAD(P) binding site [chemical binding]; other site 338963007903 active site 338963007904 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 338963007905 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 338963007906 active site 338963007907 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 338963007908 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 338963007909 intersubunit interface [polypeptide binding]; other site 338963007910 active site 338963007911 zinc binding site [ion binding]; other site 338963007912 Na+ binding site [ion binding]; other site 338963007913 glyceraldehyde-3-phosphate dehydrogenase; Reviewed; Region: PRK08289 338963007914 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 338963007915 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 338963007916 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 338963007917 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 338963007918 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 338963007919 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 338963007920 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 338963007921 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 338963007922 PilZ domain; Region: PilZ; pfam07238 338963007923 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 338963007924 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 338963007925 Clp amino terminal domain; Region: Clp_N; pfam02861 338963007926 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 338963007927 Walker A motif; other site 338963007928 ATP binding site [chemical binding]; other site 338963007929 Walker B motif; other site 338963007930 arginine finger; other site 338963007931 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 338963007932 Walker A motif; other site 338963007933 ATP binding site [chemical binding]; other site 338963007934 Walker B motif; other site 338963007935 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 338963007936 Uncharacterized conserved protein [Function unknown]; Region: COG2127 338963007937 Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflK; cd03404 338963007938 HflK protein; Region: hflK; TIGR01933 338963007939 HflC protein; Region: hflC; TIGR01932 338963007940 Band_7_HflC: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfC (High frequency of lysogenization C). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflC; cd03405 338963007941 Transposase IS200 like; Region: Y1_Tnp; pfam01797 338963007942 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 338963007943 DnaA box-binding interface [nucleotide binding]; other site 338963007944 Protein of unknown function (DUF1311); Region: DUF1311; pfam07007 338963007945 Protein of unknown function (DUF1311); Region: DUF1311; cl01530 338963007946 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 338963007947 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 338963007948 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 338963007949 putative active site [active] 338963007950 putative NTP binding site [chemical binding]; other site 338963007951 putative nucleic acid binding site [nucleotide binding]; other site 338963007952 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 338963007953 Domain of unknown function (DUF4104); Region: DUF4104; pfam13372 338963007954 YaeQ protein; Region: YaeQ; pfam07152 338963007955 RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; Region: RNase_H; cl14782 338963007956 RNA/DNA hybrid binding site [nucleotide binding]; other site 338963007957 active site 338963007958 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 338963007959 active site residue [active] 338963007960 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB; cd01045 338963007961 diiron binding motif [ion binding]; other site 338963007962 pyridine nucleotide-disulfide oxidoreductase family protein; Region: Nterm_to_SelD; TIGR03169 338963007963 LemA family; Region: LemA; pfam04011 338963007964 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]; Region: COG1512 338963007965 Repair protein; Region: Repair_PSII; pfam04536 338963007966 Repair protein; Region: Repair_PSII; cl01535 338963007967 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; pfam00690 338963007968 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 338963007969 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 338963007970 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 338963007971 motif II; other site 338963007972 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 338963007973 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 338963007974 Ligand Binding Site [chemical binding]; other site 338963007975 conserved nucleotide sequence; Pcar_R5068 338963007976 conserved nucleotide sequence; Pcar_R5069 338963007977 HIGH Nucleotidyl Transferase; Region: HIGH_NTase1; cl17673 338963007978 hypothetical protein; Provisional; Region: PRK13670 338963007979 putative DNA-binding transcriptional regulator; Reviewed; Region: PRK00347 338963007980 CT domains found N-terminal of phosphoserine phosphatase (PSP, SerB); Region: ACT_PSP_1; cd04870 338963007981 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 338963007982 phosphoserine phosphatase SerB; Region: serB; TIGR00338 338963007983 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 338963007984 motif II; other site 338963007985 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 338963007986 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 338963007987 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 338963007988 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 338963007989 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 338963007990 motif II; other site 338963007991 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_a; cd00913 338963007992 aromatic arch; other site 338963007993 DCoH dimer interaction site [polypeptide binding]; other site 338963007994 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 338963007995 DCoH tetramer interaction site [polypeptide binding]; other site 338963007996 substrate binding site [chemical binding]; other site 338963007997 palindrome; Pcar_R5085 338963007998 hypothetical protein; Provisional; Region: PRK08201 338963007999 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_3; cd05680 338963008000 metal binding site [ion binding]; metal-binding site 338963008001 putative dimer interface [polypeptide binding]; other site 338963008002 hypothetical protein; Provisional; Region: PRK11295 338963008003 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 338963008004 dimerization interface [polypeptide binding]; other site 338963008005 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963008006 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963008007 metal binding site [ion binding]; metal-binding site 338963008008 active site 338963008009 I-site; other site 338963008010 Cupin domain; Region: Cupin_2; cl17218 338963008011 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 338963008012 active site 338963008013 Protein of unknown function (DUF3405); Region: DUF3405; pfam11885 338963008014 conserved nucleotide sequence fragment; Pcar_R1022 338963008015 dihydropyrimidine dehydrogenase subunit A; Provisional; Region: PRK11749 338963008016 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 338963008017 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 338963008018 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 338963008019 PAS fold; Region: PAS_4; pfam08448 338963008020 PAS domain; Region: PAS_9; pfam13426 338963008021 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963008022 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963008023 metal binding site [ion binding]; metal-binding site 338963008024 active site 338963008025 I-site; other site 338963008026 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963008027 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963008028 metal binding site [ion binding]; metal-binding site 338963008029 active site 338963008030 I-site; other site 338963008031 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 338963008032 conserved nucleotide sequence; Pcar_R1023 338963008033 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 338963008034 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 338963008035 dimerization interface [polypeptide binding]; other site 338963008036 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 338963008037 dimer interface [polypeptide binding]; other site 338963008038 putative CheW interface [polypeptide binding]; other site 338963008039 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 338963008040 active site 338963008041 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 338963008042 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 338963008043 conserved nucleotide sequence; Pcar_R2014 338963008044 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 338963008045 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 338963008046 putative acyl-acceptor binding pocket; other site 338963008047 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; pfam13444 338963008048 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 338963008049 Glutamine amidotransferases class-II (Gn-AT)_YafJ-type. YafJ is a glutamine amidotransferase-like protein of unknown function found in prokaryotes, eukaryotes and archaea. YafJ has a conserved structural fold similar to those of other class II...; Region: YafJ; cd01908 338963008050 putative active site [active] 338963008051 putative dimer interface [polypeptide binding]; other site 338963008052 conserved nucleotide sequence; Pcar_R1024 338963008053 Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones]; Region: COG4067 338963008054 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 338963008055 RimK-like ATP-grasp domain; Region: RimK; pfam08443 338963008056 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]; Region: COG3357 338963008057 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 338963008058 putative Zn2+ binding site [ion binding]; other site 338963008059 [FeFe] hydrogenase, group A; Region: FeFe_hydrog_A; TIGR02512 338963008060 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 338963008061 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 338963008062 Putative Fe-S cluster; Region: FeS; cl17515 338963008063 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 338963008064 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 338963008065 Walker A motif; other site 338963008066 ATP binding site [chemical binding]; other site 338963008067 Walker B motif; other site 338963008068 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 338963008069 GAF domain; Region: GAF_2; pfam13185 338963008070 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 338963008071 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 338963008072 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 338963008073 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 338963008074 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 338963008075 CHASE4 domain; Region: CHASE4; pfam05228 338963008076 PAS domain S-box; Region: sensory_box; TIGR00229 338963008077 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 338963008078 putative active site [active] 338963008079 heme pocket [chemical binding]; other site 338963008080 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963008081 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963008082 metal binding site [ion binding]; metal-binding site 338963008083 active site 338963008084 I-site; other site 338963008085 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 338963008086 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 338963008087 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 338963008088 HIGH motif; other site 338963008089 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 338963008090 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 338963008091 active site 338963008092 KMSKS motif; other site 338963008093 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 338963008094 tRNA binding surface [nucleotide binding]; other site 338963008095 anticodon binding site; other site 338963008096 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 338963008097 Response regulator receiver domain; Region: Response_reg; pfam00072 338963008098 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963008099 active site 338963008100 phosphorylation site [posttranslational modification] 338963008101 intermolecular recognition site; other site 338963008102 dimerization interface [polypeptide binding]; other site 338963008103 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 338963008104 BED zinc finger; Region: zf-BED; cl02703 338963008105 Protein of unknown function (DUF2914); Region: DUF2914; pfam11141 338963008106 PilZ domain; Region: PilZ; pfam07238 338963008107 phosphopentomutase; Provisional; Region: PRK05362 338963008108 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 338963008109 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 338963008110 intersubunit interface [polypeptide binding]; other site 338963008111 active site 338963008112 catalytic residue [active] 338963008113 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 338963008114 heterotetramer interface [polypeptide binding]; other site 338963008115 active site pocket [active] 338963008116 cleavage site 338963008117 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 338963008118 DEAD/DEAH box helicase; Region: DEAD; pfam00270 338963008119 ATP binding site [chemical binding]; other site 338963008120 putative Mg++ binding site [ion binding]; other site 338963008121 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 338963008122 SEC-C motif; Region: SEC-C; pfam02810 338963008123 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 338963008124 Peptidase family M23; Region: Peptidase_M23; pfam01551 338963008125 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 338963008126 Coenzyme A binding pocket [chemical binding]; other site 338963008127 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 338963008128 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 338963008129 Walker A/P-loop; other site 338963008130 ATP binding site [chemical binding]; other site 338963008131 Q-loop/lid; other site 338963008132 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 338963008133 ABC transporter signature motif; other site 338963008134 Walker B; other site 338963008135 D-loop; other site 338963008136 H-loop/switch region; other site 338963008137 NAD kinase [Coenzyme metabolism]; Region: nadF; COG0061 338963008138 ATP-NAD kinase; Region: NAD_kinase; pfam01513 338963008139 recombination factor protein RarA; Reviewed; Region: PRK13342 338963008140 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 338963008141 Walker A motif; other site 338963008142 ATP binding site [chemical binding]; other site 338963008143 Walker B motif; other site 338963008144 arginine finger; other site 338963008145 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 338963008146 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 338963008147 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 338963008148 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 338963008149 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 338963008150 Zn2+ binding site [ion binding]; other site 338963008151 Mg2+ binding site [ion binding]; other site 338963008152 PilZ domain; Region: PilZ; cl01260 338963008153 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 338963008154 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 338963008155 catalytic triad [active] 338963008156 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 338963008157 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 338963008158 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 338963008159 motif II; other site 338963008160 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 338963008161 Glycerophosphoryl diester phosphodiesterase family; Region: GDPD; pfam03009 338963008162 active site 338963008163 catalytic site [active] 338963008164 Bacterial fructose-1,6-bisphosphatase, glpX-encoded. A dimeric enzyme dependent on Mg(2+). glpX-encoded FPBase (FBPase class II) differs from other members of the inositol-phosphatase superfamily by permutation of secondary structure elements. The core...; Region: FBPase_glpX; cd01516 338963008165 Bacterial fructose-1,6-bisphosphatase, glpX-encoded; Region: FBPase_glpX; pfam03320 338963008166 putative active site [active] 338963008167 hypothetical protein; Validated; Region: PRK00110 338963008168 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 338963008169 active site 338963008170 putative DNA-binding cleft [nucleotide binding]; other site 338963008171 dimer interface [polypeptide binding]; other site 338963008172 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 338963008173 RuvA N terminal domain; Region: RuvA_N; pfam01330 338963008174 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 338963008175 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 338963008176 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 338963008177 Walker A motif; other site 338963008178 ATP binding site [chemical binding]; other site 338963008179 Walker B motif; other site 338963008180 arginine finger; other site 338963008181 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 338963008182 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 338963008183 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 338963008184 nucleophile elbow; other site 338963008185 Uncharacterized conserved protein [Function unknown]; Region: COG3937 338963008186 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 338963008187 ABC1 family; Region: ABC1; pfam03109 338963008188 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 338963008189 active site 338963008190 ATP binding site [chemical binding]; other site 338963008191 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 338963008192 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 338963008193 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 338963008194 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 338963008195 dimerization interface [polypeptide binding]; other site 338963008196 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 338963008197 putative active site [active] 338963008198 heme pocket [chemical binding]; other site 338963008199 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 338963008200 dimer interface [polypeptide binding]; other site 338963008201 phosphorylation site [posttranslational modification] 338963008202 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 338963008203 ATP binding site [chemical binding]; other site 338963008204 Mg2+ binding site [ion binding]; other site 338963008205 G-X-G motif; other site 338963008206 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 338963008207 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963008208 active site 338963008209 phosphorylation site [posttranslational modification] 338963008210 intermolecular recognition site; other site 338963008211 dimerization interface [polypeptide binding]; other site 338963008212 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 338963008213 Walker A motif; other site 338963008214 ATP binding site [chemical binding]; other site 338963008215 Walker B motif; other site 338963008216 arginine finger; other site 338963008217 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 338963008218 Rubrerythrin [Energy production and conversion]; Region: COG1592 338963008219 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 338963008220 binuclear metal center [ion binding]; other site 338963008221 Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and...; Region: rubredoxin_SM; cd00729 338963008222 iron binding site [ion binding]; other site 338963008223 desulfoferrodoxin; Region: dfx_rbo; TIGR00320 338963008224 Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small; Region: DSRD; cd00974 338963008225 non-heme iron binding site [ion binding]; other site 338963008226 dimer interface [polypeptide binding]; other site 338963008227 Superoxide reductase-like (SORL) domain, class I; SORL-domains are present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin. Superoxide reductase-like proteins scavenge superoxide anion radicals...; Region: SORL_Dfx_classI; cd03171 338963008228 non-heme iron binding site [ion binding]; other site 338963008229 dimer interface [polypeptide binding]; other site 338963008230 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 338963008231 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 338963008232 active site 338963008233 HIGH motif; other site 338963008234 dimer interface [polypeptide binding]; other site 338963008235 KMSKS motif; other site 338963008236 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 338963008237 RNA binding surface [nucleotide binding]; other site 338963008238 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain; Region: MPP_DR1281; cd07382 338963008239 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 338963008240 putative active site [active] 338963008241 metal binding site [ion binding]; metal-binding site 338963008242 homodimer binding site [polypeptide binding]; other site 338963008243 ribonuclease Y; Region: RNase_Y; TIGR03319 338963008244 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 338963008245 Zn2+ binding site [ion binding]; other site 338963008246 Mg2+ binding site [ion binding]; other site 338963008247 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 338963008248 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 338963008249 Cell division protein ZapA; Region: ZapA; pfam05164 338963008250 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 338963008251 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 338963008252 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 338963008253 P loop; other site 338963008254 GTP binding site [chemical binding]; other site 338963008255 Roadblock/LC7 domain; Region: Robl_LC7; smart00960 338963008256 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 338963008257 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 338963008258 Walker A/P-loop; other site 338963008259 ATP binding site [chemical binding]; other site 338963008260 Q-loop/lid; other site 338963008261 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; pfam06470 338963008262 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 338963008263 ABC transporter signature motif; other site 338963008264 Walker B; other site 338963008265 D-loop; other site 338963008266 H-loop/switch region; other site 338963008267 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 338963008268 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 338963008269 active site 338963008270 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 338963008271 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 338963008272 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 338963008273 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 338963008274 S-adenosylmethionine binding site [chemical binding]; other site 338963008275 The MutT pyrophosphohydrolase is a prototypical Nudix hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic...; Region: MutT_pyrophosphohydrolase; cd03425 338963008276 active site 338963008277 8-oxo-dGMP binding site [chemical binding]; other site 338963008278 nudix motif; other site 338963008279 metal binding site [ion binding]; metal-binding site 338963008280 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 338963008281 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 338963008282 putative active site [active] 338963008283 heme pocket [chemical binding]; other site 338963008284 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 338963008285 putative active site [active] 338963008286 heme pocket [chemical binding]; other site 338963008287 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 338963008288 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 338963008289 putative active site [active] 338963008290 heme pocket [chemical binding]; other site 338963008291 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 338963008292 dimer interface [polypeptide binding]; other site 338963008293 phosphorylation site [posttranslational modification] 338963008294 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 338963008295 ATP binding site [chemical binding]; other site 338963008296 Mg2+ binding site [ion binding]; other site 338963008297 G-X-G motif; other site 338963008298 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 338963008299 homodimer interaction site [polypeptide binding]; other site 338963008300 cofactor binding site; other site 338963008301 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 338963008302 Cache domain; Region: Cache_1; pfam02743 338963008303 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 338963008304 dimer interface [polypeptide binding]; other site 338963008305 putative CheW interface [polypeptide binding]; other site 338963008306 Response regulator receiver domain; Region: Response_reg; pfam00072 338963008307 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963008308 active site 338963008309 phosphorylation site [posttranslational modification] 338963008310 intermolecular recognition site; other site 338963008311 dimerization interface [polypeptide binding]; other site 338963008312 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 338963008313 PAS domain; Region: PAS_9; pfam13426 338963008314 putative active site [active] 338963008315 heme pocket [chemical binding]; other site 338963008316 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 338963008317 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 338963008318 Walker A motif; other site 338963008319 ATP binding site [chemical binding]; other site 338963008320 Walker B motif; other site 338963008321 arginine finger; other site 338963008322 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 338963008323 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 338963008324 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 338963008325 putative active site [active] 338963008326 heme pocket [chemical binding]; other site 338963008327 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 338963008328 putative active site [active] 338963008329 heme pocket [chemical binding]; other site 338963008330 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 338963008331 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 338963008332 putative active site [active] 338963008333 heme pocket [chemical binding]; other site 338963008334 PAS domain; Region: PAS_8; pfam13188 338963008335 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 338963008336 dimer interface [polypeptide binding]; other site 338963008337 phosphorylation site [posttranslational modification] 338963008338 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 338963008339 ATP binding site [chemical binding]; other site 338963008340 Mg2+ binding site [ion binding]; other site 338963008341 G-X-G motif; other site 338963008342 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 338963008343 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 338963008344 active site 338963008345 dimer interface [polypeptide binding]; other site 338963008346 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 338963008347 dimer interface [polypeptide binding]; other site 338963008348 active site 338963008349 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 338963008350 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 338963008351 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 338963008352 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 338963008353 TRAM domain; Region: TRAM; cl01282 338963008354 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 338963008355 S-adenosylmethionine binding site [chemical binding]; other site 338963008356 heptanucleotide repeats; Pcar_R7025 338963008357 palindrome; Pcar_R5086 338963008358 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 338963008359 DNA-binding site [nucleotide binding]; DNA binding site 338963008360 RNA-binding motif; other site 338963008361 Domain of unknown function (DUF4292); Region: DUF4292; pfam14125 338963008362 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 338963008363 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 338963008364 FtsX-like permease family; Region: FtsX; pfam02687 338963008365 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 338963008366 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 338963008367 FtsX-like permease family; Region: FtsX; pfam02687 338963008368 heptanucleotide repeats; Pcar_R7026 338963008369 cell division ATP-binding protein FtsE; Region: FtsE; TIGR02673 338963008370 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 338963008371 Walker A/P-loop; other site 338963008372 ATP binding site [chemical binding]; other site 338963008373 Q-loop/lid; other site 338963008374 ABC transporter signature motif; other site 338963008375 Walker B; other site 338963008376 D-loop; other site 338963008377 H-loop/switch region; other site 338963008378 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 338963008379 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 338963008380 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 338963008381 ligand binding site [chemical binding]; other site 338963008382 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 338963008383 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 338963008384 putative catalytic site [active] 338963008385 putative phosphate binding site [ion binding]; other site 338963008386 active site 338963008387 metal binding site A [ion binding]; metal-binding site 338963008388 DNA binding site [nucleotide binding] 338963008389 putative AP binding site [nucleotide binding]; other site 338963008390 putative metal binding site B [ion binding]; other site 338963008391 ATP-dependent DNA helicase RecQ; Provisional; Region: PRK11057 338963008392 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 338963008393 ATP binding site [chemical binding]; other site 338963008394 putative Mg++ binding site [ion binding]; other site 338963008395 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 338963008396 nucleotide binding region [chemical binding]; other site 338963008397 ATP-binding site [chemical binding]; other site 338963008398 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 338963008399 HRDC domain; Region: HRDC; pfam00570 338963008400 Putative rRNA methylase; Region: rRNA_methylase; pfam06962 338963008401 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 338963008402 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 338963008403 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 338963008404 DNA binding residues [nucleotide binding] 338963008405 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 338963008406 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 338963008407 binding surface 338963008408 TPR motif; other site 338963008409 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 338963008410 succinate CoA transferase; Region: YgfH_subfam; TIGR03458 338963008411 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 338963008412 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 338963008413 nucleotide binding site [chemical binding]; other site 338963008414 substrate binding site [chemical binding]; other site 338963008415 Lysine 2,3-aminomutase [Amino acid transport and metabolism]; Region: KamA; COG1509 338963008416 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 338963008417 FeS/SAM binding site; other site 338963008418 geranylgeranyl reductase family; Region: GG-red-SF; TIGR02032 338963008419 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 338963008420 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 338963008421 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 338963008422 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 338963008423 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 338963008424 methanogenesis imperfect marker protein 11; Region: methan_mark_11; TIGR03280 338963008425 Cobalt transport protein; Region: CbiQ; cl00463 338963008426 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 338963008427 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 338963008428 Walker A/P-loop; other site 338963008429 ATP binding site [chemical binding]; other site 338963008430 Q-loop/lid; other site 338963008431 ABC transporter signature motif; other site 338963008432 Walker B; other site 338963008433 D-loop; other site 338963008434 H-loop/switch region; other site 338963008435 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 338963008436 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 338963008437 Walker A/P-loop; other site 338963008438 ATP binding site [chemical binding]; other site 338963008439 Q-loop/lid; other site 338963008440 ABC transporter signature motif; other site 338963008441 Walker B; other site 338963008442 D-loop; other site 338963008443 H-loop/switch region; other site 338963008444 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 338963008445 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 338963008446 N-terminal plug; other site 338963008447 ligand-binding site [chemical binding]; other site 338963008448 AAA domain; Region: AAA_26; pfam13500 338963008449 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 338963008450 ABC-type tungstate transport system, permease component [Coenzyme metabolism]; Region: TupB; COG2998 338963008451 PBP superfamily domain; Region: PBP_like_2; pfam12849 338963008452 NCAIR mutase (PurE)-related proteins [General function prediction only]; Region: COG1691 338963008453 AIR carboxylase; Region: AIRC; smart01001 338963008454 hypothetical protein; Provisional; Region: PRK04194 338963008455 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 338963008456 tetramer interfaces [polypeptide binding]; other site 338963008457 binuclear metal-binding site [ion binding]; other site 338963008458 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 338963008459 competence damage-inducible protein A; Provisional; Region: PRK00549 338963008460 putative MPT binding site; other site 338963008461 Competence-damaged protein; Region: CinA; pfam02464 338963008462 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 338963008463 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 338963008464 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 338963008465 recombinase A; Provisional; Region: recA; PRK09354 338963008466 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 338963008467 hexamer interface [polypeptide binding]; other site 338963008468 Walker A motif; other site 338963008469 ATP binding site [chemical binding]; other site 338963008470 Walker B motif; other site 338963008471 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 338963008472 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 338963008473 Walker A motif; other site 338963008474 ATP binding site [chemical binding]; other site 338963008475 Walker B motif; other site 338963008476 recombination regulator RecX; Reviewed; Region: recX; PRK00117 338963008477 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 338963008478 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 338963008479 motif 1; other site 338963008480 active site 338963008481 motif 2; other site 338963008482 motif 3; other site 338963008483 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 338963008484 Cupin domain; Region: Cupin_2; pfam07883 338963008485 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 338963008486 active site 338963008487 HslU subunit interaction site [polypeptide binding]; other site 338963008488 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 338963008489 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 338963008490 Walker A motif; other site 338963008491 ATP binding site [chemical binding]; other site 338963008492 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 338963008493 Walker B motif; other site 338963008494 arginine finger; other site 338963008495 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 338963008496 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 338963008497 feedback inhibition sensing region; other site 338963008498 homohexameric interface [polypeptide binding]; other site 338963008499 nucleotide binding site [chemical binding]; other site 338963008500 N-acetyl-L-glutamate binding site [chemical binding]; other site 338963008501 acetylornithine aminotransferase; Provisional; Region: PRK02627 338963008502 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 338963008503 inhibitor-cofactor binding pocket; inhibition site 338963008504 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963008505 catalytic residue [active] 338963008506 ornithine carbamoyltransferase; Provisional; Region: PRK00779 338963008507 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 338963008508 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 338963008509 zinc-ribbon domain; Region: zinc_ribbon_5; cl11777 338963008510 RDD family; Region: RDD; pfam06271 338963008511 argininosuccinate synthase; Provisional; Region: PRK13820 338963008512 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 338963008513 ANP binding site [chemical binding]; other site 338963008514 Substrate Binding Site II [chemical binding]; other site 338963008515 Substrate Binding Site I [chemical binding]; other site 338963008516 argininosuccinate lyase; Provisional; Region: PRK00855 338963008517 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 338963008518 active sites [active] 338963008519 tetramer interface [polypeptide binding]; other site 338963008520 diaminopimelate decarboxylase; Region: lysA; TIGR01048 338963008521 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 338963008522 active site 338963008523 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 338963008524 substrate binding site [chemical binding]; other site 338963008525 catalytic residues [active] 338963008526 dimer interface [polypeptide binding]; other site 338963008527 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 338963008528 dihydrodipicolinate synthase; Region: dapA; TIGR00674 338963008529 dimer interface [polypeptide binding]; other site 338963008530 active site 338963008531 catalytic residue [active] 338963008532 dihydrodipicolinate reductase; Provisional; Region: PRK00048 338963008533 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 338963008534 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 338963008535 octanucleotide repeats; Pcar_R8052 338963008536 L,L-diaminopimelate aminotransferase; Validated; Region: PRK07590 338963008537 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 338963008538 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963008539 homodimer interface [polypeptide binding]; other site 338963008540 catalytic residue [active] 338963008541 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 338963008542 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 338963008543 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 338963008544 conserved nucleotide sequence; Pcar_R5012 338963008545 conserved nucleotide sequence fragment; Pcar_R5007 338963008546 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 338963008547 conserved nucleotide sequence fragment; Pcar_R5008 338963008548 conserved nucleotide sequence fragment; Pcar_R5009 338963008549 Acetokinase family; Region: Acetate_kinase; cl17229 338963008550 propionate/acetate kinase; Provisional; Region: PRK12379 338963008551 Predicted ATPases of PP-loop superfamily [General function prediction only]; Region: COG2102 338963008552 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_IV; cd01994 338963008553 Ligand Binding Site [chemical binding]; other site 338963008554 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 338963008555 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 338963008556 dimer interface [polypeptide binding]; other site 338963008557 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963008558 catalytic residue [active] 338963008559 ATP-utilizing enzymes of the PP-loop superfamily [General function prediction only]; Region: COG1606 338963008560 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily. Adenine 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_I; cd01990 338963008561 Ligand Binding Site [chemical binding]; other site 338963008562 Staphylococcal nuclease homologues; Region: SNc; smart00318 338963008563 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 338963008564 Catalytic site; other site 338963008565 hypothetical protein; Provisional; Region: PRK04164 338963008566 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 338963008567 phosphoenolpyruvate synthase; Validated; Region: PRK06464 338963008568 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 338963008569 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 338963008570 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 338963008571 Transglycosylase SLT domain; Region: SLT_2; pfam13406 338963008572 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 338963008573 N-acetyl-D-glucosamine binding site [chemical binding]; other site 338963008574 Kinase/pyrophosphorylase; Region: Kinase-PPPase; pfam03618 338963008575 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 338963008576 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 338963008577 active site 338963008578 dimerization interface [polypeptide binding]; other site 338963008579 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 338963008580 FAD binding domain; Region: FAD_binding_4; pfam01565 338963008581 L-lysine aminotransferase; Provisional; Region: PRK08297 338963008582 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 338963008583 inhibitor-cofactor binding pocket; inhibition site 338963008584 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963008585 catalytic residue [active] 338963008586 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 338963008587 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 338963008588 trimerization site [polypeptide binding]; other site 338963008589 active site 338963008590 FlgN protein; Region: FlgN; pfam05130 338963008591 flagellar hook-associated protein FlgK; Region: flgK_ends; TIGR02492 338963008592 Uncharacterized conserved protein [Function unknown]; Region: COG1359 338963008593 butyryl-CoA:acetate CoA-transferase; Region: butyr_acet_CoA; TIGR03948 338963008594 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 338963008595 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 338963008596 Flavodoxin-like fold; Region: Flavodoxin_2; pfam02525 338963008597 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 338963008598 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 338963008599 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 338963008600 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 338963008601 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963008602 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963008603 metal binding site [ion binding]; metal-binding site 338963008604 active site 338963008605 I-site; other site 338963008606 aconitate hydratase; Validated; Region: PRK07229 338963008607 Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: AcnA_Bact; cd01585 338963008608 substrate binding site [chemical binding]; other site 338963008609 ligand binding site [chemical binding]; other site 338963008610 Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme...; Region: Aconitase_swivel; cl00215 338963008611 substrate binding site [chemical binding]; other site 338963008612 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 338963008613 Mechanosensitive ion channel; Region: MS_channel; pfam00924 338963008614 Rhomboid family; Region: Rhomboid; pfam01694 338963008615 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 338963008616 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 338963008617 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 338963008618 active site 338963008619 HIGH motif; other site 338963008620 nucleotide binding site [chemical binding]; other site 338963008621 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 338963008622 active site 338963008623 KMSKS motif; other site 338963008624 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 338963008625 tRNA binding surface [nucleotide binding]; other site 338963008626 anticodon binding site; other site 338963008627 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 338963008628 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 338963008629 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 338963008630 Alpha-acetolactate decarboxylase; Region: AAL_decarboxy; pfam03306 338963008631 NLPC_P60 stabilising domain, N term; Region: N_NLPC_P60; pfam12912 338963008632 SH3 domain of the SH3b1 type; Region: SH3_6; pfam12913 338963008633 NlpC/P60 family; Region: NLPC_P60; cl17555 338963008634 Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either...; Region: rubredoxin_like; cd00350 338963008635 iron binding site [ion binding]; other site 338963008636 Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and...; Region: rubredoxin_SM; cd00729 338963008637 Rubrerythrin [Energy production and conversion]; Region: COG1592 338963008638 iron binding site [ion binding]; other site 338963008639 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 338963008640 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 338963008641 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 338963008642 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14193 338963008643 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 338963008644 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 338963008645 homodimer interface [polypeptide binding]; other site 338963008646 NADP binding site [chemical binding]; other site 338963008647 substrate binding site [chemical binding]; other site 338963008648 2-hydroxyacid dehydrogenase; Provisional; Region: PRK08410 338963008649 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_4; cd12162 338963008650 putative ligand binding site [chemical binding]; other site 338963008651 putative NAD binding site [chemical binding]; other site 338963008652 catalytic site [active] 338963008653 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 338963008654 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 338963008655 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 338963008656 Predicted metal-binding protein (DUF2284); Region: DUF2284; pfam10050 338963008657 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 338963008658 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963008659 DNA-binding transcriptional regulator RstA; Provisional; Region: PRK10701 338963008660 active site 338963008661 phosphorylation site [posttranslational modification] 338963008662 intermolecular recognition site; other site 338963008663 dimerization interface [polypeptide binding]; other site 338963008664 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 338963008665 DNA binding site [nucleotide binding] 338963008666 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 338963008667 dimerization interface [polypeptide binding]; other site 338963008668 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 338963008669 dimer interface [polypeptide binding]; other site 338963008670 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 338963008671 putative CheW interface [polypeptide binding]; other site 338963008672 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 338963008673 Major Facilitator Superfamily; Region: MFS_1; pfam07690 338963008674 putative substrate translocation pore; other site 338963008675 Mechanosensitive ion channel; Region: MS_channel; pfam00924 338963008676 ATP-dependent helicase HrpB; Region: DEAH_box_HrpB; TIGR01970 338963008677 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 338963008678 ATP binding site [chemical binding]; other site 338963008679 putative Mg++ binding site [ion binding]; other site 338963008680 helicase superfamily c-terminal domain; Region: HELICc; smart00490 338963008681 Helicase associated domain (HA2) Add an annotation; Region: HA2; smart00847 338963008682 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 338963008683 M20 Peptidase T like enzymes specifically cleave tripeptides; Region: M20_peptT_like; cd05683 338963008684 peptidase T-like protein; Region: PepT-like; TIGR01883 338963008685 metal binding site [ion binding]; metal-binding site 338963008686 putative dimer interface [polypeptide binding]; other site 338963008687 putative peptidase; Provisional; Region: PRK11649 338963008688 Peptidase family M23; Region: Peptidase_M23; pfam01551 338963008689 Protein of unknown function, DUF479; Region: DUF479; pfam04336 338963008690 Uncharacterized conserved protein [Function unknown]; Region: COG3287 338963008691 FIST N domain; Region: FIST; pfam08495 338963008692 FIST C domain; Region: FIST_C; pfam10442 338963008693 Domain of unknown function (DUF4388); Region: DUF4388; pfam14332 338963008694 Roadblock/LC7 domain; Region: Robl_LC7; smart00960 338963008695 The V4R (vinyl 4 reductase) domain is a predicted small molecular binding domain, that may bind to hydrocarbons; Region: V4R; smart00989 338963008696 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 338963008697 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 338963008698 P-loop; other site 338963008699 Magnesium ion binding site [ion binding]; other site 338963008700 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 338963008701 Magnesium ion binding site [ion binding]; other site 338963008702 hypothetical protein; Provisional; Region: PRK11568 338963008703 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 338963008704 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 338963008705 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 338963008706 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 338963008707 putative active site [active] 338963008708 putative metal binding site [ion binding]; other site 338963008709 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 338963008710 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 338963008711 N-acetyl-D-glucosamine binding site [chemical binding]; other site 338963008712 catalytic residue [active] 338963008713 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 338963008714 B12 binding site [chemical binding]; other site 338963008715 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 338963008716 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 338963008717 FeS/SAM binding site; other site 338963008718 OsmC-like protein; Region: OsmC; pfam02566 338963008719 elongation factor P; Validated; Region: PRK00529 338963008720 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 338963008721 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 338963008722 RNA binding site [nucleotide binding]; other site 338963008723 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 338963008724 RNA binding site [nucleotide binding]; other site 338963008725 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 338963008726 EF-P lysine aminoacylase GenX; Region: genX; TIGR00462 338963008727 motif 1; other site 338963008728 dimer interface [polypeptide binding]; other site 338963008729 active site 338963008730 motif 2; other site 338963008731 motif 3; other site 338963008732 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 338963008733 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 338963008734 Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either...; Region: rubredoxin_like; cl00202 338963008735 iron binding site [ion binding]; other site 338963008736 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 338963008737 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 338963008738 Homeodomain-like domain; Region: HTH_23; pfam13384 338963008739 Winged helix-turn helix; Region: HTH_29; pfam13551 338963008740 Integrase core domain; Region: rve; pfam00665 338963008741 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 338963008742 Integrase core domain; Region: rve_3; pfam13683 338963008743 PII-like signaling protein [Signal transduction mechanisms]; Region: COG1993 338963008744 conserved nucleotide sequence; Pcar_R5041 338963008745 conserved nucleotide sequence; Pcar_R5057 338963008746 conserved nucleotide sequence; Pcar_R5022 338963008747 conserved nucleotide sequence; Pcar_R5037 338963008748 RNA 3'-terminal-phosphate cyclase; Provisional; Region: PRK04204 338963008749 RNA 3' phosphate cyclase domain (class II). These proteins function as RNA cyclase to catalyze the ATP-dependent conversion of 3'-phosphate to a 2'.3'-cyclic phosphodiester at the end of RNA molecule. A conserved catalytic histidine...; Region: RNA_Cyclase_Class_II; cd00874 338963008750 putative active site [active] 338963008751 adenylation catalytic residue [active] 338963008752 Uncharacterized conserved protein (DUF2196); Region: DUF2196; pfam09962 338963008753 RNA-binding proteins (RRM domain) [General function prediction only]; Region: COG0724 338963008754 RNA recognition motif (RRM) superfamily; Region: RRM_SF; cd00590 338963008755 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 338963008756 PAS domain; Region: PAS_9; pfam13426 338963008757 putative active site [active] 338963008758 heme pocket [chemical binding]; other site 338963008759 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963008760 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963008761 metal binding site [ion binding]; metal-binding site 338963008762 active site 338963008763 I-site; other site 338963008764 Transcriptional regulators [Transcription]; Region: FadR; COG2186 338963008765 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 338963008766 DNA-binding site [nucleotide binding]; DNA binding site 338963008767 FCD domain; Region: FCD; pfam07729 338963008768 Homeodomain-like domain; Region: HTH_23; cl17451 338963008769 Transposase; Region: HTH_Tnp_1; cl17663 338963008770 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 338963008771 catalytic loop [active] 338963008772 iron binding site [ion binding]; other site 338963008773 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 338963008774 [FeFe] hydrogenase, group A; Region: FeFe_hydrog_A; TIGR02512 338963008775 4Fe-4S binding domain; Region: Fer4; pfam00037 338963008776 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 338963008777 Iron hydrogenase small subunit; Region: Fe_hyd_SSU; pfam02256 338963008778 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 338963008779 putative oxidoreductase; Provisional; Region: PRK12831 338963008780 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 338963008781 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 338963008782 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 338963008783 tetrameric interface [polypeptide binding]; other site 338963008784 NAD binding site [chemical binding]; other site 338963008785 catalytic residues [active] 338963008786 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 338963008787 Iron-containing alcohol dehydrogenases-like; Region: Fe-ADH6; cd08194 338963008788 putative active site [active] 338963008789 metal binding site [ion binding]; metal-binding site 338963008790 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 338963008791 PII-like signaling protein [Signal transduction mechanisms]; Region: COG1993 338963008792 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 338963008793 Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria; Region: LPO; cd08176 338963008794 dimer interface [polypeptide binding]; other site 338963008795 active site 338963008796 metal binding site [ion binding]; metal-binding site 338963008797 thiamine biosynthesis protein ThiF; Provisional; Region: PRK08644 338963008798 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 338963008799 ATP binding site [chemical binding]; other site 338963008800 substrate interface [chemical binding]; other site 338963008801 Ubiquitin-like proteins; Region: UBQ; cl00155 338963008802 charged pocket; other site 338963008803 hydrophobic patch; other site 338963008804 Aldehyde:ferredoxin oxidoreductase [Energy production and conversion]; Region: COG2414 338963008805 Aldehyde ferredoxin oxidoreductase, N-terminal domain; Region: AFOR_N; pfam02730 338963008806 Aldehyde ferredoxin oxidoreductase, domains 2 & 3; Region: AFOR_C; pfam01314 338963008807 putative metalloenzyme radical SAM/SPASM domain maturase; Region: rSAM_Geo_metal; TIGR04311 338963008808 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 338963008809 FeS/SAM binding site; other site 338963008810 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 338963008811 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 338963008812 Uncharacterized conserved protein [Function unknown]; Region: COG2006 338963008813 Domain of unknown function (DUF362); Region: DUF362; pfam04015 338963008814 ketol-acid reductoisomerase; Validated; Region: PRK05225 338963008815 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 338963008816 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 338963008817 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 338963008818 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 338963008819 DNA-binding transcriptional regulator IlvY; Provisional; Region: PRK11716 338963008820 The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic bindin; Region: PBP2_IlvY; cd08430 338963008821 putative dimerization interface [polypeptide binding]; other site 338963008822 Lysine 2,3-aminomutase [Amino acid transport and metabolism]; Region: KamA; COG1509 338963008823 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 338963008824 FeS/SAM binding site; other site 338963008825 Lysine-2,3-aminomutase; Region: LAM_C; pfam12544 338963008826 B12 binding domain; Region: B12-binding; pfam02310 338963008827 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 338963008828 Radical SAM superfamily; Region: Radical_SAM; pfam04055 338963008829 FeS/SAM binding site; other site 338963008830 Methylamine utilisation protein MauE; Region: MauE; pfam07291 338963008831 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 338963008832 active site residue [active] 338963008833 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 338963008834 Cu(I) binding site [ion binding]; other site 338963008835 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 338963008836 cytochrome c oxidase, subunit I; Region: CtaD_CoxA; TIGR02891 338963008837 Heme-copper oxidase subunit III. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The...; Region: Heme_Cu_Oxidase_III_like; cl00211 338963008838 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; cl01204 338963008839 cytochrome c oxidase, subunit II; Region: CoxB; TIGR02866 338963008840 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 338963008841 UbiA prenyltransferase family; Region: UbiA; pfam01040 338963008842 4-hydroxybenzoate polyprenyltransferase and related prenyltransferases [Coenzyme metabolism]; Region: UbiA; cl00337 338963008843 Ion channel; Region: Ion_trans_2; pfam07885 338963008844 conserved nucleotide sequence; Pcar_R2015 338963008845 RF-1 domain; Region: RF-1; pfam00472 338963008846 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 338963008847 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 338963008848 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 338963008849 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 338963008850 active site 338963008851 catalytic residues [active] 338963008852 metal binding site [ion binding]; metal-binding site 338963008853 mercuric reductase; Validated; Region: PRK06370 338963008854 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 338963008855 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 338963008856 Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on...; Region: cytidine_deaminase; cd01283 338963008857 active site 338963008858 catalytic motif [active] 338963008859 Zn binding site [ion binding]; other site 338963008860 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 338963008861 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 338963008862 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 338963008863 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 338963008864 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963008865 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963008866 metal binding site [ion binding]; metal-binding site 338963008867 active site 338963008868 I-site; other site 338963008869 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 338963008870 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and...; Region: GCS_H; cd06848 338963008871 lipoyl attachment site [posttranslational modification]; other site 338963008872 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 338963008873 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 338963008874 phosphotransacetylase; Reviewed; Region: eutD; PRK09653 338963008875 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 338963008876 propionate/acetate kinase; Provisional; Region: PRK12379 338963008877 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 338963008878 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 338963008879 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 338963008880 zinc-ribbon domain; Region: zinc_ribbon_5; pfam13719 338963008881 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 338963008882 active site 338963008883 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 338963008884 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 338963008885 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cd08168 338963008886 heme-binding residues [chemical binding]; other site 338963008887 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 338963008888 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 338963008889 molybdopterin cofactor binding site; other site 338963008890 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 338963008891 molybdopterin cofactor binding site; other site 338963008892 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 338963008893 Polysulphide reductase [Energy production and conversion]; Region: COG5557; cl17901 338963008894 Protein of unknown function (DUF3341); Region: DUF3341; pfam11821 338963008895 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 338963008896 Ferritin-like domain; Region: Ferritin; pfam00210 338963008897 ferroxidase diiron center [ion binding]; other site 338963008898 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 338963008899 binding surface 338963008900 TPR motif; other site 338963008901 penicillin-binding protein 1B; Region: PBP_1b; TIGR02071 338963008902 Transglycosylase; Region: Transgly; pfam00912 338963008903 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 338963008904 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 338963008905 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 338963008906 PAS fold; Region: PAS_3; pfam08447 338963008907 putative active site [active] 338963008908 heme pocket [chemical binding]; other site 338963008909 PAS domain S-box; Region: sensory_box; TIGR00229 338963008910 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 338963008911 putative active site [active] 338963008912 heme pocket [chemical binding]; other site 338963008913 PAS domain S-box; Region: sensory_box; TIGR00229 338963008914 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 338963008915 putative active site [active] 338963008916 heme pocket [chemical binding]; other site 338963008917 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963008918 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963008919 metal binding site [ion binding]; metal-binding site 338963008920 active site 338963008921 I-site; other site 338963008922 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 338963008923 conserved nucleotide sequence; Pcar_R3007 338963008924 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 338963008925 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 338963008926 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 338963008927 PhoU domain; Region: PhoU; pfam01895 338963008928 PhoU domain; Region: PhoU; pfam01895 338963008929 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 338963008930 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 338963008931 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 338963008932 ligand binding site [chemical binding]; other site 338963008933 flexible hinge region; other site 338963008934 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 338963008935 non-specific DNA interactions [nucleotide binding]; other site 338963008936 DNA binding site [nucleotide binding] 338963008937 sequence specific DNA binding site [nucleotide binding]; other site 338963008938 putative cAMP binding site [chemical binding]; other site 338963008939 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 338963008940 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 338963008941 catalytic triad [active] 338963008942 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963008943 Response regulator receiver domain; Region: Response_reg; pfam00072 338963008944 active site 338963008945 phosphorylation site [posttranslational modification] 338963008946 intermolecular recognition site; other site 338963008947 PAS domain S-box; Region: sensory_box; TIGR00229 338963008948 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 338963008949 putative active site [active] 338963008950 heme pocket [chemical binding]; other site 338963008951 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963008952 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963008953 metal binding site [ion binding]; metal-binding site 338963008954 active site 338963008955 I-site; other site 338963008956 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 338963008957 Response regulator receiver domain; Region: Response_reg; pfam00072 338963008958 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963008959 active site 338963008960 phosphorylation site [posttranslational modification] 338963008961 intermolecular recognition site; other site 338963008962 dimerization interface [polypeptide binding]; other site 338963008963 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 338963008964 HAMP domain; Region: HAMP; pfam00672 338963008965 dimerization interface [polypeptide binding]; other site 338963008966 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 338963008967 dimer interface [polypeptide binding]; other site 338963008968 phosphorylation site [posttranslational modification] 338963008969 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 338963008970 ATP binding site [chemical binding]; other site 338963008971 Mg2+ binding site [ion binding]; other site 338963008972 G-X-G motif; other site 338963008973 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 338963008974 ABC transporter substrate binding protein; Region: ABC_sub_bind; cl17301 338963008975 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 338963008976 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 338963008977 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]; Region: COG2231 338963008978 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 338963008979 minor groove reading motif; other site 338963008980 helix-hairpin-helix signature motif; other site 338963008981 substrate binding pocket [chemical binding]; other site 338963008982 active site 338963008983 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 338963008984 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 338963008985 active site 338963008986 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 338963008987 phosphoglyceromutase; Provisional; Region: PRK05434 338963008988 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 338963008989 binding surface 338963008990 TPR repeat; Region: TPR_11; pfam13414 338963008991 TPR motif; other site 338963008992 tetratricopeptide repeat protein; Provisional; Region: PRK11788 338963008993 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 338963008994 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 338963008995 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 338963008996 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 338963008997 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 338963008998 active site 338963008999 (T/H)XGH motif; other site 338963009000 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 338963009001 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 338963009002 putative catalytic cysteine [active] 338963009003 gamma-glutamyl kinase; Provisional; Region: PRK05429 338963009004 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 338963009005 nucleotide binding site [chemical binding]; other site 338963009006 homotetrameric interface [polypeptide binding]; other site 338963009007 putative phosphate binding site [ion binding]; other site 338963009008 putative allosteric binding site; other site 338963009009 PUA domain; Region: PUA; pfam01472 338963009010 GTPase CgtA; Reviewed; Region: obgE; PRK12299 338963009011 GTP1/OBG; Region: GTP1_OBG; pfam01018 338963009012 Obg GTPase; Region: Obg; cd01898 338963009013 G1 box; other site 338963009014 GTP/Mg2+ binding site [chemical binding]; other site 338963009015 Switch I region; other site 338963009016 G2 box; other site 338963009017 G3 box; other site 338963009018 Switch II region; other site 338963009019 G4 box; other site 338963009020 G5 box; other site 338963009021 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 338963009022 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 338963009023 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 338963009024 ribonuclease G; Provisional; Region: PRK11712 338963009025 S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and...; Region: S1_RNase_E; cd04453 338963009026 homodimer interface [polypeptide binding]; other site 338963009027 oligonucleotide binding site [chemical binding]; other site 338963009028 radical SAM family uncharacterized protein; Region: rSAM_fuse_unch; TIGR03960 338963009029 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 338963009030 FeS/SAM binding site; other site 338963009031 radical SAM-linked protein; Region: sam_1_link_chp; TIGR03936 338963009032 Uncharacterized protein conserved in bacteria (DUF2344); Region: DUF2344; pfam10105 338963009033 putative hydrolase; Validated; Region: PRK09248 338963009034 Polymerase and Histidinol Phosphatase domain of Ycdx like; Region: PHP_HisPPase_Ycdx_like; cd07437 338963009035 active site 338963009036 Tic20-like protein; Region: Tic20; pfam09685 338963009037 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 338963009038 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 338963009039 homodimer interface [polypeptide binding]; other site 338963009040 substrate-cofactor binding pocket; other site 338963009041 catalytic residue [active] 338963009042 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 338963009043 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 338963009044 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 338963009045 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 338963009046 active site 338963009047 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 338963009048 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 338963009049 active site 338963009050 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 338963009051 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 338963009052 NAD binding site [chemical binding]; other site 338963009053 substrate binding site [chemical binding]; other site 338963009054 homodimer interface [polypeptide binding]; other site 338963009055 active site 338963009056 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 338963009057 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 338963009058 NADP binding site [chemical binding]; other site 338963009059 active site 338963009060 putative substrate binding site [chemical binding]; other site 338963009061 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 338963009062 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 338963009063 substrate binding site; other site 338963009064 tetramer interface; other site 338963009065 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: rmlC; TIGR01221 338963009066 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 338963009067 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 338963009068 Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to...; Region: Gn_AT_II; cl00319 338963009069 Glutamine amidotransferases class-II (Gn-AT)_GlxB-type. GlxB is a glutamine amidotransferase-like protein of unknown function found in bacteria and archaea. GlxB has a structural fold similar to that of other class II glutamine amidotransferases...; Region: GlxB; cd01907 338963009070 putative active site [active] 338963009071 4Fe-4S binding domain; Region: Fer4; pfam00037 338963009072 4Fe-4S double cluster binding domain; Region: Fer4_16; pfam13484 338963009073 4Fe-4S binding domain; Region: Fer4; pfam00037 338963009074 Conserved region in glutamate synthase; Region: Glu_synthase; pfam01645 338963009075 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 338963009076 active site 338963009077 FMN binding site [chemical binding]; other site 338963009078 substrate binding site [chemical binding]; other site 338963009079 3Fe-4S cluster binding site [ion binding]; other site 338963009080 GXGXG domain. This domain of unknown function is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS), in subunit C of tungsten formylmethanofuran dehydrogenase (FwdC) and in subunit C of molybdenum formylmethanofuran...; Region: GXGXG; cl00239 338963009081 domain_subunit interface; other site 338963009082 putative glutamate synthase (NADPH) small subunit; Provisional; Region: PRK12771 338963009083 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 338963009084 Alanine dehydrogenase/PNT, C-terminal domain; Region: AlaDh_PNT_C; smart01002 338963009085 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 338963009086 Domain of unknown function (DUF1858); Region: DUF1858; cl14817 338963009087 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 338963009088 Low molecular weight phosphatase family; Region: LMWPc; cl00105 338963009089 active site 338963009090 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 338963009091 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 338963009092 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 338963009093 serine/threonine protein kinase; Provisional; Region: PRK11768 338963009094 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 338963009095 Tic20-like protein; Region: Tic20; pfam09685 338963009096 CHASE3 domain; Region: CHASE3; pfam05227 338963009097 Sensory domain found in PocR; Region: PocR; pfam10114 338963009098 Predicted sensor domain [Signal transduction mechanisms / Transcription]; Region: PocR; COG4936 338963009099 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 338963009100 dimerization interface [polypeptide binding]; other site 338963009101 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 338963009102 dimer interface [polypeptide binding]; other site 338963009103 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 338963009104 putative CheW interface [polypeptide binding]; other site 338963009105 Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]; Region: PaaD; COG2151 338963009106 Family description; Region: DsbD_2; pfam13386 338963009107 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 338963009108 Zn2+ binding site [ion binding]; other site 338963009109 Mg2+ binding site [ion binding]; other site 338963009110 Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: MsrA; COG0225 338963009111 methionine sulfoxide reductase B; Provisional; Region: PRK00222 338963009112 SelR domain; Region: SelR; pfam01641 338963009113 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 338963009114 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 338963009115 heptanucleotide repeats; Pcar_R7027 338963009116 octanucleotide repeats; Pcar_R8053 338963009117 octanucleotide repeats; Pcar_R8054 338963009118 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 338963009119 active site 338963009120 catalytic site [active] 338963009121 substrate binding site [chemical binding]; other site 338963009122 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 338963009123 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 338963009124 A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity...; Region: APP_MetAP; cd01066 338963009125 active site 338963009126 Uncharacterized protein family (UPF0160); Region: UPF0160; cl01749 338963009127 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 338963009128 Multiple resistance and pH regulation protein F (MrpF / PhaF); Region: MrpF_PhaF; cl09154 338963009129 Na+/H+ ion antiporter subunit; Region: MNHE; pfam01899 338963009130 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12663 338963009131 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 338963009132 Multisubunit Na+/H+ antiporter, MnhC subunit [Inorganic ion transport and metabolism]; Region: MnhC; COG1006 338963009133 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 338963009134 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12647 338963009135 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 338963009136 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 338963009137 Multisubunit Na+/H+ antiporter, MnhB subunit [Inorganic ion transport and metabolism]; Region: MnhB; COG2111 338963009138 universal stress protein UspE; Provisional; Region: PRK11175 338963009139 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 338963009140 Ligand Binding Site [chemical binding]; other site 338963009141 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 338963009142 Ligand Binding Site [chemical binding]; other site 338963009143 cytosolic glyceraldehyde 3-phosphate dehydrogenase; Provisional; Region: PTZ00434 338963009144 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 338963009145 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 338963009146 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 338963009147 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 338963009148 putative substrate translocation pore; other site 338963009149 AMP nucleosidase; Provisional; Region: PRK07115 338963009150 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 338963009151 active site 338963009152 FMN binding site [chemical binding]; other site 338963009153 substrate binding site [chemical binding]; other site 338963009154 3Fe-4S cluster binding site [ion binding]; other site 338963009155 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 338963009156 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963009157 active site 338963009158 phosphorylation site [posttranslational modification] 338963009159 intermolecular recognition site; other site 338963009160 dimerization interface [polypeptide binding]; other site 338963009161 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 338963009162 DNA binding site [nucleotide binding] 338963009163 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 338963009164 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 338963009165 dimer interface [polypeptide binding]; other site 338963009166 phosphorylation site [posttranslational modification] 338963009167 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 338963009168 ATP binding site [chemical binding]; other site 338963009169 Mg2+ binding site [ion binding]; other site 338963009170 G-X-G motif; other site 338963009171 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 338963009172 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG2304 338963009173 metal ion-dependent adhesion site (MIDAS); other site 338963009174 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; pfam02639 338963009175 Methyltransferase domain; Region: Methyltransf_32; pfam13679 338963009176 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 338963009177 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963009178 Walker A/P-loop; other site 338963009179 ATP binding site [chemical binding]; other site 338963009180 Q-loop/lid; other site 338963009181 ABC transporter signature motif; other site 338963009182 Walker B; other site 338963009183 D-loop; other site 338963009184 H-loop/switch region; other site 338963009185 ABC transporter; Region: ABC_tran_2; pfam12848 338963009186 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 338963009187 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 338963009188 S4 domain; Region: S4_2; pfam13275 338963009189 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 338963009190 Transcriptional regulator [Transcription]; Region: LysR; COG0583 338963009191 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 338963009192 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 338963009193 dimerization interface [polypeptide binding]; other site 338963009194 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 338963009195 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 338963009196 FeS/SAM binding site; other site 338963009197 Transposase IS200 like; Region: Y1_Tnp; cl00848 338963009198 DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both...; Region: POLBc; cl10023 338963009199 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 338963009200 DnaA box-binding interface [nucleotide binding]; other site 338963009201 Transposase domain (DUF772); Region: DUF772; pfam05598 338963009202 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 338963009203 conserved nucleotide sequence; Pcar_R5045 338963009204 integron integrase; Region: integrase_gron; TIGR02249 338963009205 IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and...; Region: INT_IntI; cd01193 338963009206 Int/Topo IB signature motif; other site 338963009207 adenylosuccinate lyase; Provisional; Region: PRK09285 338963009208 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 338963009209 tetramer interface [polypeptide binding]; other site 338963009210 active site 338963009211 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 338963009212 S1 domain; Region: S1_2; pfam13509 338963009213 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 338963009214 RNA binding site [nucleotide binding]; other site 338963009215 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 338963009216 AMP binding site [chemical binding]; other site 338963009217 active site 338963009218 acyl-activating enzyme (AAE) consensus motif; other site 338963009219 CoA binding site [chemical binding]; other site 338963009220 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 338963009221 active site 338963009222 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 338963009223 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK05952 338963009224 dimer interface [polypeptide binding]; other site 338963009225 active site 338963009226 Phosphopantetheine attachment site; Region: PP-binding; cl09936 338963009227 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 338963009228 putative acyl-acceptor binding pocket; other site 338963009229 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 338963009230 Ligand binding site; other site 338963009231 Putative Catalytic site; other site 338963009232 DXD motif; other site 338963009233 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; cl01261 338963009234 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 338963009235 active site 338963009236 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 338963009237 active site 2 [active] 338963009238 active site 1 [active] 338963009239 Predicted exporter [General function prediction only]; Region: COG4258 338963009240 hopanoid biosynthesis associated RND transporter like protein HpnN; Region: HpnN; TIGR03480 338963009241 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 338963009242 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl17548 338963009243 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 338963009244 active site 2 [active] 338963009245 active site 1 [active] 338963009246 putative heme d1 biosynthesis radical SAM protein NirJ2; Region: rSAM_NirJ2; TIGR04055 338963009247 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 338963009248 FeS/SAM binding site; other site 338963009249 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 338963009250 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 338963009251 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 338963009252 putative acyl-acceptor binding pocket; other site 338963009253 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK09116 338963009254 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 338963009255 dimer interface [polypeptide binding]; other site 338963009256 active site 338963009257 Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG1233 338963009258 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 338963009259 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 338963009260 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 338963009261 dimer interface [polypeptide binding]; other site 338963009262 active site 338963009263 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 338963009264 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 338963009265 NAD(P) binding site [chemical binding]; other site 338963009266 active site 338963009267 Protein of unknown function (DUF1653); Region: DUF1653; pfam07866 338963009268 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 338963009269 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 338963009270 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 338963009271 MarR family; Region: MarR_2; cl17246 338963009272 Methyltransferase domain; Region: Methyltransf_31; pfam13847 338963009273 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 338963009274 S-adenosylmethionine binding site [chemical binding]; other site 338963009275 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06676 338963009276 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 338963009277 RNA binding site [nucleotide binding]; other site 338963009278 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 338963009279 RNA binding site [nucleotide binding]; other site 338963009280 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 338963009281 RNA binding site [nucleotide binding]; other site 338963009282 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 338963009283 RNA binding site [nucleotide binding]; other site 338963009284 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_16; cd04674 338963009285 nudix motif; other site 338963009286 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 338963009287 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 338963009288 The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; Region: BAR; cl12013 338963009289 Putative zinc ribbon domain; Region: DUF164; pfam02591 338963009290 Uncharacterized conserved protein [Function unknown]; Region: COG0327 338963009291 NIF3 (NGG1p interacting factor 3); Region: NIF3; pfam01784 338963009292 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3323 338963009293 NIF3 (NGG1p interacting factor 3); Region: NIF3; pfam01784 338963009294 Uncharacterized conserved protein [Function unknown]; Region: COG0327 338963009295 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 338963009296 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 338963009297 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 338963009298 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 338963009299 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 338963009300 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 338963009301 DNA binding residues [nucleotide binding] 338963009302 DNA primase; Validated; Region: dnaG; PRK05667 338963009303 CHC2 zinc finger; Region: zf-CHC2; pfam01807 338963009304 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 338963009305 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 338963009306 active site 338963009307 metal binding site [ion binding]; metal-binding site 338963009308 interdomain interaction site; other site 338963009309 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 338963009310 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; smart00766 338963009311 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 338963009312 MutS domain III; Region: MutS_III; pfam05192 338963009313 ATP-binding cassette domain of MutS2; Region: ABC_MutS2; cd03280 338963009314 Walker A/P-loop; other site 338963009315 ATP binding site [chemical binding]; other site 338963009316 Q-loop/lid; other site 338963009317 ABC transporter signature motif; other site 338963009318 Walker B; other site 338963009319 D-loop; other site 338963009320 H-loop/switch region; other site 338963009321 Smr domain; Region: Smr; pfam01713 338963009322 Colicin V production protein; Region: Colicin_V; pfam02674 338963009323 Yqey-like protein; Region: YqeY; pfam09424 338963009324 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 338963009325 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; pfam01502 338963009326 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 338963009327 metal binding site [ion binding]; metal-binding site 338963009328 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 338963009329 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 338963009330 substrate binding site [chemical binding]; other site 338963009331 glutamase interaction surface [polypeptide binding]; other site 338963009332 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 338963009333 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 338963009334 catalytic residues [active] 338963009335 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13141 338963009336 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 338963009337 putative active site [active] 338963009338 oxyanion strand; other site 338963009339 catalytic triad [active] 338963009340 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 338963009341 putative active site pocket [active] 338963009342 4-fold oligomerization interface [polypeptide binding]; other site 338963009343 metal binding residues [ion binding]; metal-binding site 338963009344 3-fold/trimer interface [polypeptide binding]; other site 338963009345 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 338963009346 histidinol dehydrogenase; Region: hisD; TIGR00069 338963009347 NAD binding site [chemical binding]; other site 338963009348 dimerization interface [polypeptide binding]; other site 338963009349 product binding site; other site 338963009350 substrate binding site [chemical binding]; other site 338963009351 zinc binding site [ion binding]; other site 338963009352 catalytic residues [active] 338963009353 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 338963009354 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 338963009355 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 338963009356 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 338963009357 hinge; other site 338963009358 active site 338963009359 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 338963009360 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 338963009361 S-adenosylmethionine binding site [chemical binding]; other site 338963009362 peptide chain release factor 1; Validated; Region: prfA; PRK00591 338963009363 This domain is found in peptide chain release factors; Region: PCRF; smart00937 338963009364 RF-1 domain; Region: RF-1; pfam00472 338963009365 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 338963009366 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 338963009367 transcription termination factor Rho; Provisional; Region: rho; PRK09376 338963009368 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 338963009369 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 338963009370 RNA binding site [nucleotide binding]; other site 338963009371 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 338963009372 multimer interface [polypeptide binding]; other site 338963009373 Walker A motif; other site 338963009374 ATP binding site [chemical binding]; other site 338963009375 Walker B motif; other site 338963009376 Glutamyl- and glutaminyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]; Region: GlnS; COG0008 338963009377 glutamyl-queuosine tRNA(Asp) synthetase; Region: queuosine_YadB; TIGR03838 338963009378 active site 338963009379 HIGH motif; other site 338963009380 nucleotide binding site [chemical binding]; other site 338963009381 active site 338963009382 KMSKS motif; other site 338963009383 Trm112p-like protein; Region: Trm112p; pfam03966 338963009384 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 338963009385 S-adenosylmethionine binding site [chemical binding]; other site 338963009386 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 338963009387 The MopB_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. Members...; Region: MopB_Acetylene-hydratase; cd02759 338963009388 putative [Fe4-S4] binding site [ion binding]; other site 338963009389 putative molybdopterin cofactor binding site [chemical binding]; other site 338963009390 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 338963009391 molybdopterin cofactor binding site; other site 338963009392 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5339 338963009393 Bacterial protein of unknown function (DUF945); Region: DUF945; pfam06097 338963009394 putative molybdenum transport ATP-binding protein ModF; Provisional; Region: PRK10938 338963009395 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963009396 Walker A/P-loop; other site 338963009397 ATP binding site [chemical binding]; other site 338963009398 Q-loop/lid; other site 338963009399 ABC transporter signature motif; other site 338963009400 Walker B; other site 338963009401 D-loop; other site 338963009402 H-loop/switch region; other site 338963009403 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963009404 Walker A/P-loop; other site 338963009405 ATP binding site [chemical binding]; other site 338963009406 Q-loop/lid; other site 338963009407 ABC transporter signature motif; other site 338963009408 Walker B; other site 338963009409 D-loop; other site 338963009410 H-loop/switch region; other site 338963009411 Protein of unknown function (DUF502); Region: DUF502; cl01107 338963009412 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 338963009413 SLBB domain; Region: SLBB; pfam10531 338963009414 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 338963009415 4Fe-4S binding domain; Region: Fer4; pfam00037 338963009416 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 338963009417 4Fe-4S binding domain; Region: Fer4; pfam00037 338963009418 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 338963009419 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963009420 active site 338963009421 phosphorylation site [posttranslational modification] 338963009422 intermolecular recognition site; other site 338963009423 dimerization interface [polypeptide binding]; other site 338963009424 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 338963009425 PAS fold; Region: PAS_3; pfam08447 338963009426 putative active site [active] 338963009427 heme pocket [chemical binding]; other site 338963009428 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963009429 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963009430 metal binding site [ion binding]; metal-binding site 338963009431 active site 338963009432 I-site; other site 338963009433 hypothetical protein; Provisional; Region: PRK13560 338963009434 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 338963009435 putative active site [active] 338963009436 heme pocket [chemical binding]; other site 338963009437 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 338963009438 putative active site [active] 338963009439 heme pocket [chemical binding]; other site 338963009440 PAS domain; Region: PAS; smart00091 338963009441 putative active site [active] 338963009442 heme pocket [chemical binding]; other site 338963009443 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 338963009444 putative active site [active] 338963009445 heme pocket [chemical binding]; other site 338963009446 Histidine kinase; Region: HisKA_2; pfam07568 338963009447 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 338963009448 ATP binding site [chemical binding]; other site 338963009449 Mg2+ binding site [ion binding]; other site 338963009450 G-X-G motif; other site 338963009451 Response regulator receiver domain; Region: Response_reg; pfam00072 338963009452 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963009453 active site 338963009454 phosphorylation site [posttranslational modification] 338963009455 intermolecular recognition site; other site 338963009456 dimerization interface [polypeptide binding]; other site 338963009457 Protein of unknown function (DUF523); Region: DUF523; pfam04463 338963009458 Uncharacterized conserved protein [Function unknown]; Region: COG3272 338963009459 Protein of unknown function (DUF1722); Region: DUF1722; pfam08349 338963009460 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 338963009461 Thermotoga maritima CorA_like subfamily; Region: TmCorA-like_1; cd12828 338963009462 oligomer interface [polypeptide binding]; other site 338963009463 metal binding site [ion binding]; metal-binding site 338963009464 metal binding site [ion binding]; metal-binding site 338963009465 Cl binding site [ion binding]; other site 338963009466 aspartate ring; other site 338963009467 basic sphincter; other site 338963009468 putative hydrophobic gate; other site 338963009469 periplasmic entrance; other site 338963009470 AAA ATPase domain; Region: AAA_16; pfam13191 338963009471 AAA domain; Region: AAA_22; pfam13401 338963009472 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 338963009473 Mechanosensitive ion channel; Region: MS_channel; pfam00924 338963009474 photolyase PhrII; Region: phr2; TIGR00591 338963009475 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 338963009476 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 338963009477 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963009478 active site 338963009479 phosphorylation site [posttranslational modification] 338963009480 intermolecular recognition site; other site 338963009481 dimerization interface [polypeptide binding]; other site 338963009482 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 338963009483 Walker A motif; other site 338963009484 ATP binding site [chemical binding]; other site 338963009485 Walker B motif; other site 338963009486 arginine finger; other site 338963009487 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 338963009488 Transketolase, C-terminal subunit [Carbohydrate transport and metabolism]; Region: COG3958 338963009489 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 338963009490 PYR/PP interface [polypeptide binding]; other site 338963009491 dimer interface [polypeptide binding]; other site 338963009492 TPP binding site [chemical binding]; other site 338963009493 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 338963009494 transketolase; Reviewed; Region: PRK05899 338963009495 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 338963009496 TPP-binding site [chemical binding]; other site 338963009497 dimer interface [polypeptide binding]; other site 338963009498 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 338963009499 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 338963009500 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 338963009501 substrate binding pocket [chemical binding]; other site 338963009502 dimer interface [polypeptide binding]; other site 338963009503 inhibitor binding site; inhibition site 338963009504 methyltransferase cognate corrinoid proteins, Methanosarcina family; Region: pyl_corrinoid; TIGR02370 338963009505 B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or...; Region: corrinoid_protein_B12-BD; cd02070 338963009506 B12 binding site [chemical binding]; other site 338963009507 cobalt ligand [ion binding]; other site 338963009508 Sporulation and spore germination; Region: Germane; pfam10646 338963009509 glutamate racemase; Provisional; Region: PRK00865 338963009510 2-hydroxyglutaryl-CoA dehydratase, D-component; Region: HGD-D; pfam06050 338963009511 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 338963009512 Homeodomain-like domain; Region: HTH_23; pfam13384 338963009513 Winged helix-turn helix; Region: HTH_29; pfam13551 338963009514 Integrase core domain; Region: rve; pfam00665 338963009515 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 338963009516 Integrase core domain; Region: rve_3; pfam13683 338963009517 Restriction endonuclease [Defense mechanisms]; Region: COG3587 338963009518 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 338963009519 ATP binding site [chemical binding]; other site 338963009520 putative Mg++ binding site [ion binding]; other site 338963009521 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]; Region: COG2865 338963009522 Divergent AAA domain; Region: AAA_4; pfam04326 338963009523 ATP-dependent DNA helicase recG C-terminal; Region: HATPase_c_4; pfam13749 338963009524 conserved nucleotide sequence fragment; Pcar_R1110 338963009525 conserved nucleotide sequence; Pcar_R5063 338963009526 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: NrdG2; TIGR02495 338963009527 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 338963009528 FeS/SAM binding site; other site 338963009529 Viral polyprotein N-terminal; Region: Calici_PP_N; pfam08405 338963009530 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK08270 338963009531 ATP cone domain; Region: ATP-cone; pfam03477 338963009532 Class III ribonucleotide reductase; Region: RNR_III; cd01675 338963009533 effector binding site; other site 338963009534 active site 338963009535 Zn binding site [ion binding]; other site 338963009536 conserved nucleotide sequence; Pcar_R2016 338963009537 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 338963009538 nudix motif; other site 338963009539 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]; Region: MDN1; COG5271 338963009540 Precorrin-6Y methyltransferase, the cobalamin biosynthesis enzyme CbiE; Region: Precorrin-6Y-methylase; cd11644 338963009541 active site 338963009542 putative homodimer interface [polypeptide binding]; other site 338963009543 SAM binding site [chemical binding]; other site 338963009544 Precorrin-6B methylase 2 [Coenzyme metabolism]; Region: CobL; COG2242 338963009545 precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunit; Region: CbiT; TIGR02469 338963009546 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_N; cd03416 338963009547 putative active site [active] 338963009548 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 338963009549 catalytic core [active] 338963009550 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 338963009551 G1 box; other site 338963009552 GTP/Mg2+ binding site [chemical binding]; other site 338963009553 Switch I region; other site 338963009554 G2 box; other site 338963009555 G3 box; other site 338963009556 Switch II region; other site 338963009557 G4 box; other site 338963009558 G5 box; other site 338963009559 Protein of unknown function, DUF393; Region: DUF393; pfam04134 338963009560 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB; cd01045 338963009561 diiron binding motif [ion binding]; other site 338963009562 Cytochrome c; Region: Cytochrom_C; pfam00034 338963009563 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 338963009564 Walker A motif; other site 338963009565 Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity; Region: Lysophospholipase_L1_like; cd01822 338963009566 active site 338963009567 catalytic triad [active] 338963009568 oxyanion hole [active] 338963009569 switch loop; other site 338963009570 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 338963009571 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 338963009572 anti sigma factor interaction site; other site 338963009573 regulatory phosphorylation site [posttranslational modification]; other site 338963009574 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 338963009575 Permease; Region: Permease; pfam02405 338963009576 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 338963009577 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 338963009578 Walker A/P-loop; other site 338963009579 ATP binding site [chemical binding]; other site 338963009580 Q-loop/lid; other site 338963009581 ABC transporter signature motif; other site 338963009582 Walker B; other site 338963009583 D-loop; other site 338963009584 H-loop/switch region; other site 338963009585 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 338963009586 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 338963009587 Protein of unknown function (DUF330); Region: DUF330; cl01135 338963009588 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 338963009589 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 338963009590 Zn2+ binding site [ion binding]; other site 338963009591 Mg2+ binding site [ion binding]; other site 338963009592 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cd00209 338963009593 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 338963009594 folate binding site [chemical binding]; other site 338963009595 NADP+ binding site [chemical binding]; other site 338963009596 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 338963009597 putative FMN binding site [chemical binding]; other site 338963009598 NADPH bind site [chemical binding]; other site 338963009599 putative iron-only hydrogenase system regulator; Region: hyd_TM1266; TIGR03959 338963009600 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 338963009601 putative catalytic cysteine [active] 338963009602 conserved nucleotide sequence fragment; Pcar_R2017 338963009603 conserved nucleotide sequence; Pcar_R2018 338963009604 GAF domain; Region: GAF; cl17456 338963009605 GAF domain; Region: GAF; pfam01590 338963009606 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 338963009607 dimer interface [polypeptide binding]; other site 338963009608 phosphorylation site [posttranslational modification] 338963009609 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 338963009610 ATP binding site [chemical binding]; other site 338963009611 Mg2+ binding site [ion binding]; other site 338963009612 G-X-G motif; other site 338963009613 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 338963009614 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 338963009615 trimer interface [polypeptide binding]; other site 338963009616 dimer interface [polypeptide binding]; other site 338963009617 putative active site [active] 338963009618 poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB; Region: deacetyl_PgaB; TIGR03938 338963009619 DNA repair protein RadA; Provisional; Region: PRK11823 338963009620 Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of...; Region: Sms; cd01121 338963009621 Walker A motif/ATP binding site; other site 338963009622 ATP binding site [chemical binding]; other site 338963009623 Walker B motif; other site 338963009624 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 338963009625 FAD binding domain; Region: FAD_binding_4; pfam01565 338963009626 glycolate oxidase, subunit GlcD; Region: glcD; TIGR00387 338963009627 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 338963009628 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 338963009629 Cysteine-rich domain; Region: CCG; pfam02754 338963009630 Cysteine-rich domain; Region: CCG; pfam02754 338963009631 c(7)-type cytochrome triheme domain; Region: nanowire_3heme; TIGR04257 338963009632 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 338963009633 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 338963009634 FeS/SAM binding site; other site 338963009635 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 338963009636 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 338963009637 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 338963009638 Ligand Binding Site [chemical binding]; other site 338963009639 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 338963009640 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 338963009641 ring oligomerisation interface [polypeptide binding]; other site 338963009642 ATP/Mg binding site [chemical binding]; other site 338963009643 stacking interactions; other site 338963009644 hinge regions; other site 338963009645 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 338963009646 oligomerisation interface [polypeptide binding]; other site 338963009647 mobile loop; other site 338963009648 roof hairpin; other site 338963009649 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 338963009650 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 338963009651 catalytic residue [active] 338963009652 TM2 domain; Region: TM2; pfam05154 338963009653 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 338963009654 Walker B motif; other site 338963009655 Amidohydrolase; Region: Amidohydro_2; pfam04909 338963009656 2-acyl-glycerophospho-ethanolamine acyltransferase; Validated; Region: PRK08633 338963009657 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 338963009658 putative substrate translocation pore; other site 338963009659 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 338963009660 putative acyl-acceptor binding pocket; other site 338963009661 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 338963009662 acyl-activating enzyme (AAE) consensus motif; other site 338963009663 AMP binding site [chemical binding]; other site 338963009664 active site 338963009665 CoA binding site [chemical binding]; other site 338963009666 Phosphatidylglycerophosphate synthase [Lipid metabolism]; Region: PgsA; COG0558 338963009667 Predicted CDP-diglyceride synthetase/phosphatidate cytidylyltransferase [General function prediction only]; Region: COG4589 338963009668 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 338963009669 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 338963009670 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 338963009671 putative acyl-acceptor binding pocket; other site 338963009672 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 338963009673 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 338963009674 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 338963009675 S-adenosylmethionine binding site [chemical binding]; other site 338963009676 PAP2_like proteins, Aur1_like subfamily. Yeast Aur1p or Ipc1p is necessary for the addition of inositol phosphate to ceramide, an essential step in yeast sphingolipid synthesis, and is the target of several antifungal compounds such as aureobasidin; Region: PAP2_Aur1_like; cd03386 338963009677 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 338963009678 active site 338963009679 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr; Region: PTPc; cl00053 338963009680 active site 338963009681 catalytic residues [active] 338963009682 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 338963009683 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 338963009684 sulfate transport protein; Provisional; Region: cysT; CHL00187 338963009685 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 338963009686 dimer interface [polypeptide binding]; other site 338963009687 conserved gate region; other site 338963009688 putative PBP binding loops; other site 338963009689 ABC-ATPase subunit interface; other site 338963009690 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 338963009691 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 338963009692 Walker A/P-loop; other site 338963009693 ATP binding site [chemical binding]; other site 338963009694 Q-loop/lid; other site 338963009695 ABC transporter signature motif; other site 338963009696 Walker B; other site 338963009697 D-loop; other site 338963009698 H-loop/switch region; other site 338963009699 TOBE domain; Region: TOBE; pfam03459 338963009700 integral membrane protein, YkoY family; Region: R_switched_YkoY; TIGR03716 338963009701 diaminopimelate dehydrogenase; Region: DAP-DH; TIGR01921 338963009702 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 338963009703 Uncharacterized conserved protein [Function unknown]; Region: COG5316 338963009704 N-terminal domain of unknown function (DUF4140); Region: DUF4140; pfam13600 338963009705 Domain of unknown function (DUF4139); Region: DUF4139; pfam13598 338963009706 poly-beta-1,6-N-acetyl-D-glucosamine biosynthesis protein PgaD; Region: PGA_PgaD; TIGR03940 338963009707 N-glycosyltransferase; Provisional; Region: PRK11204 338963009708 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 338963009709 DXD motif; other site 338963009710 poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB; Region: deacetyl_PgaB; TIGR03938 338963009711 N-terminal putative catalytic polysaccharide deacetylase domain of bacterial poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, and similar proteins; Region: CE4_PgaB_5s; cd10964 338963009712 putative active site [active] 338963009713 putative metal binding site [ion binding]; other site 338963009714 Uncharacterized BCR, COG1649; Region: DUF187; pfam02638 338963009715 poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA; Region: PGA_TPR_OMP; TIGR03939 338963009716 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 338963009717 binding surface 338963009718 TPR motif; other site 338963009719 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 338963009720 Part of AAA domain; Region: AAA_19; pfam13245 338963009721 Family description; Region: UvrD_C_2; pfam13538 338963009722 putative voltage-gated ClC-type chloride channel ClcB; Provisional; Region: PRK01862 338963009723 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cd00400 338963009724 Cl- selectivity filter; other site 338963009725 Cl- binding residues [ion binding]; other site 338963009726 pore gating glutamate residue; other site 338963009727 dimer interface [polypeptide binding]; other site 338963009728 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC; Region: CBS_pair_SpoIVFB_EriC_assoc2; cd04613 338963009729 metallo-beta-lactamase/flavodoxin domain-containing protein; Provisional; Region: PRK11921 338963009730 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 338963009731 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 338963009732 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 338963009733 Rubredoxin; Region: Rubredoxin; pfam00301 338963009734 iron binding site [ion binding]; other site 338963009735 Rubrerythrin [Energy production and conversion]; Region: COG1592 338963009736 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 338963009737 binuclear metal center [ion binding]; other site 338963009738 Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either...; Region: rubredoxin_like; cl00202 338963009739 iron binding site [ion binding]; other site 338963009740 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 338963009741 metal binding site 2 [ion binding]; metal-binding site 338963009742 putative DNA binding helix; other site 338963009743 metal binding site 1 [ion binding]; metal-binding site 338963009744 dimer interface [polypeptide binding]; other site 338963009745 structural Zn2+ binding site [ion binding]; other site 338963009746 Cupin domain; Region: Cupin_2; pfam07883 338963009747 Protein of unknown function (DUF3024); Region: DUF3024; pfam11225 338963009748 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 338963009749 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 338963009750 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 338963009751 Autotransporter beta-domain; Region: Autotransporter; smart00869 338963009752 fructose-bisphosphate aldolase; Provisional; Region: PRK09250 338963009753 Class I fructose-1,6-bisphosphate (FBP) aldolases of the archaeal type (DhnA homologs); Region: DhnA; cd00958 338963009754 putative active site; other site 338963009755 catalytic residue [active] 338963009756 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 338963009757 active site 338963009758 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 338963009759 DNA-binding site [nucleotide binding]; DNA binding site 338963009760 RNA-binding motif; other site 338963009761 Type VI secretion lipoprotein; Region: T6SS-SciN; pfam12790 338963009762 type VI secretion protein, VC_A0114 family; Region: VI_chp_4; TIGR03353 338963009763 Bacterial protein of unknown function (DUF876); Region: DUF876; pfam05936 338963009764 type IV / VI secretion system protein, DotU family; Region: IV_VI_DotU; TIGR03349 338963009765 type VI secretion protein IcmF; Region: VI_IcmF; TIGR03348 338963009766 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 338963009767 G1 box; other site 338963009768 GTP/Mg2+ binding site [chemical binding]; other site 338963009769 G2 box; other site 338963009770 G3 box; other site 338963009771 Switch II region; other site 338963009772 G4 box; other site 338963009773 Intracellular multiplication and human macrophage-killing; Region: IcmF-related; pfam06761 338963009774 Protein of unknown function (DUF1215); Region: DUF1215; pfam06744 338963009775 type VI secretion-associated protein, BMA_A0400 family; Region: VI_minor_4; TIGR03373 338963009776 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 338963009777 type VI secretion-associated protein, VC_A0119 family; Region: VI_chp_7; TIGR03362 338963009778 Protein of unknown function (DUF770); Region: DUF770; pfam05591 338963009779 type VI secretion protein, EvpB/VC_A0108 family; Region: VI_chp_2; TIGR03355 338963009780 Protein of unknown function (DUF877); Region: DUF877; pfam05943 338963009781 type VI secretion system effector, Hcp1 family; Region: VI_effect_Hcp1; TIGR03344 338963009782 type VI secretion system lysozyme-like protein; Region: VI_zyme; TIGR03357 338963009783 Type VI protein secretion system component VasA [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3519 338963009784 type VI secretion protein, VC_A0110 family; Region: VI_chp_6; TIGR03359 338963009785 type VI secretion protein, VC_A0111 family; Region: VI_chp_1; TIGR03347 338963009786 type VI secretion ATPase, ClpV1 family; Region: VI_ClpV1; TIGR03345 338963009787 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 338963009788 Walker A motif; other site 338963009789 ATP binding site [chemical binding]; other site 338963009790 Walker B motif; other site 338963009791 arginine finger; other site 338963009792 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 338963009793 Walker A motif; other site 338963009794 ATP binding site [chemical binding]; other site 338963009795 Walker B motif; other site 338963009796 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 338963009797 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 338963009798 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 338963009799 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 338963009800 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 338963009801 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 338963009802 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 338963009803 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 338963009804 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 338963009805 Uncharacterized protein conserved in bacteria (DUF2169); Region: DUF2169; pfam09937 338963009806 3-oxoacyl-(acyl carrier protein) synthase; Validated; Region: PRK06147 338963009807 Domain of unknown function (DUF4150); Region: DUF4150; pfam13665 338963009808 putative transposase OrfB; Reviewed; Region: PHA02517 338963009809 HTH-like domain; Region: HTH_21; pfam13276 338963009810 Integrase core domain; Region: rve; pfam00665 338963009811 Integrase core domain; Region: rve_3; pfam13683 338963009812 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 338963009813 Transposase; Region: HTH_Tnp_1; pfam01527 338963009814 Uncharacterized protein family UPF0027; Region: UPF0027; pfam01139 338963009815 hypothetical protein; Reviewed; Region: PRK09588 338963009816 RNA 3'-terminal-phosphate cyclase; Provisional; Region: PRK04204 338963009817 RNA 3' phosphate cyclase domain (class II). These proteins function as RNA cyclase to catalyze the ATP-dependent conversion of 3'-phosphate to a 2'.3'-cyclic phosphodiester at the end of RNA molecule. A conserved catalytic histidine...; Region: RNA_Cyclase_Class_II; cd00874 338963009818 putative active site [active] 338963009819 adenylation catalytic residue [active] 338963009820 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 338963009821 Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form...; Region: Band_7_stomatin_like; cd03403 338963009822 tRNA-Asn-related sequence; Pcar_R0061 338963009823 Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: RtcR; COG4650 338963009824 Regulator of RNA terminal phosphate cyclase; Region: RtcR; pfam06956 338963009825 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 338963009826 Walker A motif; other site 338963009827 ATP binding site [chemical binding]; other site 338963009828 Walker B motif; other site 338963009829 arginine finger; other site 338963009830 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 338963009831 dimerization interface [polypeptide binding]; other site 338963009832 putative DNA binding site [nucleotide binding]; other site 338963009833 putative Zn2+ binding site [ion binding]; other site 338963009834 Protein tyrosine/serine phosphatase [Signal transduction mechanisms]; Region: COG2365 338963009835 Protein tyrosine phosphatase, catalytic domain motif; Region: PTPc_motif; smart00404 338963009836 active site 338963009837 Orthopoxvirus protein of unknown function (DUF830); Region: DUF830; cl13998 338963009838 Glycosyl transferase family 1; Region: Glyco_trans_1_3; pfam13528 338963009839 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 338963009840 conserved palindrome; Pcar_R5067 338963009841 peroxiredoxin, OsmC subfamily; Region: osmo_induc_OsmC; TIGR03562 338963009842 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; pfam04307 338963009843 octanucleotide repeats; Pcar_R8055 338963009844 octanucleotide repeats; Pcar_R8056 338963009845 SprT-like family; Region: SprT-like; pfam10263 338963009846 SprT homologues; Region: SprT; cl01182 338963009847 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; pfam13557 338963009848 Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria; Region: LPO; cd08176 338963009849 dimer interface [polypeptide binding]; other site 338963009850 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 338963009851 active site 338963009852 metal binding site [ion binding]; metal-binding site 338963009853 Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria; Region: LPO; cd08176 338963009854 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 338963009855 dimer interface [polypeptide binding]; other site 338963009856 active site 338963009857 metal binding site [ion binding]; metal-binding site 338963009858 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 338963009859 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963009860 active site 338963009861 phosphorylation site [posttranslational modification] 338963009862 intermolecular recognition site; other site 338963009863 dimerization interface [polypeptide binding]; other site 338963009864 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 338963009865 Walker A motif; other site 338963009866 ATP binding site [chemical binding]; other site 338963009867 Walker B motif; other site 338963009868 arginine finger; other site 338963009869 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 338963009870 phosphotransacetylase; Reviewed; Region: eutD; PRK09653 338963009871 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 338963009872 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 338963009873 putative catalytic cysteine [active] 338963009874 Homeodomain-like domain; Region: HTH_23; cl17451 338963009875 butyrate kinase; Provisional; Region: PRK03011 338963009876 conserved nucleotide sequence; Pcar_R7208 338963009877 Aldehyde:ferredoxin oxidoreductase [Energy production and conversion]; Region: COG2414 338963009878 Aldehyde ferredoxin oxidoreductase, N-terminal domain; Region: AFOR_N; smart00790 338963009879 Aldehyde ferredoxin oxidoreductase, domains 2 & 3; Region: AFOR_C; pfam01314 338963009880 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 338963009881 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 338963009882 putative active site [active] 338963009883 heme pocket [chemical binding]; other site 338963009884 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 338963009885 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 338963009886 putative active site [active] 338963009887 heme pocket [chemical binding]; other site 338963009888 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 338963009889 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 338963009890 putative active site [active] 338963009891 heme pocket [chemical binding]; other site 338963009892 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 338963009893 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 338963009894 putative active site [active] 338963009895 heme pocket [chemical binding]; other site 338963009896 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 338963009897 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 338963009898 dimer interface [polypeptide binding]; other site 338963009899 phosphorylation site [posttranslational modification] 338963009900 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 338963009901 ATP binding site [chemical binding]; other site 338963009902 G-X-G motif; other site 338963009903 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 338963009904 active site 338963009905 Sulphur transport; Region: Sulf_transp; pfam04143 338963009906 Pyruvate decarboxylase and related thiamine pyrophosphate-requiring enzymes [Carbohydrate transport and metabolism / Coenzyme metabolism / General function prediction only]; Region: COG3961 338963009907 Pyrimidine (PYR) binding domain of pyruvate decarboxylase (PDC), indolepyruvate decarboxylase (IPDC) and related proteins; Region: TPP_PYR_PDC_IPDC_like; cd07038 338963009908 dimer interface [polypeptide binding]; other site 338963009909 PYR/PP interface [polypeptide binding]; other site 338963009910 TPP binding site [chemical binding]; other site 338963009911 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 338963009912 Thiamine pyrophosphate (TPP) family, PDC_IPDC subfamily, TPP-binding module; composed of proteins similar to pyruvate decarboxylase (PDC) and indolepyruvate decarboxylase (IPDC). PDC, a key enzyme in alcoholic fermentation, catalyzes the conversion of...; Region: TPP_PDC_IPDC; cd02005 338963009913 TPP-binding site [chemical binding]; other site 338963009914 dimer interface [polypeptide binding]; other site 338963009915 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 338963009916 putative acyl-acceptor binding pocket; other site 338963009917 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 338963009918 This family is most closely related to the GT1 family of glycosyltransferases. UDP-glucose-diacylglycerol glucosyltransferase (UGDG; also known as 1,2-diacylglycerol 3-glucosyltransferase) catalyzes the transfer of glucose from UDP-glucose to 1; Region: GT1_UGDG_like; cd03817 338963009919 putative ADP-binding pocket [chemical binding]; other site 338963009920 Uncharacterized protein family (UPF0270); Region: UPF0270; cl01180 338963009921 5'-3' exonuclease; Region: 53EXOc; smart00475 338963009922 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 338963009923 active site 338963009924 metal binding site 1 [ion binding]; metal-binding site 338963009925 putative 5' ssDNA interaction site; other site 338963009926 metal binding site 3; metal-binding site 338963009927 metal binding site 2 [ion binding]; metal-binding site 338963009928 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 338963009929 putative DNA binding site [nucleotide binding]; other site 338963009930 putative metal binding site [ion binding]; other site 338963009931 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 338963009932 RNA/DNA hybrid binding site [nucleotide binding]; other site 338963009933 active site 338963009934 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 338963009935 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 338963009936 Coenzyme A binding pocket [chemical binding]; other site 338963009937 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 338963009938 conserved nucleotide sequence; Pcar_R5038 338963009939 group II intron 3' sequence; Pcar_R0106 338963009940 group II intron 5' sequence; Pcar_R0102 338963009941 Cytochrome c552; Region: Cytochrom_C552; pfam02335 338963009942 cytochrome c nitrate reductase, small subunit; Region: cytochr_NrfH; TIGR03153 338963009943 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 338963009944 Hexameric tyrosine-coordinated heme protein (HTHP); Region: HTHP; pfam11534 338963009945 Cupin domain; Region: Cupin_2; pfam07883 338963009946 metallo-beta-lactamase/flavodoxin domain-containing protein; Provisional; Region: PRK11921 338963009947 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 338963009948 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 338963009949 hybrid cluster protein; Provisional; Region: PRK05290 338963009950 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 338963009951 ACS interaction site; other site 338963009952 CODH interaction site; other site 338963009953 Hybrid cluster protein (HCP), formerly known as prismane, is thought to play a role in nitrogen metabolism but its specific function is unknown. HCP has three structural domains, an N-terminal alpha-helical domain, and two similar domains comprising a...; Region: HCP; cd01914 338963009954 hybrid metal cluster; other site 338963009955 PAS domain; Region: PAS_10; pfam13596 338963009956 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 338963009957 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 338963009958 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 338963009959 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 338963009960 Walker A/P-loop; other site 338963009961 ATP binding site [chemical binding]; other site 338963009962 Q-loop/lid; other site 338963009963 ABC transporter signature motif; other site 338963009964 Walker B; other site 338963009965 D-loop; other site 338963009966 H-loop/switch region; other site 338963009967 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 338963009968 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 338963009969 FtsX-like permease family; Region: FtsX; pfam02687 338963009970 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 338963009971 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 338963009972 HlyD family secretion protein; Region: HlyD_3; pfam13437 338963009973 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 338963009974 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 338963009975 palindrome; Pcar_R5087 338963009976 nitrite reductase subunit NirD; Provisional; Region: PRK14989 338963009977 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 338963009978 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 338963009979 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 338963009980 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 338963009981 Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain while...; Region: Rieske_NirD; cd03529 338963009982 PPIC-type PPIASE domain; Region: Rotamase_2; cl08278 338963009983 S-adenosylmethionine-dependent methyltransferase; Region: Methyltrans_SAM; pfam10672 338963009984 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 338963009985 S-adenosylmethionine binding site [chemical binding]; other site 338963009986 hypothetical protein; Provisional; Region: PRK02250 338963009987 SEC-C motif; Region: SEC-C; pfam02810 338963009988 putative metalloenzyme radical SAM/SPASM domain maturase; Region: rSAM_Geo_metal; TIGR04311 338963009989 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 338963009990 FeS/SAM binding site; other site 338963009991 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 338963009992 phage tail protein domain; Region: tail_TIGR02242 338963009993 conserved hypothetical protein, phage tail-like region; Region: TIGR02243 338963009994 conserved hypothetical protein, phage tail-like region; Region: TIGR02243 338963009995 Gene 25-like lysozyme; Region: GPW_gp25; pfam04965 338963009996 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 338963009997 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 338963009998 T4-like virus tail tube protein gp19; Region: Phage_T4_gp19; pfam06841 338963009999 Phage tail sheath protein FI [General function prediction only]; Region: COG3497 338963010000 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl17499 338963010001 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 338963010002 active site 338963010003 Mannosyltransferase OCH1 and related enzymes [Cell envelope biogenesis, outer membrane]; Region: OCH1; COG3774 338963010004 Glycosyltransferase sugar-binding region containing DXD motif; Region: Gly_transf_sug; pfam04488 338963010005 GTPase RsgA; Reviewed; Region: PRK01889 338963010006 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 338963010007 RNA binding site [nucleotide binding]; other site 338963010008 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 338963010009 GTPase/Zn-binding domain interface [polypeptide binding]; other site 338963010010 GTP/Mg2+ binding site [chemical binding]; other site 338963010011 G4 box; other site 338963010012 G5 box; other site 338963010013 G1 box; other site 338963010014 Switch I region; other site 338963010015 G2 box; other site 338963010016 G3 box; other site 338963010017 Switch II region; other site 338963010018 Protein of unknown function DUF89; Region: DUF89; cl15397 338963010019 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 338963010020 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 338963010021 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 338963010022 Prokaryotic protein of unknown function (DUF849); Region: DUF849; pfam05853 338963010023 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 338963010024 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 338963010025 Coenzyme A binding pocket [chemical binding]; other site 338963010026 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 338963010027 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 338963010028 HlyD family secretion protein; Region: HlyD_3; pfam13437 338963010029 Protein of unknown function (DUF1656); Region: DUF1656; pfam07869 338963010030 Fusaric acid resistance protein family; Region: FUSC; pfam04632 338963010031 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 338963010032 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 338963010033 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 338963010034 MarR family; Region: MarR; pfam01047 338963010035 MarR family; Region: MarR_2; cl17246 338963010036 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 338963010037 Part of AAA domain; Region: AAA_19; pfam13245 338963010038 Family description; Region: UvrD_C_2; pfam13538 338963010039 TIR domain; Region: TIR_2; pfam13676 338963010040 MTH538 TIR-like domain (DUF1863); Region: DUF1863; pfam08937 338963010041 TIR domain; Region: TIR_2; pfam13676 338963010042 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 338963010043 FeS/SAM binding site; other site 338963010044 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 338963010045 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 338963010046 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 338963010047 ATP binding site [chemical binding]; other site 338963010048 putative Mg++ binding site [ion binding]; other site 338963010049 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 338963010050 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 338963010051 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 338963010052 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 338963010053 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 338963010054 HsdM N-terminal domain; Region: HsdM_N; pfam12161 338963010055 Methyltransferase domain; Region: Methyltransf_26; pfam13659 338963010056 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 338963010057 HsdM N-terminal domain; Region: HsdM_N; pfam12161 338963010058 Methyltransferase domain; Region: Methyltransf_26; pfam13659 338963010059 Helix-turn-helix domain; Region: HTH_28; pfam13518 338963010060 Winged helix-turn helix; Region: HTH_29; pfam13551 338963010061 Winged helix-turn helix; Region: HTH_29; pfam13551 338963010062 DDE superfamily endonuclease; Region: DDE_3; pfam13358 338963010063 AAA ATPase domain; Region: AAA_16; pfam13191 338963010064 AAA domain; Region: AAA_22; pfam13401 338963010065 Integrase core domain; Region: rve; pfam00665 338963010066 TnsA endonuclease N terminal; Region: Tn7_Tnp_TnsA_N; pfam08722 338963010067 TnsA endonuclease C terminal; Region: Tn7_Tnp_TnsA_C; pfam08721 338963010068 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 338963010069 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 338963010070 glutaminase active site [active] 338963010071 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 338963010072 dimer interface [polypeptide binding]; other site 338963010073 active site 338963010074 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 338963010075 dimer interface [polypeptide binding]; other site 338963010076 active site 338963010077 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14355 338963010078 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 338963010079 Substrate binding site; other site 338963010080 Mg++ binding site; other site 338963010081 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 338963010082 active site 338963010083 substrate binding site [chemical binding]; other site 338963010084 CoA binding site [chemical binding]; other site 338963010085 Thioredoxin domain; Region: Thioredoxin_3; pfam13192 338963010086 PAS domain S-box; Region: sensory_box; TIGR00229 338963010087 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 338963010088 putative active site [active] 338963010089 heme pocket [chemical binding]; other site 338963010090 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 338963010091 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963010092 metal binding site [ion binding]; metal-binding site 338963010093 active site 338963010094 I-site; other site 338963010095 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 338963010096 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 338963010097 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 338963010098 dimer interface [polypeptide binding]; other site 338963010099 phosphorylation site [posttranslational modification] 338963010100 Response regulator receiver domain; Region: Response_reg; pfam00072 338963010101 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963010102 active site 338963010103 phosphorylation site [posttranslational modification] 338963010104 intermolecular recognition site; other site 338963010105 dimerization interface [polypeptide binding]; other site 338963010106 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_cladeC; cd03378 338963010107 active site clefts [active] 338963010108 zinc binding site [ion binding]; other site 338963010109 dimer interface [polypeptide binding]; other site 338963010110 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 338963010111 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 338963010112 TPP-binding site [chemical binding]; other site 338963010113 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 338963010114 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 338963010115 2-oxoglutarate dehydrogenase complex dihydrolipoamide succinyltransferase (E2 component); Region: sucB; TIGR01347 338963010116 E3 interaction surface; other site 338963010117 lipoyl attachment site [posttranslational modification]; other site 338963010118 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 338963010119 conserved nucleotide sequence; Pcar_R1025 338963010120 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; cl00399 338963010121 MoaD interaction [polypeptide binding]; other site 338963010122 active site residues [active] 338963010123 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 338963010124 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 338963010125 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 338963010126 heptanucleotide repeats; Pcar_R7028 338963010127 heptanucleotide repeats; Pcar_R7029 338963010128 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 338963010129 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 338963010130 active site 338963010131 dimer interface [polypeptide binding]; other site 338963010132 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 338963010133 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 338963010134 active site 338963010135 FMN binding site [chemical binding]; other site 338963010136 substrate binding site [chemical binding]; other site 338963010137 3Fe-4S cluster binding site [ion binding]; other site 338963010138 GXGXG domain. This domain of unknown function is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS), in subunit C of tungsten formylmethanofuran dehydrogenase (FwdC) and in subunit C of molybdenum formylmethanofuran...; Region: GXGXG; cd00504 338963010139 domain_subunit interface; other site 338963010140 isoprenoid biosynthesis protein with amidotransferase-like domain; Provisional; Region: PRK11780 338963010141 Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1; Region: GATase1_ES1; cd03133 338963010142 conserved cys residue [active] 338963010143 conserved nucleotide sequence; Pcar_R2019 338963010144 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 338963010145 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 338963010146 non-specific DNA binding site [nucleotide binding]; other site 338963010147 salt bridge; other site 338963010148 sequence-specific DNA binding site [nucleotide binding]; other site 338963010149 Cupin domain; Region: Cupin_2; pfam07883 338963010150 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 338963010151 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 338963010152 motif II; other site 338963010153 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 338963010154 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 338963010155 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 338963010156 protein binding site [polypeptide binding]; other site 338963010157 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 338963010158 protein binding site [polypeptide binding]; other site 338963010159 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 338963010160 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 338963010161 RNA binding surface [nucleotide binding]; other site 338963010162 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 338963010163 active site 338963010164 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 338963010165 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; pfam02578 338963010166 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 338963010167 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 338963010168 active site 338963010169 glycogen synthase; Provisional; Region: glgA; PRK00654 338963010170 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 338963010171 ADP-binding pocket [chemical binding]; other site 338963010172 homodimer interface [polypeptide binding]; other site 338963010173 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 338963010174 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 338963010175 active site 338963010176 catalytic site [active] 338963010177 ADP-glucose phosphorylase; Region: PLN02643 338963010178 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 338963010179 nucleotide binding site/active site [active] 338963010180 HIT family signature motif; other site 338963010181 catalytic residue [active] 338963010182 Alpha-amylase/alpha-mannosidase [Carbohydrate transport and metabolism]; Region: COG1449 338963010183 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 338963010184 N-terminal catalytic domain of thermoactive amylopullulanases; glycoside hydrolase family 57 (GH57); Region: GH57N_APU; cd10796 338963010185 putative active site [active] 338963010186 catalytic site [active] 338963010187 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 338963010188 NTP_transferases catalyze the transfer of nucleotides onto phosphosugars; Region: NTP_transferase; cd04181 338963010189 active site 338963010190 Substrate binding site; other site 338963010191 Mg++ binding site; other site 338963010192 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 338963010193 putative trimer interface [polypeptide binding]; other site 338963010194 putative CoA binding site [chemical binding]; other site 338963010195 GTP-mannose-1-phosphate guanyltransferase (MPG1 transferase), also known as GDP-mannose pyrophosphorylase, is a bifunctional enzyme with both phosphomannose isomerase (PMI) activity and GDP-mannose phosphorylase (GMP) activity. The protein contains an...; Region: MPG1_transferase; cd05805 338963010196 phosphoglucosamine mutase; Region: Arch_GlmM; TIGR03990 338963010197 Response regulator receiver domain; Region: Response_reg; pfam00072 338963010198 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963010199 active site 338963010200 phosphorylation site [posttranslational modification] 338963010201 intermolecular recognition site; other site 338963010202 dimerization interface [polypeptide binding]; other site 338963010203 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 338963010204 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 338963010205 FeS/SAM binding site; other site 338963010206 conserved nucleotide sequence; Pcar_R3008 338963010207 conserved nucleotide sequence; Pcar_R3009 338963010208 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 338963010209 Part of AAA domain; Region: AAA_19; pfam13245 338963010210 Family description; Region: UvrD_C_2; pfam13538 338963010211 Fasciclin domain; Region: Fasciclin; pfam02469 338963010212 Membrane protein of unknown function; Region: DUF360; pfam04020 338963010213 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 338963010214 Peptidase family M23; Region: Peptidase_M23; pfam01551 338963010215 BON domain; Region: BON; pfam04972 338963010216 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 338963010217 BON domain; Region: BON; pfam04972 338963010218 Cache domain; Region: Cache_1; pfam02743 338963010219 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 338963010220 dimerization interface [polypeptide binding]; other site 338963010221 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 338963010222 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 338963010223 dimer interface [polypeptide binding]; other site 338963010224 putative CheW interface [polypeptide binding]; other site 338963010225 conserved nucleotide sequence; Pcar_R2020 338963010226 Predicted amidohydrolase [General function prediction only]; Region: COG0388 338963010227 Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases); Region: nitrilase_7; cd07585 338963010228 putative active site [active] 338963010229 catalytic triad [active] 338963010230 putative dimer interface [polypeptide binding]; other site 338963010231 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 338963010232 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 338963010233 N-terminal plug; other site 338963010234 ligand-binding site [chemical binding]; other site 338963010235 Secreted and surface protein containing fasciclin-like repeats [Cell envelope biogenesis, outer membrane]; Region: COG2335 338963010236 Fasciclin domain; Region: Fasciclin; pfam02469 338963010237 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 338963010238 Tetratricopeptide repeat; Region: TPR_6; pfam13174 338963010239 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 338963010240 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 338963010241 ligand binding site [chemical binding]; other site 338963010242 tol-pal system beta propeller repeat protein TolB; Region: propeller_TolB; TIGR02800 338963010243 TolB amino-terminal domain; Region: TolB_N; pfam04052 338963010244 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 338963010245 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 338963010246 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 338963010247 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 338963010248 TonB C terminal; Region: TonB_2; pfam13103 338963010249 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 338963010250 TolR protein; Region: tolR; TIGR02801 338963010251 TolQ protein; Region: tolQ; TIGR02796 338963010252 threonine dehydratase; Provisional; Region: PRK08198 338963010253 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 338963010254 tetramer interface [polypeptide binding]; other site 338963010255 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963010256 catalytic residue [active] 338963010257 C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains; Region: ACT_ThrD-II-like; cd04886 338963010258 transferase 1, rSAM/selenodomain-associated; Region: glyco_like_cofC; TIGR04282 338963010259 putative GTP cyclohydrolase; Provisional; Region: PRK13674 338963010260 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 338963010261 Ligand Binding Site [chemical binding]; other site 338963010262 Pyruvate kinase [Carbohydrate transport and metabolism]; Region: PykF; COG0469 338963010263 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 338963010264 domain interfaces; other site 338963010265 active site 338963010266 AmiS/UreI family transporter; Region: AmiS_UreI; pfam02293 338963010267 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 338963010268 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 338963010269 dimer interface [polypeptide binding]; other site 338963010270 active site 338963010271 CoA binding pocket [chemical binding]; other site 338963010272 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 338963010273 Mechanosensitive ion channel; Region: MS_channel; pfam00924 338963010274 alternate F1F0 ATPase, F1 subunit beta; Region: alt_F1F0_F1_bet; TIGR03305 338963010275 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 338963010276 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 338963010277 alpha subunit interaction interface [polypeptide binding]; other site 338963010278 Walker A motif; other site 338963010279 ATP binding site [chemical binding]; other site 338963010280 Walker B motif; other site 338963010281 inhibitor binding site; inhibition site 338963010282 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 338963010283 F0F1 ATP synthase subunit epsilon; Validated; Region: PRK06228 338963010284 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 338963010285 gamma subunit interface [polypeptide binding]; other site 338963010286 epsilon subunit interface [polypeptide binding]; other site 338963010287 LBP interface [polypeptide binding]; other site 338963010288 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; cl09754 338963010289 F1/F0 ATPase, Methanosarcina type, subunit 2; Region: F1F0_chp_2; TIGR03165 338963010290 alternate F1F0 ATPase, F0 subunit A; Region: altF1_A; TIGR03306 338963010291 alternate F1F0 ATPase, F0 subunit C; Region: alt_F1F0_F0_C; TIGR03322 338963010292 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 338963010293 alternate F1F0 ATPase, F0 subunit B; Region: alt_F1F0_F0_B; TIGR03321 338963010294 alternate F1F0 ATPase, F1 subunit alpha; Region: alt_F1F0_F1_al; TIGR03324 338963010295 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 338963010296 Walker A motif; other site 338963010297 ATP binding site [chemical binding]; other site 338963010298 Walker B motif; other site 338963010299 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 338963010300 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 338963010301 core domain interface [polypeptide binding]; other site 338963010302 delta subunit interface [polypeptide binding]; other site 338963010303 epsilon subunit interface [polypeptide binding]; other site 338963010304 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 338963010305 dinuclear metal binding motif [ion binding]; other site 338963010306 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 338963010307 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 338963010308 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 338963010309 DNA binding site [nucleotide binding] 338963010310 active site 338963010311 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 338963010312 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 338963010313 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 338963010314 HlyD family secretion protein; Region: HlyD_3; pfam13437 338963010315 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 338963010316 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 338963010317 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 338963010318 MarR family; Region: MarR_2; pfam12802 338963010319 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 338963010320 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 338963010321 dimer interface [polypeptide binding]; other site 338963010322 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963010323 catalytic residue [active] 338963010324 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; pfam01977 338963010325 Short C-terminal domain; Region: SHOCT; pfam09851 338963010326 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 338963010327 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 338963010328 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 338963010329 Dodecin; Region: Dodecin; pfam07311 338963010330 conserved nucleotide sequence; Pcar_R2021 338963010331 hypothetical protein; Provisional; Region: PRK10621 338963010332 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 338963010333 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 338963010334 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 338963010335 putative ATP binding site [chemical binding]; other site 338963010336 putative substrate interface [chemical binding]; other site 338963010337 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 338963010338 active site 338963010339 TSCPD domain; Region: TSCPD; cl14834 338963010340 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 338963010341 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 338963010342 DctM-like transporters; Region: DctM; pfam06808 338963010343 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 338963010344 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 338963010345 Ligand Binding Site [chemical binding]; other site 338963010346 Scramblase; Region: Scramblase; pfam03803 338963010347 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 338963010348 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 338963010349 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 338963010350 ABC-ATPase subunit interface; other site 338963010351 dimer interface [polypeptide binding]; other site 338963010352 putative PBP binding regions; other site 338963010353 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 338963010354 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 338963010355 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 338963010356 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 338963010357 putative metal binding residues [ion binding]; other site 338963010358 Multiple antibiotic transporter [Intracellular trafficking and secretion]; Region: MarC; COG2095 338963010359 Putative thioesterase (yiiD_Cterm); Region: YiiD_Cterm; cl17557 338963010360 Multiple antibiotic transporter [Intracellular trafficking and secretion]; Region: MarC; COG2095 338963010361 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 338963010362 intersubunit interface [polypeptide binding]; other site 338963010363 active site 338963010364 Zn2+ binding site [ion binding]; other site 338963010365 putative C-S lyase; Region: C_S_lyase_PatB; TIGR04350 338963010366 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 338963010367 pyridoxal 5'-phosphate binding site [chemical binding]; other site 338963010368 homodimer interface [polypeptide binding]; other site 338963010369 catalytic residue [active] 338963010370 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl17448 338963010371 conserved nucleotide sequence; Pcar_R5049 338963010372 CARDB; Region: CARDB; pfam07705 338963010373 conserved nucleotide sequence; Pcar_R5070 338963010374 pyrophosphatase PpaX; Provisional; Region: PRK13288 338963010375 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 338963010376 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 338963010377 motif II; other site 338963010378 conserved nucleotide sequence; Pcar_R5071 338963010379 Transposase domain (DUF772); Region: DUF772; pfam05598 338963010380 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 338963010381 conserved nucleotide sequence; Pcar_R5046 338963010382 conserved nucleotide sequence; Pcar_R5051 338963010383 Uncharacterized protein conserved in bacteria (DUF2321); Region: DUF2321; pfam10083 338963010384 T5orf172 domain; Region: T5orf172; pfam10544 338963010385 conserved nucleotide sequence; Pcar_R5025 338963010386 conserved nucleotide sequence; Pcar_R5026 338963010387 conserved nucleotide sequence; Pcar_R5029 338963010388 conserved nucleotide sequence; Pcar_R5047 338963010389 conserved nucleotide sequence; Pcar_R5004 338963010390 conserved nucleotide sequence; Pcar_R5072 338963010391 conserved nucleotide sequence; Pcar_R5013 338963010392 Protein of unknown function (DUF1847); Region: DUF1847; pfam08901 338963010393 conserved nucleotide sequence; Pcar_R5074 338963010394 Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: MetG; COG0143 338963010395 conserved nucleotide sequence; Pcar_R5076 338963010396 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963010397 I-site; other site 338963010398 active site 338963010399 metal binding site [ion binding]; metal-binding site 338963010400 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 338963010401 Methyltransferase domain; Region: Methyltransf_31; pfam13847 338963010402 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 338963010403 S-adenosylmethionine binding site [chemical binding]; other site 338963010404 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 338963010405 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_10; cd07251 338963010406 conserved nucleotide sequence fragment; Pcar_R5010 338963010407 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 338963010408 UV radiation resistance protein and autophagy-related subunit 14; Region: Atg14; pfam10186 338963010409 Transposase domain (DUF772); Region: DUF772; pfam05598 338963010410 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 338963010411 conserved nucleotide sequence; Pcar_R5005 338963010412 conserved nucleotide sequence; Pcar_R5073 338963010413 conserved nucleotide sequence; Pcar_R5014 338963010414 Protein of unknown function (DUF1847); Region: DUF1847; pfam08901 338963010415 conserved nucleotide sequence; Pcar_R5075 338963010416 Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: MetG; COG0143 338963010417 conserved nucleotide sequence; Pcar_R5077 338963010418 cyclic-di-GMP phosphodiesterase; Provisional; Region: PRK11359 338963010419 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 338963010420 putative active site [active] 338963010421 heme pocket [chemical binding]; other site 338963010422 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 338963010423 putative active site [active] 338963010424 heme pocket [chemical binding]; other site 338963010425 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 338963010426 putative active site [active] 338963010427 heme pocket [chemical binding]; other site 338963010428 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 338963010429 metal binding site [ion binding]; metal-binding site 338963010430 active site 338963010431 I-site; other site 338963010432 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 338963010433 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 338963010434 Metal binding protein HemV-2. 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: HemV-2; cd01147 338963010435 putative metal binding site [ion binding]; other site 338963010436 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 338963010437 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 338963010438 Walker A/P-loop; other site 338963010439 ATP binding site [chemical binding]; other site 338963010440 Q-loop/lid; other site 338963010441 ABC transporter signature motif; other site 338963010442 Walker B; other site 338963010443 D-loop; other site 338963010444 H-loop/switch region; other site 338963010445 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 338963010446 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 338963010447 dimer interface [polypeptide binding]; other site 338963010448 ABC-ATPase subunit interface; other site 338963010449 putative PBP binding regions; other site 338963010450 Protein of unknown function (DUF1407); Region: DUF1407; pfam07191 338963010451 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 338963010452 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 338963010453 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 338963010454 Predicted integral membrane protein (DUF2270); Region: DUF2270; pfam10028 338963010455 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 338963010456 dimer interface [polypeptide binding]; other site 338963010457 active site 338963010458 Schiff base residues; other site 338963010459 conserved nucleotide sequence; Pcar_R1026 338963010460 conserved nucleotide sequence; Pcar_R1111 338963010461 conserved nucleotide sequence; Pcar_R1027 338963010462 conserved nucleotide sequence; Pcar_R1028 338963010463 Diphthamide biosynthesis methyltransferase [Translation, ribosomal structure and biogenesis]; Region: DPH5; COG1798 338963010464 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 338963010465 active site 338963010466 SAM binding site [chemical binding]; other site 338963010467 homodimer interface [polypeptide binding]; other site 338963010468 Uroporphyrinogen-III synthase [Coenzyme metabolism]; Region: HemD; COG1587 338963010469 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 338963010470 active site 338963010471 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 338963010472 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 338963010473 domain interfaces; other site 338963010474 active site 338963010475 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 338963010476 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 338963010477 tRNA; other site 338963010478 putative tRNA binding site [nucleotide binding]; other site 338963010479 putative NADP binding site [chemical binding]; other site 338963010480 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 338963010481 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 338963010482 Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme metabolism]; Region: CysG; COG1648 338963010483 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 338963010484 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 338963010485 dimer interface [polypeptide binding]; other site 338963010486 active site 338963010487 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 338963010488 catalytic residues [active] 338963010489 Protein of unknown function (DUF615); Region: DUF615; pfam04751 338963010490 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 338963010491 putative active site [active] 338963010492 dimerization interface [polypeptide binding]; other site 338963010493 putative tRNAtyr binding site [nucleotide binding]; other site 338963010494 endonuclease IV; Provisional; Region: PRK01060 338963010495 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 338963010496 AP (apurinic/apyrimidinic) site pocket; other site 338963010497 DNA interaction; other site 338963010498 Metal-binding active site; metal-binding site 338963010499 pyrimidine 5'-nucleotidase; Region: Pyr-5-nucltdase; TIGR01993 338963010500 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 338963010501 motif II; other site 338963010502 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 338963010503 nucleotide binding site/active site [active] 338963010504 HIT family signature motif; other site 338963010505 catalytic residue [active] 338963010506 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 338963010507 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 338963010508 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 338963010509 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 338963010510 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 338963010511 RDD family; Region: RDD; pfam06271 338963010512 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 338963010513 RNA methyltransferase, RsmE family; Region: TIGR00046 338963010514 Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis]; Region: PrmA; COG2264 338963010515 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 338963010516 S-adenosylmethionine binding site [chemical binding]; other site 338963010517 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 338963010518 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963010519 active site 338963010520 phosphorylation site [posttranslational modification] 338963010521 intermolecular recognition site; other site 338963010522 dimerization interface [polypeptide binding]; other site 338963010523 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 338963010524 DNA binding site [nucleotide binding] 338963010525 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 338963010526 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 338963010527 dimerization interface [polypeptide binding]; other site 338963010528 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 338963010529 dimer interface [polypeptide binding]; other site 338963010530 phosphorylation site [posttranslational modification] 338963010531 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 338963010532 ATP binding site [chemical binding]; other site 338963010533 Mg2+ binding site [ion binding]; other site 338963010534 G-X-G motif; other site 338963010535 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 338963010536 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 338963010537 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 338963010538 protein binding site [polypeptide binding]; other site 338963010539 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 338963010540 protein binding site [polypeptide binding]; other site 338963010541 ribonuclease Z; Provisional; Region: PRK02126 338963010542 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 338963010543 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 338963010544 dimerization interface [polypeptide binding]; other site 338963010545 Histidine kinase; Region: HisKA_3; pfam07730 338963010546 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 338963010547 ATP binding site [chemical binding]; other site 338963010548 Mg2+ binding site [ion binding]; other site 338963010549 G-X-G motif; other site 338963010550 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 338963010551 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 338963010552 active site 338963010553 phosphorylation site [posttranslational modification] 338963010554 intermolecular recognition site; other site 338963010555 dimerization interface [polypeptide binding]; other site 338963010556 helix_turn_helix, Lux Regulon; Region: HTH_LUXR; smart00421 338963010557 DNA binding residues [nucleotide binding] 338963010558 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 338963010559 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 338963010560 Domain of unknown function DUF20; Region: UPF0118; pfam01594 338963010561 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 338963010562 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 338963010563 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 338963010564 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 338963010565 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 338963010566 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 338963010567 HlyD family secretion protein; Region: HlyD_3; pfam13437 338963010568 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 338963010569 DNA-binding transcriptional repressor AcrR; Provisional; Region: PRK10668 338963010570 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 338963010571 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 338963010572 PilZ domain; Region: PilZ; cl01260 338963010573 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 338963010574 active site 338963010575 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 338963010576 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 338963010577 poly(A) polymerase; Region: pcnB; TIGR01942 338963010578 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 338963010579 active site 338963010580 NTP binding site [chemical binding]; other site 338963010581 metal binding triad [ion binding]; metal-binding site 338963010582 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 338963010583 Double zinc ribbon; Region: DZR; pfam12773 338963010584 TPR repeat; Region: TPR_11; pfam13414 338963010585 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 338963010586 binding surface 338963010587 TPR motif; other site 338963010588 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 338963010589 binding surface 338963010590 Tetratricopeptide repeat; Region: TPR_16; pfam13432 338963010591 TPR motif; other site 338963010592 Tetratricopeptide repeat; Region: TPR_16; pfam13432 338963010593 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 338963010594 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 338963010595 binding surface 338963010596 TPR motif; other site 338963010597 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 338963010598 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 338963010599 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 338963010600 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 338963010601 Hydantoinase B/oxoprolinase; Region: Hydantoinase_B; pfam02538 338963010602 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; pfam01977 338963010603 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 338963010604 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; Region: CobA_CobO_BtuR; pfam02572 338963010605 Outer membrane lipoprotein Slp family; Region: Slp; pfam03843 338963010606 The SYLF domain (also called DUF500), a novel lipid-binding module; Region: SYLF; cd11524 338963010607 putative amphipathic alpha helix; other site 338963010608 heptanucleotide repeats; Pcar_R7030 338963010609 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 338963010610 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 338963010611 Trehalose phosphorylase (TP) reversibly catalyzes trehalose synthesis and degradation from alpha-glucose-1-phosphate (alpha-Glc-1-P) and glucose. The catalyzing activity includes the phosphorolysis of trehalose, which produce alpha-Glc-1-P and glucose; Region: GT1_Trehalose_phosphorylase; cd03792 338963010612 Trehalose-6-Phosphate Synthase (TPS) is a glycosyltransferase that catalyses the synthesis of alpha,alpha-1,1-trehalose-6-phosphate from glucose-6-phosphate using a UDP-glucose donor. It is a key enzyme in the trehalose synthesis pathway. Trehalose is a...; Region: GT1_TPS; cd03788 338963010613 alpha,alpha-trehalose-phosphate synthase [UDP-forming]; Region: trehalose_OtsA; TIGR02400 338963010614 active site 338963010615 homotetramer interface [polypeptide binding]; other site 338963010616 3-deoxy-7-phosphoheptulonate synthase; Reviewed; Region: PRK08673 338963010617 phospho-2-dehydro-3-deoxyheptonate aldolase; Region: DAHP_synth_Bsub; TIGR01361 338963010618 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK13581 338963010619 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 338963010620 ligand binding site [chemical binding]; other site 338963010621 NAD binding site [chemical binding]; other site 338963010622 dimerization interface [polypeptide binding]; other site 338963010623 catalytic site [active] 338963010624 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 338963010625 putative L-serine binding site [chemical binding]; other site 338963010626 Menaquinone biosynthesis; Region: VitK2_biosynth; cl17475 338963010627 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 338963010628 futalosine nucleosidase; Region: fut_nucase; TIGR03664 338963010629 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 338963010630 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 338963010631 catalytic residues [active] 338963010632 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 338963010633 Putative zinc-finger; Region: zf-HC2; pfam13490 338963010634 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 338963010635 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 338963010636 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 338963010637 DNA binding residues [nucleotide binding] 338963010638 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 338963010639 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 338963010640 TPP-binding site [chemical binding]; other site 338963010641 dimer interface [polypeptide binding]; other site 338963010642 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 338963010643 PYR/PP interface [polypeptide binding]; other site 338963010644 dimer interface [polypeptide binding]; other site 338963010645 TPP binding site [chemical binding]; other site 338963010646 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 338963010647 glutamate--cysteine ligase; Region: PLN02611 338963010648 carboxylate-amine ligase, YbdK family; Region: gshA_cyan_rel; TIGR02050 338963010649 Ion channel; Region: Ion_trans_2; pfam07885 338963010650 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 338963010651 TrkA-N domain; Region: TrkA_N; pfam02254 338963010652 TrkA-C domain; Region: TrkA_C; pfam02080 338963010653 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 338963010654 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; cl12060 338963010655 Metal-binding active site; metal-binding site 338963010656 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 338963010657 active site 338963010658 DNA polymerase IV; Validated; Region: PRK02406 338963010659 DNA binding site [nucleotide binding] 338963010660 F0F1 ATP synthase subunit epsilon; Provisional; Region: atpC; PRK13446 338963010661 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 338963010662 gamma subunit interface [polypeptide binding]; other site 338963010663 epsilon subunit interface [polypeptide binding]; other site 338963010664 LBP interface [polypeptide binding]; other site 338963010665 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 338963010666 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 338963010667 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 338963010668 alpha subunit interaction interface [polypeptide binding]; other site 338963010669 Walker A motif; other site 338963010670 ATP binding site [chemical binding]; other site 338963010671 Walker B motif; other site 338963010672 inhibitor binding site; inhibition site 338963010673 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 338963010674 octanucleotide repeats; Pcar_R8057 338963010675 octanucleotide repeats; Pcar_R8058 338963010676 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 338963010677 core domain interface [polypeptide binding]; other site 338963010678 delta subunit interface [polypeptide binding]; other site 338963010679 epsilon subunit interface [polypeptide binding]; other site 338963010680 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 338963010681 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 338963010682 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 338963010683 beta subunit interaction interface [polypeptide binding]; other site 338963010684 Walker A motif; other site 338963010685 ATP binding site [chemical binding]; other site 338963010686 Walker B motif; other site 338963010687 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 338963010688 F0F1 ATP synthase subunit delta; Provisional; Region: PRK13429 338963010689 F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]; Region: AtpH; cl17210 338963010690 F0F1 ATP synthase subunit B; Validated; Region: PRK07352 338963010691 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 338963010692 ATP synthase CF0 B' subunit; Validated; Region: atpG; CHL00118 338963010693 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 338963010694 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 338963010695 ParB-like nuclease domain; Region: ParB; smart00470 338963010696 KorB domain; Region: KorB; pfam08535 338963010697 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 338963010698 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 338963010699 P-loop; other site 338963010700 Magnesium ion binding site [ion binding]; other site 338963010701 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 338963010702 Magnesium ion binding site [ion binding]; other site 338963010703 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 338963010704 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 338963010705 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 338963010706 tRNA:m(5)U-54 methyltransferase; Region: gid_trmFO; TIGR00137 338963010707 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 338963010708 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 338963010709 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 338963010710 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 338963010711 trmE is a tRNA modification GTPase; Region: trmE; cd04164 338963010712 G1 box; other site 338963010713 GTP/Mg2+ binding site [chemical binding]; other site 338963010714 Switch I region; other site 338963010715 G2 box; other site 338963010716 Switch II region; other site 338963010717 G3 box; other site 338963010718 G4 box; other site 338963010719 G5 box; other site 338963010720 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 338963010721 membrane protein insertase; Provisional; Region: PRK01318 338963010722 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 338963010723 Haemolytic domain; Region: Haemolytic; pfam01809 338963010724 Ribonuclease P; Region: Ribonuclease_P; pfam00825 338963010725 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399