-- dump date 20140619_130057 -- class Genbank::misc_feature -- table misc_feature_note -- id note 423212000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 423212000002 DnaA N-terminal domain; Region: DnaA_N; pfam11638 423212000003 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 423212000004 Walker A motif; other site 423212000005 ATP binding site [chemical binding]; other site 423212000006 Walker B motif; other site 423212000007 arginine finger; other site 423212000008 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 423212000009 DnaA box-binding interface [nucleotide binding]; other site 423212000010 DNA polymerase III subunit beta; Validated; Region: PRK05643 423212000011 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 423212000012 putative DNA binding surface [nucleotide binding]; other site 423212000013 dimer interface [polypeptide binding]; other site 423212000014 beta-clamp/clamp loader binding surface; other site 423212000015 beta-clamp/translesion DNA polymerase binding surface; other site 423212000016 Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair]; Region: RecF; COG1195 423212000017 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 423212000018 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 423212000019 ABC transporter signature motif; other site 423212000020 Walker B; other site 423212000021 D-loop; other site 423212000022 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 423212000023 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 423212000024 Mg2+ binding site [ion binding]; other site 423212000025 G-X-G motif; other site 423212000026 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 423212000027 anchoring element; other site 423212000028 dimer interface [polypeptide binding]; other site 423212000029 ATP binding site [chemical binding]; other site 423212000030 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 423212000031 active site 423212000032 putative metal-binding site [ion binding]; other site 423212000033 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 423212000034 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957; cl01113 423212000035 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 423212000036 arginine decarboxylase; Provisional; Region: PRK05354 423212000037 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 423212000038 dimer interface [polypeptide binding]; other site 423212000039 active site 423212000040 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 423212000041 catalytic residues [active] 423212000042 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 423212000043 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 423212000044 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 423212000045 putative active site; other site 423212000046 catalytic triad [active] 423212000047 putative dimer interface [polypeptide binding]; other site 423212000048 bacterial Hfq-like; Region: Hfq; cd01716 423212000049 hexamer interface [polypeptide binding]; other site 423212000050 Sm1 motif; other site 423212000051 RNA binding site [nucleotide binding]; other site 423212000052 Sm2 motif; other site 423212000053 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 423212000054 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 423212000055 HflX GTPase family; Region: HflX; cd01878 423212000056 G1 box; other site 423212000057 GTP/Mg2+ binding site [chemical binding]; other site 423212000058 Switch I region; other site 423212000059 G2 box; other site 423212000060 G3 box; other site 423212000061 Switch II region; other site 423212000062 G4 box; other site 423212000063 G5 box; other site 423212000064 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 423212000065 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 423212000066 catalytic residues [active] 423212000067 Pirin-related protein [General function prediction only]; Region: COG1741 423212000068 Pirin; Region: Pirin; pfam02678 423212000069 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 423212000070 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 423212000071 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 423212000072 active site 423212000073 nucleophile elbow; other site 423212000074 Patatin phospholipase; Region: DUF3734; pfam12536 423212000075 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 423212000076 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 423212000077 HlyD family secretion protein; Region: HlyD_3; pfam13437 423212000078 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 423212000079 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 423212000080 Zinc metalloprotease (elastase) [Amino acid transport and metabolism]; Region: LasB; COG3227 423212000081 Fungalysin/Thermolysin Propeptide Motif; Region: FTP; pfam07504 423212000082 Peptidase M4 family includes thermolysin, protealysin, aureolysin and neutral protease; Region: M4_neutral_protease; cd09597 423212000083 active site 423212000084 Zn binding site [ion binding]; other site 423212000085 hypothetical protein; Provisional; Region: PRK05255 423212000086 23S rRNA m(2)G2445 methyltransferase; Provisional; Region: rlmL; PRK11783 423212000087 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 423212000088 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 423212000089 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 423212000090 Protein of unknown function (DUF962); Region: DUF962; cl01879 423212000091 phospholipid:lipid A palmitoyltransferase; Provisional; Region: pagP; PRK11045 423212000092 amino acid transporter; Region: 2A0306; TIGR00909 423212000093 C-terminus of AA_permease; Region: AA_permease_C; pfam13906 423212000094 Phosphate transporter family; Region: PHO4; pfam01384 423212000095 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 423212000096 diiron binding motif [ion binding]; other site 423212000097 PAS domain; Region: PAS_9; pfam13426 423212000098 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 423212000099 putative active site [active] 423212000100 heme pocket [chemical binding]; other site 423212000101 PAS domain S-box; Region: sensory_box; TIGR00229 423212000102 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 423212000103 putative active site [active] 423212000104 heme pocket [chemical binding]; other site 423212000105 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 423212000106 PAS domain; Region: PAS_9; pfam13426 423212000107 putative active site [active] 423212000108 heme pocket [chemical binding]; other site 423212000109 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212000110 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212000111 metal binding site [ion binding]; metal-binding site 423212000112 active site 423212000113 I-site; other site 423212000114 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 423212000115 M28 Zn-Peptidase Aeromonas (Vibrio) proteolytica aminopeptidase; Region: M28_AAP; cd03879 423212000116 Peptidase family M28; Region: Peptidase_M28; pfam04389 423212000117 active site 423212000118 metal binding site [ion binding]; metal-binding site 423212000119 Protein of unknown function (DUF2490); Region: DUF2490; pfam10677 423212000120 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 423212000121 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 423212000122 substrate binding pocket [chemical binding]; other site 423212000123 membrane-bound complex binding site; other site 423212000124 hinge residues; other site 423212000125 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 423212000126 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 423212000127 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; pfam04307 423212000128 Metallo-peptidase family M12B Reprolysin-like; Region: Reprolysin_2; pfam13574 423212000129 active site 423212000130 Ser-Thr-rich glycosyl-phosphatidyl-inositol-anchored membrane family; Region: GPI-anchored; pfam10342 423212000131 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 423212000132 Bestrophin, RFP-TM, chloride channel; Region: Bestrophin; cl01544 423212000133 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 423212000134 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 423212000135 trimer interface [polypeptide binding]; other site 423212000136 active site 423212000137 substrate binding site [chemical binding]; other site 423212000138 CoA binding site [chemical binding]; other site 423212000139 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 423212000140 amino acid transporter; Region: 2A0306; TIGR00909 423212000141 Entericidin EcnA/B family; Region: Entericidin; cl02322 423212000142 Predicted membrane protein [Function unknown]; Region: COG2323 423212000143 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 423212000144 tetramer interface [polypeptide binding]; other site 423212000145 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 423212000146 active site 423212000147 Mg2+/Mn2+ binding site [ion binding]; other site 423212000148 Domain of Unknown Function with PDB structure (DUF3865); Region: DUF3865; pfam12981 423212000149 Transcriptional regulator [Transcription]; Region: LysR; COG0583 423212000150 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 423212000151 LysR substrate binding domain; Region: LysR_substrate; pfam03466 423212000152 dimerization interface [polypeptide binding]; other site 423212000153 Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic); Region: Peptidase_C39_like; cl00296 423212000154 Radial spokehead-like protein; Region: Radial_spoke; pfam04712 423212000155 zinc-responsive transcriptional regulator; Provisional; Region: zntR; PRK09514 423212000156 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Region: HTH_MerR1; cd04783 423212000157 DNA binding residues [nucleotide binding] 423212000158 dimer interface [polypeptide binding]; other site 423212000159 mercury binding site [ion binding]; other site 423212000160 Glutaredoxin and related proteins [Posttranslational modification, protein turnover, chaperones]; Region: GrxC; COG0695 423212000161 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212000162 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212000163 metal binding site [ion binding]; metal-binding site 423212000164 active site 423212000165 I-site; other site 423212000166 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 423212000167 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 423212000168 S-AdoMet dependent tetrapyrrole methylases; Region: TP_methylase; cl00304 423212000169 active site 423212000170 SAM binding site [chemical binding]; other site 423212000171 homodimer interface [polypeptide binding]; other site 423212000172 Major Facilitator Superfamily; Region: MFS_1; pfam07690 423212000173 Class-II DAHP synthetase family; Region: DAHP_synth_2; pfam01474 423212000174 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 423212000175 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 423212000176 Serine hydrolase; Region: Ser_hydrolase; cl17834 423212000177 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 423212000178 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 423212000179 EamA-like transporter family; Region: EamA; pfam00892 423212000180 EamA-like transporter family; Region: EamA; pfam00892 423212000181 Helix-turn-helix domain of transposase family ISL3; Region: HTH_Tnp_ISL3; pfam13542 423212000182 integrase; Provisional; Region: PRK09692 423212000183 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 423212000184 active site 423212000185 Int/Topo IB signature motif; other site 423212000186 Phage derived protein Gp49-like (DUF891); Region: Gp49; pfam05973 423212000187 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 423212000188 non-specific DNA binding site [nucleotide binding]; other site 423212000189 salt bridge; other site 423212000190 sequence-specific DNA binding site [nucleotide binding]; other site 423212000191 exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase; Region: EPS_sugtrans; TIGR03025 423212000192 aspartate aminotransferase; Provisional; Region: PRK05764 423212000193 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 423212000194 pyridoxal 5'-phosphate binding site [chemical binding]; other site 423212000195 homodimer interface [polypeptide binding]; other site 423212000196 catalytic residue [active] 423212000197 excinuclease ABC subunit B; Provisional; Region: PRK05298 423212000198 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 423212000199 ATP binding site [chemical binding]; other site 423212000200 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 423212000201 nucleotide binding region [chemical binding]; other site 423212000202 ATP-binding site [chemical binding]; other site 423212000203 Ultra-violet resistance protein B; Region: UvrB; pfam12344 423212000204 UvrB/uvrC motif; Region: UVR; pfam02151 423212000205 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212000206 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212000207 metal binding site [ion binding]; metal-binding site 423212000208 active site 423212000209 I-site; other site 423212000210 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 423212000211 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 423212000212 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 423212000213 active site 423212000214 FMN binding site [chemical binding]; other site 423212000215 substrate binding site [chemical binding]; other site 423212000216 3Fe-4S cluster binding site [ion binding]; other site 423212000217 Cell division protein ZapA; Region: ZapA; pfam05164 423212000218 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 423212000219 proline aminopeptidase P II; Provisional; Region: PRK10879 423212000220 Aminopeptidase P, N-terminal domain; Region: AMP_N; pfam05195 423212000221 Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on...; Region: Prolidase; cd01087 423212000222 active site 423212000223 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 423212000224 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 423212000225 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 423212000226 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 423212000227 alpha-L-glutamate ligase-related protein; Region: rimK_rel_E_lig; TIGR02291 423212000228 Inactive transglutaminase fused to 7 transmembrane helices; Region: Transglut_i_TM; pfam14400 423212000229 7 transmembrane helices usually fused to an inactive transglutaminase; Region: 7TM_transglut; pfam14402 423212000230 Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones]; Region: COG4067 423212000231 Protein of unknown function (DUF4254); Region: DUF4254; pfam14063 423212000232 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 423212000233 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 423212000234 substrate binding pocket [chemical binding]; other site 423212000235 membrane-bound complex binding site; other site 423212000236 hinge residues; other site 423212000237 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; pfam02639 423212000238 ribonuclease R; Region: RNase_R; TIGR02063 423212000239 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 423212000240 RNB domain; Region: RNB; pfam00773 423212000241 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 423212000242 RNA binding site [nucleotide binding]; other site 423212000243 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 423212000244 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 423212000245 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 423212000246 RPI_A: Ribose 5-phosphate isomerase type A (RPI_A) subfamily; RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. This reaction leads to the...; Region: RPI_A; cd01398 423212000247 tetramer (dimer of dimers) interface [polypeptide binding]; other site 423212000248 active site 423212000249 dimer interface [polypeptide binding]; other site 423212000250 5' nucleotidase family; Region: 5_nucleotid; cl17687 423212000251 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 423212000252 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 423212000253 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 423212000254 PhnA protein; Region: PhnA; pfam03831 423212000255 Response regulator receiver domain; Region: Response_reg; pfam00072 423212000256 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 423212000257 active site 423212000258 phosphorylation site [posttranslational modification] 423212000259 intermolecular recognition site; other site 423212000260 DNA polymerase I; Provisional; Region: PRK05755 423212000261 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 423212000262 active site 423212000263 metal binding site 1 [ion binding]; metal-binding site 423212000264 putative 5' ssDNA interaction site; other site 423212000265 metal binding site 3; metal-binding site 423212000266 metal binding site 2 [ion binding]; metal-binding site 423212000267 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 423212000268 putative DNA binding site [nucleotide binding]; other site 423212000269 putative metal binding site [ion binding]; other site 423212000270 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 423212000271 active site 423212000272 catalytic site [active] 423212000273 substrate binding site [chemical binding]; other site 423212000274 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 423212000275 active site 423212000276 DNA binding site [nucleotide binding] 423212000277 catalytic site [active] 423212000278 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 423212000279 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 423212000280 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 423212000281 trimer interface [polypeptide binding]; other site 423212000282 active site 423212000283 UDP-GlcNAc binding site [chemical binding]; other site 423212000284 lipid binding site [chemical binding]; lipid-binding site 423212000285 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 423212000286 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 423212000287 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 423212000288 dimer interface [polypeptide binding]; other site 423212000289 active site 423212000290 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 423212000291 Coenzyme A binding pocket [chemical binding]; other site 423212000292 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 423212000293 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 423212000294 Coenzyme A binding pocket [chemical binding]; other site 423212000295 Peptide methionine sulfoxide reductase; Region: PMSR; pfam01625 423212000296 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 423212000297 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 423212000298 Uncharacterized ACR, YagE family COG1723; Region: DUF155; pfam02582 423212000299 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 423212000300 Isoprenoid Biosynthesis enzymes, Class 1; Region: Isoprenoid_Biosyn_C1; cl00210 423212000301 substrate binding pocket [chemical binding]; other site 423212000302 substrate-Mg2+ binding site; other site 423212000303 aspartate-rich region 1; other site 423212000304 aspartate-rich region 2; other site 423212000305 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 423212000306 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 423212000307 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 423212000308 tetramer interface [polypeptide binding]; other site 423212000309 pyridoxal 5'-phosphate binding site [chemical binding]; other site 423212000310 catalytic residue [active] 423212000311 YCII-related domain; Region: YCII; cl00999 423212000312 Glycine cleavage system protein P (pyridoxal-binding), N-terminal domain [Amino acid transport and metabolism]; Region: GcvP; COG0403 423212000313 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 423212000314 tetramer interface [polypeptide binding]; other site 423212000315 pyridoxal 5'-phosphate binding site [chemical binding]; other site 423212000316 catalytic residue [active] 423212000317 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 423212000318 lipoyl attachment site [posttranslational modification]; other site 423212000319 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 423212000320 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 423212000321 Protein of unknown function (DUF3592); Region: DUF3592; pfam12158 423212000322 Macrophage killing protein with similarity to conjugation protein; Region: IcmL; pfam11393 423212000323 ABC-type anion transport system, duplicated permease component [Inorganic ion transport and metabolism]; Region: COG4986 423212000324 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 423212000325 dimer interface [polypeptide binding]; other site 423212000326 conserved gate region; other site 423212000327 putative PBP binding loops; other site 423212000328 ABC-ATPase subunit interface; other site 423212000329 Binding-protein-dependent transport system inner membrane component; Region: BPD_transp_1; pfam00528 423212000330 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 423212000331 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 423212000332 Walker A/P-loop; other site 423212000333 ATP binding site [chemical binding]; other site 423212000334 Q-loop/lid; other site 423212000335 ABC transporter signature motif; other site 423212000336 Walker B; other site 423212000337 D-loop; other site 423212000338 H-loop/switch region; other site 423212000339 ABC nitrate/sulfonate/bicarbonate family transporter, ATPase subunit; Region: ABC_transp; pfam09821 423212000340 DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol...; Region: DsbA_DsbA; cd03019 423212000341 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 423212000342 catalytic residues [active] 423212000343 hinge region; other site 423212000344 alpha helical domain; other site 423212000345 Cytochrome c553 [Energy production and conversion]; Region: COG2863 423212000346 Cytochrome c; Region: Cytochrom_C; cl11414 423212000347 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 423212000348 G1 box; other site 423212000349 GTP/Mg2+ binding site [chemical binding]; other site 423212000350 Switch I region; other site 423212000351 G2 box; other site 423212000352 G3 box; other site 423212000353 Switch II region; other site 423212000354 G4 box; other site 423212000355 G5 box; other site 423212000356 acetyl-CoA synthetase; Provisional; Region: PRK00174 423212000357 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 423212000358 active site 423212000359 CoA binding site [chemical binding]; other site 423212000360 acyl-activating enzyme (AAE) consensus motif; other site 423212000361 AMP binding site [chemical binding]; other site 423212000362 acetate binding site [chemical binding]; other site 423212000363 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 423212000364 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 423212000365 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 423212000366 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 423212000367 tetrameric interface [polypeptide binding]; other site 423212000368 NAD binding site [chemical binding]; other site 423212000369 catalytic residues [active] 423212000370 Dodecin; Region: Dodecin; cl01328 423212000371 dihydrodipicolinate reductase; Provisional; Region: PRK00048 423212000372 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 423212000373 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 423212000374 ProQ/FINO family; Region: ProQ; pfam04352 423212000375 putative RNA binding sites [nucleotide binding]; other site 423212000376 pyruvate kinase; Provisional; Region: PRK05826 423212000377 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 423212000378 domain interfaces; other site 423212000379 active site 423212000380 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 423212000381 Phosphoglycerate kinase; Region: PGK; pfam00162 423212000382 substrate binding site [chemical binding]; other site 423212000383 hinge regions; other site 423212000384 ADP binding site [chemical binding]; other site 423212000385 catalytic site [active] 423212000386 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 423212000387 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 423212000388 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 423212000389 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 423212000390 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 423212000391 TPP-binding site [chemical binding]; other site 423212000392 dimer interface [polypeptide binding]; other site 423212000393 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 423212000394 PYR/PP interface [polypeptide binding]; other site 423212000395 dimer interface [polypeptide binding]; other site 423212000396 TPP binding site [chemical binding]; other site 423212000397 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 423212000398 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 423212000399 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 423212000400 active site 423212000401 Zn binding site [ion binding]; other site 423212000402 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 423212000403 Sel1-like repeats; Region: SEL1; smart00671 423212000404 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 423212000405 sequence-specific DNA binding site [nucleotide binding]; other site 423212000406 salt bridge; other site 423212000407 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 423212000408 Catalytic site [active] 423212000409 Global regulator protein family; Region: CsrA; pfam02599 423212000410 conjugal transfer ATPase TrbB; Provisional; Region: PRK13894 423212000411 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 423212000412 ATP binding site [chemical binding]; other site 423212000413 Walker A motif; other site 423212000414 hexamer interface [polypeptide binding]; other site 423212000415 Walker B motif; other site 423212000416 TrbC/VIRB2 family; Region: TrbC; cl01583 423212000417 conjugal transfer protein TrbD; Provisional; Region: PRK13823 423212000418 conjugal transfer protein TrbE; Provisional; Region: PRK13891 423212000419 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 423212000420 conjugal transfer protein TrbF; Provisional; Region: PRK13887 423212000421 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 423212000422 VirB7 interaction site; other site 423212000423 conjugal transfer protein TrbH; Provisional; Region: PRK13883 423212000424 Conjugal transfer protein TrbH; Region: TrbH; pfam07283 423212000425 conjugal transfer protein TrbI; Provisional; Region: PRK13881 423212000426 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 423212000427 conjugal transfer protein TrbJ; Provisional; Region: PRK13879 423212000428 P-type conjugative transfer protein TrbL; Region: TrbL_P; TIGR02783 423212000429 conjugal transfer coupling protein TraG; Provisional; Region: PRK13880 423212000430 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 423212000431 Walker A motif; other site 423212000432 ATP binding site [chemical binding]; other site 423212000433 Walker B motif; other site 423212000434 conjugal transfer peptidase TraF; Provisional; Region: PRK13884 423212000435 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 423212000436 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 423212000437 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 423212000438 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4643 423212000439 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 423212000440 active site 423212000441 metal binding site [ion binding]; metal-binding site 423212000442 interdomain interaction site; other site 423212000443 Uncharacterized conserved protein [Function unknown]; Region: COG4933 423212000444 Phagosome trafficking protein DotA; Region: DotA; pfam11388 423212000445 conjugal transfer relaxase TraI; Provisional; Region: PRK13878 423212000446 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 423212000447 conjugal transfer relaxosome component TraJ; Provisional; Region: PRK13877 423212000448 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 423212000449 P-loop; other site 423212000450 Transcriptional activator TraM; Region: Activator-TraM; pfam11657 423212000451 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 423212000452 nucleoside/Zn binding site; other site 423212000453 dimer interface [polypeptide binding]; other site 423212000454 catalytic motif [active] 423212000455 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 423212000456 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 423212000457 sequence-specific DNA binding site [nucleotide binding]; other site 423212000458 salt bridge; other site 423212000459 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 423212000460 Catalytic site [active] 423212000461 Putative excisionase (DUF1233); Region: DUF1233; pfam06806 423212000462 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 423212000463 phiCTX phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various phage and bacterial integrases, including those similar to phage integrases: Bordetella and...; Region: INT_phiCTX_C; cd01191 423212000464 Int/Topo IB signature motif; other site 423212000465 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 423212000466 Predicted transcriptional regulator [Transcription]; Region: COG5340 423212000467 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 423212000468 integrase; Provisional; Region: PRK09692 423212000469 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 423212000470 active site 423212000471 Int/Topo IB signature motif; other site 423212000472 DNA-damage-inducible protein D; Provisional; Region: dinD; PRK11525 423212000473 BRO family, N-terminal domain; Region: Bro-N; pfam02498 423212000474 Peptidase family M48; Region: Peptidase_M48; cl12018 423212000475 tellurium resistance terB-like protein; Region: terB_like; cd07177 423212000476 metal binding site [ion binding]; metal-binding site 423212000477 Predicted transcriptional regulator [Transcription]; Region: AlpA; COG3311 423212000478 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4643 423212000479 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 423212000480 active site 423212000481 metal binding site [ion binding]; metal-binding site 423212000482 interdomain interaction site; other site 423212000483 Protein of unknown function (DUF3987); Region: DUF3987; pfam13148 423212000484 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 423212000485 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 423212000486 non-specific DNA binding site [nucleotide binding]; other site 423212000487 salt bridge; other site 423212000488 sequence-specific DNA binding site [nucleotide binding]; other site 423212000489 Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]; Region: SecA; COG0653 423212000490 Transposase; Region: DDE_Tnp_ISL3; pfam01610 423212000491 Restriction endonuclease [Defense mechanisms]; Region: Mrr; COG1715 423212000492 Mrr N-terminal domain; Region: Mrr_N; pfam14338 423212000493 Restriction endonuclease; Region: Mrr_cat; pfam04471 423212000494 hypothetical protein; Provisional; Region: PRK10040 423212000495 Staphylococcal nuclease homologues; Region: SNc; smart00318 423212000496 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cd00175 423212000497 Catalytic site; other site 423212000498 nuc_hydro: Nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity. This group contains eukaryotic, bacterial and archeal...; Region: nuc_hydro; cl00226 423212000499 active site 423212000500 reticulocyte binding/rhoptry protein; Region: 235kDa-fam; TIGR01612 423212000501 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 423212000502 Coenzyme A binding pocket [chemical binding]; other site 423212000503 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 423212000504 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 423212000505 Walker A/P-loop; other site 423212000506 ATP binding site [chemical binding]; other site 423212000507 Q-loop/lid; other site 423212000508 ABC transporter signature motif; other site 423212000509 Walker B; other site 423212000510 D-loop; other site 423212000511 H-loop/switch region; other site 423212000512 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 423212000513 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 423212000514 FtsX-like permease family; Region: FtsX; pfam02687 423212000515 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 423212000516 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 423212000517 HlyD family secretion protein; Region: HlyD_3; pfam13437 423212000518 PAS domain; Region: PAS_9; pfam13426 423212000519 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 423212000520 putative active site [active] 423212000521 heme pocket [chemical binding]; other site 423212000522 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212000523 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212000524 metal binding site [ion binding]; metal-binding site 423212000525 active site 423212000526 I-site; other site 423212000527 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 423212000528 active site 423212000529 Protein of unknown function (DUF3423); Region: DUF3423; pfam11903 423212000530 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 423212000531 Uncharacterized conserved protein [Function unknown]; Region: COG0432 423212000532 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 423212000533 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 423212000534 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 423212000535 Protein of unknown function (DUF808); Region: DUF808; cl01002 423212000536 RF-1 domain; Region: RF-1; pfam00472 423212000537 Protein of unknown function (DUF330); Region: DUF330; pfam03886 423212000538 mce related protein; Region: MCE; pfam02470 423212000539 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 423212000540 Permease; Region: Permease; pfam02405 423212000541 Transcriptional regulator [Transcription]; Region: LysR; COG0583 423212000542 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 423212000543 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 423212000544 dimerization interface [polypeptide binding]; other site 423212000545 Pyoverdine/dityrosine biosynthesis protein; Region: DIT1_PvcA; pfam05141 423212000546 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 423212000547 Taurine catabolism dioxygenase TauD, TfdA family; Region: TauD; pfam02668 423212000548 substrate binding pocket [chemical binding]; other site 423212000549 active site 423212000550 iron coordination sites [ion binding]; other site 423212000551 hypothetical protein; Provisional; Region: PRK07190 423212000552 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 423212000553 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 423212000554 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 423212000555 Major Facilitator Superfamily; Region: MFS_1; pfam07690 423212000556 putative substrate translocation pore; other site 423212000557 hypothetical protein; Provisional; Region: PRK07206 423212000558 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 423212000559 Methyltransferase domain; Region: Methyltransf_31; pfam13847 423212000560 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 423212000561 S-adenosylmethionine binding site [chemical binding]; other site 423212000562 M48 family peptidase; Provisional; Region: PRK03001 423212000563 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 423212000564 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 423212000565 hypothetical protein; Provisional; Region: PRK09133 423212000566 M20 Peptidase, carboxypeptidase yscS-like; Region: M20_yscS_like; cd05675 423212000567 putative metal binding site [ion binding]; other site 423212000568 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 423212000569 CoA-transferase family III; Region: CoA_transf_3; pfam02515 423212000570 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 423212000571 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 423212000572 putative dimer interface [polypeptide binding]; other site 423212000573 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 423212000574 dimer interface [polypeptide binding]; other site 423212000575 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 423212000576 active site 423212000577 heme binding site [chemical binding]; other site 423212000578 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 423212000579 Uncharacterized conserved protein [Function unknown]; Region: COG0393 423212000580 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 423212000581 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 423212000582 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 423212000583 Protein of unknown function (DUF1295); Region: DUF1295; cl17837 423212000584 Protein of unknown function (DUF2878); Region: DUF2878; pfam11086 423212000585 Predicted kinase related to dihydroxyacetone kinase [General function prediction only]; Region: COG1461 423212000586 DAK2 domain; Region: Dak2; pfam02734 423212000587 EDD domain protein, DegV family; Region: DegV; TIGR00762 423212000588 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 423212000589 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 423212000590 classical (c) SDRs; Region: SDR_c; cd05233 423212000591 NAD(P) binding site [chemical binding]; other site 423212000592 active site 423212000593 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 423212000594 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 423212000595 Predicted membrane protein (DUF2177); Region: DUF2177; pfam09945 423212000596 Catalytic domain of Protein Kinases; Region: PKc; cd00180 423212000597 active site 423212000598 ATP binding site [chemical binding]; other site 423212000599 substrate binding site [chemical binding]; other site 423212000600 activation loop (A-loop); other site 423212000601 TspO/MBR family; Region: TspO_MBR; pfam03073 423212000602 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 423212000603 DNA photolyase; Region: DNA_photolyase; pfam00875 423212000604 Putative effector of murein hydrolase [Cell envelope biogenesis, outer membrane]; Region: LrgB; COG1346 423212000605 Putative effector of murein hydrolase LrgA [General function prediction only]; Region: COG1380 423212000606 Transcriptional regulator [Transcription]; Region: LysR; COG0583 423212000607 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 423212000608 The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; Region: PBP2_CidR; cd08438 423212000609 putative dimerization interface [polypeptide binding]; other site 423212000610 Domain of unknown function (DUF329); Region: DUF329; pfam03884 423212000611 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 423212000612 ATP-grasp domain; Region: ATP-grasp; pfam02222 423212000613 Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]; Region: PurE; COG0041 423212000614 Double zinc ribbon; Region: DZR; pfam12773 423212000615 Nitrogen regulatory protein P-II; Region: P-II; cl00412 423212000616 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 423212000617 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 423212000618 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 423212000619 Transcriptional regulator [Transcription]; Region: LysR; COG0583 423212000620 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 423212000621 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 423212000622 dimerization interface [polypeptide binding]; other site 423212000623 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 423212000624 ATP binding site [chemical binding]; other site 423212000625 Q-loop/lid; other site 423212000626 ABC transporter signature motif; other site 423212000627 Walker B; other site 423212000628 D-loop; other site 423212000629 H-loop/switch region; other site 423212000630 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 423212000631 HlyD family secretion protein; Region: HlyD_3; pfam13437 423212000632 Outer membrane efflux protein; Region: OEP; pfam02321 423212000633 Outer membrane efflux protein; Region: OEP; pfam02321 423212000634 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cl17299 423212000635 heme binding pocket [chemical binding]; other site 423212000636 heme ligand [chemical binding]; other site 423212000637 CHASE3 domain; Region: CHASE3; pfam05227 423212000638 PAS domain; Region: PAS_9; pfam13426 423212000639 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 423212000640 GAF domain; Region: GAF; cl17456 423212000641 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212000642 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212000643 metal binding site [ion binding]; metal-binding site 423212000644 active site 423212000645 I-site; other site 423212000646 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 423212000647 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 423212000648 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 423212000649 motif II; other site 423212000650 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 423212000651 metal binding site 2 [ion binding]; metal-binding site 423212000652 putative DNA binding helix; other site 423212000653 metal binding site 1 [ion binding]; metal-binding site 423212000654 dimer interface [polypeptide binding]; other site 423212000655 structural Zn2+ binding site [ion binding]; other site 423212000656 Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase] [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvB; COG0028 423212000657 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 423212000658 PYR/PP interface [polypeptide binding]; other site 423212000659 dimer interface [polypeptide binding]; other site 423212000660 TPP binding site [chemical binding]; other site 423212000661 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 423212000662 Thiamine pyrophosphate (TPP) family, BFDC subfamily, TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of...; Region: TPP_BFDC; cd02002 423212000663 TPP-binding site [chemical binding]; other site 423212000664 dimer interface [polypeptide binding]; other site 423212000665 Dot/Icm substrate protein; Region: SidE; pfam12252 423212000666 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 423212000667 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 423212000668 TAP-like protein; Region: Abhydrolase_4; pfam08386 423212000669 Bacillus subtilis NAD+-dependent betaine aldehyde dehydrogenase-like; Region: ALDH_BADH-GbsA; cd07119 423212000670 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 423212000671 tetramerization interface [polypeptide binding]; other site 423212000672 NAD(P) binding site [chemical binding]; other site 423212000673 catalytic residues [active] 423212000674 4-aminobutyrate aminotransferase; Provisional; Region: PRK06058 423212000675 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 423212000676 inhibitor-cofactor binding pocket; inhibition site 423212000677 pyridoxal 5'-phosphate binding site [chemical binding]; other site 423212000678 catalytic residue [active] 423212000679 Glutaminase [Amino acid transport and metabolism]; Region: GlsA; COG2066 423212000680 glutaminase A; Region: Gln_ase; TIGR03814 423212000681 Lin1944 and related proteins, classical (c) SDRs; Region: Lin1944_like_SDR_c; cd11731 423212000682 putative NAD(P) binding site [chemical binding]; other site 423212000683 homodimer interface [polypeptide binding]; other site 423212000684 mercuric reductase; Validated; Region: PRK06370 423212000685 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 423212000686 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 423212000687 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 423212000688 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 423212000689 Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the...; Region: ArsC_ArsC; cd03034 423212000690 ArsC family; Region: ArsC; pfam03960 423212000691 catalytic residues [active] 423212000692 Fatty acid desaturase; Region: FA_desaturase; pfam00487 423212000693 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 423212000694 Di-iron ligands [ion binding]; other site 423212000695 Transposase; Region: DDE_Tnp_ISL3; pfam01610 423212000696 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 423212000697 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 423212000698 ATP binding site [chemical binding]; other site 423212000699 Mg++ binding site [ion binding]; other site 423212000700 motif III; other site 423212000701 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 423212000702 nucleotide binding region [chemical binding]; other site 423212000703 ATP-binding site [chemical binding]; other site 423212000704 RNA-binding proteins (RRM domain) [General function prediction only]; Region: COG0724 423212000705 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 423212000706 hypothetical protein; Provisional; Region: PRK11212 423212000707 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 423212000708 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 423212000709 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 423212000710 HlyD family secretion protein; Region: HlyD; pfam00529 423212000711 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 423212000712 HlyD family secretion protein; Region: HlyD_3; pfam13437 423212000713 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 423212000714 Fe-S cluster binding site [ion binding]; other site 423212000715 active site 423212000716 Permeases of the major facilitator superfamily [General function prediction only]; Region: COG2270 423212000717 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 423212000718 amidase catalytic site [active] 423212000719 Zn binding residues [ion binding]; other site 423212000720 substrate binding site [chemical binding]; other site 423212000721 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 423212000722 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 423212000723 Multicopper oxidase; Region: Cu-oxidase; pfam00394 423212000724 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 423212000725 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 423212000726 Thermotoga maritima CorA-like family; Region: TmCorA-like; cd12822 423212000727 oligomer interface [polypeptide binding]; other site 423212000728 metal binding site [ion binding]; metal-binding site 423212000729 metal binding site [ion binding]; metal-binding site 423212000730 putative Cl binding site [ion binding]; other site 423212000731 aspartate ring; other site 423212000732 hydrophobic gate; other site 423212000733 basic sphincter; other site 423212000734 periplasmic entrance; other site 423212000735 HD domain; Region: HD_3; pfam13023 423212000736 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 423212000737 nicotinate phosphoribosyltransferase; Validated; Region: PRK09243 423212000738 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 423212000739 active site 423212000740 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 423212000741 Isochorismatase family; Region: Isochorismatase; pfam00857 423212000742 catalytic triad [active] 423212000743 metal binding site [ion binding]; metal-binding site 423212000744 conserved cis-peptide bond; other site 423212000745 ChaP, an enzyme involved in the biosynthesis of the antitumor agent chartreusin (cha); and similar proteins; Region: ChaP_like; cd08351 423212000746 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 423212000747 metal binding site [ion binding]; metal-binding site 423212000748 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 423212000749 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 423212000750 putative substrate translocation pore; other site 423212000751 Transcriptional regulator [Transcription]; Region: LysR; COG0583 423212000752 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 423212000753 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 423212000754 putative effector binding pocket; other site 423212000755 dimerization interface [polypeptide binding]; other site 423212000756 Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking; Region: RasGEF; cl02485 423212000757 Ras interaction site [polypeptide binding]; other site 423212000758 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 423212000759 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 423212000760 active site 423212000761 phosphorylation site [posttranslational modification] 423212000762 intermolecular recognition site; other site 423212000763 dimerization interface [polypeptide binding]; other site 423212000764 PAS domain; Region: PAS; smart00091 423212000765 PAS fold; Region: PAS_7; pfam12860 423212000766 putative active site [active] 423212000767 heme pocket [chemical binding]; other site 423212000768 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212000769 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212000770 metal binding site [ion binding]; metal-binding site 423212000771 active site 423212000772 I-site; other site 423212000773 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 423212000774 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 423212000775 PAS fold; Region: PAS_3; pfam08447 423212000776 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 423212000777 ATP binding site [chemical binding]; other site 423212000778 Mg2+ binding site [ion binding]; other site 423212000779 G-X-G motif; other site 423212000780 FIST N domain; Region: FIST; pfam08495 423212000781 Uncharacterized conserved protein [Function unknown]; Region: COG3287 423212000782 FIST C domain; Region: FIST_C; pfam10442 423212000783 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 423212000784 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 423212000785 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 423212000786 dimerization interface [polypeptide binding]; other site 423212000787 amino acid transporter; Region: 2A0306; TIGR00909 423212000788 Methyltransferase domain; Region: Methyltransf_31; pfam13847 423212000789 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 423212000790 S-adenosylmethionine binding site [chemical binding]; other site 423212000791 formate dehydrogenase; Provisional; Region: PRK07574 423212000792 NAD-dependent Formate Dehydrogenase (FDH); Region: FDH; cd05302 423212000793 dimerization interface [polypeptide binding]; other site 423212000794 ligand binding site [chemical binding]; other site 423212000795 NAD binding site [chemical binding]; other site 423212000796 catalytic site [active] 423212000797 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 423212000798 classical (c) SDR, subgroup 5; Region: SDR_c5; cd05346 423212000799 putative NAD(P) binding site [chemical binding]; other site 423212000800 homodimer interface [polypeptide binding]; other site 423212000801 homotetramer interface [polypeptide binding]; other site 423212000802 active site 423212000803 elongation factor P; Validated; Region: PRK00529 423212000804 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 423212000805 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 423212000806 RNA binding site [nucleotide binding]; other site 423212000807 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 423212000808 RNA binding site [nucleotide binding]; other site 423212000809 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 423212000810 Radical SAM superfamily; Region: Radical_SAM; pfam04055 423212000811 FeS/SAM binding site; other site 423212000812 polyphosphate kinase; Provisional; Region: PRK05443 423212000813 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 423212000814 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 423212000815 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 423212000816 putative active site [active] 423212000817 catalytic site [active] 423212000818 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 423212000819 putative domain interface [polypeptide binding]; other site 423212000820 putative active site [active] 423212000821 catalytic site [active] 423212000822 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 423212000823 nucleophile elbow; other site 423212000824 Chromate transporter; Region: Chromate_transp; pfam02417 423212000825 acyl-CoA dehydrogenase; Reviewed; Region: PRK13026 423212000826 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 423212000827 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 423212000828 active site 423212000829 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 423212000830 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 423212000831 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 423212000832 Substrate binding site; other site 423212000833 metal-binding site 423212000834 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 423212000835 Phosphotransferase enzyme family; Region: APH; pfam01636 423212000836 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 423212000837 OstA-like protein; Region: OstA; cl00844 423212000838 Organic solvent tolerance protein; Region: OstA_C; pfam04453 423212000839 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 423212000840 SurA N-terminal domain; Region: SurA_N; pfam09312 423212000841 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 423212000842 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 423212000843 4-hydroxythreonine-4-phosphate dehydrogenase; Region: pdxA; TIGR00557 423212000844 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 423212000845 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 423212000846 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 423212000847 folate binding site [chemical binding]; other site 423212000848 NADP+ binding site [chemical binding]; other site 423212000849 Repeats found in Drosophila proteins; Region: DM9; smart00696 423212000850 Protein of unknown function (DUF3421); Region: DUF3421; pfam11901 423212000851 Repeats found in Drosophila proteins; Region: DM9; smart00696 423212000852 elongation factor Tu; Reviewed; Region: PRK00049 423212000853 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 423212000854 G1 box; other site 423212000855 GEF interaction site [polypeptide binding]; other site 423212000856 GTP/Mg2+ binding site [chemical binding]; other site 423212000857 Switch I region; other site 423212000858 G2 box; other site 423212000859 G3 box; other site 423212000860 Switch II region; other site 423212000861 G4 box; other site 423212000862 G5 box; other site 423212000863 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 423212000864 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 423212000865 Antibiotic Binding Site [chemical binding]; other site 423212000866 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 423212000867 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 423212000868 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 423212000869 putative homodimer interface [polypeptide binding]; other site 423212000870 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 423212000871 heterodimer interface [polypeptide binding]; other site 423212000872 homodimer interface [polypeptide binding]; other site 423212000873 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 423212000874 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 423212000875 23S rRNA interface [nucleotide binding]; other site 423212000876 L7/L12 interface [polypeptide binding]; other site 423212000877 putative thiostrepton binding site; other site 423212000878 L25 interface [polypeptide binding]; other site 423212000879 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 423212000880 mRNA/rRNA interface [nucleotide binding]; other site 423212000881 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 423212000882 23S rRNA interface [nucleotide binding]; other site 423212000883 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 423212000884 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 423212000885 peripheral dimer interface [polypeptide binding]; other site 423212000886 core dimer interface [polypeptide binding]; other site 423212000887 L10 interface [polypeptide binding]; other site 423212000888 L11 interface [polypeptide binding]; other site 423212000889 putative EF-Tu interaction site [polypeptide binding]; other site 423212000890 putative EF-G interaction site [polypeptide binding]; other site 423212000891 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 423212000892 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 423212000893 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 423212000894 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 423212000895 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 423212000896 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 423212000897 RPB3 interaction site [polypeptide binding]; other site 423212000898 RPB1 interaction site [polypeptide binding]; other site 423212000899 RPB11 interaction site [polypeptide binding]; other site 423212000900 RPB10 interaction site [polypeptide binding]; other site 423212000901 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 423212000902 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 423212000903 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 423212000904 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 423212000905 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 423212000906 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 423212000907 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 423212000908 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 423212000909 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 423212000910 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 423212000911 DNA binding site [nucleotide binding] 423212000912 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 423212000913 30S ribosomal protein S12; Validated; Region: rpsL; PRK05163 423212000914 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 423212000915 30S ribosomal protein S7; Validated; Region: PRK05302 423212000916 elongation factor G; Reviewed; Region: PRK00007 423212000917 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 423212000918 G1 box; other site 423212000919 putative GEF interaction site [polypeptide binding]; other site 423212000920 GTP/Mg2+ binding site [chemical binding]; other site 423212000921 Switch I region; other site 423212000922 G2 box; other site 423212000923 G3 box; other site 423212000924 Switch II region; other site 423212000925 G4 box; other site 423212000926 G5 box; other site 423212000927 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 423212000928 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 423212000929 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 423212000930 elongation factor Tu; Reviewed; Region: PRK00049 423212000931 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 423212000932 GEF interaction site [polypeptide binding]; other site 423212000933 GTP/Mg2+ binding site [chemical binding]; other site 423212000934 Switch I region; other site 423212000935 G2 box; other site 423212000936 G3 box; other site 423212000937 Switch II region; other site 423212000938 G4 box; other site 423212000939 G5 box; other site 423212000940 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 423212000941 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 423212000942 Antibiotic Binding Site [chemical binding]; other site 423212000943 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 423212000944 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 423212000945 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 423212000946 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 423212000947 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 423212000948 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 423212000949 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 423212000950 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 423212000951 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 423212000952 putative translocon binding site; other site 423212000953 protein-rRNA interface [nucleotide binding]; other site 423212000954 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 423212000955 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 423212000956 G-X-X-G motif; other site 423212000957 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 423212000958 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 423212000959 23S rRNA interface [nucleotide binding]; other site 423212000960 5S rRNA interface [nucleotide binding]; other site 423212000961 putative antibiotic binding site [chemical binding]; other site 423212000962 L25 interface [polypeptide binding]; other site 423212000963 L27 interface [polypeptide binding]; other site 423212000964 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 423212000965 putative translocon interaction site; other site 423212000966 23S rRNA interface [nucleotide binding]; other site 423212000967 signal recognition particle (SRP54) interaction site; other site 423212000968 L23 interface [polypeptide binding]; other site 423212000969 trigger factor interaction site; other site 423212000970 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 423212000971 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 423212000972 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 423212000973 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 423212000974 RNA binding site [nucleotide binding]; other site 423212000975 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 423212000976 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 423212000977 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 423212000978 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK06911 423212000979 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 423212000980 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 423212000981 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 423212000982 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 423212000983 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 423212000984 23S rRNA interface [nucleotide binding]; other site 423212000985 L21e interface [polypeptide binding]; other site 423212000986 5S rRNA interface [nucleotide binding]; other site 423212000987 L27 interface [polypeptide binding]; other site 423212000988 L5 interface [polypeptide binding]; other site 423212000989 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 423212000990 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 423212000991 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 423212000992 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that...; Region: Ribosomal_L30; cd01658 423212000993 23S rRNA binding site [nucleotide binding]; other site 423212000994 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 423212000995 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 423212000996 SecY translocase; Region: SecY; pfam00344 423212000997 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 423212000998 30S ribosomal protein S13; Region: bact_S13; TIGR03631 423212000999 30S ribosomal protein S11; Validated; Region: PRK05309 423212001000 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 423212001001 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 423212001002 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 423212001003 RNA binding surface [nucleotide binding]; other site 423212001004 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 423212001005 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 423212001006 alphaNTD homodimer interface [polypeptide binding]; other site 423212001007 alphaNTD - beta interaction site [polypeptide binding]; other site 423212001008 alphaNTD - beta' interaction site [polypeptide binding]; other site 423212001009 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 423212001010 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 423212001011 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 423212001012 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 423212001013 dimer interface [polypeptide binding]; other site 423212001014 ssDNA binding site [nucleotide binding]; other site 423212001015 tetramer (dimer of dimers) interface [polypeptide binding]; other site 423212001016 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 423212001017 Major Facilitator Superfamily; Region: MFS_1; pfam07690 423212001018 putative substrate translocation pore; other site 423212001019 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08063 423212001020 1-cyclohexenylcarbonyl_coenzyme A_reductase (ChcA)_like, classical (c) SDRs; Region: ChcA_like_SDR_c; cd05359 423212001021 putative NAD(P) binding site [chemical binding]; other site 423212001022 active site 423212001023 Phosphopantetheine attachment site; Region: PP-binding; cl09936 423212001024 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 423212001025 active site 2 [active] 423212001026 active site 1 [active] 423212001027 FabA/Z, beta-hydroxyacyl-acyl carrier protein (ACP)-dehydratases: One of several distinct enzyme types of the dissociative, type II, fatty acid synthase system (found in bacteria and plants) required to complete successive cycles of fatty acid elongation; Region: FabA_FabZ; cd00493 423212001028 active site 2 [active] 423212001029 dimer interface [polypeptide binding]; other site 423212001030 active site 1 [active] 423212001031 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 423212001032 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 423212001033 dimer interface [polypeptide binding]; other site 423212001034 active site 423212001035 3-oxoacyl-(acyl-carrier-protein) synthase [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: FabB; COG0304 423212001036 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 423212001037 dimer interface [polypeptide binding]; other site 423212001038 active site 423212001039 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 423212001040 putative acyl-acceptor binding pocket; other site 423212001041 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 423212001042 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 423212001043 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 423212001044 Prokaryotic lipoprotein-attachment site; Region: LPAM_2; pfam13627 423212001045 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 423212001046 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 423212001047 putative coenzyme Q binding site [chemical binding]; other site 423212001048 hypothetical protein; Validated; Region: PRK01777 423212001049 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 423212001050 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 423212001051 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 423212001052 metal binding site 2 [ion binding]; metal-binding site 423212001053 putative DNA binding helix; other site 423212001054 metal binding site 1 [ion binding]; metal-binding site 423212001055 dimer interface [polypeptide binding]; other site 423212001056 structural Zn2+ binding site [ion binding]; other site 423212001057 choline dehydrogenase; Validated; Region: PRK02106 423212001058 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212001059 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212001060 metal binding site [ion binding]; metal-binding site 423212001061 active site 423212001062 I-site; other site 423212001063 N-formylglutamate amidohydrolase; Region: FGase; pfam05013 423212001064 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 423212001065 RimK-like ATPgrasp N-terminal domain; Region: RLAN; pfam14401 423212001066 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis]; Region: RimK; COG0189 423212001067 ATP-grasp domain; Region: ATP-grasp_4; cl17255 423212001068 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 423212001069 CoenzymeA binding site [chemical binding]; other site 423212001070 subunit interaction site [polypeptide binding]; other site 423212001071 PHB binding site; other site 423212001072 BON domain; Region: BON; pfam04972 423212001073 BON domain; Region: BON; pfam04972 423212001074 Macrophage killing protein with similarity to conjugation protein; Region: IcmL; pfam11393 423212001075 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 423212001076 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 423212001077 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 423212001078 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 423212001079 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 423212001080 heat shock protein HtpX; Provisional; Region: PRK02870 423212001081 inner membrane transport permease; Provisional; Region: PRK15066 423212001082 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 423212001083 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 423212001084 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 423212001085 Walker A/P-loop; other site 423212001086 ATP binding site [chemical binding]; other site 423212001087 Q-loop/lid; other site 423212001088 ABC transporter signature motif; other site 423212001089 Walker B; other site 423212001090 D-loop; other site 423212001091 H-loop/switch region; other site 423212001092 Predicted proline hydroxylase [Posttranslational modification, protein turnover, chaperones]; Region: EGL-9; COG3751 423212001093 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; pfam13640 423212001094 Protein of unknown function DUF45; Region: DUF45; pfam01863 423212001095 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 423212001096 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 423212001097 DNA binding site [nucleotide binding] 423212001098 active site 423212001099 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 423212001100 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 423212001101 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 423212001102 RimM N-terminal domain; Region: RimM; pfam01782 423212001103 PRC-barrel domain; Region: PRC; pfam05239 423212001104 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 423212001105 signal recognition particle protein; Provisional; Region: PRK10867 423212001106 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 423212001107 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 423212001108 P loop; other site 423212001109 GTP binding site [chemical binding]; other site 423212001110 Signal peptide binding domain; Region: SRP_SPB; pfam02978 423212001111 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 423212001112 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 423212001113 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 423212001114 putative glutamate/gamma-aminobutyrate antiporter; Region: put_Glu_GABA_T; TIGR03813 423212001115 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 423212001116 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 423212001117 Protein of unknown function (DUF2909); Region: DUF2909; pfam11137 423212001118 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cd06662 423212001119 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 423212001120 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 423212001121 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 423212001122 UbiA prenyltransferase family; Region: UbiA; pfam01040 423212001123 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 423212001124 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 423212001125 Cu(I) binding site [ion binding]; other site 423212001126 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 423212001127 RimK-like ATP-grasp domain; Region: RimK; pfam08443 423212001128 bifunctional HTH-domain containing protein/aminotransferase; Provisional; Region: PRK13355 423212001129 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 423212001130 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 423212001131 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 423212001132 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 423212001133 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 423212001134 putative active site [active] 423212001135 phosphogluconate dehydratase; Validated; Region: PRK09054 423212001136 6-phosphogluconate dehydratase; Region: edd; TIGR01196 423212001137 Glucokinase; Region: Glucokinase; pfam02685 423212001138 glucokinase, proteobacterial type; Region: glk; TIGR00749 423212001139 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 423212001140 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 423212001141 active site 423212001142 intersubunit interface [polypeptide binding]; other site 423212001143 catalytic residue [active] 423212001144 MFS transporter, sugar porter (SP) family; Region: SP; TIGR00879 423212001145 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 423212001146 putative substrate translocation pore; other site 423212001147 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 423212001148 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 423212001149 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 423212001150 salt bridge; other site 423212001151 non-specific DNA binding site [nucleotide binding]; other site 423212001152 sequence-specific DNA binding site [nucleotide binding]; other site 423212001153 Protein of unknown function (DUF2975); Region: DUF2975; pfam11188 423212001154 ferrochelatase; Reviewed; Region: hemH; PRK00035 423212001155 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 423212001156 C-terminal domain interface [polypeptide binding]; other site 423212001157 active site 423212001158 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 423212001159 active site 423212001160 N-terminal domain interface [polypeptide binding]; other site 423212001161 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 423212001162 DNA-binding site [nucleotide binding]; DNA binding site 423212001163 RNA-binding motif; other site 423212001164 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 423212001165 HIT family signature motif; other site 423212001166 catalytic residue [active] 423212001167 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 423212001168 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 423212001169 active site 423212001170 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 423212001171 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 423212001172 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 423212001173 HlyD family secretion protein; Region: HlyD_3; pfam13437 423212001174 Predicted membrane protein [Function unknown]; Region: COG1289 423212001175 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 423212001176 Predicted transcriptional regulators [Transcription]; Region: COG1733 423212001177 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 423212001178 Uncharacterized conserved protein [Function unknown]; Region: COG4278 423212001179 Methyltransferase domain; Region: Methyltransf_23; pfam13489 423212001180 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 423212001181 S-adenosylmethionine binding site [chemical binding]; other site 423212001182 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 423212001183 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 423212001184 Protein of unknown function (DUF3773); Region: DUF3773; pfam12608 423212001185 Dot/Icm secretion system protein (dot_icm_IcmQ); Region: Dot_icm_IcmQ; pfam09475 423212001186 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 423212001187 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 423212001188 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 423212001189 ligand binding site [chemical binding]; other site 423212001190 Macrophage killing protein with similarity to conjugation protein; Region: IcmL; pfam11393 423212001191 Protein of unknown function (DUF3625); Region: DUF3625; pfam12293 423212001192 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 423212001193 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 423212001194 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 423212001195 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 423212001196 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 423212001197 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 423212001198 HNH nucleases; Region: HNHc; smart00507 423212001199 AAA-like domain; Region: AAA_10; pfam12846 423212001200 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 423212001201 metabolite-proton symporter; Region: 2A0106; TIGR00883 423212001202 putative substrate translocation pore; other site 423212001203 type VI secretion protein IcmF; Region: VI_IcmF; TIGR03348 423212001204 Intracellular multiplication and human macrophage-killing; Region: IcmF-related; pfam06761 423212001205 Protein of unknown function (DUF1215); Region: DUF1215; pfam06744 423212001206 type IV / VI secretion system protein, DotU family; Region: IV_VI_DotU; TIGR03349 423212001207 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 423212001208 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 423212001209 purine monophosphate binding site [chemical binding]; other site 423212001210 dimer interface [polypeptide binding]; other site 423212001211 putative catalytic residues [active] 423212001212 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 423212001213 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 423212001214 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 423212001215 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 423212001216 S-adenosylmethionine binding site [chemical binding]; other site 423212001217 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 423212001218 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 423212001219 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 423212001220 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 423212001221 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 423212001222 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 423212001223 carboxyltransferase (CT) interaction site; other site 423212001224 biotinylation site [posttranslational modification]; other site 423212001225 Dehydroquinase class II; Region: DHquinase_II; pfam01220 423212001226 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 423212001227 trimer interface [polypeptide binding]; other site 423212001228 active site 423212001229 dimer interface [polypeptide binding]; other site 423212001230 pyruvate carboxylase subunit B; Provisional; Region: PRK14042 423212001231 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 423212001232 active site 423212001233 catalytic residues [active] 423212001234 metal binding site [ion binding]; metal-binding site 423212001235 homodimer binding site [polypeptide binding]; other site 423212001236 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 423212001237 carboxyltransferase (CT) interaction site; other site 423212001238 biotinylation site [posttranslational modification]; other site 423212001239 Zinc metalloprotease (elastase) [Amino acid transport and metabolism]; Region: LasB; COG3227 423212001240 Fungalysin/Thermolysin Propeptide Motif; Region: FTP; pfam07504 423212001241 Peptidase M4 family includes thermolysin, protealysin, aureolysin and neutral protease; Region: M4_neutral_protease; cd09597 423212001242 active site 423212001243 Zn binding site [ion binding]; other site 423212001244 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 423212001245 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 423212001246 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 423212001247 putative catalytic site [active] 423212001248 putative metal binding site [ion binding]; other site 423212001249 putative phosphate binding site [ion binding]; other site 423212001250 Fructose-1,6-bisphosphate aldolase; Region: FBP_aldolase_I_a; cd00948 423212001251 active site 423212001252 intersubunit interface [polypeptide binding]; other site 423212001253 catalytic residue [active] 423212001254 Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently...; Region: FNR1; cd06195 423212001255 ferredoxin-NADP reductase; Provisional; Region: PRK10926 423212001256 FAD binding pocket [chemical binding]; other site 423212001257 FAD binding motif [chemical binding]; other site 423212001258 phosphate binding motif [ion binding]; other site 423212001259 beta-alpha-beta structure motif; other site 423212001260 NAD binding pocket [chemical binding]; other site 423212001261 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 423212001262 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 423212001263 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 423212001264 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 423212001265 dimerization domain swap beta strand [polypeptide binding]; other site 423212001266 regulatory protein interface [polypeptide binding]; other site 423212001267 active site 423212001268 regulatory phosphorylation site [posttranslational modification]; other site 423212001269 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 423212001270 30S subunit binding site; other site 423212001271 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 423212001272 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 423212001273 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 423212001274 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 423212001275 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 423212001276 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 423212001277 tRNA (guanine-N(7)-)-methyltransferase; Reviewed; Region: trmB; PRK00121 423212001278 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 423212001279 M42 Peptidase, Endoglucanases; Region: M42_Frv; cd05656 423212001280 oligomer interface [polypeptide binding]; other site 423212001281 active site 423212001282 metal binding site [ion binding]; metal-binding site 423212001283 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 423212001284 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 423212001285 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 423212001286 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 423212001287 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 423212001288 HflK protein; Region: hflK; TIGR01933 423212001289 FtsH protease regulator HflC; Provisional; Region: PRK11029 423212001290 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 423212001291 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 423212001292 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 423212001293 GDP-binding site [chemical binding]; other site 423212001294 ACT binding site; other site 423212001295 IMP binding site; other site 423212001296 Predicted metal-dependent enzyme of the double-stranded beta helix superfamily [General function prediction only]; Region: COG5553 423212001297 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 423212001298 Arginine repressor [Transcription]; Region: ArgR; COG1438 423212001299 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 423212001300 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 423212001301 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 423212001302 substrate binding pocket [chemical binding]; other site 423212001303 membrane-bound complex binding site; other site 423212001304 hinge residues; other site 423212001305 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 423212001306 dimer interface [polypeptide binding]; other site 423212001307 conserved gate region; other site 423212001308 putative PBP binding loops; other site 423212001309 ABC-ATPase subunit interface; other site 423212001310 glutamine ABC transporter ATP-binding protein; Reviewed; Region: glnQ; PRK09493 423212001311 ATP-binding cassette domain of the binding protein-dependent transport systems; Region: ABC_Class3; cd03229 423212001312 Walker A/P-loop; other site 423212001313 ATP binding site [chemical binding]; other site 423212001314 Q-loop/lid; other site 423212001315 ABC transporter signature motif; other site 423212001316 Walker B; other site 423212001317 D-loop; other site 423212001318 H-loop/switch region; other site 423212001319 argininosuccinate synthase; Provisional; Region: PRK13820 423212001320 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 423212001321 ANP binding site [chemical binding]; other site 423212001322 Substrate Binding Site II [chemical binding]; other site 423212001323 Substrate Binding Site I [chemical binding]; other site 423212001324 Lyase; Region: Lyase_1; pfam00206 423212001325 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 423212001326 active sites [active] 423212001327 tetramer interface [polypeptide binding]; other site 423212001328 ornithine carbamoyltransferase; Provisional; Region: PRK00779 423212001329 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 423212001330 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 423212001331 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 423212001332 active site 423212001333 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 423212001334 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 423212001335 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 423212001336 C-terminal peptidase (prc); Region: prc; TIGR00225 423212001337 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 423212001338 protein binding site [polypeptide binding]; other site 423212001339 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 423212001340 Catalytic dyad [active] 423212001341 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 423212001342 TATA element modulatory factor 1 TATA binding; Region: TMF_TATA_bd; pfam12325 423212001343 Peptidase family M23; Region: Peptidase_M23; pfam01551 423212001344 phosphoglyceromutase; Provisional; Region: PRK05434 423212001345 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 423212001346 undecaprenyl pyrophosphate synthase; Provisional; Region: PRK14836 423212001347 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 423212001348 catalytic residue [active] 423212001349 putative FPP diphosphate binding site; other site 423212001350 putative FPP binding hydrophobic cleft; other site 423212001351 dimer interface [polypeptide binding]; other site 423212001352 putative IPP diphosphate binding site; other site 423212001353 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 423212001354 CDP-diglyceride synthase; Provisional; Region: cdsA; PRK11624 423212001355 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 423212001356 zinc metallopeptidase RseP; Provisional; Region: PRK10779 423212001357 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 423212001358 protein binding site [polypeptide binding]; other site 423212001359 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 423212001360 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 423212001361 putative substrate binding region [chemical binding]; other site 423212001362 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 423212001363 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 423212001364 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 423212001365 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 423212001366 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 423212001367 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 423212001368 Surface antigen; Region: Bac_surface_Ag; pfam01103 423212001369 periplasmic chaperone; Provisional; Region: PRK10780 423212001370 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 423212001371 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 423212001372 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 423212001373 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 423212001374 trimer interface [polypeptide binding]; other site 423212001375 active site 423212001376 UDP-GlcNAc binding site [chemical binding]; other site 423212001377 lipid binding site [chemical binding]; lipid-binding site 423212001378 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 423212001379 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK12461 423212001380 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 423212001381 active site 423212001382 camphor resistance protein CrcB; Provisional; Region: PRK14217 423212001383 seryl-tRNA synthetase; Provisional; Region: PRK05431 423212001384 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 423212001385 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 423212001386 dimer interface [polypeptide binding]; other site 423212001387 active site 423212001388 motif 1; other site 423212001389 motif 2; other site 423212001390 motif 3; other site 423212001391 Uncharacterized protein family (UPF0157); Region: UPF0157; cl00987 423212001392 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; pfam05721 423212001393 Methyltransferase domain; Region: Methyltransf_23; pfam13489 423212001394 Methyltransferase domain; Region: Methyltransf_12; pfam08242 423212001395 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 423212001396 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 423212001397 active site 423212001398 catalytic tetrad [active] 423212001399 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 423212001400 S-adenosylmethionine binding site [chemical binding]; other site 423212001401 Methyltransferase domain; Region: Methyltransf_23; pfam13489 423212001402 hypothetical protein; Provisional; Region: PRK08233 423212001403 AAA domain; Region: AAA_18; pfam13238 423212001404 active site 423212001405 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 423212001406 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 423212001407 Coenzyme A binding pocket [chemical binding]; other site 423212001408 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 423212001409 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 423212001410 Siderophore biosynthesis protein domain; Region: AlcB; smart01006 423212001411 Abi-like protein; Region: Abi_2; pfam07751 423212001412 Domain of unknown function (DUF4102); Region: DUF4102; pfam13356 423212001413 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 423212001414 active site 423212001415 DNA binding site [nucleotide binding] 423212001416 Int/Topo IB signature motif; other site 423212001417 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 423212001418 non-specific DNA binding site [nucleotide binding]; other site 423212001419 Predicted transcriptional regulator [Transcription]; Region: COG2932 423212001420 salt bridge; other site 423212001421 sequence-specific DNA binding site [nucleotide binding]; other site 423212001422 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 423212001423 Catalytic site [active] 423212001424 Global regulator protein family; Region: CsrA; pfam02599 423212001425 conjugal transfer ATPase TrbB; Provisional; Region: PRK13894 423212001426 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 423212001427 ATP binding site [chemical binding]; other site 423212001428 Walker A motif; other site 423212001429 hexamer interface [polypeptide binding]; other site 423212001430 Walker B motif; other site 423212001431 TrbC/VIRB2 family; Region: TrbC; cl01583 423212001432 conjugal transfer protein TrbD; Provisional; Region: PRK13823 423212001433 conjugal transfer protein TrbE; Provisional; Region: PRK13891 423212001434 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 423212001435 conjugal transfer protein TrbF; Provisional; Region: PRK13887 423212001436 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 423212001437 VirB7 interaction site; other site 423212001438 conjugal transfer protein TrbH; Provisional; Region: PRK13883 423212001439 Conjugal transfer protein TrbH; Region: TrbH; pfam07283 423212001440 conjugal transfer protein TrbI; Provisional; Region: PRK13881 423212001441 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 423212001442 conjugal transfer protein TrbJ; Provisional; Region: PRK13879 423212001443 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 423212001444 conjugal transfer coupling protein TraG; Provisional; Region: PRK13880 423212001445 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 423212001446 Walker A motif; other site 423212001447 ATP binding site [chemical binding]; other site 423212001448 Walker B motif; other site 423212001449 conjugal transfer peptidase TraF; Provisional; Region: PRK13884 423212001450 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 423212001451 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 423212001452 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 423212001453 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4643 423212001454 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 423212001455 active site 423212001456 metal binding site [ion binding]; metal-binding site 423212001457 interdomain interaction site; other site 423212001458 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cd02883 423212001459 nudix motif; other site 423212001460 conjugal transfer relaxase TraI; Provisional; Region: PRK13878 423212001461 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 423212001462 conjugal transfer relaxosome component TraJ; Provisional; Region: PRK13877 423212001463 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 423212001464 P-loop; other site 423212001465 conjugal transfer protein TraM; Provisional; Region: PRK13895 423212001466 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 423212001467 HsdM N-terminal domain; Region: HsdM_N; pfam12161 423212001468 Methyltransferase domain; Region: Methyltransf_26; pfam13659 423212001469 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 423212001470 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 423212001471 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 423212001472 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 423212001473 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 423212001474 ATP binding site [chemical binding]; other site 423212001475 putative Mg++ binding site [ion binding]; other site 423212001476 FRG domain; Region: FRG; cl07460 423212001477 FRG domain; Region: FRG; cl07460 423212001478 RecB family nuclease, putative, TM0106 family; Region: TIGR03491 423212001479 RNase_H superfamily; Region: RNase_H_2; pfam13482 423212001480 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 423212001481 AAA domain; Region: AAA_11; pfam13086 423212001482 Walker A motif; other site 423212001483 ATP binding site [chemical binding]; other site 423212001484 AAA domain; Region: AAA_12; pfam13087 423212001485 Autoinducer binding domain; Region: Autoind_bind; pfam03472 423212001486 metabolite-proton symporter; Region: 2A0106; TIGR00883 423212001487 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 423212001488 putative substrate translocation pore; other site 423212001489 Domain of unknown function (DUF4286); Region: DUF4286; pfam14114 423212001490 Helix-turn-helix domain; Region: HTH_17; pfam12728 423212001491 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; cl15777 423212001492 RDD family; Region: RDD; cl00746 423212001493 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 423212001494 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the...; Region: SQR_TypeC_SdhC; cd03499 423212001495 Iron-sulfur protein interface; other site 423212001496 proximal quinone binding site [chemical binding]; other site 423212001497 SdhD (CybS) interface [polypeptide binding]; other site 423212001498 proximal heme binding site [chemical binding]; other site 423212001499 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. E. coli SQR, a member of this subfamily, reduces the...; Region: SQR_TypeC_SdhD; cd03494 423212001500 SdhC subunit interface [polypeptide binding]; other site 423212001501 proximal heme binding site [chemical binding]; other site 423212001502 cardiolipin binding site; other site 423212001503 Iron-sulfur protein interface; other site 423212001504 proximal quinone binding site [chemical binding]; other site 423212001505 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK08958 423212001506 L-aspartate oxidase; Provisional; Region: PRK06175 423212001507 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 423212001508 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 423212001509 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 423212001510 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 423212001511 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 423212001512 TPP-binding site [chemical binding]; other site 423212001513 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 423212001514 dimer interface [polypeptide binding]; other site 423212001515 PYR/PP interface [polypeptide binding]; other site 423212001516 TPP binding site [chemical binding]; other site 423212001517 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 423212001518 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 423212001519 E3 interaction surface; other site 423212001520 lipoyl attachment site [posttranslational modification]; other site 423212001521 e3 binding domain; Region: E3_binding; pfam02817 423212001522 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 423212001523 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 423212001524 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 423212001525 CoA-ligase; Region: Ligase_CoA; pfam00549 423212001526 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 423212001527 CoA binding domain; Region: CoA_binding; smart00881 423212001528 CoA-ligase; Region: Ligase_CoA; pfam00549 423212001529 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 423212001530 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 423212001531 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 423212001532 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 423212001533 D-galactonate transporter; Region: 2A0114; TIGR00893 423212001534 putative substrate translocation pore; other site 423212001535 Bacterial protein of unknown function (DUF945); Region: DUF945; pfam06097 423212001536 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5339 423212001537 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 423212001538 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 423212001539 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 423212001540 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 423212001541 active site 423212001542 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 423212001543 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 423212001544 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 423212001545 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 423212001546 active site 423212001547 (T/H)XGH motif; other site 423212001548 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 423212001549 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 423212001550 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 423212001551 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 423212001552 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 423212001553 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 423212001554 ligand binding site [chemical binding]; other site 423212001555 1-acyl-sn-glycerol-3-phosphate acyltransferase; Provisional; Region: PRK15018 423212001556 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 423212001557 putative acyl-acceptor binding pocket; other site 423212001558 multidrug efflux system protein; Provisional; Region: PRK11431 423212001559 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 423212001560 Phosphotransferase enzyme family; Region: APH; pfam01636 423212001561 substrate binding site [chemical binding]; other site 423212001562 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 423212001563 active site 423212001564 DNA polymerase IV; Validated; Region: PRK02406 423212001565 DNA binding site [nucleotide binding] 423212001566 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 423212001567 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 423212001568 DNA binding site [nucleotide binding] 423212001569 catalytic residue [active] 423212001570 H2TH interface [polypeptide binding]; other site 423212001571 putative catalytic residues [active] 423212001572 turnover-facilitating residue; other site 423212001573 intercalation triad [nucleotide binding]; other site 423212001574 8OG recognition residue [nucleotide binding]; other site 423212001575 putative reading head residues; other site 423212001576 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 423212001577 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 423212001578 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 423212001579 Fatty acid desaturase; Region: FA_desaturase; pfam00487 423212001580 Di-iron ligands [ion binding]; other site 423212001581 Transposase; Region: DDE_Tnp_ISL3; pfam01610 423212001582 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 423212001583 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 423212001584 NAD(P) binding site [chemical binding]; other site 423212001585 active site 423212001586 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 423212001587 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 423212001588 NAD(P) binding site [chemical binding]; other site 423212001589 active site 423212001590 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 423212001591 Phasin protein; Region: Phasin_2; cl11491 423212001592 Protein of unknown function (DUF1460); Region: DUF1460; pfam07313 423212001593 Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]; Region: SpmA; COG2715 423212001594 Uncharacterized membrane protein [Function unknown]; Region: SpmB; COG0700 423212001595 putative peptidase; Provisional; Region: PRK11649 423212001596 Peptidase family M23; Region: Peptidase_M23; pfam01551 423212001597 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 423212001598 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 423212001599 active site 423212001600 HIGH motif; other site 423212001601 dimer interface [polypeptide binding]; other site 423212001602 KMSKS motif; other site 423212001603 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 423212001604 RNA binding surface [nucleotide binding]; other site 423212001605 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 423212001606 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 423212001607 hinge; other site 423212001608 active site 423212001609 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 423212001610 Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon...; Region: LbH_gamma_CA_like; cd04645 423212001611 trimer interface [polypeptide binding]; other site 423212001612 putative metal binding site [ion binding]; other site 423212001613 glutathione reductase; Validated; Region: PRK06116 423212001614 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 423212001615 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 423212001616 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 423212001617 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 423212001618 adenosine deaminase; Provisional; Region: PRK09358 423212001619 active site 423212001620 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 423212001621 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 423212001622 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 423212001623 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 423212001624 hypothetical protein; Validated; Region: PRK00228 423212001625 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 423212001626 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 423212001627 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 423212001628 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 423212001629 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 423212001630 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 423212001631 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 423212001632 Walker A motif; other site 423212001633 ATP binding site [chemical binding]; other site 423212001634 Walker B motif; other site 423212001635 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 423212001636 Membrane fusogenic activity; Region: BMFP; pfam04380 423212001637 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 423212001638 Nitrogen regulatory protein P-II; Region: P-II; smart00938 423212001639 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 423212001640 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 423212001641 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 423212001642 ADCL_like: 4-Amino-4-deoxychorismate lyase: is a member of the fold-type IV of PLP dependent enzymes that converts 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate and pyruvate. Based on the information available from the crystal structure, most...; Region: ADCL_like; cd01559 423212001643 pyridoxal 5'-phosphate binding site [chemical binding]; other site 423212001644 catalytic residue [active] 423212001645 Uncharacterized conserved protein [Function unknown]; Region: COG0398 423212001646 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 423212001647 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 423212001648 putative acyl-acceptor binding pocket; other site 423212001649 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 423212001650 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 423212001651 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 423212001652 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 423212001653 acyl-activating enzyme (AAE) consensus motif; other site 423212001654 AMP binding site [chemical binding]; other site 423212001655 active site 423212001656 CoA binding site [chemical binding]; other site 423212001657 Protein of unknown function (DUF1499); Region: DUF1499; pfam07386 423212001658 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 423212001659 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 423212001660 Transcriptional regulator; Region: Rrf2; pfam02082 423212001661 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814 423212001662 putative ABC transporter; Region: ycf24; CHL00085 423212001663 FeS assembly ATPase SufC; Region: sufC; TIGR01978 423212001664 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 423212001665 Walker A/P-loop; other site 423212001666 ATP binding site [chemical binding]; other site 423212001667 Q-loop/lid; other site 423212001668 ABC transporter signature motif; other site 423212001669 Walker B; other site 423212001670 D-loop; other site 423212001671 H-loop/switch region; other site 423212001672 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814; cl03223 423212001673 FeS assembly protein SufD; Region: sufD; TIGR01981 423212001674 Uncharacterized protein family (UPF0051); Region: UPF0051; pfam01458 423212001675 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 423212001676 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 423212001677 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 423212001678 catalytic residue [active] 423212001679 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 423212001680 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 423212001681 trimerization site [polypeptide binding]; other site 423212001682 active site 423212001683 FeS assembly SUF system protein; Region: SUF_assoc; TIGR02945 423212001684 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 423212001685 EF-P lysine aminoacylase GenX; Region: genX; TIGR00462 423212001686 motif 1; other site 423212001687 dimer interface [polypeptide binding]; other site 423212001688 active site 423212001689 motif 2; other site 423212001690 motif 3; other site 423212001691 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 423212001692 S-adenosylmethionine binding site [chemical binding]; other site 423212001693 Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]; Region: COG2872 423212001694 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 423212001695 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 423212001696 putative substrate translocation pore; other site 423212001697 Major Facilitator Superfamily; Region: MFS_1; pfam07690 423212001698 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 423212001699 Domain of unknown function DUF21; Region: DUF21; pfam01595 423212001700 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 423212001701 Transporter associated domain; Region: CorC_HlyC; smart01091 423212001702 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 423212001703 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 423212001704 putative NAD(P) binding site [chemical binding]; other site 423212001705 putative substrate binding site [chemical binding]; other site 423212001706 catalytic Zn binding site [ion binding]; other site 423212001707 structural Zn binding site [ion binding]; other site 423212001708 dimer interface [polypeptide binding]; other site 423212001709 Domain of unknown function (DUF4332); Region: DUF4332; pfam14229 423212001710 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 423212001711 active site 423212001712 catalytic residues [active] 423212001713 metal binding site [ion binding]; metal-binding site 423212001714 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 423212001715 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 423212001716 gamma-glutamyl:cysteine ligase; Provisional; Region: PRK13516 423212001717 carboxylate-amine ligase, YbdK family; Region: gshA_cyan_rel; TIGR02050 423212001718 CoA binding domain; Region: CoA_binding_2; pfam13380 423212001719 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 423212001720 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 423212001721 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 423212001722 Legionella pneumophila major outer membrane protein precursor; Region: Legionella_OMP; pfam05150 423212001723 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 423212001724 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 423212001725 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 423212001726 Protein of unknown function (DUF1810); Region: DUF1810; cl02370 423212001727 Cupin domain; Region: Cupin_2; cl17218 423212001728 StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been...; Region: StaR_like; cd05804 423212001729 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 423212001730 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 423212001731 Competence protein; Region: Competence; pfam03772 423212001732 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 423212001733 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 423212001734 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 423212001735 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 423212001736 Tfp pilus assembly protein PilX [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilX; COG4726 423212001737 PilX N-terminal; Region: PilX_N; pfam14341 423212001738 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 423212001739 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 423212001740 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 423212001741 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 423212001742 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 423212001743 Type II transport protein GspH; Region: GspH; pfam12019 423212001744 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 423212001745 Catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases; Region: CE4_NodB_like_1; cd10960 423212001746 NodB motif; other site 423212001747 putative active site [active] 423212001748 putative catalytic site [active] 423212001749 putative Zn binding site [ion binding]; other site 423212001750 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 423212001751 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 423212001752 thymidine kinase; Provisional; Region: PRK04296 423212001753 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 423212001754 Major Facilitator Superfamily; Region: MFS_1; pfam07690 423212001755 putative substrate translocation pore; other site 423212001756 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 423212001757 putative substrate translocation pore; other site 423212001758 D-galactonate transporter; Region: 2A0114; TIGR00893 423212001759 phosphopentomutase; Provisional; Region: PRK05362 423212001760 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 423212001761 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 423212001762 active site 423212001763 HslU subunit interaction site [polypeptide binding]; other site 423212001764 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 423212001765 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 423212001766 Walker A motif; other site 423212001767 ATP binding site [chemical binding]; other site 423212001768 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 423212001769 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 423212001770 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 423212001771 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 423212001772 metal ion-dependent adhesion site (MIDAS); other site 423212001773 type I secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 423212001774 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 423212001775 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 423212001776 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 423212001777 putative active site [active] 423212001778 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 423212001779 putative active site [active] 423212001780 putative catalytic site [active] 423212001781 putative DNA binding site [nucleotide binding]; other site 423212001782 putative phosphate binding site [ion binding]; other site 423212001783 metal binding site A [ion binding]; metal-binding site 423212001784 putative AP binding site [nucleotide binding]; other site 423212001785 putative metal binding site B [ion binding]; other site 423212001786 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 423212001787 putative catalytic site [active] 423212001788 putative phosphate binding site [ion binding]; other site 423212001789 active site 423212001790 metal binding site A [ion binding]; metal-binding site 423212001791 DNA binding site [nucleotide binding] 423212001792 putative AP binding site [nucleotide binding]; other site 423212001793 putative metal binding site B [ion binding]; other site 423212001794 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 423212001795 Malic enzyme, N-terminal domain; Region: malic; pfam00390 423212001796 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 423212001797 putative NAD(P) binding site [chemical binding]; other site 423212001798 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 423212001799 Major Facilitator Superfamily; Region: MFS_1; pfam07690 423212001800 putative substrate translocation pore; other site 423212001801 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 423212001802 putative substrate translocation pore; other site 423212001803 Major Facilitator Superfamily; Region: MFS_1; pfam07690 423212001804 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 423212001805 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 423212001806 aromatic amino acid transport protein; Region: araaP; TIGR00837 423212001807 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 423212001808 aromatic amino acid transport protein; Region: araaP; TIGR00837 423212001809 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 423212001810 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 423212001811 ligand binding site [chemical binding]; other site 423212001812 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39A; cd02549 423212001813 putative active site [active] 423212001814 N-acetylmuramoyl-L-alanine amidase; Region: Amidase_2; pfam01510 423212001815 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 423212001816 ABC exporter membrane fusion protein, DevB family; Region: heterocyst_DevB; TIGR02971 423212001817 HlyD family secretion protein; Region: HlyD_3; pfam13437 423212001818 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 423212001819 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 423212001820 Walker A/P-loop; other site 423212001821 ATP binding site [chemical binding]; other site 423212001822 Q-loop/lid; other site 423212001823 ABC transporter signature motif; other site 423212001824 Walker B; other site 423212001825 D-loop; other site 423212001826 H-loop/switch region; other site 423212001827 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 423212001828 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 423212001829 Walker A/P-loop; other site 423212001830 ATP binding site [chemical binding]; other site 423212001831 Q-loop/lid; other site 423212001832 ABC transporter signature motif; other site 423212001833 Walker B; other site 423212001834 D-loop; other site 423212001835 H-loop/switch region; other site 423212001836 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 423212001837 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 423212001838 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 423212001839 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 423212001840 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 423212001841 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 423212001842 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 423212001843 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 423212001844 N-acetyl-D-glucosamine binding site [chemical binding]; other site 423212001845 catalytic residue [active] 423212001846 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 423212001847 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 423212001848 substrate binding site [chemical binding]; other site 423212001849 hexamer interface [polypeptide binding]; other site 423212001850 metal binding site [ion binding]; metal-binding site 423212001851 DoxX; Region: DoxX; pfam07681 423212001852 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 423212001853 hypothetical protein; Provisional; Region: PRK05409 423212001854 Predicted integral membrane protein (DUF2282); Region: DUF2282; pfam10048 423212001855 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 423212001856 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 423212001857 nucleophile elbow; other site 423212001858 DoxX; Region: DoxX; pfam07681 423212001859 Predicted membrane protein [Function unknown]; Region: COG2259 423212001860 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 423212001861 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 423212001862 acetoacetate decarboxylase; Provisional; Region: PRK02265 423212001863 Predicted integral membrane protein (DUF2282); Region: DUF2282; pfam10048 423212001864 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 423212001865 cyclase homology domain; Region: CHD; cd07302 423212001866 nucleotidyl binding site; other site 423212001867 metal binding site [ion binding]; metal-binding site 423212001868 dimer interface [polypeptide binding]; other site 423212001869 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; pfam09836 423212001870 hypothetical protein; Provisional; Region: PRK05409 423212001871 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 423212001872 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 423212001873 substrate binding pocket [chemical binding]; other site 423212001874 membrane-bound complex binding site; other site 423212001875 hinge residues; other site 423212001876 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 423212001877 metal binding triad; other site 423212001878 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 423212001879 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 423212001880 metal binding triad; other site 423212001881 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 423212001882 HlyD family secretion protein; Region: HlyD_3; pfam13437 423212001883 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 423212001884 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 423212001885 Walker A/P-loop; other site 423212001886 ATP binding site [chemical binding]; other site 423212001887 Q-loop/lid; other site 423212001888 ABC transporter signature motif; other site 423212001889 Walker B; other site 423212001890 D-loop; other site 423212001891 H-loop/switch region; other site 423212001892 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 423212001893 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 423212001894 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 423212001895 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 423212001896 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 423212001897 FeS/SAM binding site; other site 423212001898 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 423212001899 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 423212001900 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 423212001901 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 423212001902 DsbD alpha interface [polypeptide binding]; other site 423212001903 catalytic residues [active] 423212001904 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 423212001905 oligomerisation interface [polypeptide binding]; other site 423212001906 mobile loop; other site 423212001907 roof hairpin; other site 423212001908 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 423212001909 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 423212001910 ring oligomerisation interface [polypeptide binding]; other site 423212001911 ATP/Mg binding site [chemical binding]; other site 423212001912 stacking interactions; other site 423212001913 hinge regions; other site 423212001914 Ferritin-like domain; Region: Ferritin; pfam00210 423212001915 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 423212001916 dimerization interface [polypeptide binding]; other site 423212001917 DPS ferroxidase diiron center [ion binding]; other site 423212001918 ion pore; other site 423212001919 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 423212001920 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 423212001921 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 423212001922 Mg2+ binding site [ion binding]; other site 423212001923 G-X-G motif; other site 423212001924 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 423212001925 anchoring element; other site 423212001926 dimer interface [polypeptide binding]; other site 423212001927 ATP binding site [chemical binding]; other site 423212001928 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 423212001929 active site 423212001930 metal binding site [ion binding]; metal-binding site 423212001931 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 423212001932 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 423212001933 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 423212001934 Walker A/P-loop; other site 423212001935 ATP binding site [chemical binding]; other site 423212001936 Q-loop/lid; other site 423212001937 ABC transporter signature motif; other site 423212001938 Walker B; other site 423212001939 D-loop; other site 423212001940 H-loop/switch region; other site 423212001941 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 423212001942 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 423212001943 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 423212001944 Walker A/P-loop; other site 423212001945 ATP binding site [chemical binding]; other site 423212001946 Q-loop/lid; other site 423212001947 ABC transporter signature motif; other site 423212001948 Walker B; other site 423212001949 D-loop; other site 423212001950 H-loop/switch region; other site 423212001951 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 423212001952 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 423212001953 prolyl-tRNA synthetase; Provisional; Region: PRK09194 423212001954 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 423212001955 dimer interface [polypeptide binding]; other site 423212001956 motif 1; other site 423212001957 active site 423212001958 motif 2; other site 423212001959 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 423212001960 putative deacylase active site [active] 423212001961 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 423212001962 active site 423212001963 motif 3; other site 423212001964 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 423212001965 anticodon binding site; other site 423212001966 FOG: Ankyrin repeat [General function prediction only]; Region: Arp; COG0666 423212001967 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 423212001968 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 423212001969 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 423212001970 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 423212001971 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 423212001972 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 423212001973 Sulfate transporter family; Region: Sulfate_transp; pfam00916 423212001974 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 423212001975 active site clefts [active] 423212001976 zinc binding site [ion binding]; other site 423212001977 dimer interface [polypeptide binding]; other site 423212001978 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 423212001979 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 423212001980 Ligand Binding Site [chemical binding]; other site 423212001981 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 423212001982 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 423212001983 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 423212001984 S-adenosylmethionine binding site [chemical binding]; other site 423212001985 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 423212001986 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 423212001987 substrate-cofactor binding pocket; other site 423212001988 pyridoxal 5'-phosphate binding site [chemical binding]; other site 423212001989 catalytic residue [active] 423212001990 L-threonine 3-dehydrogenase; Validated; Region: tdh; PRK05396 423212001991 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 423212001992 NAD(P) binding site [chemical binding]; other site 423212001993 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 423212001994 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 423212001995 Walker A/P-loop; other site 423212001996 ATP binding site [chemical binding]; other site 423212001997 Q-loop/lid; other site 423212001998 ABC transporter signature motif; other site 423212001999 Walker B; other site 423212002000 D-loop; other site 423212002001 H-loop/switch region; other site 423212002002 ABC transporter; Region: ABC_tran_2; pfam12848 423212002003 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 423212002004 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 423212002005 Domain of unknown function (DUF4341); Region: DUF4341; pfam14241 423212002006 Predicted transporter component [General function prediction only]; Region: COG2391 423212002007 Sulphur transport; Region: Sulf_transp; pfam04143 423212002008 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 423212002009 Macrophage killing protein with similarity to conjugation protein; Region: IcmL; pfam11393 423212002010 formimidoylglutamase; Provisional; Region: PRK13775 423212002011 Formimidoylglutamase or HutE; Region: Formimidoylglutamase; cd09988 423212002012 putative active site [active] 423212002013 putative metal binding site [ion binding]; other site 423212002014 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 423212002015 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 423212002016 NAD(P) binding site [chemical binding]; other site 423212002017 active site 423212002018 imidazolonepropionase; Validated; Region: PRK09356 423212002019 Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria; Region: Imidazolone-5PH; cd01296 423212002020 active site 423212002021 Domain of unknown function (DUF4163); Region: DUF4163; pfam13739 423212002022 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 423212002023 Predicted membrane protein [Function unknown]; Region: COG1297 423212002024 putative oligopeptide transporter, OPT family; Region: TIGR00733 423212002025 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 423212002026 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 423212002027 dimer interface [polypeptide binding]; other site 423212002028 phosphorylation site [posttranslational modification] 423212002029 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 423212002030 ATP binding site [chemical binding]; other site 423212002031 Mg2+ binding site [ion binding]; other site 423212002032 G-X-G motif; other site 423212002033 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 423212002034 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 423212002035 active site 423212002036 phosphorylation site [posttranslational modification] 423212002037 intermolecular recognition site; other site 423212002038 dimerization interface [polypeptide binding]; other site 423212002039 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 423212002040 DNA binding site [nucleotide binding] 423212002041 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 423212002042 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 423212002043 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 423212002044 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 423212002045 HIGH motif; other site 423212002046 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 423212002047 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 423212002048 active site 423212002049 KMSKS motif; other site 423212002050 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 423212002051 tRNA binding surface [nucleotide binding]; other site 423212002052 anticodon binding site; other site 423212002053 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 423212002054 multidrug efflux protein; Reviewed; Region: PRK09579 423212002055 TcdA/TcdB pore forming domain; Region: TcdA_TcdB_pore; pfam12920 423212002056 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 423212002057 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 423212002058 HlyD family secretion protein; Region: HlyD_3; pfam13437 423212002059 BON domain; Region: BON; pfam04972 423212002060 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 423212002061 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 423212002062 dimer interface [polypeptide binding]; other site 423212002063 active site 423212002064 glycine-pyridoxal phosphate binding site [chemical binding]; other site 423212002065 folate binding site [chemical binding]; other site 423212002066 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 423212002067 ATP cone domain; Region: ATP-cone; pfam03477 423212002068 transcription antitermination factor NusB; Region: nusB; TIGR01951 423212002069 putative RNA binding site [nucleotide binding]; other site 423212002070 thiamine monophosphate kinase; Provisional; Region: PRK05731 423212002071 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 423212002072 ATP binding site [chemical binding]; other site 423212002073 dimerization interface [polypeptide binding]; other site 423212002074 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 423212002075 tetramer interfaces [polypeptide binding]; other site 423212002076 binuclear metal-binding site [ion binding]; other site 423212002077 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 423212002078 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 423212002079 NAD synthetase; Provisional; Region: PRK13981 423212002080 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 423212002081 multimer interface [polypeptide binding]; other site 423212002082 active site 423212002083 catalytic triad [active] 423212002084 protein interface 1 [polypeptide binding]; other site 423212002085 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 423212002086 homodimer interface [polypeptide binding]; other site 423212002087 NAD binding pocket [chemical binding]; other site 423212002088 ATP binding pocket [chemical binding]; other site 423212002089 Mg binding site [ion binding]; other site 423212002090 active-site loop [active] 423212002091 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 423212002092 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 423212002093 ATP binding site [chemical binding]; other site 423212002094 putative Mg++ binding site [ion binding]; other site 423212002095 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 423212002096 nucleotide binding region [chemical binding]; other site 423212002097 ATP-binding site [chemical binding]; other site 423212002098 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 423212002099 replicative DNA helicase; Region: DnaB; TIGR00665 423212002100 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 423212002101 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 423212002102 Walker A motif; other site 423212002103 ATP binding site [chemical binding]; other site 423212002104 Walker B motif; other site 423212002105 DNA binding loops [nucleotide binding] 423212002106 alanine racemase; Reviewed; Region: alr; PRK00053 423212002107 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 423212002108 active site 423212002109 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 423212002110 substrate binding site [chemical binding]; other site 423212002111 catalytic residues [active] 423212002112 dimer interface [polypeptide binding]; other site 423212002113 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 423212002114 FOG: CBS domain [General function prediction only]; Region: COG0517 423212002115 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_10; cd04623 423212002116 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 423212002117 Iron-binding zinc finger CDGSH type; Region: zf-CDGSH; pfam09360 423212002118 Iron-binding zinc finger CDGSH type; Region: zf-CDGSH; pfam09360 423212002119 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212002120 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212002121 metal binding site [ion binding]; metal-binding site 423212002122 active site 423212002123 I-site; other site 423212002124 lipoyl synthase; Provisional; Region: PRK05481 423212002125 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 423212002126 FeS/SAM binding site; other site 423212002127 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 423212002128 GIY-YIG motif/motif A; other site 423212002129 putative active site [active] 423212002130 putative metal binding site [ion binding]; other site 423212002131 POT family; Region: PTR2; cl17359 423212002132 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 423212002133 Methyltransferase domain; Region: Methyltransf_11; pfam08241 423212002134 S-adenosylmethionine binding site [chemical binding]; other site 423212002135 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_III; cd01996 423212002136 Ligand Binding Site [chemical binding]; other site 423212002137 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 423212002138 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 423212002139 substrate binding site [chemical binding]; other site 423212002140 glutamase interaction surface [polypeptide binding]; other site 423212002141 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 423212002142 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 423212002143 putative active site [active] 423212002144 oxyanion strand; other site 423212002145 catalytic triad [active] 423212002146 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 423212002147 ligand binding site; other site 423212002148 tetramer interface; other site 423212002149 N-acetylneuraminate synthase; Region: NeuB_NnaB; TIGR03569 423212002150 NeuB family; Region: NeuB; pfam03102 423212002151 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 423212002152 NeuB binding interface [polypeptide binding]; other site 423212002153 putative substrate binding site [chemical binding]; other site 423212002154 UDP-N-acetyl-D-glucosamine 2-epimerase, UDP-hydrolysing; Region: NeuC_NnaA; TIGR03568 423212002155 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 423212002156 active site 423212002157 homodimer interface [polypeptide binding]; other site 423212002158 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 423212002159 Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing...; Region: LbH_AT_putative; cd03360 423212002160 putative trimer interface [polypeptide binding]; other site 423212002161 putative CoA binding site [chemical binding]; other site 423212002162 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain associated with the NTP (Nucleotidyl transferase) domain downstream. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently...; Region: CBS_pair_NTP_transferase_assoc; cd04607 423212002163 aminotransferase, LLPSF_NHT_00031 family; Region: NHT_00031; TIGR04181 423212002164 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 423212002165 inhibitor-cofactor binding pocket; inhibition site 423212002166 pyridoxal 5'-phosphate binding site [chemical binding]; other site 423212002167 catalytic residue [active] 423212002168 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; cl17405 423212002169 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 423212002170 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 423212002171 NADP binding site [chemical binding]; other site 423212002172 active site 423212002173 putative substrate binding site [chemical binding]; other site 423212002174 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 423212002175 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 423212002176 NAD binding site [chemical binding]; other site 423212002177 substrate binding site [chemical binding]; other site 423212002178 homodimer interface [polypeptide binding]; other site 423212002179 active site 423212002180 Phosphoglucose isomerase; Region: PGI; pfam00342 423212002181 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 423212002182 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 423212002183 active site 423212002184 dimer interface [polypeptide binding]; other site 423212002185 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 423212002186 dimer interface [polypeptide binding]; other site 423212002187 active site 423212002188 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 423212002189 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 423212002190 substrate binding site; other site 423212002191 tetramer interface; other site 423212002192 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 423212002193 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 423212002194 NAD(P) binding site [chemical binding]; other site 423212002195 active site 423212002196 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 423212002197 The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine precursor; Region: GT_WbpL_WbcO_like; cd06854 423212002198 Mg++ binding site [ion binding]; other site 423212002199 putative catalytic motif [active] 423212002200 putative substrate binding site [chemical binding]; other site 423212002201 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 423212002202 binding surface 423212002203 TPR motif; other site 423212002204 CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase; Region: Glyphos_transf; pfam04464 423212002205 Phosphotransferase enzyme family; Region: APH; pfam01636 423212002206 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 423212002207 substrate binding site [chemical binding]; other site 423212002208 Sialic acid synthase [Cell envelope biogenesis, outer membrane]; Region: SpsE; COG2089 423212002209 NeuB family; Region: NeuB; pfam03102 423212002210 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 423212002211 NeuB binding interface [polypeptide binding]; other site 423212002212 putative substrate binding site [chemical binding]; other site 423212002213 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 423212002214 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 423212002215 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 423212002216 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 423212002217 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 423212002218 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 423212002219 Walker A/P-loop; other site 423212002220 ATP binding site [chemical binding]; other site 423212002221 Q-loop/lid; other site 423212002222 ABC transporter signature motif; other site 423212002223 Walker B; other site 423212002224 D-loop; other site 423212002225 H-loop/switch region; other site 423212002226 C-Terminal domain of O-antigenic polysaccharide transporter protein Wzt and related proteins; Region: Wzt_C-like; cd10147 423212002227 putative carbohydrate binding site [chemical binding]; other site 423212002228 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 423212002229 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 423212002230 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 423212002231 Probable Catalytic site; other site 423212002232 metal-binding site 423212002233 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 423212002234 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 423212002235 Probable Catalytic site; other site 423212002236 metal-binding site 423212002237 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 423212002238 carbon storage regulator; Provisional; Region: PRK01712 423212002239 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 423212002240 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 423212002241 Biotin operon repressor [Transcription]; Region: BirA; COG1654 423212002242 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 423212002243 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 423212002244 Phosphopantetheinyl transferase [Coenzyme metabolism]; Region: Sfp; COG2091 423212002245 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; pfam01648 423212002246 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 423212002247 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 423212002248 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 423212002249 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 423212002250 Ligand Binding Site [chemical binding]; other site 423212002251 TilS substrate binding domain; Region: TilS; pfam09179 423212002252 TilS substrate C-terminal domain; Region: TilS_C; pfam11734 423212002253 Transposase IS200 like; Region: Y1_Tnp; cl00848 423212002254 Transposase domain (DUF772); Region: DUF772; pfam05598 423212002255 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 423212002256 GDSL-like Lipase/Acylhydrolase family; Region: Lipase_GDSL_2; pfam13472 423212002257 active site 423212002258 oxyanion hole [active] 423212002259 GDSL-like Lipase/Acylhydrolase family; Region: Lipase_GDSL_2; pfam13472 423212002260 catalytic triad [active] 423212002261 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 423212002262 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 423212002263 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 423212002264 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 423212002265 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 423212002266 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 423212002267 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 423212002268 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 423212002269 muropeptide transporter; Reviewed; Region: ampG; PRK11902 423212002270 putative substrate translocation pore; other site 423212002271 Protein of unknown function (DUF3757); Region: DUF3757; pfam12582 423212002272 Quinolinate synthetase A protein; Region: NadA; pfam02445 423212002273 L-aspartate oxidase; Provisional; Region: PRK09077 423212002274 L-aspartate oxidase; Provisional; Region: PRK06175 423212002275 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 423212002276 adenylosuccinate lyase; Provisional; Region: PRK09285 423212002277 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 423212002278 tetramer interface [polypeptide binding]; other site 423212002279 active site 423212002280 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 423212002281 putative transporter; Provisional; Region: PRK11660 423212002282 Sulfate transporter family; Region: Sulfate_transp; pfam00916 423212002283 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 423212002284 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 423212002285 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 423212002286 active site 423212002287 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 423212002288 Linear amide C-N hydrolases, choloylglycine hydrolase family; Region: CBAH; pfam02275 423212002289 active site 423212002290 phosphoenolpyruvate synthase; Validated; Region: PRK06464 423212002291 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 423212002292 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 423212002293 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 423212002294 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 423212002295 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 423212002296 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 423212002297 Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]; Region: NadC; COG0157 423212002298 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 423212002299 dimerization interface [polypeptide binding]; other site 423212002300 active site 423212002301 undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase; Reviewed; Region: PRK12446 423212002302 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 423212002303 active site 423212002304 homodimer interface [polypeptide binding]; other site 423212002305 hypothetical protein; Provisional; Region: PRK08201 423212002306 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_5; cd05682 423212002307 metal binding site [ion binding]; metal-binding site 423212002308 putative dimer interface [polypeptide binding]; other site 423212002309 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 423212002310 rod shape-determining protein MreB; Provisional; Region: PRK13927 423212002311 MreB and similar proteins; Region: MreB_like; cd10225 423212002312 nucleotide binding site [chemical binding]; other site 423212002313 Mg binding site [ion binding]; other site 423212002314 putative protofilament interaction site [polypeptide binding]; other site 423212002315 RodZ interaction site [polypeptide binding]; other site 423212002316 rod shape-determining protein MreC; Provisional; Region: PRK13922 423212002317 rod shape-determining protein MreC; Region: MreC; pfam04085 423212002318 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 423212002319 pseudouridine synthase; Region: TIGR00093 423212002320 active site 423212002321 isocitrate dehydrogenase; Validated; Region: PRK07362 423212002322 isocitrate dehydrogenase; Reviewed; Region: PRK07006 423212002323 Uncharacterized conserved protein [Function unknown]; Region: COG2127 423212002324 ATP-dependent Clp protease ATP-binding subunit; Provisional; Region: clpA; PRK11034 423212002325 Clp amino terminal domain; Region: Clp_N; pfam02861 423212002326 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 423212002327 Walker A motif; other site 423212002328 ATP binding site [chemical binding]; other site 423212002329 Walker B motif; other site 423212002330 arginine finger; other site 423212002331 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 423212002332 Walker A motif; other site 423212002333 ATP binding site [chemical binding]; other site 423212002334 Walker B motif; other site 423212002335 arginine finger; other site 423212002336 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 423212002337 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 423212002338 putative metal binding site; other site 423212002339 Rhomboid family; Region: Rhomboid; cl11446 423212002340 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 423212002341 Peptidase family M23; Region: Peptidase_M23; pfam01551 423212002342 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 423212002343 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 423212002344 generic binding surface II; other site 423212002345 generic binding surface I; other site 423212002346 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 423212002347 Sporulation related domain; Region: SPOR; pfam05036 423212002348 Bacterial transglutaminase-like cysteine proteinase BTLCP; Region: BTLCP; cl17596 423212002349 putative inner membrane diguanylate cyclase; Provisional; Region: PRK09966 423212002350 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 423212002351 dimerization interface [polypeptide binding]; other site 423212002352 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212002353 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212002354 metal binding site [ion binding]; metal-binding site 423212002355 active site 423212002356 I-site; other site 423212002357 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 423212002358 Thioesterase domains of type I polyketide synthases or non-ribosomal peptide synthetases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3319 423212002359 putative bacillithiol system oxidoreductase, YpdA family; Region: Bthiol_YpdA; TIGR04018 423212002360 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 423212002361 hypothetical protein; Provisional; Region: PRK06194 423212002362 classical (c) SDRs; Region: SDR_c; cd05233 423212002363 NAD(P) binding site [chemical binding]; other site 423212002364 active site 423212002365 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 423212002366 active site 423212002367 ribulose/triose binding site [chemical binding]; other site 423212002368 phosphate binding site [ion binding]; other site 423212002369 substrate (anthranilate) binding pocket [chemical binding]; other site 423212002370 product (indole) binding pocket [chemical binding]; other site 423212002371 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 423212002372 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 423212002373 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 423212002374 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 423212002375 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 423212002376 glutamine binding [chemical binding]; other site 423212002377 catalytic triad [active] 423212002378 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 423212002379 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 423212002380 Walker A/P-loop; other site 423212002381 ATP binding site [chemical binding]; other site 423212002382 Q-loop/lid; other site 423212002383 ABC transporter signature motif; other site 423212002384 Walker B; other site 423212002385 D-loop; other site 423212002386 H-loop/switch region; other site 423212002387 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 423212002388 OstA-like protein; Region: OstA; pfam03968 423212002389 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 423212002390 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 423212002391 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 423212002392 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 423212002393 active site 423212002394 motif I; other site 423212002395 motif II; other site 423212002396 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 423212002397 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 423212002398 putative active site [active] 423212002399 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 423212002400 putative ABC transporter ATP-binding protein YrbF; Provisional; Region: PRK11831 423212002401 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 423212002402 Walker A/P-loop; other site 423212002403 ATP binding site [chemical binding]; other site 423212002404 Q-loop/lid; other site 423212002405 ABC transporter signature motif; other site 423212002406 Walker B; other site 423212002407 D-loop; other site 423212002408 H-loop/switch region; other site 423212002409 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 423212002410 Permease; Region: Permease; cl00510 423212002411 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 423212002412 mce related protein; Region: MCE; pfam02470 423212002413 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 423212002414 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 423212002415 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 423212002416 anti sigma factor interaction site; other site 423212002417 regulatory phosphorylation site [posttranslational modification]; other site 423212002418 BolA-like protein; Region: BolA; cl00386 423212002419 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 423212002420 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 423212002421 hinge; other site 423212002422 active site 423212002423 Uncharacterized conserved protein [Function unknown]; Region: COG0327 423212002424 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 423212002425 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 423212002426 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 423212002427 Walker A/P-loop; other site 423212002428 ATP binding site [chemical binding]; other site 423212002429 Q-loop/lid; other site 423212002430 ABC transporter signature motif; other site 423212002431 Walker B; other site 423212002432 D-loop; other site 423212002433 H-loop/switch region; other site 423212002434 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 423212002435 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 423212002436 FtsX-like permease family; Region: FtsX; pfam02687 423212002437 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 423212002438 HlyD family secretion protein; Region: HlyD_3; pfam13437 423212002439 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 423212002440 Flagellar regulatory protein FleQ; Region: FleQ; pfam06490 423212002441 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 423212002442 Walker A motif; other site 423212002443 ATP binding site [chemical binding]; other site 423212002444 Walker B motif; other site 423212002445 arginine finger; other site 423212002446 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 423212002447 Peptidase family S49 N-terminal; Region: Peptidase_S49_N; pfam08496 423212002448 putative inner membrane peptidase; Provisional; Region: PRK11778 423212002449 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 423212002450 tandem repeat interface [polypeptide binding]; other site 423212002451 oligomer interface [polypeptide binding]; other site 423212002452 active site residues [active] 423212002453 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13540 423212002454 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 423212002455 Walker A/P-loop; other site 423212002456 ATP binding site [chemical binding]; other site 423212002457 Q-loop/lid; other site 423212002458 ABC transporter signature motif; other site 423212002459 Walker B; other site 423212002460 D-loop; other site 423212002461 H-loop/switch region; other site 423212002462 CcmB protein; Region: CcmB; cl17444 423212002463 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 423212002464 heme exporter protein CcmD; Region: cytochro_ccmD; TIGR03141 423212002465 CcmE; Region: CcmE; pfam03100 423212002466 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 423212002467 periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily; Region: dsbE; TIGR00385 423212002468 TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c...; Region: TlpA_like_DsbE; cd03010 423212002469 catalytic residues [active] 423212002470 central insert; other site 423212002471 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 423212002472 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 423212002473 binding surface 423212002474 TPR motif; other site 423212002475 Dodecin; Region: Dodecin; pfam07311 423212002476 Domain of unknown function (DUF4156); Region: DUF4156; pfam13698 423212002477 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 423212002478 active site 423212002479 DNA binding site [nucleotide binding] 423212002480 Superfamily II DNA helicase [DNA replication, recombination, and repair]; Region: RecQ; COG0514 423212002481 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 423212002482 ATP binding site [chemical binding]; other site 423212002483 putative Mg++ binding site [ion binding]; other site 423212002484 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 423212002485 nucleotide binding region [chemical binding]; other site 423212002486 ATP-binding site [chemical binding]; other site 423212002487 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 423212002488 HRDC domain; Region: HRDC; pfam00570 423212002489 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 423212002490 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 423212002491 active site 423212002492 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 423212002493 3-hydroxybutyryl-CoA dehydratase; Validated; Region: PRK05809 423212002494 substrate binding site [chemical binding]; other site 423212002495 oxyanion hole (OAH) forming residues; other site 423212002496 trimer interface [polypeptide binding]; other site 423212002497 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 423212002498 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 423212002499 substrate binding site [chemical binding]; other site 423212002500 oxyanion hole (OAH) forming residues; other site 423212002501 trimer interface [polypeptide binding]; other site 423212002502 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 423212002503 Polysaccharide biosynthesis protein; Region: Polysacc_synt; cl10513 423212002504 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 423212002505 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 423212002506 G1 box; other site 423212002507 putative GEF interaction site [polypeptide binding]; other site 423212002508 GTP/Mg2+ binding site [chemical binding]; other site 423212002509 Switch I region; other site 423212002510 G2 box; other site 423212002511 G3 box; other site 423212002512 Switch II region; other site 423212002513 G4 box; other site 423212002514 G5 box; other site 423212002515 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 423212002516 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 423212002517 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 423212002518 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 423212002519 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 423212002520 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 423212002521 ligand binding site [chemical binding]; other site 423212002522 homodimer interface [polypeptide binding]; other site 423212002523 NAD(P) binding site [chemical binding]; other site 423212002524 trimer interface B [polypeptide binding]; other site 423212002525 trimer interface A [polypeptide binding]; other site 423212002526 Uncharacterized protein with SCP/PR1 domains [Function unknown]; Region: COG2340 423212002527 SCP_bacterial: SCP-like extracellular protein domain, as found in bacteria and archaea. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5...; Region: SCP_bacterial; cd05379 423212002528 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212002529 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212002530 metal binding site [ion binding]; metal-binding site 423212002531 active site 423212002532 I-site; other site 423212002533 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 423212002534 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 423212002535 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 423212002536 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 423212002537 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 423212002538 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 423212002539 metal binding site [ion binding]; metal-binding site 423212002540 dimer interface [polypeptide binding]; other site 423212002541 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 423212002542 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA; Region: LbH_THP_succinylT; cd03350 423212002543 trimer interface [polypeptide binding]; other site 423212002544 active site 423212002545 substrate binding site [chemical binding]; other site 423212002546 CoA binding site [chemical binding]; other site 423212002547 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 423212002548 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 423212002549 putative acyl-acceptor binding pocket; other site 423212002550 Cys/Met metabolism PLP-dependent enzyme; Region: Cys_Met_Meta_PP; pfam01053 423212002551 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 423212002552 homodimer interface [polypeptide binding]; other site 423212002553 substrate-cofactor binding pocket; other site 423212002554 pyridoxal 5'-phosphate binding site [chemical binding]; other site 423212002555 catalytic residue [active] 423212002556 PAS fold; Region: PAS_7; pfam12860 423212002557 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 423212002558 PAS domain; Region: PAS_9; pfam13426 423212002559 putative active site [active] 423212002560 heme pocket [chemical binding]; other site 423212002561 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212002562 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212002563 metal binding site [ion binding]; metal-binding site 423212002564 active site 423212002565 I-site; other site 423212002566 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 423212002567 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 423212002568 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 423212002569 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 423212002570 FAD binding domain; Region: FAD_binding_4; pfam01565 423212002571 Cytokinin dehydrogenase 1, FAD and cytokinin binding; Region: Cytokin-bind; pfam09265 423212002572 Type IV pilus biogenesis; Region: Pilus_PilP; pfam11356 423212002573 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 423212002574 putative calcium/sodium:proton antiporter; Provisional; Region: PRK10734 423212002575 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 423212002576 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 423212002577 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 423212002578 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 423212002579 minor groove reading motif; other site 423212002580 helix-hairpin-helix signature motif; other site 423212002581 substrate binding pocket [chemical binding]; other site 423212002582 active site 423212002583 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 423212002584 DNA binding and oxoG recognition site [nucleotide binding] 423212002585 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 423212002586 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 423212002587 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 423212002588 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 423212002589 protein binding site [polypeptide binding]; other site 423212002590 Isochorismatase family; Region: Isochorismatase; pfam00857 423212002591 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them; Region: YcaC_related; cd01012 423212002592 catalytic triad [active] 423212002593 dimer interface [polypeptide binding]; other site 423212002594 conserved cis-peptide bond; other site 423212002595 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08217 423212002596 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 423212002597 NAD(P) binding site [chemical binding]; other site 423212002598 active site 423212002599 FlgN protein; Region: FlgN; pfam05130 423212002600 flagellar biosynthesis anti-sigma factor FlgM; Region: FlgM_jcvi; TIGR03824 423212002601 SAF-like; Region: SAF_2; pfam13144 423212002602 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 423212002603 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 423212002604 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 423212002605 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 423212002606 nucleotide binding site [chemical binding]; other site 423212002607 Type III pantothenate kinase; Region: Pan_kinase; cl17198 423212002608 cell division protein MraZ; Reviewed; Region: PRK00326 423212002609 MraZ protein; Region: MraZ; pfam02381 423212002610 MraZ protein; Region: MraZ; pfam02381 423212002611 MraW methylase family; Region: Methyltransf_5; cl17771 423212002612 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 423212002613 Cell division protein FtsL; Region: FtsL; pfam04999 423212002614 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 423212002615 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 423212002616 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 423212002617 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 423212002618 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 423212002619 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 423212002620 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 423212002621 erythronate-4-phosphate dehydrogenase; Validated; Region: PRK00257 423212002622 D-Erythronate-4-Phosphate Dehydrogenase NAD-binding and catalytic domains; Region: ErythrP_dh; cd12158 423212002623 ligand binding site [chemical binding]; other site 423212002624 NAD binding site [chemical binding]; other site 423212002625 catalytic site [active] 423212002626 homodimer interface [polypeptide binding]; other site 423212002627 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 423212002628 Peptidase family M50; Region: Peptidase_M50; pfam02163 423212002629 active site 423212002630 putative substrate binding region [chemical binding]; other site 423212002631 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 423212002632 PAP2_like proteins, Lipid A 1-phosphatase subfamily. Lipid A 1-phosphatase, or LpxE from Francisella novicida selectively dephosphorylates lipid A at the 1-position. Lipid A is the membrane-anchor component of lipopolysaccharides (LPS), the major...; Region: PAP2_lipid_A_1_phosphatase; cd03389 423212002633 active site 423212002634 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 423212002635 Ligand binding site [chemical binding]; other site 423212002636 Electron transfer flavoprotein domain; Region: ETF; pfam01012 423212002637 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 423212002638 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 423212002639 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 423212002640 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 423212002641 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 423212002642 hexamer interface [polypeptide binding]; other site 423212002643 ligand binding site [chemical binding]; other site 423212002644 putative active site [active] 423212002645 NAD(P) binding site [chemical binding]; other site 423212002646 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 423212002647 Transglycosylase; Region: Transgly; pfam00912 423212002648 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 423212002649 Cell division protein FtsA; Region: FtsA; cl17206 423212002650 Competence protein A; Region: Competence_A; pfam11104 423212002651 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 423212002652 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 423212002653 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 423212002654 Pilus assembly protein, PilO; Region: PilO; pfam04350 423212002655 Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilP; COG3168 423212002656 Pilus assembly protein, PilP; Region: PilP; pfam04351 423212002657 AMIN domain; Region: AMIN; pfam11741 423212002658 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 423212002659 Secretin and TonB N terminus short domain; Region: STN; smart00965 423212002660 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 423212002661 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 423212002662 shikimate kinase; Reviewed; Region: aroK; PRK00131 423212002663 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 423212002664 ADP binding site [chemical binding]; other site 423212002665 magnesium binding site [ion binding]; other site 423212002666 putative shikimate binding site; other site 423212002667 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 423212002668 active site 423212002669 dimer interface [polypeptide binding]; other site 423212002670 metal binding site [ion binding]; metal-binding site 423212002671 AAA domain; Region: AAA_22; pfam13401 423212002672 Sporulation related domain; Region: SPOR; pfam05036 423212002673 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 423212002674 Ligand Binding Site [chemical binding]; other site 423212002675 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 423212002676 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 423212002677 active site 423212002678 Riboflavin kinase; Region: Flavokinase; smart00904 423212002679 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 423212002680 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 423212002681 active site 423212002682 HIGH motif; other site 423212002683 nucleotide binding site [chemical binding]; other site 423212002684 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 423212002685 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 423212002686 active site 423212002687 KMSKS motif; other site 423212002688 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 423212002689 tRNA binding surface [nucleotide binding]; other site 423212002690 anticodon binding site; other site 423212002691 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 423212002692 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 423212002693 lipoprotein signal peptidase; Provisional; Region: PRK14787 423212002694 Class I aldolases; Region: Aldolase_Class_I; cl17187 423212002695 catalytic residue [active] 423212002696 Protein of unknown function (DUF3380); Region: DUF3380; pfam11860 423212002697 GTPase Era; Reviewed; Region: era; PRK00089 423212002698 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 423212002699 G1 box; other site 423212002700 GTP/Mg2+ binding site [chemical binding]; other site 423212002701 Switch I region; other site 423212002702 G2 box; other site 423212002703 Switch II region; other site 423212002704 G3 box; other site 423212002705 G4 box; other site 423212002706 G5 box; other site 423212002707 KH domain; Region: KH_2; pfam07650 423212002708 Recombination protein O N terminal; Region: RecO_N; pfam11967 423212002709 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 423212002710 Recombination protein O C terminal; Region: RecO_C; pfam02565 423212002711 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 423212002712 Leucine-rich repeats; other site 423212002713 Substrate binding site [chemical binding]; other site 423212002714 Leucine rich repeat; Region: LRR_8; pfam13855 423212002715 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 423212002716 active site 423212002717 hydrophilic channel; other site 423212002718 dimerization interface [polypeptide binding]; other site 423212002719 catalytic residues [active] 423212002720 active site lid [active] 423212002721 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 423212002722 2-oxoacid:acceptor oxidoreductase, alpha subunit; Region: OAFO_sf; TIGR03710 423212002723 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 423212002724 dimer interface [polypeptide binding]; other site 423212002725 PYR/PP interface [polypeptide binding]; other site 423212002726 TPP binding site [chemical binding]; other site 423212002727 substrate binding site [chemical binding]; other site 423212002728 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Reviewed; Region: PRK11867 423212002729 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 423212002730 TPP-binding site [chemical binding]; other site 423212002731 YccA-like proteins; Region: YccA_like; cd10433 423212002732 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 423212002733 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 423212002734 nitrilase; Region: PLN02798 423212002735 putative active site [active] 423212002736 catalytic triad [active] 423212002737 dimer interface [polypeptide binding]; other site 423212002738 protease TldD; Provisional; Region: tldD; PRK10735 423212002739 hypothetical protein; Provisional; Region: PRK10279 423212002740 Bacterial patatin-like phospholipase domain containing protein 6; Region: Pat_NTE_like_bacteria; cd07228 423212002741 active site 423212002742 nucleophile elbow; other site 423212002743 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 423212002744 Bacterial long-chain fatty acid CoA synthetase (LC-FACS), including Marinobacter hydrocarbonoclasticus isoprenoid Coenzyme A synthetase; Region: LC_FACS_bac; cd05932 423212002745 acyl-activating enzyme (AAE) consensus motif; other site 423212002746 putative AMP binding site [chemical binding]; other site 423212002747 putative active site [active] 423212002748 putative CoA binding site [chemical binding]; other site 423212002749 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 423212002750 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 423212002751 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 423212002752 ATP binding site [chemical binding]; other site 423212002753 putative Mg++ binding site [ion binding]; other site 423212002754 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 423212002755 nucleotide binding region [chemical binding]; other site 423212002756 ATP-binding site [chemical binding]; other site 423212002757 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 423212002758 RmuC family; Region: RmuC; pfam02646 423212002759 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 423212002760 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 423212002761 nucleotide binding pocket [chemical binding]; other site 423212002762 K-X-D-G motif; other site 423212002763 catalytic site [active] 423212002764 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 423212002765 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 423212002766 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 423212002767 Dimer interface [polypeptide binding]; other site 423212002768 BRCT sequence motif; other site 423212002769 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_18; cd08505 423212002770 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 423212002771 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 423212002772 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 423212002773 dimer interface [polypeptide binding]; other site 423212002774 conserved gate region; other site 423212002775 putative PBP binding loops; other site 423212002776 ABC-ATPase subunit interface; other site 423212002777 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 423212002778 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 423212002779 dimer interface [polypeptide binding]; other site 423212002780 conserved gate region; other site 423212002781 putative PBP binding loops; other site 423212002782 ABC-ATPase subunit interface; other site 423212002783 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 423212002784 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 423212002785 putative active site [active] 423212002786 putative PHP Thumb interface [polypeptide binding]; other site 423212002787 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 423212002788 generic binding surface II; other site 423212002789 generic binding surface I; other site 423212002790 phosphoribose diphosphate:decaprenyl-phosphate phosphoribosyltransferase; Provisional; Region: PRK12324 423212002791 UbiA prenyltransferase family; Region: UbiA; pfam01040 423212002792 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 423212002793 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 423212002794 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 423212002795 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 423212002796 NAD(P) binding site [chemical binding]; other site 423212002797 homodimer interface [polypeptide binding]; other site 423212002798 substrate binding site [chemical binding]; other site 423212002799 active site 423212002800 Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]; Region: AnsP; COG1113 423212002801 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 423212002802 nucleotide binding site [chemical binding]; other site 423212002803 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; pfam13640 423212002804 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 423212002805 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 423212002806 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 423212002807 Catalytic site [active] 423212002808 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 423212002809 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 423212002810 active site 423212002811 DNA binding site [nucleotide binding] 423212002812 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 423212002813 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-II-III; cl00656 423212002814 CRISPR/Cas system-associated protein Cas3/Cas2; Region: Cas3_Cas2_I-F; cd09673 423212002815 CRISPR/Cas system-associated protein Cas3'' Region: Cas3''_I; cd09641 423212002816 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 423212002817 CRISPR/Cas system-associated RAMP superfamily protein Cas6f; Region: Cas6_I-F; cd09739 423212002818 Antirestriction protein (ArdA); Region: ArdA; pfam07275 423212002819 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 423212002820 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 423212002821 dimer interface [polypeptide binding]; other site 423212002822 ssDNA binding site [nucleotide binding]; other site 423212002823 tetramer (dimer of dimers) interface [polypeptide binding]; other site 423212002824 Phage integrase, N-terminal; Region: Integrase_l_N; pfam12834 423212002825 Integrase; Region: Integrase_1; pfam12835 423212002826 Phage integrase, N-terminal; Region: Integrase_l_N; pfam12834 423212002827 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 423212002828 conjugative coupling factor TraD, SXT/TOL subfamily; Region: SXT_TraD; TIGR03743 423212002829 conjugative coupling factor TraD, TOL family; Region: conj_TOL_TraD; TIGR03754 423212002830 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 423212002831 integrating conjugative element protein, PFL_4711 family; Region: conj_TIGR03755 423212002832 integrating conjugative element protein, PFL_4710 family; Region: conj_TIGR03756 423212002833 conjugative transfer ATPase, PFL_4706 family; Region: traC_PFL_4706; TIGR03744 423212002834 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 423212002835 Domain of unknown function DUF87; Region: DUF87; pfam01935 423212002836 conjugative transfer region lipoprotein, TIGR03751 family; Region: conj_TIGR03751 423212002837 integrating conjugative element protein, PFL_4705 family; Region: conj_TIGR03752 423212002838 basic region leucin zipper; Region: BRLZ; smart00338 423212002839 Protein of unknown function (DUF3438); Region: DUF3438; cl13372 423212002840 Protein of unknown function (DUF3438); Region: DUF3438; cl13372 423212002841 Protein of unknown function (DUF2895); Region: DUF2895; pfam11444 423212002842 conjugative transfer region protein, TIGR03750 family; Region: conj_TIGR03750 423212002843 Plasmid protein of unknown function (Plasmid_RAQPRD); Region: Plasmid_RAQPRD; pfam09686 423212002844 Domain of unknown function (DUF4400); Region: DUF4400; cl14023 423212002845 Protein of unknown function (DUF2859); Region: DUF2859; pfam11072 423212002846 integrating conjugative element protein, PFL_4693 family; Region: conj_TIGR03759 423212002847 conjugative transfer region protein, TIGR03748 family; Region: conj_PilL 423212002848 Global regulator protein family; Region: CsrA; pfam02599 423212002849 Fructose/tagarose-bisphosphate aldolase class II. This family includes fructose-1,6-bisphosphate (FBP) and tagarose 1,6-bisphosphate (TBP) aldolases. FBP-aldolase is homodimeric and used in gluconeogenesis and glycolysis; the enzyme controls the...; Region: FTBP_aldolase_II; cl17181 423212002850 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 423212002851 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 423212002852 non-specific DNA binding site [nucleotide binding]; other site 423212002853 salt bridge; other site 423212002854 sequence-specific DNA binding site [nucleotide binding]; other site 423212002855 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 423212002856 Membrane-fusion protein [Cell envelope biogenesis, outer membrane]; Region: AcrA; COG0845 423212002857 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 423212002858 E3 interaction surface; other site 423212002859 lipoyl attachment site [posttranslational modification]; other site 423212002860 HlyD family secretion protein; Region: HlyD_3; pfam13437 423212002861 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 423212002862 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 423212002863 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 423212002864 metal-binding site [ion binding] 423212002865 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 423212002866 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 423212002867 motif II; other site 423212002868 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 423212002869 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 423212002870 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 423212002871 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 423212002872 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 423212002873 motif II; other site 423212002874 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 423212002875 Outer membrane efflux protein; Region: OEP; pfam02321 423212002876 Outer membrane efflux protein; Region: OEP; pfam02321 423212002877 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 423212002878 HlyD family secretion protein; Region: HlyD_3; pfam13437 423212002879 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 423212002880 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 423212002881 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 423212002882 Beta-Casp domain; Region: Beta-Casp; smart01027 423212002883 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 423212002884 thymidine phosphorylase; Provisional; Region: PRK04350 423212002885 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 423212002886 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 423212002887 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; smart00941 423212002888 phosphoribosylpyrophosphate synthetase; Provisional; Region: PRK07199 423212002889 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 423212002890 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 423212002891 active site 423212002892 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 423212002893 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 423212002894 Soluble P-type ATPase [General function prediction only]; Region: COG4087 423212002895 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212002896 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212002897 metal binding site [ion binding]; metal-binding site 423212002898 active site 423212002899 I-site; other site 423212002900 Domain of unknown function (DUF4156); Region: DUF4156; pfam13698 423212002901 Outer membrane efflux protein; Region: OEP; pfam02321 423212002902 Outer membrane efflux protein; Region: OEP; pfam02321 423212002903 Biotin carboxyl carrier protein [Lipid metabolism]; Region: AccB; COG0511 423212002904 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 423212002905 carboxyltransferase (CT) interaction site; other site 423212002906 biotinylation site [posttranslational modification]; other site 423212002907 HlyD family secretion protein; Region: HlyD_3; pfam13437 423212002908 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 423212002909 Protein export membrane protein; Region: SecD_SecF; cl14618 423212002910 O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3315 423212002911 Leucine carboxyl methyltransferase; Region: LCM; cl01306 423212002912 Uncharacterized conserved protein [Function unknown]; Region: COG4278 423212002913 Cytotoxic translational repressor of toxin-antitoxin stability system [Translation, ribosomal structure and biogenesis / Cell division and chromosome partitioning]; Region: RelE; COG2026 423212002914 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 423212002915 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 423212002916 HlyD family secretion protein; Region: HlyD_3; pfam13437 423212002917 Outer membrane efflux protein; Region: OEP; pfam02321 423212002918 Outer membrane efflux protein; Region: OEP; pfam02321 423212002919 Protein of unknown function (DUF3141); Region: DUF3141; pfam11339 423212002920 Predicted membrane protein (DUF2231); Region: DUF2231; cl01730 423212002921 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 423212002922 Multicopper oxidase; Region: Cu-oxidase; pfam00394 423212002923 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 423212002924 Copper resistance protein B precursor (CopB); Region: CopB; cl01476 423212002925 Domain of unknown function (DUF4156); Region: DUF4156; pfam13698 423212002926 Predicted membrane protein [Function unknown]; Region: COG3212 423212002927 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 423212002928 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 423212002929 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 423212002930 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 423212002931 substrate binding pocket [chemical binding]; other site 423212002932 membrane-bound complex binding site; other site 423212002933 hinge residues; other site 423212002934 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 423212002935 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 423212002936 HlyD family secretion protein; Region: HlyD_3; pfam13437 423212002937 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 423212002938 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 423212002939 dimerization interface [polypeptide binding]; other site 423212002940 putative DNA binding site [nucleotide binding]; other site 423212002941 putative Zn2+ binding site [ion binding]; other site 423212002942 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 423212002943 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 423212002944 metal-binding site [ion binding] 423212002945 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 423212002946 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 423212002947 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 423212002948 active site 423212002949 DNA binding site [nucleotide binding] 423212002950 Int/Topo IB signature motif; other site 423212002951 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 423212002952 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; cl14901 423212002953 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; cl14901 423212002954 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 423212002955 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron...; Region: FNR_iron_sulfur_binding_3; cd06217 423212002956 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 423212002957 FAD binding pocket [chemical binding]; other site 423212002958 FAD binding motif [chemical binding]; other site 423212002959 phosphate binding motif [ion binding]; other site 423212002960 beta-alpha-beta structure motif; other site 423212002961 NAD binding pocket [chemical binding]; other site 423212002962 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 423212002963 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 423212002964 catalytic loop [active] 423212002965 iron binding site [ion binding]; other site 423212002966 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cl00365 423212002967 core domain interface [polypeptide binding]; other site 423212002968 epsilon subunit interface [polypeptide binding]; other site 423212002969 F0F1 ATP synthase subunit alpha; Provisional; Region: PRK13343 423212002970 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 423212002971 Walker A motif; other site 423212002972 ATP binding site [chemical binding]; other site 423212002973 Walker B motif; other site 423212002974 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 423212002975 alternate F1F0 ATPase, F0 subunit B; Region: alt_F1F0_F0_B; TIGR03321 423212002976 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 423212002977 ATP synthase subunit C; Region: ATP-synt_C; cl00466 423212002978 F0F1 ATP synthase subunit A; Provisional; Region: PRK13420 423212002979 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 423212002980 F0F1 ATP synthase subunit epsilon; Validated; Region: PRK06228 423212002981 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cl10033 423212002982 gamma subunit interface [polypeptide binding]; other site 423212002983 epsilon subunit interface [polypeptide binding]; other site 423212002984 LBP interface [polypeptide binding]; other site 423212002985 F0F1 ATP synthase subunit beta; Provisional; Region: PRK12597 423212002986 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 423212002987 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 423212002988 alpha subunit interaction interface [polypeptide binding]; other site 423212002989 Walker A motif; other site 423212002990 ATP binding site [chemical binding]; other site 423212002991 Walker B motif; other site 423212002992 inhibitor binding site; inhibition site 423212002993 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 423212002994 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 423212002995 non-specific DNA binding site [nucleotide binding]; other site 423212002996 salt bridge; other site 423212002997 sequence-specific DNA binding site [nucleotide binding]; other site 423212002998 Heme NO binding; Region: HNOB; pfam07700 423212002999 potential frameshift: common BLAST hit: gi|52841291|ref|YP_095090.1| sensory box/GGDEF family protein 423212003000 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212003001 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212003002 metal binding site [ion binding]; metal-binding site 423212003003 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212003004 active site 423212003005 I-site; other site 423212003006 metal binding site [ion binding]; metal-binding site 423212003007 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 423212003008 Poly-beta-hydroxybutyrate polymerase N terminal; Region: PHBC_N; pfam12551 423212003009 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 423212003010 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 423212003011 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 423212003012 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 423212003013 NAD(P) binding site [chemical binding]; other site 423212003014 active site 423212003015 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 423212003016 DNA-binding site [nucleotide binding]; DNA binding site 423212003017 RNA-binding motif; other site 423212003018 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 423212003019 Sel1-like repeats; Region: SEL1; smart00671 423212003020 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 423212003021 Sel1-like repeats; Region: SEL1; smart00671 423212003022 Sel1-like repeats; Region: SEL1; smart00671 423212003023 Sel1-like repeats; Region: SEL1; smart00671 423212003024 Sel1 repeat; Region: Sel1; pfam08238 423212003025 Sel1-like repeats; Region: SEL1; smart00671 423212003026 citrate-proton symporter; Provisional; Region: PRK15075 423212003027 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 423212003028 putative substrate translocation pore; other site 423212003029 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 423212003030 active site 423212003031 catalytic residues [active] 423212003032 metal binding site [ion binding]; metal-binding site 423212003033 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 423212003034 non-specific DNA binding site [nucleotide binding]; other site 423212003035 salt bridge; other site 423212003036 sequence-specific DNA binding site [nucleotide binding]; other site 423212003037 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 423212003038 Abi-like protein; Region: Abi_2; pfam07751 423212003039 integrase; Provisional; Region: PRK09692 423212003040 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 423212003041 active site 423212003042 Int/Topo IB signature motif; other site 423212003043 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 423212003044 Coenzyme A binding pocket [chemical binding]; other site 423212003045 GNAT acetyltransferase 2; Region: GNAT_acetyltr_2; pfam13718 423212003046 Predicted P-loop ATPase [General function prediction only]; Region: COG4928 423212003047 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 423212003048 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 423212003049 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 423212003050 Domain of unknown function (DUF927); Region: DUF927; pfam06048 423212003051 Helix-turn-helix domain; Region: HTH_17; pfam12728 423212003052 DNA binding domain, excisionase family; Region: excise; TIGR01764 423212003053 PIN domain; Region: PIN_3; pfam13470 423212003054 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 423212003055 Retron-type reverse transcriptase [DNA replication, recombination, and repair]; Region: COG3344 423212003056 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 423212003057 putative active site [active] 423212003058 putative NTP binding site [chemical binding]; other site 423212003059 putative nucleic acid binding site [nucleotide binding]; other site 423212003060 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 423212003061 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 423212003062 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 423212003063 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 423212003064 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 423212003065 Coenzyme A binding pocket [chemical binding]; other site 423212003066 Uncharacterized protein family (UPF0157); Region: UPF0157; pfam04229 423212003067 Domain of unknown function (DUF4111); Region: DUF4111; pfam13427 423212003068 Methyltransferase domain; Region: Methyltransf_23; pfam13489 423212003069 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 423212003070 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 423212003071 S-adenosylmethionine binding site [chemical binding]; other site 423212003072 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 423212003073 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 423212003074 Coenzyme A binding pocket [chemical binding]; other site 423212003075 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 423212003076 AAA domain; Region: AAA_23; pfam13476 423212003077 AAA domain; Region: AAA_21; pfam13304 423212003078 Walker A/P-loop; other site 423212003079 ATP binding site [chemical binding]; other site 423212003080 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 423212003081 Walker B; other site 423212003082 D-loop; other site 423212003083 H-loop/switch region; other site 423212003084 TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as...; Region: TOPRIM_OLD; cd01026 423212003085 putative active site [active] 423212003086 putative metal-binding site [ion binding]; other site 423212003087 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4487 423212003088 Uncharacterized protein conserved in bacteria (DUF2130); Region: DUF2130; pfam09903 423212003089 Fic family protein [Function unknown]; Region: COG3177 423212003090 Domain of unknown function (DUF4172); Region: DUF4172; pfam13776 423212003091 Fic/DOC family; Region: Fic; pfam02661 423212003092 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 423212003093 Coenzyme A binding pocket [chemical binding]; other site 423212003094 beta-phosphoglucomutase; Region: bPGM; TIGR01990 423212003095 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 423212003096 motif II; other site 423212003097 Exopolysaccharide synthesis, ExoD; Region: ExoD; pfam06055 423212003098 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; cl14901 423212003099 putative transposase OrfB; Reviewed; Region: PHA02517 423212003100 HTH-like domain; Region: HTH_21; pfam13276 423212003101 Integrase core domain; Region: rve; pfam00665 423212003102 Integrase core domain; Region: rve_2; pfam13333 423212003103 Transposase; Region: HTH_Tnp_1; pfam01527 423212003104 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 423212003105 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 423212003106 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 423212003107 Phosphotransferase enzyme family; Region: APH; pfam01636 423212003108 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 423212003109 methionine sulfoxide reductase B; Provisional; Region: PRK00222 423212003110 SelR domain; Region: SelR; pfam01641 423212003111 Predicted membrane protein [Function unknown]; Region: COG4325 423212003112 Predicted membrane protein (DUF2254); Region: DUF2254; pfam10011 423212003113 EamA-like transporter family; Region: EamA; cl17759 423212003114 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 423212003115 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 423212003116 PAS domain; Region: PAS_9; pfam13426 423212003117 putative active site [active] 423212003118 heme pocket [chemical binding]; other site 423212003119 PAS domain; Region: PAS_9; pfam13426 423212003120 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 423212003121 putative active site [active] 423212003122 heme pocket [chemical binding]; other site 423212003123 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212003124 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212003125 metal binding site [ion binding]; metal-binding site 423212003126 active site 423212003127 I-site; other site 423212003128 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 423212003129 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 423212003130 KaiB-like family; composed of the circadian clock proteins, KaiB and the N-terminal KaiB-like sensory domain of SasA. KaiB is an essential protein in maintaining circadian rhythm. It was originally discovered from the cyanobacterium Synechococcus as part...; Region: KaiB_like; cd02978 423212003131 tetramer interface [polypeptide binding]; other site 423212003132 dimer interface [polypeptide binding]; other site 423212003133 potential frameshift: common BLAST hit: gi|148360205|ref|YP_001251412.1| DNA integration/recombination/inversion protein 423212003134 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 423212003135 Walker B motif; other site 423212003136 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 423212003137 KaiC; Region: KaiC; pfam06745 423212003138 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 423212003139 Walker A motif; other site 423212003140 Walker A motif; other site 423212003141 ATP binding site [chemical binding]; other site 423212003142 ATP binding site [chemical binding]; other site 423212003143 Walker B motif; other site 423212003144 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 423212003145 Walker A motif; other site 423212003146 Glycosyl hydrolases family 18; Region: Glyco_hydro_18; pfam00704 423212003147 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 423212003148 active site 423212003149 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 423212003150 Coenzyme A binding pocket [chemical binding]; other site 423212003151 Beta-lactamase; Region: Beta-lactamase; pfam00144 423212003152 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 423212003153 Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction; Region: HP_HAP_like; cd07061 423212003154 catalytic core [active] 423212003155 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 423212003156 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 423212003157 N-acetyl-D-glucosamine binding site [chemical binding]; other site 423212003158 catalytic residue [active] 423212003159 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 423212003160 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 423212003161 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 423212003162 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 423212003163 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 423212003164 substrate binding pocket [chemical binding]; other site 423212003165 membrane-bound complex binding site; other site 423212003166 hinge residues; other site 423212003167 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 423212003168 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 423212003169 substrate binding pocket [chemical binding]; other site 423212003170 membrane-bound complex binding site; other site 423212003171 hinge residues; other site 423212003172 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 423212003173 Soluble P-type ATPase [General function prediction only]; Region: COG4087 423212003174 putative cation:proton antiport protein; Provisional; Region: PRK10669 423212003175 Kef-type K+ transport system, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: RosB; COG4651 423212003176 TrkA-N domain; Region: TrkA_N; pfam02254 423212003177 Winged helix-turn helix; Region: HTH_29; pfam13551 423212003178 Helix-turn-helix domain; Region: HTH_28; pfam13518 423212003179 Integrase core domain; Region: rve; pfam00665 423212003180 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 423212003181 Integrase core domain; Region: rve_3; pfam13683 423212003182 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 423212003183 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 423212003184 dimerization interface [polypeptide binding]; other site 423212003185 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 423212003186 cyclase homology domain; Region: CHD; cd07302 423212003187 nucleotidyl binding site; other site 423212003188 metal binding site [ion binding]; metal-binding site 423212003189 dimer interface [polypeptide binding]; other site 423212003190 cyclopropane fatty acyl phospholipid synthase; Provisional; Region: PRK11705 423212003191 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 423212003192 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 423212003193 S-adenosylmethionine binding site [chemical binding]; other site 423212003194 Nitronate monooxygenase; Region: NMO; pfam03060 423212003195 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 423212003196 FMN binding site [chemical binding]; other site 423212003197 substrate binding site [chemical binding]; other site 423212003198 putative catalytic residue [active] 423212003199 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 423212003200 COQ9; Region: COQ9; pfam08511 423212003201 Domain of unknown function (DUF4349); Region: DUF4349; pfam14257 423212003202 spermidine/putrescine ABC transporter periplasmic substrate-binding protein; Reviewed; Region: potD; PRK09501 423212003203 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 423212003204 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 423212003205 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 423212003206 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 423212003207 dimer interface [polypeptide binding]; other site 423212003208 conserved gate region; other site 423212003209 putative PBP binding loops; other site 423212003210 ABC-ATPase subunit interface; other site 423212003211 putrescine/spermidine ABC transporter ATPase protein; Reviewed; Region: potA; PRK09452 423212003212 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 423212003213 Walker A/P-loop; other site 423212003214 ATP binding site [chemical binding]; other site 423212003215 Q-loop/lid; other site 423212003216 ABC transporter signature motif; other site 423212003217 Walker B; other site 423212003218 D-loop; other site 423212003219 H-loop/switch region; other site 423212003220 TOBE domain; Region: TOBE_2; pfam08402 423212003221 short chain dehydrogenase; Provisional; Region: PRK08219 423212003222 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 423212003223 NADP binding site [chemical binding]; other site 423212003224 active site 423212003225 steroid binding site; other site 423212003226 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 423212003227 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 423212003228 active site 423212003229 Zn binding site [ion binding]; other site 423212003230 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 423212003231 Coenzyme A binding pocket [chemical binding]; other site 423212003232 probable polyamine oxidase; Region: PLN02268 423212003233 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 423212003234 pyruvate decarboxylase; Region: PLN02573 423212003235 Pyrimidine (PYR) binding domain of pyruvate decarboxylase (PDC), indolepyruvate decarboxylase (IPDC) and related proteins; Region: TPP_PYR_PDC_IPDC_like; cd07038 423212003236 dimer interface [polypeptide binding]; other site 423212003237 PYR/PP interface [polypeptide binding]; other site 423212003238 TPP binding site [chemical binding]; other site 423212003239 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 423212003240 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 423212003241 TPP-binding site [chemical binding]; other site 423212003242 dimer interface [polypeptide binding]; other site 423212003243 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 423212003244 Peptidase family M28; Region: Peptidase_M28; pfam04389 423212003245 metal binding site [ion binding]; metal-binding site 423212003246 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 423212003247 Putative serine esterase (DUF676); Region: DUF676; pfam05057 423212003248 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 423212003249 active site 423212003250 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 423212003251 metabolite-proton symporter; Region: 2A0106; TIGR00883 423212003252 putative substrate translocation pore; other site 423212003253 acetylornithine deacetylase; Provisional; Region: PRK07522 423212003254 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 423212003255 metal binding site [ion binding]; metal-binding site 423212003256 putative dimer interface [polypeptide binding]; other site 423212003257 Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway; Region: UMPK; cd02023 423212003258 ATP-binding site [chemical binding]; other site 423212003259 Sugar specificity; other site 423212003260 Pyrimidine base specificity; other site 423212003261 7kD viral coat protein; Region: 7kD_coat; pfam02495 423212003262 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 423212003263 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 423212003264 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212003265 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212003266 metal binding site [ion binding]; metal-binding site 423212003267 active site 423212003268 I-site; other site 423212003269 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 423212003270 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 423212003271 putative ligand binding pocket/active site [active] 423212003272 putative metal binding site [ion binding]; other site 423212003273 AmmeMemoRadiSam system protein A; Region: AmmeMemoSam_A; TIGR04335 423212003274 AMMECR1; Region: AMMECR1; pfam01871 423212003275 AmmeMemoRadiSam system radical SAM enzyme; Region: AmmeMemoSam_rS; TIGR04337 423212003276 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 423212003277 FeS/SAM binding site; other site 423212003278 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 423212003279 Sel1-like repeats; Region: SEL1; smart00671 423212003280 Sel1-like repeats; Region: SEL1; smart00671 423212003281 Sel1-like repeats; Region: SEL1; smart00671 423212003282 Sel1-like repeats; Region: SEL1; smart00671 423212003283 Sel1-like repeats; Region: SEL1; smart00671 423212003284 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 423212003285 Sel1-like repeats; Region: SEL1; smart00671 423212003286 Sel1-like repeats; Region: SEL1; smart00671 423212003287 Sel1-like repeats; Region: SEL1; smart00671 423212003288 Sel1-like repeats; Region: SEL1; smart00671 423212003289 Sel1-like repeats; Region: SEL1; smart00671 423212003290 Sel1-like repeats; Region: SEL1; smart00671 423212003291 Sel1-like repeats; Region: SEL1; smart00671 423212003292 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 423212003293 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 423212003294 dimer interface [polypeptide binding]; other site 423212003295 phosphorylation site [posttranslational modification] 423212003296 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 423212003297 ATP binding site [chemical binding]; other site 423212003298 Mg2+ binding site [ion binding]; other site 423212003299 G-X-G motif; other site 423212003300 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 423212003301 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 423212003302 active site 423212003303 phosphorylation site [posttranslational modification] 423212003304 intermolecular recognition site; other site 423212003305 dimerization interface [polypeptide binding]; other site 423212003306 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 423212003307 Walker A motif; other site 423212003308 ATP binding site [chemical binding]; other site 423212003309 Walker B motif; other site 423212003310 arginine finger; other site 423212003311 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 423212003312 AsnC family; Region: AsnC_trans_reg; pfam01037 423212003313 Peptidase family M48; Region: Peptidase_M48; pfam01435 423212003314 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 423212003315 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 423212003316 catalytic motif [active] 423212003317 Zn binding site [ion binding]; other site 423212003318 RibD C-terminal domain; Region: RibD_C; cl17279 423212003319 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 423212003320 Lumazine binding domain; Region: Lum_binding; pfam00677 423212003321 Lumazine binding domain; Region: Lum_binding; pfam00677 423212003322 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 423212003323 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 423212003324 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 423212003325 dimerization interface [polypeptide binding]; other site 423212003326 active site 423212003327 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 423212003328 homopentamer interface [polypeptide binding]; other site 423212003329 active site 423212003330 CTP synthetase; Validated; Region: pyrG; PRK05380 423212003331 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 423212003332 Catalytic site [active] 423212003333 active site 423212003334 UTP binding site [chemical binding]; other site 423212003335 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 423212003336 active site 423212003337 putative oxyanion hole; other site 423212003338 catalytic triad [active] 423212003339 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 423212003340 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 423212003341 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 423212003342 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 423212003343 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 423212003344 Putative exonuclease, RdgC; Region: RdgC; pfam04381 423212003345 K+ potassium transporter; Region: K_trans; pfam02705 423212003346 Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase; Region: PUA; smart00359 423212003347 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 423212003348 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 423212003349 putative RNA binding site [nucleotide binding]; other site 423212003350 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 423212003351 S-adenosylmethionine binding site [chemical binding]; other site 423212003352 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 423212003353 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 423212003354 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 423212003355 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_2; cd03139 423212003356 conserved cys residue [active] 423212003357 Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]; Region: HisI; COG0139 423212003358 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 423212003359 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 423212003360 metal binding site [ion binding]; metal-binding site 423212003361 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 423212003362 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 423212003363 substrate binding site [chemical binding]; other site 423212003364 glutamase interaction surface [polypeptide binding]; other site 423212003365 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 423212003366 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 423212003367 catalytic residues [active] 423212003368 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13170 423212003369 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 423212003370 putative active site [active] 423212003371 oxyanion strand; other site 423212003372 catalytic triad [active] 423212003373 imidazole glycerol-phosphate dehydratase/histidinol phosphatase; Provisional; Region: PRK05446 423212003374 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 423212003375 active site 423212003376 motif I; other site 423212003377 motif II; other site 423212003378 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 423212003379 putative active site pocket [active] 423212003380 4-fold oligomerization interface [polypeptide binding]; other site 423212003381 metal binding residues [ion binding]; metal-binding site 423212003382 3-fold/trimer interface [polypeptide binding]; other site 423212003383 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 423212003384 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 423212003385 pyridoxal 5'-phosphate binding site [chemical binding]; other site 423212003386 homodimer interface [polypeptide binding]; other site 423212003387 catalytic residue [active] 423212003388 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 423212003389 histidinol dehydrogenase; Region: hisD; TIGR00069 423212003390 NAD binding site [chemical binding]; other site 423212003391 dimerization interface [polypeptide binding]; other site 423212003392 product binding site; other site 423212003393 substrate binding site [chemical binding]; other site 423212003394 zinc binding site [ion binding]; other site 423212003395 catalytic residues [active] 423212003396 ATP phosphoribosyltransferase; Reviewed; Region: hisG; PRK00489 423212003397 ATP phosphoribosyltransferase; Region: hisG; TIGR00070 423212003398 ATP phosphoribosyltransferase, C-terminal domain; Region: HisG_C-term; TIGR03455 423212003399 Trp repressor protein; Region: Trp_repressor; cl17266 423212003400 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 423212003401 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 423212003402 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 423212003403 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 423212003404 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 423212003405 active site 423212003406 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 423212003407 DNA-binding site [nucleotide binding]; DNA binding site 423212003408 RNA-binding motif; other site 423212003409 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 423212003410 30S subunit binding site; other site 423212003411 YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, ProX, and PrdX. The primary function of INS is to hydrolyze...; Region: YbaK_like; cd04332 423212003412 putative deacylase active site [active] 423212003413 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 423212003414 MarR family; Region: MarR_2; pfam12802 423212003415 MarR family; Region: MarR_2; cl17246 423212003416 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 423212003417 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 423212003418 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 423212003419 LysE type translocator; Region: LysE; cl00565 423212003420 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 423212003421 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 423212003422 Coenzyme A binding pocket [chemical binding]; other site 423212003423 Predicted ATPase [General function prediction only]; Region: COG3911 423212003424 AAA domain; Region: AAA_28; pfam13521 423212003425 Major Facilitator Superfamily; Region: MFS_1; pfam07690 423212003426 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 423212003427 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 423212003428 flagellar basal body rod protein FlgB; Provisional; Region: flgB; PRK12619 423212003429 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 423212003430 flagellar basal body rod protein FlgC; Provisional; Region: flgC; PRK12628 423212003431 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 423212003432 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK12634 423212003433 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 423212003434 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 423212003435 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 423212003436 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 423212003437 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 423212003438 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 423212003439 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 423212003440 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 423212003441 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 423212003442 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 423212003443 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 423212003444 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK12701 423212003445 Flagellar L-ring protein; Region: FlgH; pfam02107 423212003446 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 423212003447 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 423212003448 flagellar rod assembly protein/muramidase FlgJ; Provisional; Region: flgJ; PRK12710 423212003449 Rod binding protein; Region: Rod-binding; cl01626 423212003450 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 423212003451 flagellar hook-associated protein FlgK; Provisional; Region: flgK; PRK12715 423212003452 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 423212003453 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 423212003454 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 423212003455 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 423212003456 ExoU and VipD-like proteins; homologus to patatin, cPLA2, and iPLA2; Region: Pat_ExoU_VipD_like; cd07207 423212003457 active site 423212003458 nucleophile elbow; other site 423212003459 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 423212003460 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 423212003461 transmembrane helices; other site 423212003462 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 423212003463 TrkA-C domain; Region: TrkA_C; pfam02080 423212003464 TrkA-C domain; Region: TrkA_C; pfam02080 423212003465 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 423212003466 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 423212003467 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 423212003468 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 423212003469 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 423212003470 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 423212003471 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 423212003472 Walker A/P-loop; other site 423212003473 ATP binding site [chemical binding]; other site 423212003474 Q-loop/lid; other site 423212003475 ABC transporter signature motif; other site 423212003476 Walker B; other site 423212003477 D-loop; other site 423212003478 H-loop/switch region; other site 423212003479 Protein of unknown function (DUF2845); Region: DUF2845; pfam11006 423212003480 Chagasin family peptidase inhibitor I42; Region: Inhibitor_I42; pfam09394 423212003481 malate dehydrogenase; Provisional; Region: PRK13529 423212003482 Malic enzyme, N-terminal domain; Region: malic; pfam00390 423212003483 NAD(P) binding domain of malic enzyme (ME), subgroup 1; Region: NAD_bind_1_malic_enz; cd05312 423212003484 NAD(P) binding site [chemical binding]; other site 423212003485 RNA polymerase factor sigma-54; Provisional; Region: PRK12469 423212003486 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 423212003487 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 423212003488 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 423212003489 Peptidase family M23; Region: Peptidase_M23; pfam01551 423212003490 RNA polymerase sigma factor RpoS; Region: rpoS_proteo; TIGR02394 423212003491 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 423212003492 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 423212003493 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 423212003494 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 423212003495 DNA binding residues [nucleotide binding] 423212003496 homogentisate 1,2-dioxygenase; Provisional; Region: PRK05341 423212003497 hypothetical protein; Validated; Region: PRK00110 423212003498 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 423212003499 active site 423212003500 putative DNA-binding cleft [nucleotide binding]; other site 423212003501 dimer interface [polypeptide binding]; other site 423212003502 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 423212003503 RuvA N terminal domain; Region: RuvA_N; pfam01330 423212003504 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 423212003505 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 423212003506 sensor protein QseC; Provisional; Region: PRK10337 423212003507 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 423212003508 dimer interface [polypeptide binding]; other site 423212003509 phosphorylation site [posttranslational modification] 423212003510 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 423212003511 ATP binding site [chemical binding]; other site 423212003512 Mg2+ binding site [ion binding]; other site 423212003513 G-X-G motif; other site 423212003514 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 423212003515 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 423212003516 active site 423212003517 phosphorylation site [posttranslational modification] 423212003518 intermolecular recognition site; other site 423212003519 dimerization interface [polypeptide binding]; other site 423212003520 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 423212003521 DNA binding site [nucleotide binding] 423212003522 intracellular septation protein A; Reviewed; Region: PRK00259 423212003523 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 423212003524 N-acetyl-D-glucosamine binding site [chemical binding]; other site 423212003525 catalytic residue [active] 423212003526 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 423212003527 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 423212003528 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 423212003529 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 423212003530 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 423212003531 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 423212003532 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 423212003533 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 423212003534 homodimer interface [polypeptide binding]; other site 423212003535 NADP binding site [chemical binding]; other site 423212003536 substrate binding site [chemical binding]; other site 423212003537 FimV N-terminal domain; Region: FimV_core; TIGR03505 423212003538 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 423212003539 Predicted integral membrane protein (DUF2269); Region: DUF2269; pfam10027 423212003540 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 423212003541 NADH(P)-binding; Region: NAD_binding_10; pfam13460 423212003542 putative NAD(P) binding site [chemical binding]; other site 423212003543 active site 423212003544 DoxX-like family; Region: DoxX_3; pfam13781 423212003545 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 423212003546 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 423212003547 dimerization interface 3.5A [polypeptide binding]; other site 423212003548 active site 423212003549 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 423212003550 active site 423212003551 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 423212003552 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 423212003553 pyridoxal 5'-phosphate binding site [chemical binding]; other site 423212003554 catalytic residue [active] 423212003555 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 423212003556 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 423212003557 substrate binding site [chemical binding]; other site 423212003558 active site 423212003559 catalytic residues [active] 423212003560 heterodimer interface [polypeptide binding]; other site 423212003561 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 423212003562 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 423212003563 active site 423212003564 HIGH motif; other site 423212003565 nucleotide binding site [chemical binding]; other site 423212003566 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 423212003567 KMSKS motif; other site 423212003568 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 423212003569 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 423212003570 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 423212003571 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 423212003572 KMSKS motif; other site 423212003573 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 423212003574 tRNA binding surface [nucleotide binding]; other site 423212003575 anticodon binding site; other site 423212003576 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 423212003577 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 423212003578 Sulfatase; Region: Sulfatase; pfam00884 423212003579 type II secretion system protein E; Region: type_II_gspE; TIGR02533 423212003580 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 423212003581 Walker A motif; other site 423212003582 ATP binding site [chemical binding]; other site 423212003583 Walker B motif; other site 423212003584 Sporulation related domain; Region: SPOR; pfam05036 423212003585 type II secretion system protein D; Region: type_II_gspD; TIGR02517 423212003586 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 423212003587 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 423212003588 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 423212003589 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 423212003590 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 423212003591 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 423212003592 Cache domain; Region: Cache_1; pfam02743 423212003593 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 423212003594 cyclase homology domain; Region: CHD; cd07302 423212003595 nucleotidyl binding site; other site 423212003596 metal binding site [ion binding]; metal-binding site 423212003597 dimer interface [polypeptide binding]; other site 423212003598 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 423212003599 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 423212003600 putative substrate translocation pore; other site 423212003601 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 423212003602 Major Facilitator Superfamily; Region: MFS_1; pfam07690 423212003603 putative substrate translocation pore; other site 423212003604 IucA / IucC family; Region: IucA_IucC; pfam04183 423212003605 Ferric iron reductase FhuF-like transporter; Region: FhuF; pfam06276 423212003606 Domain of unknown function (DUF4286); Region: DUF4286; pfam14114 423212003607 glycoside hydrolase family 64 (beta-1,3-glucanases which produce specific pentasaccharide oligomers) and thaumatin-like proteins; Region: GH64-TLP-SF; cl02511 423212003608 glycoside hydrolase family 64 (beta-1,3-glucanases which produce specific pentasaccharide oligomers) and thaumatin-like proteins; Region: GH64-TLP-SF; cl02511 423212003609 Sporulation related domain; Region: SPOR; pfam05036 423212003610 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 423212003611 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 423212003612 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 423212003613 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 423212003614 protein binding site [polypeptide binding]; other site 423212003615 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 423212003616 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 423212003617 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 423212003618 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 423212003619 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 423212003620 RNA binding surface [nucleotide binding]; other site 423212003621 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 423212003622 active site 423212003623 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 423212003624 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 423212003625 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 423212003626 FeS/SAM binding site; other site 423212003627 TRAM domain; Region: TRAM; pfam01938 423212003628 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 423212003629 putative substrate translocation pore; other site 423212003630 Major Facilitator Superfamily; Region: MFS_1; pfam07690 423212003631 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 423212003632 Flagellar protein FliS; Region: FliS; cl00654 423212003633 flagellar capping protein; Provisional; Region: PRK12765 423212003634 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 423212003635 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 423212003636 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 423212003637 flagellin; Provisional; Region: PRK12806 423212003638 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 423212003639 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 423212003640 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 423212003641 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 423212003642 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 423212003643 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 423212003644 Uncharacterized protein conserved in bacteria [Function unknown]; Region: DedD; COG3147 423212003645 Sporulation related domain; Region: SPOR; pfam05036 423212003646 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 423212003647 Colicin V production protein; Region: Colicin_V; pfam02674 423212003648 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 423212003649 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 423212003650 active site 423212003651 (T/H)XGH motif; other site 423212003652 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 423212003653 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 423212003654 Lipopolysaccharide-assembly; Region: LptE; cl01125 423212003655 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 423212003656 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 423212003657 HIGH motif; other site 423212003658 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 423212003659 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 423212003660 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 423212003661 active site 423212003662 KMSKS motif; other site 423212003663 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 423212003664 tRNA binding surface [nucleotide binding]; other site 423212003665 apolipoprotein N-acyltransferase; Region: lnt; TIGR00546 423212003666 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 423212003667 putative active site [active] 423212003668 catalytic triad [active] 423212003669 putative dimer interface [polypeptide binding]; other site 423212003670 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 423212003671 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 423212003672 aldehyde dehydrogenase family 7 member; Region: PLN02315 423212003673 NAD+-dependent alpha-aminoadipic semialdehyde dehydrogenase, ALDH family members 7A1 and 7B; Region: ALDH_F7_AASADH; cd07130 423212003674 tetrameric interface [polypeptide binding]; other site 423212003675 NAD binding site [chemical binding]; other site 423212003676 catalytic residues [active] 423212003677 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 423212003678 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 423212003679 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 423212003680 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 423212003681 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 423212003682 substrate binding site [chemical binding]; other site 423212003683 oxyanion hole (OAH) forming residues; other site 423212003684 trimer interface [polypeptide binding]; other site 423212003685 acetyl-CoA acetyltransferase; Provisional; Region: PRK09052 423212003686 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 423212003687 dimer interface [polypeptide binding]; other site 423212003688 active site 423212003689 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 423212003690 Sel1-like repeats; Region: SEL1; smart00671 423212003691 Sel1-like repeats; Region: SEL1; smart00671 423212003692 Sel1-like repeats; Region: SEL1; smart00671 423212003693 Sel1-like repeats; Region: SEL1; smart00671 423212003694 Sel1-like repeats; Region: SEL1; smart00671 423212003695 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212003696 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212003697 metal binding site [ion binding]; metal-binding site 423212003698 active site 423212003699 I-site; other site 423212003700 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 423212003701 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 423212003702 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 423212003703 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 423212003704 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 423212003705 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 423212003706 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 423212003707 type II secretion system protein J; Region: gspJ; TIGR01711 423212003708 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 423212003709 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 423212003710 Type II transport protein GspH; Region: GspH; pfam12019 423212003711 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 423212003712 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 423212003713 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 423212003714 type II secretion system protein F; Region: GspF; TIGR02120 423212003715 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 423212003716 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 423212003717 glutamine synthetase; Provisional; Region: glnA; PRK09469 423212003718 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 423212003719 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 423212003720 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 423212003721 hypothetical protein; Validated; Region: PRK02101 423212003722 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 423212003723 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 423212003724 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 423212003725 catalytic residue [active] 423212003726 heat shock protein 90; Provisional; Region: PRK05218 423212003727 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 423212003728 ATP binding site [chemical binding]; other site 423212003729 Mg2+ binding site [ion binding]; other site 423212003730 G-X-G motif; other site 423212003731 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 423212003732 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 423212003733 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 423212003734 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 423212003735 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 423212003736 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 423212003737 RNA/DNA hybrid binding site [nucleotide binding]; other site 423212003738 active site 423212003739 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 423212003740 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 423212003741 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 423212003742 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 423212003743 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 423212003744 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 423212003745 POT family; Region: PTR2; cl17359 423212003746 amino acid/peptide transporter (Peptide:H+ symporter), bacterial; Region: yjdL_sub1_fam; TIGR00924 423212003747 urocanate hydratase; Provisional; Region: PRK05414 423212003748 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 423212003749 active sites [active] 423212003750 tetramer interface [polypeptide binding]; other site 423212003751 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 423212003752 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 423212003753 NAD(P) binding site [chemical binding]; other site 423212003754 catalytic residues [active] 423212003755 short chain dehydrogenase; Provisional; Region: PRK08278 423212003756 human hydroxysteroid dehydrogenase-like protein 2 (HSDL2), classical (c) SDRs; Region: HSDL2_SDR_c; cd09762 423212003757 NAD(P) binding site [chemical binding]; other site 423212003758 homodimer interface [polypeptide binding]; other site 423212003759 active site 423212003760 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 423212003761 RNA/DNA hybrid binding site [nucleotide binding]; other site 423212003762 active site 423212003763 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 423212003764 DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; Region: DNA_pol_III_epsilon_Ecoli_like; cd06131 423212003765 active site 423212003766 catalytic site [active] 423212003767 substrate binding site [chemical binding]; other site 423212003768 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 423212003769 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 423212003770 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 423212003771 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 423212003772 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 423212003773 Ligand Binding Site [chemical binding]; other site 423212003774 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 423212003775 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 423212003776 putative phosphate acyltransferase; Provisional; Region: PRK05331 423212003777 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 423212003778 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 423212003779 dimer interface [polypeptide binding]; other site 423212003780 active site 423212003781 CoA binding pocket [chemical binding]; other site 423212003782 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 423212003783 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 423212003784 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 423212003785 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 423212003786 NAD(P) binding site [chemical binding]; other site 423212003787 homotetramer interface [polypeptide binding]; other site 423212003788 homodimer interface [polypeptide binding]; other site 423212003789 active site 423212003790 acyl carrier protein; Provisional; Region: acpP; PRK00982 423212003791 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 423212003792 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 423212003793 dimer interface [polypeptide binding]; other site 423212003794 active site 423212003795 YceG-like family; Region: YceG; pfam02618 423212003796 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 423212003797 dimerization interface [polypeptide binding]; other site 423212003798 thymidylate kinase; Validated; Region: tmk; PRK00698 423212003799 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 423212003800 TMP-binding site; other site 423212003801 ATP-binding site [chemical binding]; other site 423212003802 DNA polymerase III, delta subunit; Region: DNA_pol3_delta2; pfam13177 423212003803 DNA polymerase III subunit delta'; Validated; Region: PRK08485 423212003804 PilZ domain; Region: PilZ; cl01260 423212003805 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 423212003806 active site 423212003807 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 423212003808 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 423212003809 Major Facilitator Superfamily; Region: MFS_1; pfam07690 423212003810 putative substrate translocation pore; other site 423212003811 multidrug efflux system translocase MdfA; Provisional; Region: PRK15402 423212003812 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 423212003813 dolichyl-phosphate beta-D-mannosyltransferase; Region: PLN02726 423212003814 DPM1_like represents putative enzymes similar to eukaryotic DPM1; Region: DPM1_like; cd06442 423212003815 Ligand binding site; other site 423212003816 Putative Catalytic site; other site 423212003817 DXD motif; other site 423212003818 GtrA-like protein; Region: GtrA; pfam04138 423212003819 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 423212003820 Choline Kinase (ChoK). The ChoK subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and...; Region: ChoK; cd05151 423212003821 Phosphotransferase enzyme family; Region: APH; pfam01636 423212003822 active site 423212003823 ATP binding site [chemical binding]; other site 423212003824 substrate binding site [chemical binding]; other site 423212003825 dimer interface [polypeptide binding]; other site 423212003826 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 423212003827 active site 423212003828 catalytic site [active] 423212003829 substrate binding site [chemical binding]; other site 423212003830 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 423212003831 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 423212003832 N-acetyl-D-glucosamine binding site [chemical binding]; other site 423212003833 catalytic residue [active] 423212003834 adenylate kinase; Reviewed; Region: adk; PRK00279 423212003835 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 423212003836 AMP-binding site [chemical binding]; other site 423212003837 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 423212003838 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 423212003839 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 423212003840 catalytic residues [active] 423212003841 glycerol-3-phosphate dehydrogenase; Reviewed; Region: glpD; PRK12266 423212003842 Glycerol kinase [Energy production and conversion]; Region: GlpK; COG0554 423212003843 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 423212003844 N- and C-terminal domain interface [polypeptide binding]; other site 423212003845 active site 423212003846 MgATP binding site [chemical binding]; other site 423212003847 catalytic site [active] 423212003848 metal binding site [ion binding]; metal-binding site 423212003849 glycerol binding site [chemical binding]; other site 423212003850 homotetramer interface [polypeptide binding]; other site 423212003851 homodimer interface [polypeptide binding]; other site 423212003852 FBP binding site [chemical binding]; other site 423212003853 protein IIAGlc interface [polypeptide binding]; other site 423212003854 Escherichia coli (Ec) citrate synthase (CS) GltA_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS...; Region: EcCS_like; cd06114 423212003855 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 423212003856 dimer interface [polypeptide binding]; other site 423212003857 active site 423212003858 citrylCoA binding site [chemical binding]; other site 423212003859 NADH binding [chemical binding]; other site 423212003860 cationic pore residues; other site 423212003861 oxalacetate/citrate binding site [chemical binding]; other site 423212003862 coenzyme A binding site [chemical binding]; other site 423212003863 catalytic triad [active] 423212003864 Phosphorylase superfamily; Region: PNP_UDP_1; pfam01048 423212003865 DNA gyrase subunit A; Validated; Region: PRK05560 423212003866 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 423212003867 CAP-like domain; other site 423212003868 active site 423212003869 primary dimer interface [polypeptide binding]; other site 423212003870 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 423212003871 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 423212003872 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 423212003873 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 423212003874 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 423212003875 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 423212003876 3-phosphoserine/phosphohydroxythreonine aminotransferase; Provisional; Region: PRK05355 423212003877 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 423212003878 catalytic residue [active] 423212003879 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 423212003880 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 423212003881 hinge; other site 423212003882 active site 423212003883 cytidylate kinase; Provisional; Region: cmk; PRK00023 423212003884 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 423212003885 CMP-binding site; other site 423212003886 The sites determining sugar specificity; other site 423212003887 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 423212003888 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 423212003889 RNA binding site [nucleotide binding]; other site 423212003890 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 423212003891 RNA binding site [nucleotide binding]; other site 423212003892 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 423212003893 RNA binding site [nucleotide binding]; other site 423212003894 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 423212003895 RNA binding site [nucleotide binding]; other site 423212003896 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 423212003897 RNA binding site [nucleotide binding]; other site 423212003898 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec6; cd05691 423212003899 RNA binding site [nucleotide binding]; other site 423212003900 Protein of unknown function (DUF1049); Region: DUF1049; pfam06305 423212003901 tetratricopeptide repeat protein; Provisional; Region: PRK11788 423212003902 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 423212003903 TPR motif; other site 423212003904 binding surface 423212003905 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 423212003906 binding surface 423212003907 TPR motif; other site 423212003908 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 423212003909 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 423212003910 inhibitor-cofactor binding pocket; inhibition site 423212003911 pyridoxal 5'-phosphate binding site [chemical binding]; other site 423212003912 catalytic residue [active] 423212003913 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 423212003914 active site 423212003915 dimer interface [polypeptide binding]; other site 423212003916 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 423212003917 ExoU and VipD-like proteins; homologus to patatin, cPLA2, and iPLA2; Region: Pat_ExoU_VipD_like; cd07207 423212003918 active site 423212003919 nucleophile elbow; other site 423212003920 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 423212003921 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 423212003922 classical (c) SDRs; Region: SDR_c; cd05233 423212003923 NAD(P) binding site [chemical binding]; other site 423212003924 active site 423212003925 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 423212003926 Chorismate lyase; Region: Chor_lyase; cl01230 423212003927 4-hydroxybenzoate polyprenyltransferase; Reviewed; Region: ubiA; PRK12847 423212003928 UbiA prenyltransferase family; Region: UbiA; pfam01040 423212003929 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 423212003930 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 423212003931 FAD binding domain; Region: FAD_binding_4; pfam01565 423212003932 Berberine and berberine like; Region: BBE; pfam08031 423212003933 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 423212003934 intersubunit interface [polypeptide binding]; other site 423212003935 active site 423212003936 catalytic residue [active] 423212003937 purine nucleoside phosphorylase; Provisional; Region: PRK08202 423212003938 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 423212003939 active site 423212003940 catalytic motif [active] 423212003941 Zn binding site [ion binding]; other site 423212003942 two-component sensor protein; Provisional; Region: cpxA; PRK09470 423212003943 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 423212003944 dimerization interface [polypeptide binding]; other site 423212003945 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 423212003946 dimer interface [polypeptide binding]; other site 423212003947 phosphorylation site [posttranslational modification] 423212003948 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 423212003949 ATP binding site [chemical binding]; other site 423212003950 Mg2+ binding site [ion binding]; other site 423212003951 G-X-G motif; other site 423212003952 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 423212003953 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 423212003954 active site 423212003955 phosphorylation site [posttranslational modification] 423212003956 intermolecular recognition site; other site 423212003957 dimerization interface [polypeptide binding]; other site 423212003958 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 423212003959 DNA binding site [nucleotide binding] 423212003960 FOG: CBS domain [General function prediction only]; Region: COG0517 423212003961 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 423212003962 Transporter associated domain; Region: CorC_HlyC; smart01091 423212003963 metal-binding heat shock protein; Provisional; Region: PRK00016 423212003964 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 423212003965 PhoH-like protein; Region: PhoH; pfam02562 423212003966 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 423212003967 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 423212003968 active site 423212003969 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 423212003970 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 423212003971 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 423212003972 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 423212003973 active site 423212003974 HIGH motif; other site 423212003975 dimer interface [polypeptide binding]; other site 423212003976 KMSKS motif; other site 423212003977 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 423212003978 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 423212003979 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 423212003980 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 423212003981 RNA binding surface [nucleotide binding]; other site 423212003982 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 423212003983 probable active site [active] 423212003984 Type I periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides; Region: PBP1_NHase; cd06358 423212003985 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 423212003986 putative ligand binding site [chemical binding]; other site 423212003987 PAS domain S-box; Region: sensory_box; TIGR00229 423212003988 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 423212003989 putative active site [active] 423212003990 heme pocket [chemical binding]; other site 423212003991 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212003992 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212003993 metal binding site [ion binding]; metal-binding site 423212003994 active site 423212003995 I-site; other site 423212003996 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 423212003997 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 423212003998 substrate binding site [chemical binding]; other site 423212003999 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 423212004000 putative transporter; Provisional; Region: PRK10504 423212004001 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 423212004002 putative substrate translocation pore; other site 423212004003 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 423212004004 TRAM domain; Region: TRAM; pfam01938 423212004005 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 423212004006 S-adenosylmethionine binding site [chemical binding]; other site 423212004007 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 423212004008 HD domain; Region: HD_4; pfam13328 423212004009 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 423212004010 synthetase active site [active] 423212004011 NTP binding site [chemical binding]; other site 423212004012 metal binding site [ion binding]; metal-binding site 423212004013 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 423212004014 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 423212004015 Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome; Region: Xcc1710_like; cd05560 423212004016 aminotransferase; Validated; Region: PRK08175 423212004017 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 423212004018 pyridoxal 5'-phosphate binding site [chemical binding]; other site 423212004019 homodimer interface [polypeptide binding]; other site 423212004020 catalytic residue [active] 423212004021 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4255 423212004022 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 423212004023 DHH family; Region: DHH; pfam01368 423212004024 DHHA1 domain; Region: DHHA1; pfam02272 423212004025 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 423212004026 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 423212004027 FMN binding site [chemical binding]; other site 423212004028 active site 423212004029 catalytic residues [active] 423212004030 substrate binding site [chemical binding]; other site 423212004031 preprotein translocase subunit SecA; Reviewed; Region: secA; PRK13104 423212004032 DEAD/DEAH box helicase; Region: DEAD; pfam00270 423212004033 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 423212004034 SEC-C motif; Region: SEC-C; pfam02810 423212004035 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 423212004036 active site 423212004037 8-oxo-dGMP binding site [chemical binding]; other site 423212004038 nudix motif; other site 423212004039 metal binding site [ion binding]; metal-binding site 423212004040 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; pfam13557 423212004041 hypothetical protein; Provisional; Region: PRK05287 423212004042 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 423212004043 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 423212004044 CoA-binding site [chemical binding]; other site 423212004045 ATP-binding [chemical binding]; other site 423212004046 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 423212004047 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 423212004048 adenosylmethionine-8-amino-7-oxononanoate transaminase; Region: bioA; TIGR00508 423212004049 inhibitor-cofactor binding pocket; inhibition site 423212004050 pyridoxal 5'-phosphate binding site [chemical binding]; other site 423212004051 catalytic residue [active] 423212004052 biotin synthase; Region: bioB; TIGR00433 423212004053 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 423212004054 FeS/SAM binding site; other site 423212004055 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 423212004056 8-amino-7-oxononanoate synthase; Reviewed; Region: PRK05958 423212004057 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 423212004058 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 423212004059 catalytic residue [active] 423212004060 pimelyl-[acyl-carrier protein] methyl ester esterase; Region: bioH; TIGR01738 423212004061 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 423212004062 AAA domain; Region: AAA_26; pfam13500 423212004063 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 423212004064 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 423212004065 Uncharacterized conserved protein [Function unknown]; Region: COG2928 423212004066 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 423212004067 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 423212004068 dimer interface [polypeptide binding]; other site 423212004069 anticodon binding site; other site 423212004070 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 423212004071 homodimer interface [polypeptide binding]; other site 423212004072 motif 1; other site 423212004073 active site 423212004074 motif 2; other site 423212004075 GAD domain; Region: GAD; pfam02938 423212004076 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 423212004077 motif 3; other site 423212004078 CENP-A-nucleosome distal (CAD) centromere subunit; Region: CENP-Q; pfam13094 423212004079 Mechanosensitive ion channel inner membrane domain 1; Region: MscS_TM; pfam12794 423212004080 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 423212004081 Mechanosensitive ion channel; Region: MS_channel; pfam00924 423212004082 MutH is a 28kD endonuclease involved in methyl-directed DNA mismatch repair in gram negative bacteria. MutH is both sequence-specific and methylation-specific, introducing a nick in the unmethylated strand of a hemi-methylated d(GATC) DNA duplex. MutH...; Region: MutH_Sau3AI; cd00583 423212004083 putative DNA-binding cleft [nucleotide binding]; other site 423212004084 putative DNA clevage site; other site 423212004085 molecular lever; other site 423212004086 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 423212004087 Catalytic domain of Protein Kinases; Region: PKc; cd00180 423212004088 active site 423212004089 ATP binding site [chemical binding]; other site 423212004090 substrate binding site [chemical binding]; other site 423212004091 activation loop (A-loop); other site 423212004092 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 423212004093 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 423212004094 putative DNA binding site [nucleotide binding]; other site 423212004095 putative Zn2+ binding site [ion binding]; other site 423212004096 AsnC family; Region: AsnC_trans_reg; pfam01037 423212004097 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 423212004098 Coenzyme A binding pocket [chemical binding]; other site 423212004099 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 423212004100 GAF domain; Region: GAF; pfam01590 423212004101 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 423212004102 cyclase homology domain; Region: CHD; cd07302 423212004103 nucleotidyl binding site; other site 423212004104 metal binding site [ion binding]; metal-binding site 423212004105 dimer interface [polypeptide binding]; other site 423212004106 Pathogenicity locus; Region: Cdd1; pfam11731 423212004107 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 423212004108 Phosphotransferase enzyme family; Region: APH; pfam01636 423212004109 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 423212004110 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 423212004111 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 423212004112 putative active site pocket [active] 423212004113 dimerization interface [polypeptide binding]; other site 423212004114 putative catalytic residue [active] 423212004115 Dot/Icm substrate protein; Region: SidE; pfam12252 423212004116 aminopeptidase N; Provisional; Region: pepN; PRK14015 423212004117 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 423212004118 Zn binding site [ion binding]; other site 423212004119 C factor cell-cell signaling protein; Provisional; Region: PRK09009 423212004120 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 423212004121 NAD(P) binding site [chemical binding]; other site 423212004122 active site 423212004123 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 423212004124 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 423212004125 Coenzyme A binding pocket [chemical binding]; other site 423212004126 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 423212004127 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 423212004128 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 423212004129 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 423212004130 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 423212004131 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 423212004132 E3 interaction surface; other site 423212004133 lipoyl attachment site [posttranslational modification]; other site 423212004134 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 423212004135 E3 interaction surface; other site 423212004136 lipoyl attachment site [posttranslational modification]; other site 423212004137 e3 binding domain; Region: E3_binding; pfam02817 423212004138 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 423212004139 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 423212004140 Thiamine pyrophosphate (TPP) family, E1 of E. coli PDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDC). PDC catalyzes the oxidative...; Region: TPP_E1_EcPDC_like; cd02017 423212004141 dimer interface [polypeptide binding]; other site 423212004142 TPP-binding site [chemical binding]; other site 423212004143 Membrane protein required for beta-lactamase induction [Defense mechanisms]; Region: AmpE; cl17896 423212004144 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 423212004145 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 423212004146 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 423212004147 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 423212004148 Sporulation related domain; Region: SPOR; pfam05036 423212004149 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 423212004150 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 423212004151 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; smart00936 423212004152 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 423212004153 D-Alanine aminotransferase (D-AAT_like): D-amino acid aminotransferase catalyzes transamination between D-amino acids and their respective alpha-keto acids. It plays a major role in the synthesis of bacterial cell wall components like D-alanine and...; Region: D-AAT_like; cd01558 423212004154 homodimer interface [polypeptide binding]; other site 423212004155 substrate-cofactor binding pocket; other site 423212004156 pyridoxal 5'-phosphate binding site [chemical binding]; other site 423212004157 catalytic residue [active] 423212004158 Protein of unknown function (DUF493); Region: DUF493; pfam04359 423212004159 lipoate-protein ligase B; Provisional; Region: PRK14342 423212004160 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 423212004161 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 423212004162 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 423212004163 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 423212004164 active site 423212004165 LssY C-terminus; Region: LssY_C; pfam14067 423212004166 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 423212004167 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 423212004168 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39_likeD; cd02421 423212004169 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 423212004170 ATP-binding cassette domain of bacteriocin exporters, subfamily C; Region: ABCC_bacteriocin_exporters; cd03245 423212004171 Walker A/P-loop; other site 423212004172 ATP binding site [chemical binding]; other site 423212004173 Q-loop/lid; other site 423212004174 ABC transporter signature motif; other site 423212004175 Walker B; other site 423212004176 D-loop; other site 423212004177 H-loop/switch region; other site 423212004178 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 423212004179 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 423212004180 HlyD family secretion protein; Region: HlyD_3; pfam13437 423212004181 PAS domain S-box; Region: sensory_box; TIGR00229 423212004182 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212004183 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212004184 metal binding site [ion binding]; metal-binding site 423212004185 active site 423212004186 I-site; other site 423212004187 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 423212004188 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 423212004189 active site 423212004190 Domain of unknown function (DUF1820); Region: DUF1820; pfam08850 423212004191 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 423212004192 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 423212004193 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 423212004194 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 423212004195 Walker A motif; other site 423212004196 ATP binding site [chemical binding]; other site 423212004197 Walker B motif; other site 423212004198 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 423212004199 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 423212004200 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 423212004201 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 423212004202 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 423212004203 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 423212004204 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 423212004205 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 423212004206 ligand binding site [chemical binding]; other site 423212004207 CAAX protease self-immunity; Region: Abi; pfam02517 423212004208 PEP synthetase regulatory protein; Provisional; Region: PRK05339 423212004209 2-methylcitrate dehydratase; Provisional; Region: prpD; PRK09425 423212004210 2-methylcitrate dehydratase; Region: prpD; TIGR02330 423212004211 Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (CS) catalyzes...; Region: Ec2MCS_like; cd06108 423212004212 dimer interface [polypeptide binding]; other site 423212004213 Citrate synthase; Region: Citrate_synt; pfam00285 423212004214 active site 423212004215 citrylCoA binding site [chemical binding]; other site 423212004216 oxalacetate/citrate binding site [chemical binding]; other site 423212004217 coenzyme A binding site [chemical binding]; other site 423212004218 catalytic triad [active] 423212004219 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 423212004220 Uncharacterized conserved protein [Function unknown]; Region: COG4121 423212004221 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 423212004222 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 423212004223 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 423212004224 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 423212004225 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 423212004226 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 423212004227 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 423212004228 inhibitor-cofactor binding pocket; inhibition site 423212004229 pyridoxal 5'-phosphate binding site [chemical binding]; other site 423212004230 catalytic residue [active] 423212004231 Rubredoxin [Energy production and conversion]; Region: COG1773 423212004232 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 423212004233 iron binding site [ion binding]; other site 423212004234 Uncharacterized protein family (UPF0093); Region: UPF0093; pfam03653 423212004235 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 423212004236 poly(A) polymerase; Region: pcnB; TIGR01942 423212004237 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 423212004238 active site 423212004239 NTP binding site [chemical binding]; other site 423212004240 metal binding triad [ion binding]; metal-binding site 423212004241 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 423212004242 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 423212004243 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 423212004244 catalytic center binding site [active] 423212004245 ATP binding site [chemical binding]; other site 423212004246 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 423212004247 Ligand Binding Site [chemical binding]; other site 423212004248 GTP-binding protein Der; Reviewed; Region: PRK00093 423212004249 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 423212004250 G1 box; other site 423212004251 GTP/Mg2+ binding site [chemical binding]; other site 423212004252 Switch I region; other site 423212004253 G2 box; other site 423212004254 Switch II region; other site 423212004255 G3 box; other site 423212004256 G4 box; other site 423212004257 G5 box; other site 423212004258 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 423212004259 G1 box; other site 423212004260 GTP/Mg2+ binding site [chemical binding]; other site 423212004261 Switch I region; other site 423212004262 G2 box; other site 423212004263 G3 box; other site 423212004264 Switch II region; other site 423212004265 G4 box; other site 423212004266 G5 box; other site 423212004267 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 423212004268 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 423212004269 Trp docking motif [polypeptide binding]; other site 423212004270 active site 423212004271 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 423212004272 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 423212004273 histidyl-tRNA synthetase; Region: hisS; TIGR00442 423212004274 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 423212004275 dimer interface [polypeptide binding]; other site 423212004276 motif 1; other site 423212004277 active site 423212004278 motif 2; other site 423212004279 motif 3; other site 423212004280 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 423212004281 anticodon binding site; other site 423212004282 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 423212004283 Helix-turn-helix domain; Region: HTH_25; pfam13413 423212004284 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 423212004285 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 423212004286 binding surface 423212004287 TPR motif; other site 423212004288 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 423212004289 binding surface 423212004290 TPR motif; other site 423212004291 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 423212004292 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 423212004293 FeS/SAM binding site; other site 423212004294 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 423212004295 active site 423212004296 multimer interface [polypeptide binding]; other site 423212004297 MiaE tRNA-modifying nonheme diiron monooxygenase, ferritin-like diiron-binding domain; Region: MiaE; cd07910 423212004298 active site 423212004299 dinuclear metal binding site [ion binding]; other site 423212004300 dimerization interface [polypeptide binding]; other site 423212004301 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 423212004302 putative active site [active] 423212004303 putative metal binding site [ion binding]; other site 423212004304 septum formation inhibitor; Reviewed; Region: minC; PRK00339 423212004305 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 423212004306 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 423212004307 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 423212004308 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 423212004309 acyl-activating enzyme (AAE) consensus motif; other site 423212004310 putative AMP binding site [chemical binding]; other site 423212004311 putative active site [active] 423212004312 putative CoA binding site [chemical binding]; other site 423212004313 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 423212004314 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 423212004315 substrate binding pocket [chemical binding]; other site 423212004316 membrane-bound complex binding site; other site 423212004317 hinge residues; other site 423212004318 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 423212004319 putative active site [active] 423212004320 putative CoA binding site [chemical binding]; other site 423212004321 nudix motif; other site 423212004322 metal binding site [ion binding]; metal-binding site 423212004323 Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]; Region: TrpE; COG0147 423212004324 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 423212004325 chorismate binding enzyme; Region: Chorismate_bind; cl10555 423212004326 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_x; TIGR03181 423212004327 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 423212004328 TPP-binding site [chemical binding]; other site 423212004329 tetramer interface [polypeptide binding]; other site 423212004330 heterodimer interface [polypeptide binding]; other site 423212004331 phosphorylation loop region [posttranslational modification] 423212004332 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 423212004333 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 423212004334 alpha subunit interface [polypeptide binding]; other site 423212004335 TPP binding site [chemical binding]; other site 423212004336 heterodimer interface [polypeptide binding]; other site 423212004337 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 423212004338 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 423212004339 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 423212004340 E3 interaction surface; other site 423212004341 lipoyl attachment site [posttranslational modification]; other site 423212004342 e3 binding domain; Region: E3_binding; pfam02817 423212004343 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 423212004344 Mechanosensitive ion channel; Region: MS_channel; pfam00924 423212004345 Uncharacterized conserved protein [Function unknown]; Region: COG0398 423212004346 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 423212004347 mercuric reductase; Validated; Region: PRK06370 423212004348 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 423212004349 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 423212004350 Predicted phosphoribosyltransferases [General function prediction only]; Region: COG2236 423212004351 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 423212004352 active site 423212004353 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_3; cd02434 423212004354 NMT1/THI5 like; Region: NMT1; pfam09084 423212004355 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 423212004356 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 423212004357 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 423212004358 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 423212004359 thiS-thiF/thiG interaction site; other site 423212004360 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 423212004361 ThiS interaction site; other site 423212004362 putative active site [active] 423212004363 tetramer interface [polypeptide binding]; other site 423212004364 HMP-P kinase/thiamin-monophosphate pyrophosphorylase; Region: PLN02898 423212004365 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 423212004366 dimer interface [polypeptide binding]; other site 423212004367 substrate binding site [chemical binding]; other site 423212004368 ATP binding site [chemical binding]; other site 423212004369 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 423212004370 thiamine phosphate binding site [chemical binding]; other site 423212004371 active site 423212004372 pyrophosphate binding site [ion binding]; other site 423212004373 molybdopterin biosynthesis-like protein MoeZ; Validated; Region: PRK07878 423212004374 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 423212004375 ATP binding site [chemical binding]; other site 423212004376 substrate interface [chemical binding]; other site 423212004377 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 423212004378 active site residue [active] 423212004379 S1/P1 nucleases and related enzymes; Region: S1-P1_nuclease; cd11010 423212004380 active site 423212004381 Zn binding site [ion binding]; other site 423212004382 tol-pal system beta propeller repeat protein TolB; Region: propeller_TolB; TIGR02800 423212004383 TolB amino-terminal domain; Region: TolB_N; pfam04052 423212004384 Uncharacterized protein conserved in bacteria (DUF2195); Region: DUF2195; cl02042 423212004385 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 423212004386 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 423212004387 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 423212004388 TolA protein; Region: tolA_full; TIGR02794 423212004389 TolA protein; Region: tolA_full; TIGR02794 423212004390 TonB C terminal; Region: TonB_2; pfam13103 423212004391 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 423212004392 TolR protein; Region: tolR; TIGR02801 423212004393 TolQ protein; Region: tolQ; TIGR02796 423212004394 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 423212004395 active site 423212004396 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 423212004397 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 423212004398 Walker A motif; other site 423212004399 ATP binding site [chemical binding]; other site 423212004400 Walker B motif; other site 423212004401 arginine finger; other site 423212004402 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 423212004403 RNA polymerase sigma factor RpoE; Provisional; Region: PRK09652 423212004404 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 423212004405 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 423212004406 DNA binding residues [nucleotide binding] 423212004407 Uncharacterized conserved protein [Function unknown]; Region: COG2938 423212004408 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 423212004409 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 423212004410 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 423212004411 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 423212004412 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 423212004413 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 423212004414 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 423212004415 Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 1-like; Region: ALDH_SSADH1_GabD1; cd07100 423212004416 NAD(P) binding site [chemical binding]; other site 423212004417 catalytic residues [active] 423212004418 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 423212004419 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 423212004420 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 423212004421 putative catalytic residue [active] 423212004422 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 423212004423 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 423212004424 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 423212004425 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 423212004426 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 423212004427 Global regulator protein family; Region: CsrA; pfam02599 423212004428 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 423212004429 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 423212004430 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 423212004431 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 423212004432 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 423212004433 substrate binding site [chemical binding]; other site 423212004434 oxyanion hole (OAH) forming residues; other site 423212004435 trimer interface [polypeptide binding]; other site 423212004436 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 423212004437 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 423212004438 acetyl-CoA acetyltransferase; Provisional; Region: PRK08170 423212004439 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 423212004440 dimer interface [polypeptide binding]; other site 423212004441 active site 423212004442 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 423212004443 Leucine-rich repeats; other site 423212004444 Substrate binding site [chemical binding]; other site 423212004445 RES domain; Region: RES; smart00953 423212004446 Protein of unknown function (DUF2384); Region: DUF2384; pfam09722 423212004447 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 423212004448 S-adenosylmethionine binding site [chemical binding]; other site 423212004449 Phosphoenolpyruvate carboxylase; Region: PEPcase; cl17418 423212004450 Phosphoenolpyruvate carboxylase; Region: PEPcase; cl17418 423212004451 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_21; cd04680 423212004452 nudix motif; other site 423212004453 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 423212004454 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 423212004455 putative catalytic cysteine [active] 423212004456 gamma-glutamyl kinase; Provisional; Region: PRK05429 423212004457 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 423212004458 nucleotide binding site [chemical binding]; other site 423212004459 homotetrameric interface [polypeptide binding]; other site 423212004460 putative phosphate binding site [ion binding]; other site 423212004461 putative allosteric binding site; other site 423212004462 PUA domain; Region: PUA; pfam01472 423212004463 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 423212004464 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 423212004465 Coenzyme A binding pocket [chemical binding]; other site 423212004466 GNAT acetyltransferase 2; Region: GNAT_acetyltr_2; pfam13718 423212004467 Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; Region: HTH_TipAL-Mta; cd01106 423212004468 DNA binding residues [nucleotide binding] 423212004469 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 423212004470 dimer interface [polypeptide binding]; other site 423212004471 TipAS antibiotic-recognition domain; Region: TipAS; pfam07739 423212004472 Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides; Region: GH20_hexosaminidase; cl02948 423212004473 active site 423212004474 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 423212004475 Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; Region: HTH_TipAL-Mta; cd01106 423212004476 DNA binding residues [nucleotide binding] 423212004477 dimer interface [polypeptide binding]; other site 423212004478 TipAS antibiotic-recognition domain; Region: TipAS; pfam07739 423212004479 BlaR1 peptidase M56; Region: Peptidase_M56; pfam05569 423212004480 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 423212004481 Penicillinase repressor; Region: Pencillinase_R; pfam03965 423212004482 tRNA pseudouridine synthase D (TruD); Region: TruD; pfam01142 423212004483 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 423212004484 Permutation of conserved domain; other site 423212004485 active site 423212004486 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 423212004487 putative hydrolase; Provisional; Region: PRK10985 423212004488 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 423212004489 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 423212004490 Soluble P-type ATPase [General function prediction only]; Region: COG4087 423212004491 putative adenylate-forming enzyme; Region: aden_form_hyp; TIGR02304 423212004492 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 423212004493 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 423212004494 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 423212004495 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 423212004496 NAD(P) binding site [chemical binding]; other site 423212004497 active site 423212004498 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK07204 423212004499 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 423212004500 dimer interface [polypeptide binding]; other site 423212004501 active site 423212004502 CoA binding pocket [chemical binding]; other site 423212004503 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 423212004504 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 423212004505 putative ADP-binding pocket [chemical binding]; other site 423212004506 PAP2 superfamily C-terminal; Region: PAP2_C; pfam14360 423212004507 potential frameshift: common BLAST hit: gi|148359169|ref|YP_001250376.1| oxidase 423212004508 FAD binding domain; Region: FAD_binding_4; pfam01565 423212004509 FAD linked oxidases, C-terminal domain; Region: FAD-oxidase_C; pfam02913 423212004510 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 423212004511 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 423212004512 FAD binding domain; Region: FAD_binding_4; pfam01565 423212004513 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 423212004514 putative urate catabolism protein; Region: uraD_N-term-dom; TIGR03212 423212004515 Catalytic domain of bacterial PuuE allantoinases, Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), and similar proteins; Region: CE4_PuuE_SpCDA1; cd10977 423212004516 active site 423212004517 catalytic site [active] 423212004518 tetramer interface [polypeptide binding]; other site 423212004519 enterobactin exporter EntS; Provisional; Region: PRK10489 423212004520 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 423212004521 putative substrate translocation pore; other site 423212004522 Predicted membrane protein [Function unknown]; Region: COG2119 423212004523 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 423212004524 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 423212004525 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 423212004526 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 423212004527 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 423212004528 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 423212004529 Chlamydia CHLPS protein (DUF818); Region: DUF818; pfam05677 423212004530 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 423212004531 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 423212004532 threonine synthase; Validated; Region: PRK09225 423212004533 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 423212004534 catalytic residue [active] 423212004535 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 423212004536 Dot/Icm substrate protein; Region: SidE; pfam12252 423212004537 YceI-like domain; Region: YceI; pfam04264 423212004538 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 423212004539 YceI-like domain; Region: YceI; smart00867 423212004540 Predicted integral membrane protein (DUF2282); Region: DUF2282; pfam10048 423212004541 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 423212004542 Acetolactate synthase [Amino acid transport and metabolism]; Region: COG3962 423212004543 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 423212004544 PYR/PP interface [polypeptide binding]; other site 423212004545 dimer interface [polypeptide binding]; other site 423212004546 TPP binding site [chemical binding]; other site 423212004547 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 423212004548 Thiamine pyrophosphate (TPP) family, IolD subfamily, TPP-binding module; composed of proteins similar to Rhizobium leguminosarum bv. viciae IolD. IolD plays an important role in myo-inositol catabolism; Region: TPP_IolD; cd02003 423212004549 TPP-binding site; other site 423212004550 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 423212004551 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 423212004552 substrate binding site [chemical binding]; other site 423212004553 ATP binding site [chemical binding]; other site 423212004554 KduI/IolB family; Region: KduI; pfam04962 423212004555 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 423212004556 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 423212004557 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 423212004558 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 423212004559 putative substrate translocation pore; other site 423212004560 Sugar (and other) transporter; Region: Sugar_tr; pfam00083 423212004561 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 423212004562 Tetratricopeptide repeat; Region: TPR_12; pfam13424 423212004563 Zinc metalloprotease (elastase) [Amino acid transport and metabolism]; Region: LasB; COG3227 423212004564 Fungalysin/Thermolysin Propeptide Motif; Region: FTP; pfam07504 423212004565 Peptidase M4 family includes thermolysin, protealysin, aureolysin and neutral protease; Region: M4_neutral_protease; cd09597 423212004566 active site 423212004567 Zn binding site [ion binding]; other site 423212004568 ATP-grasp domain; Region: ATP-grasp_4; cl17255 423212004569 N-Dimethylarginine dimethylaminohydrolase [Amino acid transport and metabolism]; Region: COG1834 423212004570 Amidinotransferase; Region: Amidinotransf; cl12043 423212004571 putative glutamate/gamma-aminobutyrate antiporter; Region: put_Glu_GABA_T; TIGR03813 423212004572 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 423212004573 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4299 423212004574 Major Facilitator Superfamily; Region: MFS_1; pfam07690 423212004575 penicillin-binding protein 1C; Region: PBP_1c; TIGR02073 423212004576 Transglycosylase; Region: Transgly; pfam00912 423212004577 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 423212004578 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 423212004579 IgD-like repeat domain of mycobacterial L,D-transpeptidases; Region: LDT_IgD_like; cl17506 423212004580 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 423212004581 MG2 domain; Region: A2M_N; pfam01835 423212004582 Alpha-2-macroglobulin family; Region: A2M; pfam00207 423212004583 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 423212004584 surface patch; other site 423212004585 thioester region; other site 423212004586 specificity defining residues; other site 423212004587 IgA Peptidase M64; Region: Peptidase_M64; pfam09471 423212004588 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 423212004589 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 423212004590 Alpha amylase catalytic domain family; Region: AmyAc_family; cd00551 423212004591 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 423212004592 active site 423212004593 catalytic site [active] 423212004594 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 423212004595 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 423212004596 active site 423212004597 substrate binding site [chemical binding]; other site 423212004598 cosubstrate binding site; other site 423212004599 catalytic site [active] 423212004600 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 423212004601 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 423212004602 ATP-grasp domain; Region: ATP-grasp_4; cl17255 423212004603 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 423212004604 amidophosphoribosyltransferase; Provisional; Region: PRK09246 423212004605 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 423212004606 active site 423212004607 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 423212004608 active site 423212004609 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 423212004610 ATP binding site [chemical binding]; other site 423212004611 active site 423212004612 substrate binding site [chemical binding]; other site 423212004613 phosphoribosylformylglycinamidine synthase I; Provisional; Region: PRK03619 423212004614 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 423212004615 putative active site [active] 423212004616 catalytic triad [active] 423212004617 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 423212004618 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 423212004619 dimerization interface [polypeptide binding]; other site 423212004620 putative ATP binding site [chemical binding]; other site 423212004621 phosphoribosylformylglycinamidine synthase II; Provisional; Region: PRK01213 423212004622 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 423212004623 dimerization interface [polypeptide binding]; other site 423212004624 ATP binding site [chemical binding]; other site 423212004625 Mitochondrial ribosomal protein subunit L20; Region: MRP-L20; pfam12824 423212004626 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 423212004627 dimerization interface [polypeptide binding]; other site 423212004628 ATP binding site [chemical binding]; other site 423212004629 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 423212004630 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 423212004631 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 423212004632 DsbD alpha interface [polypeptide binding]; other site 423212004633 catalytic residues [active] 423212004634 short chain dehydrogenase; Provisional; Region: PRK05993 423212004635 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 423212004636 NADP binding site [chemical binding]; other site 423212004637 active site 423212004638 steroid binding site; other site 423212004639 D123; Region: D123; pfam07065 423212004640 methanogenesis marker radical SAM protein; Region: methan_mark_10; TIGR03278 423212004641 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 423212004642 aconitate hydratase; Validated; Region: PRK09277 423212004643 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 423212004644 substrate binding site [chemical binding]; other site 423212004645 ligand binding site [chemical binding]; other site 423212004646 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 423212004647 substrate binding site [chemical binding]; other site 423212004648 putative glutamate/gamma-aminobutyrate antiporter; Region: put_Glu_GABA_T; TIGR03813 423212004649 DDE superfamily endonuclease; Region: DDE_3; pfam13358 423212004650 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 423212004651 Proline dehydrogenase; Region: Pro_dh; pfam01619 423212004652 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 423212004653 Glutamate binding site [chemical binding]; other site 423212004654 NAD binding site [chemical binding]; other site 423212004655 catalytic residues [active] 423212004656 L,D-transpeptidase catalytic domain; Region: YkuD_2; pfam13645 423212004657 Activator of osmoprotectant transporter ProP [Signal transduction mechanisms]; Region: ProQ; COG3109 423212004658 ProQ/FINO family; Region: ProQ; pfam04352 423212004659 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 423212004660 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 423212004661 S-adenosylmethionine binding site [chemical binding]; other site 423212004662 Uracil-DNA glycosylases (UDG) and related enzymes; Region: UDG_like; cl00483 423212004663 ligand binding site [chemical binding]; other site 423212004664 active site 423212004665 Protein of unknown function (DUF3429); Region: DUF3429; pfam11911 423212004666 cell division protein MukB; Provisional; Region: mukB; PRK04863 423212004667 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 423212004668 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 423212004669 active site 423212004670 DNA binding site [nucleotide binding] 423212004671 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 423212004672 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 423212004673 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 423212004674 Catalytic site [active] 423212004675 hypothetical protein; Provisional; Region: PRK07338 423212004676 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 423212004677 metal binding site [ion binding]; metal-binding site 423212004678 dimer interface [polypeptide binding]; other site 423212004679 Arginine/ornithine N-succinyltransferase beta subunit [Amino acid transport and metabolism]; Region: AstA; COG3138 423212004680 Arginine N-succinyltransferase beta subunit; Region: AstA; pfam04958 423212004681 succinylglutamic semialdehyde dehydrogenase; Reviewed; Region: astD; PRK09457 423212004682 N-succinylglutamate 5-semialdehyde dehydrogenase, AstD-like; Region: ALDH_SGSD_AstD; cd07095 423212004683 NAD(P) binding site [chemical binding]; other site 423212004684 catalytic residues [active] 423212004685 succinylarginine dihydrolase; Provisional; Region: PRK13281 423212004686 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 423212004687 Cytochrome c; Region: Cytochrom_C; cl11414 423212004688 ribosome recycling factor; Reviewed; Region: frr; PRK00083 423212004689 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 423212004690 hinge region; other site 423212004691 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 423212004692 putative nucleotide binding site [chemical binding]; other site 423212004693 uridine monophosphate binding site [chemical binding]; other site 423212004694 homohexameric interface [polypeptide binding]; other site 423212004695 elongation factor Ts; Provisional; Region: tsf; PRK09377 423212004696 UBA/TS-N domain; Region: UBA; pfam00627 423212004697 Elongation factor TS; Region: EF_TS; pfam00889 423212004698 Elongation factor TS; Region: EF_TS; pfam00889 423212004699 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 423212004700 rRNA interaction site [nucleotide binding]; other site 423212004701 S8 interaction site; other site 423212004702 putative laminin-1 binding site; other site 423212004703 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 423212004704 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 423212004705 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 423212004706 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 423212004707 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 423212004708 dimer interface [polypeptide binding]; other site 423212004709 Protein kinase domain; Region: Pkinase; pfam00069 423212004710 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 423212004711 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 423212004712 SET domain; Region: SET; pfam00856 423212004713 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 423212004714 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 423212004715 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 423212004716 active site 423212004717 PII uridylyl-transferase; Provisional; Region: glnD; PRK00275 423212004718 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 423212004719 metal binding triad; other site 423212004720 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 423212004721 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 423212004722 Zn2+ binding site [ion binding]; other site 423212004723 Mg2+ binding site [ion binding]; other site 423212004724 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 423212004725 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 423212004726 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 423212004727 nucleoside/Zn binding site; other site 423212004728 dimer interface [polypeptide binding]; other site 423212004729 catalytic motif [active] 423212004730 GMP synthase; Reviewed; Region: guaA; PRK00074 423212004731 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 423212004732 AMP/PPi binding site [chemical binding]; other site 423212004733 candidate oxyanion hole; other site 423212004734 catalytic triad [active] 423212004735 potential glutamine specificity residues [chemical binding]; other site 423212004736 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 423212004737 ATP Binding subdomain [chemical binding]; other site 423212004738 Ligand Binding sites [chemical binding]; other site 423212004739 Dimerization subdomain; other site 423212004740 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 423212004741 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 423212004742 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 423212004743 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 423212004744 active site 423212004745 four helix bundle protein; Region: TIGR02436 423212004746 S23 ribosomal protein; Region: Ribosomal_S23p; cl05287 423212004747 glycosyl hydrolase family 16; Region: Glyco_hydrolase_16; cl00218 423212004748 active site 423212004749 catalytic residues [active] 423212004750 four helix bundle protein; Region: TIGR02436 423212004751 S23 ribosomal protein; Region: Ribosomal_S23p; cl05287 423212004752 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 423212004753 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 423212004754 Switch I; other site 423212004755 Switch II; other site 423212004756 cell division topological specificity factor MinE; Reviewed; Region: minE; PRK00296 423212004757 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 423212004758 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 423212004759 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 423212004760 active site 423212004761 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 423212004762 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 423212004763 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 423212004764 The N-terminal ATPase domain of the maltose transporter, MalK; Region: ABC_MalK_N; cd03301 423212004765 Walker A/P-loop; other site 423212004766 ATP binding site [chemical binding]; other site 423212004767 Q-loop/lid; other site 423212004768 ABC transporter signature motif; other site 423212004769 Walker B; other site 423212004770 D-loop; other site 423212004771 H-loop/switch region; other site 423212004772 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 423212004773 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 423212004774 dimer interface [polypeptide binding]; other site 423212004775 conserved gate region; other site 423212004776 putative PBP binding loops; other site 423212004777 ABC-ATPase subunit interface; other site 423212004778 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 423212004779 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 423212004780 dimer interface [polypeptide binding]; other site 423212004781 conserved gate region; other site 423212004782 putative PBP binding loops; other site 423212004783 ABC-ATPase subunit interface; other site 423212004784 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 423212004785 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 423212004786 NAD(P) binding site [chemical binding]; other site 423212004787 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 423212004788 ClC chloride channel EriC. This domain is found in the EriC chloride transporters that mediate the extreme acid resistance response in eubacteria and archaea. This response allows bacteria to survive in the acidic environments by decarboxylation-linked...; Region: EriC; cd01031 423212004789 Cl- selectivity filter; other site 423212004790 Cl- binding residues [ion binding]; other site 423212004791 pore gating glutamate residue; other site 423212004792 dimer interface [polypeptide binding]; other site 423212004793 H+/Cl- coupling transport residue; other site 423212004794 anthranilate synthase; Provisional; Region: PRK13566 423212004795 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 423212004796 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 423212004797 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 423212004798 glutamine binding [chemical binding]; other site 423212004799 catalytic triad [active] 423212004800 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 423212004801 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 423212004802 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 423212004803 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 423212004804 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 423212004805 GatB domain; Region: GatB_Yqey; smart00845 423212004806 Autotransporter beta-domain; Region: Autotransporter; smart00869 423212004807 CHASE2 domain; Region: CHASE2; pfam05226 423212004808 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 423212004809 cyclase homology domain; Region: CHD; cd07302 423212004810 nucleotidyl binding site; other site 423212004811 metal binding site [ion binding]; metal-binding site 423212004812 dimer interface [polypeptide binding]; other site 423212004813 FecR protein; Region: FecR; pfam04773 423212004814 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 423212004815 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 423212004816 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cl00528 423212004817 trimerization site [polypeptide binding]; other site 423212004818 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 423212004819 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 423212004820 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 423212004821 catalytic residue [active] 423212004822 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 423212004823 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 423212004824 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 423212004825 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 423212004826 active site 423212004827 dimerization interface [polypeptide binding]; other site 423212004828 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 423212004829 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 423212004830 tandem repeat interface [polypeptide binding]; other site 423212004831 oligomer interface [polypeptide binding]; other site 423212004832 active site residues [active] 423212004833 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 423212004834 Clp amino terminal domain; Region: Clp_N; pfam02861 423212004835 Clp amino terminal domain; Region: Clp_N; pfam02861 423212004836 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 423212004837 Walker A motif; other site 423212004838 ATP binding site [chemical binding]; other site 423212004839 Walker B motif; other site 423212004840 arginine finger; other site 423212004841 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; cl00148 423212004842 primary dimer interface [polypeptide binding]; other site 423212004843 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 423212004844 Walker A motif; other site 423212004845 ATP binding site [chemical binding]; other site 423212004846 Walker B motif; other site 423212004847 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 423212004848 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 423212004849 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 423212004850 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 423212004851 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 423212004852 TIGR02099 family protein; Region: TIGR02099 423212004853 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 423212004854 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 423212004855 Flagellar FliJ protein; Region: FliJ; pfam02050 423212004856 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 423212004857 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 423212004858 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 423212004859 Walker A motif/ATP binding site; other site 423212004860 Walker B motif; other site 423212004861 Flagellar assembly protein FliH; Region: FliH; pfam02108 423212004862 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 423212004863 FliG C-terminal domain; Region: FliG_C; pfam01706 423212004864 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 423212004865 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 423212004866 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 423212004867 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK00253 423212004868 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 423212004869 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 423212004870 active site 423212004871 phosphorylation site [posttranslational modification] 423212004872 intermolecular recognition site; other site 423212004873 dimerization interface [polypeptide binding]; other site 423212004874 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 423212004875 Walker A motif; other site 423212004876 ATP binding site [chemical binding]; other site 423212004877 Walker B motif; other site 423212004878 arginine finger; other site 423212004879 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 423212004880 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 423212004881 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 423212004882 putative active site [active] 423212004883 heme pocket [chemical binding]; other site 423212004884 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 423212004885 dimer interface [polypeptide binding]; other site 423212004886 phosphorylation site [posttranslational modification] 423212004887 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 423212004888 ATP binding site [chemical binding]; other site 423212004889 G-X-G motif; other site 423212004890 recombination factor protein RarA; Reviewed; Region: PRK13342 423212004891 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 423212004892 Walker A motif; other site 423212004893 ATP binding site [chemical binding]; other site 423212004894 Walker B motif; other site 423212004895 arginine finger; other site 423212004896 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 423212004897 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 423212004898 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 423212004899 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 423212004900 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 423212004901 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 423212004902 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 423212004903 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 423212004904 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 423212004905 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 423212004906 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 423212004907 active site residue [active] 423212004908 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 423212004909 rRNA binding site [nucleotide binding]; other site 423212004910 predicted 30S ribosome binding site; other site 423212004911 peptidase PmbA; Provisional; Region: PRK11040 423212004912 Predicted periplasmic protein [Function unknown]; Region: COG3698 423212004913 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 423212004914 Cupin-like domain; Region: Cupin_8; pfam13621 423212004915 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 423212004916 ATP cone domain; Region: ATP-cone; pfam03477 423212004917 ATP cone domain; Region: ATP-cone; pfam03477 423212004918 Class I ribonucleotide reductase; Region: RNR_I; cd01679 423212004919 active site 423212004920 dimer interface [polypeptide binding]; other site 423212004921 catalytic residues [active] 423212004922 effector binding site; other site 423212004923 R2 peptide binding site; other site 423212004924 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 423212004925 dimer interface [polypeptide binding]; other site 423212004926 putative radical transfer pathway; other site 423212004927 diiron center [ion binding]; other site 423212004928 tyrosyl radical; other site 423212004929 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 423212004930 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 423212004931 dimer interface [polypeptide binding]; other site 423212004932 putative anticodon binding site; other site 423212004933 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 423212004934 motif 1; other site 423212004935 active site 423212004936 motif 2; other site 423212004937 motif 3; other site 423212004938 peptide chain release factor 2; Validated; Region: prfB; PRK00578 423212004939 This domain is found in peptide chain release factors; Region: PCRF; smart00937 423212004940 RF-1 domain; Region: RF-1; pfam00472 423212004941 Protein of unknown function (DUF2802); Region: DUF2802; pfam10975 423212004942 flagellar motor protein MotD; Reviewed; Region: PRK09038 423212004943 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 423212004944 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 423212004945 ligand binding site [chemical binding]; other site 423212004946 flagellar motor protein; Reviewed; Region: motC; PRK09109 423212004947 flagellar motor protein MotA; Validated; Region: PRK08124 423212004948 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 423212004949 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 423212004950 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 423212004951 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 423212004952 DNA binding residues [nucleotide binding] 423212004953 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 423212004954 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 423212004955 P-loop; other site 423212004956 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 423212004957 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 423212004958 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 423212004959 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 423212004960 FHIPEP family; Region: FHIPEP; pfam00771 423212004961 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 423212004962 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 423212004963 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 423212004964 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 423212004965 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 423212004966 Flagellar biosynthesis protein, FliO; Region: FliO; pfam04347 423212004967 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 423212004968 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 423212004969 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 423212004970 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 423212004971 FAD binding domain; Region: FAD_binding_4; pfam01565 423212004972 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 423212004973 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 423212004974 NAD(P) binding site [chemical binding]; other site 423212004975 active site 423212004976 Transcriptional regulator [Transcription]; Region: LysR; COG0583 423212004977 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 423212004978 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 423212004979 dimerization interface [polypeptide binding]; other site 423212004980 Transposase; Region: HTH_Tnp_IS630; pfam01710 423212004981 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 423212004982 RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when...; Region: RhoGAP; cl02570 423212004983 GTPase interaction site; other site 423212004984 catalytic residue [active] 423212004985 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 423212004986 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 423212004987 motif 1; other site 423212004988 active site 423212004989 motif 2; other site 423212004990 motif 3; other site 423212004991 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 423212004992 recombination regulator RecX; Reviewed; Region: recX; PRK00117 423212004993 recombinase A; Provisional; Region: recA; PRK09354 423212004994 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 423212004995 hexamer interface [polypeptide binding]; other site 423212004996 Walker A motif; other site 423212004997 ATP binding site [chemical binding]; other site 423212004998 Walker B motif; other site 423212004999 Competence-damaged protein; Region: CinA; pfam02464 423212005000 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 423212005001 MutS domain I; Region: MutS_I; pfam01624 423212005002 MutS domain II; Region: MutS_II; pfam05188 423212005003 MutS domain III; Region: MutS_III; pfam05192 423212005004 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 423212005005 Walker A/P-loop; other site 423212005006 ATP binding site [chemical binding]; other site 423212005007 Q-loop/lid; other site 423212005008 ABC transporter signature motif; other site 423212005009 Walker B; other site 423212005010 D-loop; other site 423212005011 H-loop/switch region; other site 423212005012 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 423212005013 Surface antigen; Region: Bac_surface_Ag; pfam01103 423212005014 Family of unknown function (DUF490); Region: DUF490; pfam04357 423212005015 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 423212005016 dimer interface [polypeptide binding]; other site 423212005017 active site 423212005018 Schiff base residues; other site 423212005019 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 423212005020 bifunctional aspartate kinase/diaminopimelate decarboxylase protein; Provisional; Region: PRK08961 423212005021 AAK_AK-DapDC: Amino Acid Kinase Superfamily (AAK), AK-DapDC; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the bifunctional enzyme AK - DAP decarboxylase (DapDC) found in some bacteria. Aspartokinase is the first enzyme in the...; Region: AAK_AK-DapDC; cd04259 423212005022 putative catalytic residues [active] 423212005023 putative nucleotide binding site [chemical binding]; other site 423212005024 putative aspartate binding site [chemical binding]; other site 423212005025 ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein; Region: ACT_AKiii-DAPDC_1; cd04935 423212005026 ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC); Region: ACT_AKiii-DAPDC_2; cd04920 423212005027 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bifunctional Aspartate Kinase/Diaminopimelate Decarboxylase; Region: PLPDE_III_Bif_AspK_DapDC; cd06840 423212005028 active site 423212005029 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 423212005030 substrate binding site [chemical binding]; other site 423212005031 catalytic residues [active] 423212005032 dimer interface [polypeptide binding]; other site 423212005033 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 423212005034 Part of AAA domain; Region: AAA_19; pfam13245 423212005035 Family description; Region: UvrD_C_2; pfam13538 423212005036 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 423212005037 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 423212005038 Protein of unknown function (DUF2803); Region: DUF2803; pfam10972 423212005039 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 423212005040 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 423212005041 The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_OxyR; cd08411 423212005042 dimerization interface [polypeptide binding]; other site 423212005043 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 423212005044 Major Facilitator Superfamily; Region: MFS_1; pfam07690 423212005045 putative substrate translocation pore; other site 423212005046 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 423212005047 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 423212005048 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 423212005049 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 423212005050 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 423212005051 Walker A/P-loop; other site 423212005052 ATP binding site [chemical binding]; other site 423212005053 Q-loop/lid; other site 423212005054 ABC transporter signature motif; other site 423212005055 Walker B; other site 423212005056 D-loop; other site 423212005057 H-loop/switch region; other site 423212005058 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 423212005059 Coenzyme A binding pocket [chemical binding]; other site 423212005060 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 423212005061 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires...; Region: DHOD_2_like; cd04738 423212005062 quinone interaction residues [chemical binding]; other site 423212005063 active site 423212005064 catalytic residues [active] 423212005065 FMN binding site [chemical binding]; other site 423212005066 substrate binding site [chemical binding]; other site 423212005067 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 423212005068 isovaleryl-CoA dehydrogenase; Region: PLN02519 423212005069 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 423212005070 substrate binding site [chemical binding]; other site 423212005071 FAD binding site [chemical binding]; other site 423212005072 catalytic base [active] 423212005073 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 423212005074 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 423212005075 dimer interface [polypeptide binding]; other site 423212005076 active site 423212005077 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 423212005078 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 423212005079 enoyl-CoA hydratase; Provisional; Region: PRK05995 423212005080 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 423212005081 substrate binding site [chemical binding]; other site 423212005082 oxyanion hole (OAH) forming residues; other site 423212005083 trimer interface [polypeptide binding]; other site 423212005084 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cl15762 423212005085 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 423212005086 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 423212005087 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 423212005088 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 423212005089 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 423212005090 carboxyltransferase (CT) interaction site; other site 423212005091 biotinylation site [posttranslational modification]; other site 423212005092 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 423212005093 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 423212005094 active site 423212005095 catalytic residues [active] 423212005096 metal binding site [ion binding]; metal-binding site 423212005097 acetoacetyl-CoA synthetase; Provisional; Region: PRK03584 423212005098 Acetoacetyl-CoA synthetase (acetoacetate-CoA ligase, AACS); Region: AACS; cd05943 423212005099 acyl-activating enzyme (AAE) consensus motif; other site 423212005100 putative AMP binding site [chemical binding]; other site 423212005101 putative active site [active] 423212005102 putative CoA binding site [chemical binding]; other site 423212005103 VirK protein; Region: VirK; pfam06903 423212005104 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 423212005105 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 423212005106 Walker A/P-loop; other site 423212005107 ATP binding site [chemical binding]; other site 423212005108 Q-loop/lid; other site 423212005109 ABC transporter signature motif; other site 423212005110 Walker B; other site 423212005111 D-loop; other site 423212005112 H-loop/switch region; other site 423212005113 This domain is found at the C-terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins; Region: NIL; smart00930 423212005114 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 423212005115 dimer interface [polypeptide binding]; other site 423212005116 conserved gate region; other site 423212005117 ABC-ATPase subunit interface; other site 423212005118 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 423212005119 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 423212005120 Putative SAM-dependent methyltransferase; Region: SAM_MT; cl17517 423212005121 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 423212005122 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 423212005123 active site 423212005124 motif I; other site 423212005125 motif II; other site 423212005126 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 423212005127 DALR anticodon binding domain; Region: DALR_1; pfam05746 423212005128 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 423212005129 dimer interface [polypeptide binding]; other site 423212005130 motif 1; other site 423212005131 active site 423212005132 motif 2; other site 423212005133 motif 3; other site 423212005134 DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC...; Region: DsbA_Com1_like; cd03023 423212005135 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 423212005136 catalytic residues [active] 423212005137 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 423212005138 Part of AAA domain; Region: AAA_19; pfam13245 423212005139 Family description; Region: UvrD_C_2; pfam13538 423212005140 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 423212005141 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 423212005142 putative active site [active] 423212005143 dimerization interface [polypeptide binding]; other site 423212005144 putative tRNAtyr binding site [nucleotide binding]; other site 423212005145 VacJ like lipoprotein; Region: VacJ; cl01073 423212005146 glutathione synthetase; Provisional; Region: PRK05246 423212005147 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 423212005148 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 423212005149 Glutamate-cysteine ligase; Region: GshA; pfam08886 423212005150 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 423212005151 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 423212005152 EamA-like transporter family; Region: EamA; pfam00892 423212005153 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 423212005154 active site residue [active] 423212005155 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 423212005156 PglZ domain; Region: PglZ; pfam08665 423212005157 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 423212005158 Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway; Region: UMPK; cd02023 423212005159 Sugar specificity; other site 423212005160 Pyrimidine base specificity; other site 423212005161 ATP-binding site [chemical binding]; other site 423212005162 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 423212005163 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 423212005164 NAD binding site [chemical binding]; other site 423212005165 homotetramer interface [polypeptide binding]; other site 423212005166 homodimer interface [polypeptide binding]; other site 423212005167 substrate binding site [chemical binding]; other site 423212005168 active site 423212005169 periplasmic folding chaperone; Provisional; Region: PRK10788 423212005170 SurA N-terminal domain; Region: SurA_N_3; cl07813 423212005171 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 423212005172 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 423212005173 IHF dimer interface [polypeptide binding]; other site 423212005174 IHF - DNA interface [nucleotide binding]; other site 423212005175 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 423212005176 Found in ATP-dependent protease La (LON); Region: LON; smart00464 423212005177 Found in ATP-dependent protease La (LON); Region: LON; smart00464 423212005178 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 423212005179 Walker A motif; other site 423212005180 ATP binding site [chemical binding]; other site 423212005181 Walker B motif; other site 423212005182 arginine finger; other site 423212005183 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 423212005184 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 423212005185 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 423212005186 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 423212005187 Walker A motif; other site 423212005188 ATP binding site [chemical binding]; other site 423212005189 Walker B motif; other site 423212005190 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 423212005191 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 423212005192 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 423212005193 oligomer interface [polypeptide binding]; other site 423212005194 active site residues [active] 423212005195 trigger factor; Provisional; Region: tig; PRK01490 423212005196 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 423212005197 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 423212005198 potential protein location (hypothetical protein lpa_02689 [Legionella pneumophila 2300/99 Alcoy]) that overlaps RNA (tRNA-H) 423212005199 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 423212005200 INT_SG1, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 1, C-terminal catalytic domain. The CD contains mainly predicted integrase/recombinase and site-specific XerD recombinases. The members of this CD are found predominantly in...; Region: INT_SG1_C; cd01183 423212005201 Int/Topo IB signature motif; other site 423212005202 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 423212005203 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 423212005204 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 423212005205 ABC transporter; Region: ABC_tran_2; pfam12848 423212005206 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 423212005207 ribonuclease III; Reviewed; Region: rnc; PRK00102 423212005208 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 423212005209 dimerization interface [polypeptide binding]; other site 423212005210 active site 423212005211 metal binding site [ion binding]; metal-binding site 423212005212 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 423212005213 dsRNA binding site [nucleotide binding]; other site 423212005214 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 423212005215 signal peptidase I; Provisional; Region: PRK10861 423212005216 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 423212005217 Catalytic site [active] 423212005218 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 423212005219 GTP-binding protein LepA; Provisional; Region: PRK05433 423212005220 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 423212005221 G1 box; other site 423212005222 putative GEF interaction site [polypeptide binding]; other site 423212005223 GTP/Mg2+ binding site [chemical binding]; other site 423212005224 Switch I region; other site 423212005225 G2 box; other site 423212005226 G3 box; other site 423212005227 Switch II region; other site 423212005228 G4 box; other site 423212005229 G5 box; other site 423212005230 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 423212005231 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 423212005232 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 423212005233 Transglycosylase SLT domain; Region: SLT_2; pfam13406 423212005234 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 423212005235 N-acetyl-D-glucosamine binding site [chemical binding]; other site 423212005236 type II secretion system protein L; Region: typeII_sec_gspL; TIGR01709 423212005237 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 423212005238 GspL periplasmic domain; Region: GspL_C; cl14909 423212005239 Type II secretion system (T2SS), protein M; Region: T2SM; pfam04612 423212005240 Sporulation related domain; Region: SPOR; cl10051 423212005241 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK05318 423212005242 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 423212005243 Zn2+ binding site [ion binding]; other site 423212005244 Mg2+ binding site [ion binding]; other site 423212005245 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 423212005246 DNA repair protein RecN; Region: recN; TIGR00634 423212005247 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 423212005248 Trehalase; Region: Trehalase; cl17346 423212005249 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 423212005250 dimer interface [polypeptide binding]; other site 423212005251 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 423212005252 active site 423212005253 metal binding site [ion binding]; metal-binding site 423212005254 glutathione binding site [chemical binding]; other site 423212005255 hypothetical protein; Provisional; Region: PRK05208 423212005256 JNK_SAPK-associated protein-1; Region: Jnk-SapK_ap_N; pfam09744 423212005257 acylphosphatase; Provisional; Region: PRK14451 423212005258 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 423212005259 putative active site [active] 423212005260 catalytic site [active] 423212005261 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 423212005262 PLD-like domain; Region: PLDc_2; pfam13091 423212005263 putative active site [active] 423212005264 catalytic site [active] 423212005265 Protein of unknown function (DUF2424); Region: DUF2424; pfam10340 423212005266 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 423212005267 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 423212005268 Leucine-rich repeats; other site 423212005269 Substrate binding site [chemical binding]; other site 423212005270 Leucine rich repeat; Region: LRR_8; pfam13855 423212005271 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 423212005272 D-galactonate transporter; Region: 2A0114; TIGR00893 423212005273 putative substrate translocation pore; other site 423212005274 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 423212005275 Putative ClC chloride channel. Clc proteins are putative halogen ion (Cl-, Br- and I-) transporters found in eubacteria. They belong to the ClC superfamily of halogen ion channels, which share a unique double-barreled architecture and voltage-dependent...; Region: ClC_like; cd01033 423212005276 putative ion selectivity filter; other site 423212005277 putative pore gating glutamate residue; other site 423212005278 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3012 423212005279 SEC-C motif; Region: SEC-C; pfam02810 423212005280 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 423212005281 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 423212005282 TrkA-N domain; Region: TrkA_N; pfam02254 423212005283 MoxR-like ATPases [General function prediction only]; Region: COG0714 423212005284 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 423212005285 Walker A motif; other site 423212005286 ATP binding site [chemical binding]; other site 423212005287 Walker B motif; other site 423212005288 arginine finger; other site 423212005289 Protein of unknown function DUF58; Region: DUF58; pfam01882 423212005290 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 423212005291 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 423212005292 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 423212005293 Uncharacterized conserved protein [Function unknown]; Region: COG2850 423212005294 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 423212005295 GIY-YIG motif/motif A; other site 423212005296 putative active site [active] 423212005297 putative metal binding site [ion binding]; other site 423212005298 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 423212005299 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 423212005300 EamA-like transporter family; Region: EamA; pfam00892 423212005301 EamA-like transporter family; Region: EamA; pfam00892 423212005302 GDA1/CD39 (nucleoside phosphatase) family; Region: GDA1_CD39; cl17763 423212005303 Protein of unknown function, DUF462; Region: DUF462; pfam04315 423212005304 glutathionine S-transferase; Provisional; Region: PRK10542 423212005305 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Beta; cd03057 423212005306 C-terminal domain interface [polypeptide binding]; other site 423212005307 GSH binding site (G-site) [chemical binding]; other site 423212005308 dimer interface [polypeptide binding]; other site 423212005309 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 423212005310 N-terminal domain interface [polypeptide binding]; other site 423212005311 dimer interface [polypeptide binding]; other site 423212005312 substrate binding pocket (H-site) [chemical binding]; other site 423212005313 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 423212005314 Beta-lactamase; Region: Beta-lactamase; pfam00144 423212005315 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 423212005316 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 423212005317 HIGH motif; other site 423212005318 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 423212005319 active site 423212005320 KMSKS motif; other site 423212005321 hybrid sensory histidine kinase BarA; Provisional; Region: PRK11107 423212005322 HAMP domain; Region: HAMP; pfam00672 423212005323 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 423212005324 dimer interface [polypeptide binding]; other site 423212005325 phosphorylation site [posttranslational modification] 423212005326 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 423212005327 ATP binding site [chemical binding]; other site 423212005328 Mg2+ binding site [ion binding]; other site 423212005329 G-X-G motif; other site 423212005330 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 423212005331 active site 423212005332 phosphorylation site [posttranslational modification] 423212005333 intermolecular recognition site; other site 423212005334 dimerization interface [polypeptide binding]; other site 423212005335 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 423212005336 putative binding surface; other site 423212005337 active site 423212005338 6-phosphofructokinase; Provisional; Region: PRK14072 423212005339 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 423212005340 active site 423212005341 ADP/pyrophosphate binding site [chemical binding]; other site 423212005342 dimerization interface [polypeptide binding]; other site 423212005343 allosteric effector site; other site 423212005344 fructose-1,6-bisphosphate binding site; other site 423212005345 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 423212005346 Pilin (bacterial filament); Region: Pilin; pfam00114 423212005347 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 423212005348 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 423212005349 Pilin (bacterial filament); Region: Pilin; pfam00114 423212005350 BolA-like protein; Region: BolA; cl00386 423212005351 putative glutamate/gamma-aminobutyrate antiporter; Region: put_Glu_GABA_T; TIGR03813 423212005352 Calcium-activated chloride channel; Region: Anoctamin; pfam04547 423212005353 Cellulase (glycosyl hydrolase family 5); Region: Cellulase; pfam00150 423212005354 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 423212005355 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 423212005356 Ligand binding site; other site 423212005357 oligomer interface; other site 423212005358 Uncharacterized conserved protein [Function unknown]; Region: COG2835 423212005359 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 423212005360 Glycoprotease family; Region: Peptidase_M22; pfam00814 423212005361 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 423212005362 DEAD/DEAH box helicase; Region: DEAD; pfam00270 423212005363 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 423212005364 Ferredoxin [Energy production and conversion]; Region: COG1146 423212005365 4Fe-4S binding domain; Region: Fer4; cl02805 423212005366 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 423212005367 PilZ domain; Region: PilZ; pfam07238 423212005368 oxidative damage protection protein; Provisional; Region: PRK05408 423212005369 Indigoidine synthase A like protein; Region: Indigoidine_A; pfam04227 423212005370 Integrase; Region: Integrase_1; pfam12835 423212005371 Domain of unknown function (DUF927); Region: DUF927; pfam06048 423212005372 Helix-turn-helix domain; Region: HTH_17; pfam12728 423212005373 AAA domain; Region: AAA_14; pfam13173 423212005374 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 423212005375 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 423212005376 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 423212005377 active site 423212005378 DNA binding site [nucleotide binding] 423212005379 Int/Topo IB signature motif; other site 423212005380 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 423212005381 Transposase; Region: DDE_Tnp_ISL3; pfam01610 423212005382 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 423212005383 active site clefts [active] 423212005384 zinc binding site [ion binding]; other site 423212005385 dimer interface [polypeptide binding]; other site 423212005386 HipA N-terminal domain; Region: Couple_hipA; pfam13657 423212005387 HipA-like N-terminal domain; Region: HipA_N; pfam07805 423212005388 HipA-like C-terminal domain; Region: HipA_C; pfam07804 423212005389 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 423212005390 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 423212005391 non-specific DNA binding site [nucleotide binding]; other site 423212005392 salt bridge; other site 423212005393 sequence-specific DNA binding site [nucleotide binding]; other site 423212005394 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 423212005395 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 423212005396 S-adenosylmethionine binding site [chemical binding]; other site 423212005397 Taurine catabolism dioxygenase TauD, TfdA family; Region: TauD; pfam02668 423212005398 putative adenylate-forming enzyme; Region: aden_form_hyp; TIGR02304 423212005399 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 423212005400 polyketide synthases (PKSs) polymerize simple fatty acids into a large variety of different products, called polyketides, by successive decarboxylating Claisen condensations. PKSs can be divided into 2 groups, modular type I PKSs consisting of one or...; Region: PKS; cd00833 423212005401 Beta-ketoacyl synthase; Region: PKS_KS; smart00825 423212005402 active site 423212005403 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 423212005404 amino acid adenylation domain; Region: AA-adenyl-dom; TIGR01733 423212005405 acyl-activating enzyme (AAE) consensus motif; other site 423212005406 AMP binding site [chemical binding]; other site 423212005407 cyclohexanecarboxyl-CoA dehydrogenase; Region: cyc_hxne_CoA_dh; TIGR03207 423212005408 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 423212005409 active site 423212005410 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK05808 423212005411 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 423212005412 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 423212005413 Phosphopantetheine attachment site; Region: PP-binding; cl09936 423212005414 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 423212005415 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 423212005416 active site 423212005417 nucleophile elbow; other site 423212005418 Patatin phospholipase; Region: DUF3734; pfam12536 423212005419 cAMP phosphodiesterases class-II; Region: PDEase_II; cl17776 423212005420 PAS fold; Region: PAS_4; pfam08448 423212005421 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 423212005422 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 423212005423 Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor...; Region: Sec7; cd00171 423212005424 active site/putative ARF binding site [active] 423212005425 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 423212005426 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 423212005427 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 423212005428 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 423212005429 active site 423212005430 metal binding site [ion binding]; metal-binding site 423212005431 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 423212005432 L-Ala-D/L-Glu epimerase catalyzes the epimerization of L-Ala-D/L-Glu and other dipeptides. The genomic context and the substrate specificity of characterized members of this family from E.coli and B.subtilis indicates a possible role in the metabolism of...; Region: L-Ala-DL-Glu_epimerase; cd03319 423212005433 active site 423212005434 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 423212005435 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 423212005436 DNA binding residues [nucleotide binding] 423212005437 Fic/DOC family; Region: Fic; cl00960 423212005438 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 423212005439 Glycosyltransferase sugar-binding region containing DXD motif; Region: Gly_transf_sug; pfam04488 423212005440 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional; Region: PRK10903 423212005441 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cd00317 423212005442 active site 423212005443 potential frameshift: common BLAST hit: gi|289165842|ref|YP_003455980.1| Hypothetical protein, weakly similar to eukaryotic proteins 423212005444 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 423212005445 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 423212005446 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 423212005447 Legionella pneumophila major outer membrane protein precursor; Region: Legionella_OMP; pfam05150 423212005448 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 423212005449 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 423212005450 active site 423212005451 AMP binding site [chemical binding]; other site 423212005452 acyl-activating enzyme (AAE) consensus motif; other site 423212005453 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 423212005454 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 423212005455 C-terminal domain interface [polypeptide binding]; other site 423212005456 GSH binding site (G-site) [chemical binding]; other site 423212005457 dimer interface [polypeptide binding]; other site 423212005458 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 423212005459 N-terminal domain interface [polypeptide binding]; other site 423212005460 dimer interface [polypeptide binding]; other site 423212005461 substrate binding pocket (H-site) [chemical binding]; other site 423212005462 peroxiredoxin, Ohr subfamily; Region: organ_hyd_perox; TIGR03561 423212005463 Legionella pneumophila major outer membrane protein precursor; Region: Legionella_OMP; pfam05150 423212005464 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 423212005465 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 423212005466 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 423212005467 intracellular protease, PfpI family; Region: PfpI; TIGR01382 423212005468 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_1; cd03169 423212005469 conserved cys residue [active] 423212005470 Glycosyltransferase sugar-binding region containing DXD motif; Region: Gly_transf_sug; pfam04488 423212005471 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 423212005472 substrate binding site [chemical binding]; other site 423212005473 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 423212005474 guanine deaminase; Provisional; Region: PRK09228 423212005475 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 423212005476 active site 423212005477 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 423212005478 Toprim domain; Region: Toprim_3; pfam13362 423212005479 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 423212005480 catalytic core [active] 423212005481 RibD C-terminal domain; Region: RibD_C; cl17279 423212005482 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 423212005483 MAPEG family; Region: MAPEG; cl09190 423212005484 YhhN-like protein; Region: YhhN; pfam07947 423212005485 Catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases; Region: CE4_NodB_like_1; cd10960 423212005486 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 423212005487 NodB motif; other site 423212005488 putative active site [active] 423212005489 putative catalytic site [active] 423212005490 putative Zn binding site [ion binding]; other site 423212005491 Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane]; Region: MltA; COG2821 423212005492 MltA specific insert domain; Region: MltA; pfam03562 423212005493 3D domain; Region: 3D; pfam06725 423212005494 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 423212005495 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 423212005496 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 423212005497 pyridoxal 5'-phosphate binding site [chemical binding]; other site 423212005498 homodimer interface [polypeptide binding]; other site 423212005499 catalytic residue [active] 423212005500 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 423212005501 aromatic arch; other site 423212005502 DCoH dimer interaction site [polypeptide binding]; other site 423212005503 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 423212005504 DCoH tetramer interaction site [polypeptide binding]; other site 423212005505 substrate binding site [chemical binding]; other site 423212005506 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 423212005507 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 423212005508 Protein export membrane protein; Region: SecD_SecF; pfam02355 423212005509 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 423212005510 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 423212005511 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 423212005512 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 423212005513 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 423212005514 Queuosine biosynthesis protein; Region: Queuosine_synth; pfam02547 423212005515 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 423212005516 ABC transporter ATPase component; Reviewed; Region: PRK11147 423212005517 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 423212005518 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 423212005519 ABC transporter; Region: ABC_tran_2; pfam12848 423212005520 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 423212005521 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 423212005522 catalytic motif [active] 423212005523 Catalytic residue [active] 423212005524 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 423212005525 homotrimer interaction site [polypeptide binding]; other site 423212005526 putative active site [active] 423212005527 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional; Region: PRK11092 423212005528 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 423212005529 Zn2+ binding site [ion binding]; other site 423212005530 Mg2+ binding site [ion binding]; other site 423212005531 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 423212005532 synthetase active site [active] 423212005533 NTP binding site [chemical binding]; other site 423212005534 metal binding site [ion binding]; metal-binding site 423212005535 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 423212005536 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 423212005537 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 423212005538 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 423212005539 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 423212005540 catalytic site [active] 423212005541 G-X2-G-X-G-K; other site 423212005542 hypothetical protein; Provisional; Region: PRK11820 423212005543 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 423212005544 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 423212005545 ribonuclease PH; Reviewed; Region: rph; PRK00173 423212005546 Ribonuclease PH; Region: RNase_PH_bact; cd11362 423212005547 hexamer interface [polypeptide binding]; other site 423212005548 active site 423212005549 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 423212005550 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 423212005551 Walker A motif; other site 423212005552 ATP binding site [chemical binding]; other site 423212005553 Walker B motif; other site 423212005554 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 423212005555 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 423212005556 catalytic residue [active] 423212005557 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 423212005558 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 423212005559 YGGT family; Region: YGGT; pfam02325 423212005560 Protein of unknown function (DUF2845); Region: DUF2845; pfam11006 423212005561 Protein of unknown function (DUF2845); Region: DUF2845; pfam11006 423212005562 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 423212005563 active site 423212005564 catalytic residues [active] 423212005565 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 423212005566 Helix-turn-helix domain; Region: HTH_18; pfam12833 423212005567 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 423212005568 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 423212005569 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 423212005570 homotetramer interface [polypeptide binding]; other site 423212005571 ligand binding site [chemical binding]; other site 423212005572 catalytic site [active] 423212005573 NAD binding site [chemical binding]; other site 423212005574 S-adenosylmethionine synthetase; Validated; Region: PRK05250 423212005575 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 423212005576 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 423212005577 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 423212005578 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 423212005579 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 423212005580 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 423212005581 catalytic site [active] 423212005582 subunit interface [polypeptide binding]; other site 423212005583 chaperone protein DnaJ; Provisional; Region: PRK10767 423212005584 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 423212005585 HSP70 interaction site [polypeptide binding]; other site 423212005586 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 423212005587 substrate binding site [polypeptide binding]; other site 423212005588 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 423212005589 Zn binding sites [ion binding]; other site 423212005590 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 423212005591 dimer interface [polypeptide binding]; other site 423212005592 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 423212005593 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 423212005594 nucleotide binding site [chemical binding]; other site 423212005595 GrpE; Region: GrpE; pfam01025 423212005596 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 423212005597 dimer interface [polypeptide binding]; other site 423212005598 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 423212005599 Class-II DAHP synthetase family; Region: DAHP_synth_2; pfam01474 423212005600 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 423212005601 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 423212005602 substrate binding site [chemical binding]; other site 423212005603 active site 423212005604 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 423212005605 homooctamer interface [polypeptide binding]; other site 423212005606 active site 423212005607 Uncharacterized protein conserved in bacteria [Function unknown]; Region: DedD; COG3147 423212005608 Sporulation related domain; Region: SPOR; pfam05036 423212005609 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 423212005610 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 423212005611 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 423212005612 active site 423212005613 HIGH motif; other site 423212005614 nucleotide binding site [chemical binding]; other site 423212005615 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 423212005616 KMSK motif region; other site 423212005617 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 423212005618 tRNA binding surface [nucleotide binding]; other site 423212005619 anticodon binding site; other site 423212005620 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 423212005621 Domain of unknown function DUF20; Region: UPF0118; pfam01594 423212005622 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 423212005623 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 423212005624 generic binding surface II; other site 423212005625 ssDNA binding site; other site 423212005626 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 423212005627 ATP binding site [chemical binding]; other site 423212005628 putative Mg++ binding site [ion binding]; other site 423212005629 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 423212005630 nucleotide binding region [chemical binding]; other site 423212005631 ATP-binding site [chemical binding]; other site 423212005632 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 423212005633 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 423212005634 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 423212005635 ZIP Zinc transporter; Region: Zip; pfam02535 423212005636 Maf-like protein; Region: Maf; pfam02545 423212005637 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 423212005638 active site 423212005639 dimer interface [polypeptide binding]; other site 423212005640 enolase; Provisional; Region: eno; PRK00077 423212005641 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 423212005642 dimer interface [polypeptide binding]; other site 423212005643 metal binding site [ion binding]; metal-binding site 423212005644 substrate binding pocket [chemical binding]; other site 423212005645 Septum formation initiator; Region: DivIC; cl17659 423212005646 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 423212005647 mevalonate kinase; Region: mevalon_kin; TIGR00549 423212005648 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 423212005649 Mevalonate pyrophosphate decarboxylase [Lipid metabolism]; Region: MVD1; COG3407 423212005650 diphosphomevalonate decarboxylase; Region: PLN02407 423212005651 diphosphomevalonate decarboxylase; Region: PLN02407 423212005652 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type; Region: rSAM_QueE_gams; TIGR04349 423212005653 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 423212005654 FeS/SAM binding site; other site 423212005655 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 423212005656 binding surface 423212005657 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 423212005658 TPR motif; other site 423212005659 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 423212005660 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 423212005661 ligand binding site [chemical binding]; other site 423212005662 Protein of unknown function (DUF330); Region: DUF330; cl01135 423212005663 virulence factor Mce family protein; Region: Mtu_fam_mce; TIGR00996 423212005664 mce related protein; Region: MCE; pfam02470 423212005665 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 423212005666 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 423212005667 Walker A/P-loop; other site 423212005668 ATP binding site [chemical binding]; other site 423212005669 Q-loop/lid; other site 423212005670 ABC transporter signature motif; other site 423212005671 Walker B; other site 423212005672 D-loop; other site 423212005673 H-loop/switch region; other site 423212005674 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 423212005675 Permease; Region: Permease; pfam02405 423212005676 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 423212005677 active site 423212005678 ATP binding site [chemical binding]; other site 423212005679 substrate binding site [chemical binding]; other site 423212005680 activation loop (A-loop); other site 423212005681 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 423212005682 Isopentenyl-diphosphate:dimethylallyl diphosphate isomerase type 2 (IDI-2) FMN-binding domain. Two types of IDIs have been characterized at present. The long known IDI-1 is only dependent on divalent metals for activity, whereas IDI-2 requires a metal; Region: IDI-2_FMN; cd02811 423212005683 homotetramer interface [polypeptide binding]; other site 423212005684 FMN binding site [chemical binding]; other site 423212005685 homodimer contacts [polypeptide binding]; other site 423212005686 putative active site [active] 423212005687 putative substrate binding site [chemical binding]; other site 423212005688 Class II hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR); Region: HMG-CoA_reductase_classII; cd00644 423212005689 homodimer interface [polypeptide binding]; other site 423212005690 catalytic residues [active] 423212005691 NAD binding site [chemical binding]; other site 423212005692 substrate binding pocket [chemical binding]; other site 423212005693 flexible flap; other site 423212005694 Mevalonate kinase [Lipid metabolism]; Region: ERG12; COG1577 423212005695 potential frameshift: common BLAST hit: gi|148359628|ref|YP_001250835.1| polyhydroxyalkanoic synthase 423212005696 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 423212005697 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 423212005698 Poly-beta-hydroxybutyrate polymerase N terminal; Region: PHBC_N; pfam12551 423212005699 Transposase; Region: DDE_Tnp_ISL3; pfam01610 423212005700 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 423212005701 DNA-binding site [nucleotide binding]; DNA binding site 423212005702 RNA-binding motif; other site 423212005703 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 423212005704 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 423212005705 ATP binding site [chemical binding]; other site 423212005706 Mg++ binding site [ion binding]; other site 423212005707 motif III; other site 423212005708 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 423212005709 nucleotide binding region [chemical binding]; other site 423212005710 ATP-binding site [chemical binding]; other site 423212005711 RNA recognition motif in Escherichia coli RNA helicase dbpA and similar proteins; Region: RRM_EcDbpA_like; cd12501 423212005712 putative RNA binding site [nucleotide binding]; other site 423212005713 Cation efflux family; Region: Cation_efflux; cl00316 423212005714 Predicted acetamidase/formamidase [Energy production and conversion]; Region: COG2421 423212005715 Carbohydrate-selective porin, OprB family; Region: OprB; cl17816 423212005716 Winged helix-turn helix; Region: HTH_29; pfam13551 423212005717 Helix-turn-helix domain; Region: HTH_28; pfam13518 423212005718 Integrase core domain; Region: rve; pfam00665 423212005719 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 423212005720 Integrase core domain; Region: rve_3; pfam13683 423212005721 Domain of unknown function (DUF1768); Region: DUF1768; cl01271 423212005722 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 423212005723 GIY-YIG motif/motif A; other site 423212005724 putative active site [active] 423212005725 putative metal binding site [ion binding]; other site 423212005726 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 423212005727 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 423212005728 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 423212005729 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 423212005730 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 423212005731 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 423212005732 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 423212005733 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 423212005734 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 423212005735 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 423212005736 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 423212005737 DNA-directed RNA polymerase, beta' subunit, predominant form; Region: rpoC_TIGR; TIGR02386 423212005738 Transcriptional regulator [Transcription]; Region: LysR; COG0583 423212005739 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 423212005740 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 423212005741 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 423212005742 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 423212005743 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 423212005744 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 423212005745 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 423212005746 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 423212005747 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 423212005748 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 423212005749 Dot/Icm substrate protein; Region: SidE; pfam12252 423212005750 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 423212005751 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 423212005752 ligand binding site [chemical binding]; other site 423212005753 K+ potassium transporter; Region: K_trans; pfam02705 423212005754 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 423212005755 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 423212005756 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 423212005757 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 423212005758 PAS domain S-box; Region: sensory_box; TIGR00229 423212005759 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 423212005760 putative active site [active] 423212005761 heme pocket [chemical binding]; other site 423212005762 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212005763 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212005764 metal binding site [ion binding]; metal-binding site 423212005765 active site 423212005766 I-site; other site 423212005767 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 423212005768 putative substrate translocation pore; other site 423212005769 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 423212005770 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 423212005771 metabolite-proton symporter; Region: 2A0106; TIGR00883 423212005772 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 423212005773 Protein export membrane protein; Region: SecD_SecF; cl14618 423212005774 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 423212005775 carboxyltransferase (CT) interaction site; other site 423212005776 biotinylation site [posttranslational modification]; other site 423212005777 HlyD family secretion protein; Region: HlyD_3; pfam13437 423212005778 Outer membrane efflux protein; Region: OEP; pfam02321 423212005779 Outer membrane efflux protein; Region: OEP; pfam02321 423212005780 Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair]; Region: SPS1; COG0515 423212005781 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 423212005782 active site 423212005783 ATP binding site [chemical binding]; other site 423212005784 substrate binding site [chemical binding]; other site 423212005785 activation loop (A-loop); other site 423212005786 Transcriptional regulator [Transcription]; Region: LysR; COG0583 423212005787 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 423212005788 The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; Region: PBP2_LeuO; cd08466 423212005789 putative substrate binding pocket [chemical binding]; other site 423212005790 putative dimerization interface [polypeptide binding]; other site 423212005791 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 423212005792 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 423212005793 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 423212005794 Predicted transcriptional regulators [Transcription]; Region: COG1733 423212005795 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 423212005796 classical (c) SDRs; Region: SDR_c; cd05233 423212005797 NAD(P) binding site [chemical binding]; other site 423212005798 active site 423212005799 F-box-like; Region: F-box-like; pfam12937 423212005800 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 423212005801 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 423212005802 Response regulator receiver domain; Region: Response_reg; pfam00072 423212005803 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 423212005804 active site 423212005805 phosphorylation site [posttranslational modification] 423212005806 intermolecular recognition site; other site 423212005807 dimerization interface [polypeptide binding]; other site 423212005808 PAS domain; Region: PAS; smart00091 423212005809 PAS fold; Region: PAS_4; pfam08448 423212005810 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 423212005811 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 423212005812 dimer interface [polypeptide binding]; other site 423212005813 phosphorylation site [posttranslational modification] 423212005814 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 423212005815 ATP binding site [chemical binding]; other site 423212005816 Mg2+ binding site [ion binding]; other site 423212005817 G-X-G motif; other site 423212005818 Response regulator receiver domain; Region: Response_reg; pfam00072 423212005819 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 423212005820 active site 423212005821 phosphorylation site [posttranslational modification] 423212005822 intermolecular recognition site; other site 423212005823 dimerization interface [polypeptide binding]; other site 423212005824 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 423212005825 dimer interface [polypeptide binding]; other site 423212005826 phosphorylation site [posttranslational modification] 423212005827 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 423212005828 ATP binding site [chemical binding]; other site 423212005829 Mg2+ binding site [ion binding]; other site 423212005830 G-X-G motif; other site 423212005831 Streptomycin adenylyltransferase; Region: Adenyl_transf; pfam04439 423212005832 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 423212005833 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 423212005834 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 423212005835 Walker A/P-loop; other site 423212005836 ATP binding site [chemical binding]; other site 423212005837 Q-loop/lid; other site 423212005838 ABC transporter signature motif; other site 423212005839 Walker B; other site 423212005840 D-loop; other site 423212005841 H-loop/switch region; other site 423212005842 Dot/Icm substrate protein; Region: SidE; pfam12252 423212005843 Dot/Icm substrate protein; Region: SidE; pfam12252 423212005844 Dot/Icm substrate protein; Region: SidE; pfam12252 423212005845 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 423212005846 Integrase core domain; Region: rve; pfam00665 423212005847 Protein of unknown function (DUF3638); Region: DUF3638; pfam12340 423212005848 Cdc37 N terminal kinase binding; Region: CDC37_N; cl03951 423212005849 Helix-turn-helix domain; Region: HTH_28; pfam13518 423212005850 Winged helix-turn helix; Region: HTH_29; pfam13551 423212005851 Homeodomain-like domain; Region: HTH_32; pfam13565 423212005852 Integrase core domain; Region: rve; pfam00665 423212005853 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 423212005854 Integrase core domain; Region: rve_3; pfam13683 423212005855 Dot/Icm substrate protein; Region: SidE; pfam12252 423212005856 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 423212005857 S-adenosylmethionine binding site [chemical binding]; other site 423212005858 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 423212005859 C-20 methyltransferase BchU; Region: C20_methyl_CrtF; TIGR02716 423212005860 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 423212005861 S-adenosylmethionine binding site [chemical binding]; other site 423212005862 Protein of unknown function (DUF3141); Region: DUF3141; pfam11339 423212005863 Glycosyltransferase sugar-binding region containing DXD motif; Region: Gly_transf_sug; pfam04488 423212005864 Predicted transcriptional regulator [Transcription]; Region: COG2378 423212005865 HTH domain; Region: HTH_11; pfam08279 423212005866 WYL domain; Region: WYL; pfam13280 423212005867 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 423212005868 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 423212005869 Coenzyme A binding pocket [chemical binding]; other site 423212005870 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_11; cd07261 423212005871 putative dimer interface [polypeptide binding]; other site 423212005872 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 423212005873 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 423212005874 Coenzyme A binding pocket [chemical binding]; other site 423212005875 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 423212005876 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 423212005877 Coenzyme A binding pocket [chemical binding]; other site 423212005878 S-adenosylhomocysteine hydrolase [Coenzyme metabolism]; Region: SAM1; COG0499 423212005879 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 423212005880 NAD binding site [chemical binding]; other site 423212005881 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 423212005882 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 423212005883 active site 423212005884 Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism]; Region: GadB; COG0076 423212005885 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 423212005886 catalytic residue [active] 423212005887 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 423212005888 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 423212005889 HlyD family secretion protein; Region: HlyD_3; pfam13437 423212005890 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 423212005891 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 423212005892 putative binding surface; other site 423212005893 active site 423212005894 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 423212005895 amino acid adenylation domain; Region: AA-adenyl-dom; TIGR01733 423212005896 acyl-activating enzyme (AAE) consensus motif; other site 423212005897 AMP binding site [chemical binding]; other site 423212005898 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 423212005899 polyketide synthases (PKSs) polymerize simple fatty acids into a large variety of different products, called polyketides, by successive decarboxylating Claisen condensations. PKSs can be divided into 2 groups, modular type I PKSs consisting of one or...; Region: PKS; cd00833 423212005900 Beta-ketoacyl synthase; Region: PKS_KS; smart00825 423212005901 active site 423212005902 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 423212005903 Acyl transferase domain in polyketide synthase (PKS) enzymes; Region: PKS_AT; smart00827 423212005904 ketoreductase (KR), subgroup 2, complex (x) SDRs; Region: KR_2_SDR_x; cd08953 423212005905 putative NADP binding site [chemical binding]; other site 423212005906 This enzymatic domain is part of bacterial polyketide synthases; Region: PKS_KR; smart00822 423212005907 active site 423212005908 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 423212005909 Thioesterase domains of type I polyketide synthases or non-ribosomal peptide synthetases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3319 423212005910 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 423212005911 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 423212005912 dimer interface [polypeptide binding]; other site 423212005913 phosphorylation site [posttranslational modification] 423212005914 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 423212005915 ATP binding site [chemical binding]; other site 423212005916 Mg2+ binding site [ion binding]; other site 423212005917 G-X-G motif; other site 423212005918 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 423212005919 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 423212005920 active site 423212005921 phosphorylation site [posttranslational modification] 423212005922 intermolecular recognition site; other site 423212005923 dimerization interface [polypeptide binding]; other site 423212005924 Response regulator receiver domain; Region: Response_reg; pfam00072 423212005925 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 423212005926 active site 423212005927 phosphorylation site [posttranslational modification] 423212005928 intermolecular recognition site; other site 423212005929 dimerization interface [polypeptide binding]; other site 423212005930 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 423212005931 Methyltransferase domain; Region: Methyltransf_31; pfam13847 423212005932 S-adenosylmethionine binding site [chemical binding]; other site 423212005933 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cl00184 423212005934 tuzin; Provisional; Region: PTZ00202 423212005935 polyketide synthases (PKSs) polymerize simple fatty acids into a large variety of different products, called polyketides, by successive decarboxylating Claisen condensations. PKSs can be divided into 2 groups, modular type I PKSs consisting of one or...; Region: PKS; cd00833 423212005936 Beta-ketoacyl synthase; Region: PKS_KS; smart00825 423212005937 active site 423212005938 polyketide synthases (PKSs) polymerize simple fatty acids into a large variety of different products, called polyketides, by successive decarboxylating Claisen condensations. PKSs can be divided into 2 groups, modular type I PKSs consisting of one or...; Region: PKS; cd00833 423212005939 Beta-ketoacyl synthase; Region: PKS_KS; smart00825 423212005940 active site 423212005941 ketoreductase (KR) and fatty acid synthase (FAS), complex (x) SDRs; Region: KR_FAS_SDR_x; cd05274 423212005942 KR domain; Region: KR; pfam08659 423212005943 NADP binding site [chemical binding]; other site 423212005944 active site 423212005945 Phosphopantetheine attachment site; Region: PKS_PP; smart00823 423212005946 polyketide synthases (PKSs) polymerize simple fatty acids into a large variety of different products, called polyketides, by successive decarboxylating Claisen condensations. PKSs can be divided into 2 groups, modular type I PKSs consisting of one or...; Region: PKS; cd00833 423212005947 Beta-ketoacyl synthase; Region: PKS_KS; smart00825 423212005948 active site 423212005949 Dehydratase domain in polyketide synthase (PKS) enzymes; Region: PKS_DH; smart00826 423212005950 beta-ketoacyl reductase (KR) domain of fatty acid synthase (FAS), subgroup 2, complex (x); Region: KR_2_FAS_SDR_x; cd08955 423212005951 KR domain; Region: KR; pfam08659 423212005952 putative NADP binding site [chemical binding]; other site 423212005953 active site 423212005954 Phosphopantetheine attachment site; Region: PKS_PP; smart00823 423212005955 Condensation domain; Region: Condensation; pfam00668 423212005956 integral membrane protein, TerC family; Region: R_switched_Alx; TIGR03718 423212005957 Macrophage killing protein with similarity to conjugation protein; Region: IcmL; pfam11393 423212005958 Macrophage killing protein with similarity to conjugation protein; Region: IcmL; pfam11393 423212005959 Macrophage killing protein with similarity to conjugation protein; Region: IcmL; pfam11393 423212005960 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 423212005961 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation...; Region: ACD_IbpA-B_like; cd06470 423212005962 putative dimer interface [polypeptide binding]; other site 423212005963 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 423212005964 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 423212005965 putative dimer interface [polypeptide binding]; other site 423212005966 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 423212005967 Sulfate transporter family; Region: Sulfate_transp; pfam00916 423212005968 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 423212005969 active site clefts [active] 423212005970 zinc binding site [ion binding]; other site 423212005971 dimer interface [polypeptide binding]; other site 423212005972 Predicted ornithine cyclodeaminase, mu-crystallin homolog [Amino acid transport and metabolism]; Region: COG2423 423212005973 ornithine cyclodeaminase; Validated; Region: PRK06823; cl17400 423212005974 Ketosteroid isomerase homolog [Function unknown]; Region: COG4319 423212005975 SnoaL-like domain; Region: SnoaL_3; pfam13474 423212005976 Methyltransferase domain; Region: Methyltransf_23; pfam13489 423212005977 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 423212005978 S-adenosylmethionine binding site [chemical binding]; other site 423212005979 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 423212005980 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 423212005981 putative substrate translocation pore; other site 423212005982 POT family; Region: PTR2; cl17359 423212005983 Uncharacterized protein family UPF0027; Region: UPF0027; pfam01139 423212005984 hypothetical protein; Reviewed; Region: PRK09588 423212005985 Archease protein family (MTH1598/TM1083); Region: Archease; pfam01951 423212005986 Protein of unknown function (DUF3175); Region: DUF3175; pfam11373 423212005987 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 423212005988 L,D-transpeptidase catalytic domain; Region: YkuD_2; pfam13645 423212005989 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 423212005990 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 423212005991 putative NAD(P) binding site [chemical binding]; other site 423212005992 dimer interface [polypeptide binding]; other site 423212005993 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 423212005994 substrate binding site [chemical binding]; other site 423212005995 Domain of unknown function (DUF4424); Region: DUF4424; pfam14415 423212005996 YARHG domain; Region: YARHG; pfam13308 423212005997 Uncharacterized protein family UPF0047; Region: UPF0047; pfam01894 423212005998 Arginase-like and histone-like hydrolases; Region: Arginase_HDAC; cl17011 423212005999 active site 423212006000 metal binding site [ion binding]; metal-binding site 423212006001 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 423212006002 Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]; Region: COG1090 423212006003 NAD(P) binding site [chemical binding]; other site 423212006004 active site 423212006005 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 423212006006 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 423212006007 PF-ChiA is an uncharacterized chitinase found in the hyperthermophilic archaeon Pyrococcus furiosus with a glycosyl hydrolase family 18 (GH18) catalytic domain as well as a cellulose-binding domain. Members of this domain family are found not only in...; Region: GH18_PF-ChiA-like; cd06543 423212006008 active site 423212006009 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 423212006010 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 423212006011 iron-sulfur cluster [ion binding]; other site 423212006012 [2Fe-2S] cluster binding site [ion binding]; other site 423212006013 C-terminal catalytic domain of plant choline monooxygenase (CMO) and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_CMO-like; cd08883 423212006014 putative alpha subunit interface [polypeptide binding]; other site 423212006015 putative active site [active] 423212006016 putative substrate binding site [chemical binding]; other site 423212006017 Fe binding site [ion binding]; other site 423212006018 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 423212006019 putative trimer interface [polypeptide binding]; other site 423212006020 putative CoA binding site [chemical binding]; other site 423212006021 Sel1 repeat; Region: Sel1; cl02723 423212006022 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 423212006023 Sel1-like repeats; Region: SEL1; smart00671 423212006024 Sel1 repeat; Region: Sel1; pfam08238 423212006025 Sel1-like repeats; Region: SEL1; smart00671 423212006026 Sel1-like repeats; Region: SEL1; smart00671 423212006027 Sel1-like repeats; Region: SEL1; smart00671 423212006028 Legionella pneumophila major outer membrane protein precursor; Region: Legionella_OMP; pfam05150 423212006029 GH3 auxin-responsive promoter; Region: GH3; pfam03321 423212006030 cyclohexanecarboxyl-CoA dehydrogenase; Region: cyc_hxne_CoA_dh; TIGR03207 423212006031 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 423212006032 active site 423212006033 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 423212006034 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 423212006035 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 423212006036 3-oxoacyl-[acyl-carrier-protein]; Region: FabH; COG0332 423212006037 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 423212006038 active site 423212006039 acyl-CoA synthetase; Validated; Region: PRK05850 423212006040 Fatty acyl-AMP ligase (FAAL); Region: FAAL; cd05931 423212006041 acyl-activating enzyme (AAE) consensus motif; other site 423212006042 active site 423212006043 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 423212006044 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 423212006045 acyl-activating enzyme (AAE) consensus motif; other site 423212006046 AMP binding site [chemical binding]; other site 423212006047 active site 423212006048 CoA binding site [chemical binding]; other site 423212006049 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 423212006050 classical (c) SDRs; Region: SDR_c; cd05233 423212006051 NAD(P) binding site [chemical binding]; other site 423212006052 active site 423212006053 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 423212006054 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 423212006055 dimer interface [polypeptide binding]; other site 423212006056 active site 423212006057 CoA binding pocket [chemical binding]; other site 423212006058 Phosphopantetheine attachment site; Region: PP-binding; cl09936 423212006059 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 423212006060 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 423212006061 putative substrate translocation pore; other site 423212006062 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 423212006063 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 423212006064 Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]; Region: NorB; COG3256 423212006065 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 423212006066 Binuclear center (active site) [active] 423212006067 K-pathway; other site 423212006068 Putative proton exit pathway; other site 423212006069 Putative water exit pathway; other site 423212006070 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 423212006071 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 423212006072 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 423212006073 Walker A/P-loop; other site 423212006074 ATP binding site [chemical binding]; other site 423212006075 Q-loop/lid; other site 423212006076 ABC transporter signature motif; other site 423212006077 Walker B; other site 423212006078 D-loop; other site 423212006079 H-loop/switch region; other site 423212006080 MAPEG family; Region: MAPEG; cl09190 423212006081 ExoU and VipD-like proteins; homologus to patatin, cPLA2, and iPLA2; Region: Pat_ExoU_VipD_like; cd07207 423212006082 active site 423212006083 nucleophile elbow; other site 423212006084 DDE superfamily endonuclease; Region: DDE_4_2; pfam13613 423212006085 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 423212006086 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 423212006087 hypothetical protein; Validated; Region: PRK07198 423212006088 GTP cyclohydrolase N terminal; Region: GTP_CH_N; pfam12471 423212006089 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 423212006090 dimerization interface [polypeptide binding]; other site 423212006091 active site 423212006092 Protein of unknown function (DUF1688); Region: DUF1688; pfam07958 423212006093 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 423212006094 active site 423212006095 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 423212006096 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 423212006097 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 423212006098 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 423212006099 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 423212006100 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 423212006101 catalytic triad [active] 423212006102 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 423212006103 Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway; Region: Fe-ADH7; cd08192 423212006104 putative active site [active] 423212006105 metal binding site [ion binding]; metal-binding site 423212006106 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 423212006107 Uncharacterized aldehyde dehydrogenase of Synechococcus sp. PCC 7335 (EDX86601); Region: ALDH_EDX86601; cd07102 423212006108 NAD(P) binding site [chemical binding]; other site 423212006109 catalytic residues [active] 423212006110 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 423212006111 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 423212006112 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; pfam09836 423212006113 hypothetical protein; Provisional; Region: PRK05409 423212006114 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 423212006115 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 423212006116 Beta-Casp domain; Region: Beta-Casp; pfam10996 423212006117 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 423212006118 BON domain; Region: BON; pfam04972 423212006119 Poly-beta-hydroxybutyrate polymerase N terminal; Region: PHBC_N; pfam12551 423212006120 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 423212006121 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 423212006122 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated; Region: PRK08190 423212006123 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 423212006124 dimer interaction site [polypeptide binding]; other site 423212006125 substrate-binding tunnel; other site 423212006126 active site 423212006127 catalytic site [active] 423212006128 substrate binding site [chemical binding]; other site 423212006129 phosphate acetyltransferase; Provisional; Region: PRK11890 423212006130 Acetokinase family; Region: Acetate_kinase; cl17229 423212006131 propionate/acetate kinase; Provisional; Region: PRK12379 423212006132 curved DNA-binding protein CbpA; Provisional; Region: PRK10266 423212006133 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 423212006134 HSP70 interaction site [polypeptide binding]; other site 423212006135 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 423212006136 substrate binding site [polypeptide binding]; other site 423212006137 dimer interface [polypeptide binding]; other site 423212006138 chaperone-modulator protein CbpM; Provisional; Region: PRK10265 423212006139 MerR HTH family regulatory protein; Region: MerR_2; pfam13591 423212006140 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 423212006141 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ABO13168; Region: LPLAT_ABO13168-like; cd07988 423212006142 putative acyl-acceptor binding pocket; other site 423212006143 Protein of unknown function (DUF1415); Region: DUF1415; pfam07209 423212006144 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 423212006145 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 423212006146 Metallo-dependent hydrolases, subgroup A is part of the superfamily of metallo-dependent hydrolases, 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...; Region: Met_dep_hydrolase_A; cd01299 423212006147 active site 423212006148 probable DNA repair protein; Region: TIGR03623 423212006149 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 423212006150 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 423212006151 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 423212006152 putative NAD(P) binding site [chemical binding]; other site 423212006153 Predicted small integral membrane protein (DUF2165); Region: DUF2165; pfam09933 423212006154 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 423212006155 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 423212006156 cytoplasmic glycerophosphodiester phosphodiesterase; Provisional; Region: ugpQ; PRK09454 423212006157 Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins; Region: GDPD_EcUgpQ_like; cd08562 423212006158 putative active site [active] 423212006159 catalytic site [active] 423212006160 putative metal binding site [ion binding]; other site 423212006161 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 423212006162 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; pfam00208 423212006163 NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase; Region: NAD_bind_Leu_Phe_Val_DH; cd01075 423212006164 NAD binding site [chemical binding]; other site 423212006165 Phe binding site; other site 423212006166 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 423212006167 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 423212006168 S-adenosylmethionine binding site [chemical binding]; other site 423212006169 4-hydroxyphenylpyruvate dioxygenase; Region: 4HPPD; TIGR01263 423212006170 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 423212006171 dimer interface [polypeptide binding]; other site 423212006172 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 423212006173 active site 423212006174 Fe binding site [ion binding]; other site 423212006175 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 423212006176 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 423212006177 GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Zeta; cd03042 423212006178 maleylacetoacetate isomerase; Region: maiA; TIGR01262 423212006179 C-terminal domain interface [polypeptide binding]; other site 423212006180 GSH binding site (G-site) [chemical binding]; other site 423212006181 putative dimer interface [polypeptide binding]; other site 423212006182 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 423212006183 dimer interface [polypeptide binding]; other site 423212006184 N-terminal domain interface [polypeptide binding]; other site 423212006185 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 423212006186 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 423212006187 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 423212006188 putative dimer interface [polypeptide binding]; other site 423212006189 putative anticodon binding site; other site 423212006190 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 423212006191 homodimer interface [polypeptide binding]; other site 423212006192 motif 1; other site 423212006193 motif 2; other site 423212006194 active site 423212006195 motif 3; other site 423212006196 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 423212006197 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 423212006198 Walker A/P-loop; other site 423212006199 ATP binding site [chemical binding]; other site 423212006200 Q-loop/lid; other site 423212006201 ABC transporter signature motif; other site 423212006202 Walker B; other site 423212006203 D-loop; other site 423212006204 H-loop/switch region; other site 423212006205 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 423212006206 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 423212006207 FtsX-like permease family; Region: FtsX; pfam02687 423212006208 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 423212006209 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 423212006210 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 423212006211 motif II; other site 423212006212 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 423212006213 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 423212006214 RNA binding surface [nucleotide binding]; other site 423212006215 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 423212006216 active site 423212006217 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 423212006218 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 423212006219 homodimer interface [polypeptide binding]; other site 423212006220 oligonucleotide binding site [chemical binding]; other site 423212006221 Domain of unknown function (DUF4372); Region: DUF4372; pfam14294 423212006222 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 423212006223 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 423212006224 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 423212006225 ATP-dependent helicase HepA; Validated; Region: PRK04914 423212006226 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 423212006227 ATP binding site [chemical binding]; other site 423212006228 putative Mg++ binding site [ion binding]; other site 423212006229 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 423212006230 nucleotide binding region [chemical binding]; other site 423212006231 ATP-binding site [chemical binding]; other site 423212006232 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 423212006233 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 423212006234 Smr domain; Region: Smr; pfam01713 423212006235 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 423212006236 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 423212006237 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 423212006238 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 423212006239 Tetramer interface [polypeptide binding]; other site 423212006240 active site 423212006241 FMN-binding site [chemical binding]; other site 423212006242 HemK family putative methylases; Region: hemK_fam; TIGR00536 423212006243 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 423212006244 S-adenosylmethionine binding site [chemical binding]; other site 423212006245 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 423212006246 Smr domain; Region: Smr; pfam01713 423212006247 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 423212006248 active site residue [active] 423212006249 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 423212006250 GSH binding site [chemical binding]; other site 423212006251 catalytic residues [active] 423212006252 preprotein translocase subunit SecB; Validated; Region: PRK05751 423212006253 SecA binding site; other site 423212006254 Preprotein binding site; other site 423212006255 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 423212006256 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 423212006257 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 423212006258 glutamate racemase; Provisional; Region: PRK00865 423212006259 Domain of unknown function (DUF1704); Region: DUF1704; pfam08014 423212006260 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 423212006261 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 423212006262 dihydrodipicolinate synthase; Region: dapA; TIGR00674 423212006263 dimer interface [polypeptide binding]; other site 423212006264 active site 423212006265 catalytic residue [active] 423212006266 3-hydroxybutyrate dehydrogenase; Provisional; Region: PRK12429 423212006267 classical (c) SDRs; Region: SDR_c; cd05233 423212006268 NAD(P) binding site [chemical binding]; other site 423212006269 active site 423212006270 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 423212006271 nucleophile elbow; other site 423212006272 Patatin phospholipase; Region: DUF3734; pfam12536 423212006273 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 423212006274 flagellar motor protein MotA; Validated; Region: PRK09110 423212006275 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 423212006276 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 423212006277 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 423212006278 ligand binding site [chemical binding]; other site 423212006279 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 423212006280 serine transporter; Region: stp; TIGR00814 423212006281 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 423212006282 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 423212006283 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 423212006284 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 423212006285 ATP binding site [chemical binding]; other site 423212006286 Walker B motif; other site 423212006287 sugar 1,4-lactone oxidases; Region: FAD_lactone_ox; TIGR01678 423212006288 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; pfam05721 423212006289 DNA repair protein RadA; Provisional; Region: PRK11823 423212006290 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 423212006291 Walker A motif; other site 423212006292 ATP binding site [chemical binding]; other site 423212006293 Walker B motif; other site 423212006294 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 423212006295 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 423212006296 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 423212006297 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 423212006298 substrate binding pocket [chemical binding]; other site 423212006299 chain length determination region; other site 423212006300 substrate-Mg2+ binding site; other site 423212006301 catalytic residues [active] 423212006302 aspartate-rich region 1; other site 423212006303 active site lid residues [active] 423212006304 aspartate-rich region 2; other site 423212006305 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 423212006306 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 423212006307 S-adenosylmethionine binding site [chemical binding]; other site 423212006308 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 423212006309 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 423212006310 active site 423212006311 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 423212006312 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 423212006313 active site 423212006314 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 423212006315 protein binding site [polypeptide binding]; other site 423212006316 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 423212006317 putative substrate binding region [chemical binding]; other site 423212006318 GrpE; Region: GrpE; pfam01025 423212006319 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 423212006320 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 423212006321 tRNA; other site 423212006322 putative tRNA binding site [nucleotide binding]; other site 423212006323 putative NADP binding site [chemical binding]; other site 423212006324 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 423212006325 peptide chain release factor 1; Validated; Region: prfA; PRK00591 423212006326 This domain is found in peptide chain release factors; Region: PCRF; smart00937 423212006327 RF-1 domain; Region: RF-1; pfam00472 423212006328 protein-(glutamine-N5) methyltransferase, release factor-specific; Region: RF_mod_PrmC; TIGR03534 423212006329 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 423212006330 S-adenosylmethionine binding site [chemical binding]; other site 423212006331 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 423212006332 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 423212006333 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 423212006334 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 423212006335 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 423212006336 Dna-J like membrane chaperone protein; Provisional; Region: djlA; PRK09430 423212006337 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 423212006338 putative metal binding site [ion binding]; other site 423212006339 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 423212006340 HSP70 interaction site [polypeptide binding]; other site 423212006341 Protein of unknown function (DUF3530); Region: DUF3530; pfam12048 423212006342 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 423212006343 Fatty acyltransferase-like subfamily of the SGNH hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its...; Region: fatty_acyltransferase_like; cd01846 423212006344 active site 423212006345 catalytic triad [active] 423212006346 oxyanion hole [active] 423212006347 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 423212006348 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 423212006349 ATP binding site [chemical binding]; other site 423212006350 Mg++ binding site [ion binding]; other site 423212006351 motif III; other site 423212006352 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 423212006353 nucleotide binding region [chemical binding]; other site 423212006354 ATP-binding site [chemical binding]; other site 423212006355 RNA recognition motif in Escherichia coli cold-shock DEAD box protein A (CsdA) and similar proteins; Region: RRM_EcCsdA_like; cd12499 423212006356 putative RNA binding site [nucleotide binding]; other site 423212006357 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 423212006358 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 423212006359 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 423212006360 2,4-dienoyl-CoA reductase (DCR) FMN-binding domain. DCR in E. coli is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the...; Region: DCR_FMN; cd02930 423212006361 active site 423212006362 FMN binding site [chemical binding]; other site 423212006363 2,4-decadienoyl-CoA binding site; other site 423212006364 catalytic residue [active] 423212006365 4Fe-4S cluster binding site [ion binding]; other site 423212006366 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 423212006367 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 423212006368 Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the...; Region: Cu-Zn_Superoxide_Dismutase; cd00305 423212006369 Cu/Zn superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodC; COG2032 423212006370 E-class dimer interface [polypeptide binding]; other site 423212006371 P-class dimer interface [polypeptide binding]; other site 423212006372 active site 423212006373 Cu2+ binding site [ion binding]; other site 423212006374 Zn2+ binding site [ion binding]; other site 423212006375 alkylhydroperoxidase, AhpD family; Region: ahpD; TIGR00777 423212006376 alkylhydroperoxidase AhpD family core domain; Region: ahpD_dom; TIGR00778 423212006377 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 423212006378 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 423212006379 dimer interface [polypeptide binding]; other site 423212006380 decamer (pentamer of dimers) interface [polypeptide binding]; other site 423212006381 catalytic triad [active] 423212006382 peroxidatic and resolving cysteines [active] 423212006383 malate dehydrogenase; Provisional; Region: PRK05442 423212006384 Chloroplast-like malate dehydrogenases; Region: MDH_choloroplast_like; cd01338 423212006385 NAD(P) binding site [chemical binding]; other site 423212006386 dimer interface [polypeptide binding]; other site 423212006387 malate binding site [chemical binding]; other site 423212006388 adenosine nucleotide hydrolase NudE; Provisional; Region: nudE; PRK11762 423212006389 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 423212006390 dimer interface [polypeptide binding]; other site 423212006391 ADP-ribose binding site [chemical binding]; other site 423212006392 active site 423212006393 nudix motif; other site 423212006394 metal binding site [ion binding]; metal-binding site 423212006395 HemN family oxidoreductase; Provisional; Region: PRK05660 423212006396 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 423212006397 FeS/SAM binding site; other site 423212006398 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 423212006399 Amidase; Region: Amidase; pfam01425 423212006400 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 423212006401 UGMP family protein; Validated; Region: PRK09604 423212006402 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 423212006403 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 423212006404 Yqey-like protein; Region: YqeY; pfam09424 423212006405 DNA primase; Validated; Region: dnaG; PRK05667 423212006406 CHC2 zinc finger; Region: zf-CHC2; pfam01807 423212006407 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 423212006408 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 423212006409 active site 423212006410 metal binding site [ion binding]; metal-binding site 423212006411 interdomain interaction site; other site 423212006412 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 423212006413 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; smart00766 423212006414 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 423212006415 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 423212006416 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 423212006417 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 423212006418 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 423212006419 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 423212006420 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 423212006421 DNA binding residues [nucleotide binding] 423212006422 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 423212006423 Transposase; Region: DDE_Tnp_ISL3; pfam01610 423212006424 Helix-turn-helix domain of transposase family ISL3; Region: HTH_Tnp_ISL3; pfam13542 423212006425 Domain of unknown function (DUF927); Region: DUF927; pfam06048 423212006426 Helix-turn-helix domain; Region: HTH_17; pfam12728 423212006427 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 423212006428 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 423212006429 metal binding site [ion binding]; metal-binding site 423212006430 Protein of unknown function (DUF2433); Region: DUF2433; pfam10360 423212006431 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 423212006432 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 423212006433 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 423212006434 active site 423212006435 catalytic residues [active] 423212006436 DNA binding site [nucleotide binding] 423212006437 Int/Topo IB signature motif; other site 423212006438 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 423212006439 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 423212006440 pyridoxal 5'-phosphate binding site [chemical binding]; other site 423212006441 homodimer interface [polypeptide binding]; other site 423212006442 catalytic residue [active] 423212006443 Chorismate mutase type II; Region: CM_2; smart00830 423212006444 hypothetical protein; Provisional; Region: PRK07206 423212006445 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 423212006446 EamA-like transporter family; Region: EamA; pfam00892 423212006447 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 423212006448 classical (c) SDRs; Region: SDR_c; cd05233 423212006449 NAD(P) binding site [chemical binding]; other site 423212006450 active site 423212006451 short chain dehydrogenase; Provisional; Region: PRK06125 423212006452 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 423212006453 NAD(P) binding site [chemical binding]; other site 423212006454 active site 423212006455 Cupin domain; Region: Cupin_2; pfam07883 423212006456 Cupin domain; Region: Cupin_2; pfam07883 423212006457 Prephenate dehydratase; Region: PDT; pfam00800 423212006458 Class-II DAHP synthetase family; Region: DAHP_synth_2; pfam01474 423212006459 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 423212006460 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 423212006461 sequence-specific DNA binding site [nucleotide binding]; other site 423212006462 salt bridge; other site 423212006463 Plant viral coat protein nucleocapsid; Region: Nucleocap_ssRNA; pfam11128 423212006464 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 423212006465 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism]; Region: ThiF; COG0476 423212006466 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 423212006467 ATP binding site [chemical binding]; other site 423212006468 substrate interface [chemical binding]; other site 423212006469 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 423212006470 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 423212006471 DNA binding site [nucleotide binding] 423212006472 active site 423212006473 Int/Topo IB signature motif; other site 423212006474 Transcriptional regulator [Transcription]; Region: LysR; COG0583 423212006475 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 423212006476 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 423212006477 putative effector binding pocket; other site 423212006478 dimerization interface [polypeptide binding]; other site 423212006479 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 423212006480 Cupin domain; Region: Cupin_2; cl17218 423212006481 hypothetical protein; Provisional; Region: PRK07206 423212006482 Transcriptional regulator [Transcription]; Region: LysR; COG0583 423212006483 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 423212006484 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 423212006485 substrate binding pocket [chemical binding]; other site 423212006486 dimerization interface [polypeptide binding]; other site 423212006487 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 423212006488 salt bridge; other site 423212006489 non-specific DNA binding site [nucleotide binding]; other site 423212006490 sequence-specific DNA binding site [nucleotide binding]; other site 423212006491 HipA N-terminal domain; Region: couple_hipA; TIGR03071 423212006492 HipA-like N-terminal domain; Region: HipA_N; pfam07805 423212006493 HipA-like C-terminal domain; Region: HipA_C; pfam07804 423212006494 Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in...; Region: t_SNARE; cd00193 423212006495 flanking leucine-zipper layers; other site 423212006496 zero layer; other site 423212006497 Transcriptional regulator [Transcription]; Region: LysR; COG0583 423212006498 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 423212006499 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 423212006500 putative effector binding pocket; other site 423212006501 dimerization interface [polypeptide binding]; other site 423212006502 Protein required for attachment to host cells; Region: Host_attach; pfam10116 423212006503 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 423212006504 putative FMN binding site [chemical binding]; other site 423212006505 NADPH bind site [chemical binding]; other site 423212006506 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 423212006507 potassium uptake protein; Region: kup; TIGR00794 423212006508 K+ potassium transporter; Region: K_trans; pfam02705 423212006509 pH-dependent sodium/proton antiporter; Provisional; Region: nhaA; PRK14854 423212006510 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 423212006511 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 423212006512 NAD(P) binding site [chemical binding]; other site 423212006513 active site 423212006514 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 423212006515 Ligand Binding Site [chemical binding]; other site 423212006516 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 423212006517 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 423212006518 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 423212006519 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 423212006520 haloacid dehalogenase-like hydrolase; Region: HAD; pfam12710 423212006521 Soluble P-type ATPase [General function prediction only]; Region: COG4087 423212006522 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 423212006523 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 423212006524 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 423212006525 TrkA-N domain; Region: TrkA_N; pfam02254 423212006526 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 423212006527 Ligand Binding Site [chemical binding]; other site 423212006528 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 423212006529 Ligand Binding Site [chemical binding]; other site 423212006530 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 423212006531 AAA domain; Region: AAA_18; pfam13238 423212006532 active site 423212006533 outer membrane protease; Reviewed; Region: PRK10993 423212006534 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 423212006535 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 423212006536 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 423212006537 dimer interface [polypeptide binding]; other site 423212006538 active site 423212006539 heme binding site [chemical binding]; other site 423212006540 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 423212006541 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 423212006542 metabolite-proton symporter; Region: 2A0106; TIGR00883 423212006543 putative substrate translocation pore; other site 423212006544 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 423212006545 Substrate binding site [chemical binding]; other site 423212006546 Ferritin-like domain; Region: Ferritin; pfam00210 423212006547 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 423212006548 dinuclear metal binding motif [ion binding]; other site 423212006549 Methyltransferase domain; Region: Methyltransf_31; pfam13847 423212006550 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 423212006551 S-adenosylmethionine binding site [chemical binding]; other site 423212006552 OsmC-like protein; Region: OsmC; pfam02566 423212006553 Peptidase family M23; Region: Peptidase_M23; pfam01551 423212006554 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 423212006555 Acetyltransferase (GNAT) domain; Region: Acetyltransf_8; pfam13523 423212006556 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 423212006557 Bacterial protein of unknown function (DUF945); Region: DUF945; pfam06097 423212006558 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5339 423212006559 Beta-lactamase; Region: Beta-lactamase; pfam00144 423212006560 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 423212006561 Transcriptional regulator [Transcription]; Region: LysR; COG0583 423212006562 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 423212006563 The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; Region: PBP2_LeuO; cd08466 423212006564 putative substrate binding pocket [chemical binding]; other site 423212006565 putative dimerization interface [polypeptide binding]; other site 423212006566 Cytochrome P450; Region: p450; cl12078 423212006567 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 423212006568 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cd02883 423212006569 nudix motif; other site 423212006570 Domain of unknown function (DUF4116); Region: DUF4116; pfam13475 423212006571 Domain of unknown function (DUF4116); Region: DUF4116; pfam13475 423212006572 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 423212006573 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 423212006574 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 423212006575 GAF domain; Region: GAF_3; pfam13492 423212006576 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212006577 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212006578 metal binding site [ion binding]; metal-binding site 423212006579 active site 423212006580 I-site; other site 423212006581 ExoU and VipD-like proteins; homologus to patatin, cPLA2, and iPLA2; Region: Pat_ExoU_VipD_like; cd07207 423212006582 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 423212006583 active site 423212006584 nucleophile elbow; other site 423212006585 beta-lactamase/D-alanine carboxypeptidase; Provisional; Region: ampC; PRK11289 423212006586 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 423212006587 Ras GTPase Activating Domain; Region: RasGAP; cl02569 423212006588 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 423212006589 Coenzyme A binding pocket [chemical binding]; other site 423212006590 malonate decarboxylase, alpha subunit; Region: mdcA; TIGR01110 423212006591 Coenzyme A transferase; Region: CoA_trans; cl17247 423212006592 malonate decarboxylase acyl carrier protein; Region: malonate_delta; TIGR03130 423212006593 malonate decarboxylase, beta subunit; Region: malonate_beta; TIGR03133 423212006594 malonate decarboxylase, gamma subunit; Region: malonate_gamma; TIGR03134 423212006595 Phosphoribosyl-dephospho-CoA transferase MdcG; Region: MdcG; pfam10620 423212006596 malonate decarboxylase holo-[acyl-carrier-protein] synthase; Region: malonate_mdcG; TIGR03135 423212006597 triphosphoribosyl-dephospho-CoA synthase MdcB; Region: malonate_mdcB; TIGR03132 423212006598 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 423212006599 malonate decarboxylase, epsilon subunit; Region: malonate_mdcH; TIGR03131 423212006600 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 423212006601 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 423212006602 active site 423212006603 metal binding site [ion binding]; metal-binding site 423212006604 Cupin domain; Region: Cupin_2; cl17218 423212006605 Protein of unknown function (DUF1311); Region: DUF1311; pfam07007 423212006606 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 423212006607 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 423212006608 putative substrate translocation pore; other site 423212006609 Predicted flavoprotein [General function prediction only]; Region: COG0431 423212006610 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 423212006611 Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: ECM4; COG0435 423212006612 Glutathione S-transferase, N-terminal domain; Region: GST_N_2; pfam13409 423212006613 C-terminal, alpha helical domain of Class Omega-like Glutathione S-transferases; Region: GST_C_Omega_like; cd03190 423212006614 putative dimer interface [polypeptide binding]; other site 423212006615 N-terminal domain interface [polypeptide binding]; other site 423212006616 putative substrate binding pocket (H-site) [chemical binding]; other site 423212006617 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 423212006618 dimer interface [polypeptide binding]; other site 423212006619 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 423212006620 dimer interface [polypeptide binding]; other site 423212006621 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 423212006622 N-acetyltransferase; Region: Acetyltransf_2; cl00949 423212006623 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 423212006624 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 423212006625 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 423212006626 Coenzyme A binding pocket [chemical binding]; other site 423212006627 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 423212006628 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 423212006629 active site 423212006630 phosphorylation site [posttranslational modification] 423212006631 intermolecular recognition site; other site 423212006632 dimerization interface [polypeptide binding]; other site 423212006633 PAS domain S-box; Region: sensory_box; TIGR00229 423212006634 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 423212006635 putative active site [active] 423212006636 heme pocket [chemical binding]; other site 423212006637 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 423212006638 dimer interface [polypeptide binding]; other site 423212006639 phosphorylation site [posttranslational modification] 423212006640 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 423212006641 ATP binding site [chemical binding]; other site 423212006642 Mg2+ binding site [ion binding]; other site 423212006643 G-X-G motif; other site 423212006644 Heme NO binding; Region: HNOB; pfam07700 423212006645 SAM-dependent methyltransferases [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: SmtA; COG0500 423212006646 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 423212006647 Aspartyl/asparaginyl beta-hydroxylase and related dioxygenases [Posttranslational modification, protein turnover, chaperones]; Region: COG3555 423212006648 Hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). These enzymes belong to the peptidase family M52. Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing...; Region: H2MP; cd00518 423212006649 nickel binding site [ion binding]; other site 423212006650 Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]; Region: FrhA; COG3259 423212006651 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 423212006652 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 423212006653 cytochrome-c3 hydrogenase subunit gamma; Provisional; Region: PRK08345 423212006654 Anaerobic sulfite reductase contains an FAD and NADPH binding module with structural similarity to ferredoxin reductase and sequence similarity to dihydroorotate dehydrogenases. Clostridium pasteurianum inducible dissimilatory type sulfite reductase is...; Region: sulfite_reductase_like; cd06221 423212006655 FAD binding pocket [chemical binding]; other site 423212006656 FAD binding motif [chemical binding]; other site 423212006657 phosphate binding motif [ion binding]; other site 423212006658 beta-alpha-beta structure motif; other site 423212006659 NAD binding pocket [chemical binding]; other site 423212006660 Iron coordination center [ion binding]; other site 423212006661 4Fe-4S dicluster domain; Region: Fer4_18; pfam13746 423212006662 HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis. HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the...; Region: HypE; cd02197 423212006663 dimerization interface [polypeptide binding]; other site 423212006664 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 423212006665 ATP binding site [chemical binding]; other site 423212006666 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 423212006667 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 423212006668 HupF/HypC family; Region: HupF_HypC; pfam01455 423212006669 Acylphosphatase; Region: Acylphosphatase; pfam00708 423212006670 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 423212006671 HypF finger; Region: zf-HYPF; pfam07503 423212006672 HypF finger; Region: zf-HYPF; pfam07503 423212006673 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 423212006674 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 423212006675 Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]; Region: HybF; COG0375 423212006676 Hydrogenase expression/synthesis hypA family; Region: HypA; cl17671 423212006677 High-affinity nickel-transport protein; Region: NicO; cl00964 423212006678 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 423212006679 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 423212006680 Ligand binding site; other site 423212006681 Putative Catalytic site; other site 423212006682 DXD motif; other site 423212006683 GtrA-like protein; Region: GtrA; pfam04138 423212006684 uncharacterized YdjC-like family proteins from bacteria; Region: YdjC_like_3; cd10807 423212006685 putative active site [active] 423212006686 YdjC motif; other site 423212006687 Mg binding site [ion binding]; other site 423212006688 putative homodimer interface [polypeptide binding]; other site 423212006689 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 423212006690 EamA-like transporter family; Region: EamA; pfam00892 423212006691 EamA-like transporter family; Region: EamA; pfam00892 423212006692 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 423212006693 Uncharacterized conserved protein [Function unknown]; Region: COG2128 423212006694 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 423212006695 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 423212006696 active site 423212006697 dimerization interface [polypeptide binding]; other site 423212006698 TPR repeat; Region: TPR_11; pfam13414 423212006699 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 423212006700 binding surface 423212006701 TPR motif; other site 423212006702 TPR repeat; Region: TPR_11; pfam13414 423212006703 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 423212006704 binding surface 423212006705 TPR repeat; Region: TPR_11; pfam13414 423212006706 TPR motif; other site 423212006707 TPR repeat; Region: TPR_11; pfam13414 423212006708 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 423212006709 binding surface 423212006710 TPR repeat; Region: TPR_11; pfam13414 423212006711 TPR motif; other site 423212006712 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 423212006713 binding surface 423212006714 TPR motif; other site 423212006715 Predicted methyltransferase (contains TPR repeat) [General function prediction only]; Region: COG4976 423212006716 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 423212006717 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 423212006718 S-adenosylmethionine binding site [chemical binding]; other site 423212006719 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 423212006720 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 423212006721 active site 423212006722 substrate binding site [chemical binding]; other site 423212006723 metal binding site [ion binding]; metal-binding site 423212006724 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 423212006725 trimer interface [polypeptide binding]; other site 423212006726 active site 423212006727 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 423212006728 Flavoprotein; Region: Flavoprotein; pfam02441 423212006729 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 423212006730 hypothetical protein; Reviewed; Region: PRK00024 423212006731 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 423212006732 MPN+ (JAMM) motif; other site 423212006733 Zinc-binding site [ion binding]; other site 423212006734 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 423212006735 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 423212006736 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 423212006737 FOG: CBS domain [General function prediction only]; Region: COG0517 423212006738 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 423212006739 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 423212006740 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD2; cd08298 423212006741 putative NAD(P) binding site [chemical binding]; other site 423212006742 putative substrate binding site [chemical binding]; other site 423212006743 catalytic Zn binding site [ion binding]; other site 423212006744 structural Zn binding site [ion binding]; other site 423212006745 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 423212006746 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 423212006747 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 423212006748 putative dimer interface [polypeptide binding]; other site 423212006749 Kynurenine formamidase [Amino acid transport and metabolism]; Region: COG1878 423212006750 Homospermidine synthase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG5310 423212006751 Saccharopine dehydrogenase; Region: Saccharop_dh; pfam03435 423212006752 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 423212006753 Thiamine pyrophosphokinase; Region: TPK; cd07995 423212006754 thiamine pyrophosphokinase; Region: thi_PPkinase; TIGR01378 423212006755 active site 423212006756 dimerization interface [polypeptide binding]; other site 423212006757 thiamine binding site [chemical binding]; other site 423212006758 PQ loop repeat; Region: PQ-loop; pfam04193 423212006759 LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for...; Region: LigD_Pol_like; cd04861 423212006760 nucleotide binding site [chemical binding]; other site 423212006761 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 423212006762 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 423212006763 active site clefts [active] 423212006764 zinc binding site [ion binding]; other site 423212006765 dimer interface [polypeptide binding]; other site 423212006766 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 423212006767 Major Facilitator Superfamily; Region: MFS_1; pfam07690 423212006768 putative substrate translocation pore; other site 423212006769 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 423212006770 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 423212006771 dimer interface [polypeptide binding]; other site 423212006772 phosphorylation site [posttranslational modification] 423212006773 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 423212006774 ATP binding site [chemical binding]; other site 423212006775 Mg2+ binding site [ion binding]; other site 423212006776 G-X-G motif; other site 423212006777 Dot/Icm substrate protein; Region: SidE; pfam12252 423212006778 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 423212006779 Protein export membrane protein; Region: SecD_SecF; cl14618 423212006780 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 423212006781 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 423212006782 HlyD family secretion protein; Region: HlyD_3; pfam13437 423212006783 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 423212006784 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3323 423212006785 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 423212006786 putative substrate translocation pore; other site 423212006787 Major Facilitator Superfamily; Region: MFS_1; pfam07690 423212006788 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 423212006789 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 423212006790 putative DNA binding site [nucleotide binding]; other site 423212006791 putative Zn2+ binding site [ion binding]; other site 423212006792 AsnC family; Region: AsnC_trans_reg; pfam01037 423212006793 MutS2 family protein; Region: mutS2; TIGR01069 423212006794 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Low Specificity D-Threonine Aldolase; Region: PLPDE_III_LS_D-TA; cd06819 423212006795 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]; Region: COG3616 423212006796 dimer interface [polypeptide binding]; other site 423212006797 active site 423212006798 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 423212006799 substrate binding site [chemical binding]; other site 423212006800 catalytic residue [active] 423212006801 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 423212006802 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 423212006803 active site 423212006804 catalytic site [active] 423212006805 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 423212006806 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 423212006807 Prephenate dehydratase; Region: PDT; pfam00800 423212006808 Chorismate mutase type II; Region: CM_2; smart00830 423212006809 aspartate aminotransferase; Provisional; Region: PRK05764 423212006810 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 423212006811 pyridoxal 5'-phosphate binding site [chemical binding]; other site 423212006812 homodimer interface [polypeptide binding]; other site 423212006813 catalytic residue [active] 423212006814 tellurite resistance protein TehB; Provisional; Region: PRK12335 423212006815 Domain of unknown function (DUF1971); Region: DUF1971; pfam09313 423212006816 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 423212006817 S-adenosylmethionine binding site [chemical binding]; other site 423212006818 Transcriptional regulator; Region: Rrf2; cl17282 423212006819 Rrf2 family protein; Region: rrf2_super; TIGR00738 423212006820 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 423212006821 apolar tunnel; other site 423212006822 heme binding site [chemical binding]; other site 423212006823 dimerization interface [polypeptide binding]; other site 423212006824 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 423212006825 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 423212006826 catalytic loop [active] 423212006827 iron binding site [ion binding]; other site 423212006828 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an N-terminal Iron-Sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible...; Region: FNR_N-term_Iron_sulfur_binding; cd06194 423212006829 FAD binding pocket [chemical binding]; other site 423212006830 FAD binding motif [chemical binding]; other site 423212006831 phosphate binding motif [ion binding]; other site 423212006832 beta-alpha-beta structure motif; other site 423212006833 NAD binding pocket [chemical binding]; other site 423212006834 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG2159 423212006835 Large-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscL; COG1970 423212006836 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 423212006837 NHLM bacteriocin system ABC transporter, ATP-binding protein; Region: NHLM_micro_ABC2; TIGR03797 423212006838 MltA specific insert domain; Region: MltA; smart00925 423212006839 3D domain; Region: 3D; pfam06725 423212006840 tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain; Region: tRNA_bind_CsaA; cd02798 423212006841 dimer interface [polypeptide binding]; other site 423212006842 putative tRNA-binding site [nucleotide binding]; other site 423212006843 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 423212006844 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 423212006845 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 423212006846 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; cl15777 423212006847 putative active site pocket [active] 423212006848 dimerization interface [polypeptide binding]; other site 423212006849 putative catalytic residue [active] 423212006850 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 423212006851 EamA-like transporter family; Region: EamA; pfam00892 423212006852 EamA-like transporter family; Region: EamA; pfam00892 423212006853 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 423212006854 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 423212006855 putative substrate translocation pore; other site 423212006856 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 423212006857 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 423212006858 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 423212006859 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 423212006860 active site 423212006861 motif I; other site 423212006862 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 423212006863 motif II; other site 423212006864 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 423212006865 Catalytic domain of Protein Kinases; Region: PKc; cd00180 423212006866 active site 423212006867 ATP binding site [chemical binding]; other site 423212006868 substrate binding site [chemical binding]; other site 423212006869 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 423212006870 substrate binding site [chemical binding]; other site 423212006871 activation loop (A-loop); other site 423212006872 activation loop (A-loop); other site 423212006873 PAS domain; Region: PAS_9; pfam13426 423212006874 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 423212006875 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 423212006876 DNA binding residues [nucleotide binding] 423212006877 dimerization interface [polypeptide binding]; other site 423212006878 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 423212006879 HSP70 interaction site [polypeptide binding]; other site 423212006880 Domain of unknown function (DUF4365); Region: DUF4365; pfam14280 423212006881 RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA...; Region: RT_Bac_retron_II; cd03487 423212006882 putative active site [active] 423212006883 putative NTP binding site [chemical binding]; other site 423212006884 putative nucleic acid binding site [nucleotide binding]; other site 423212006885 Phage integrase, N-terminal; Region: Integrase_l_N; pfam12834 423212006886 Integrase; Region: Integrase_1; pfam12835 423212006887 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 423212006888 Transposase; Region: DDE_Tnp_ISL3; pfam01610 423212006889 Uncharacterized conserved protein [Function unknown]; Region: COG3189 423212006890 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 423212006891 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 423212006892 active site 423212006893 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 423212006894 tetramer interface [polypeptide binding]; other site 423212006895 TPP-binding site [chemical binding]; other site 423212006896 heterodimer interface [polypeptide binding]; other site 423212006897 phosphorylation loop region [posttranslational modification] 423212006898 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 423212006899 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 423212006900 PYR/PP interface [polypeptide binding]; other site 423212006901 dimer interface [polypeptide binding]; other site 423212006902 TPP binding site [chemical binding]; other site 423212006903 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 423212006904 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 423212006905 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 423212006906 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 423212006907 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some...; Region: Peptidase_C1; cd02619 423212006908 active site 423212006909 Fatty acyltransferase-like subfamily of the SGNH hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its...; Region: fatty_acyltransferase_like; cd01846 423212006910 active site 423212006911 catalytic triad [active] 423212006912 oxyanion hole [active] 423212006913 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 423212006914 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 423212006915 active site 423212006916 metal binding site [ion binding]; metal-binding site 423212006917 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; cl17429 423212006918 D-alanyl-D-alanine carboxypeptidase, serine-type, PBP4 family; Region: PBP4; TIGR00666 423212006919 ParB-like nuclease domain; Region: ParBc; pfam02195 423212006920 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 423212006921 16S rRNA methyltransferase B; Provisional; Region: PRK10901 423212006922 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 423212006923 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 423212006924 S-adenosylmethionine binding site [chemical binding]; other site 423212006925 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 423212006926 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 423212006927 putative active site [active] 423212006928 substrate binding site [chemical binding]; other site 423212006929 putative cosubstrate binding site; other site 423212006930 catalytic site [active] 423212006931 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 423212006932 substrate binding site [chemical binding]; other site 423212006933 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 423212006934 active site 423212006935 catalytic residues [active] 423212006936 metal binding site [ion binding]; metal-binding site 423212006937 Uncharacterized protein containing LysM domain [Function unknown]; Region: XkdP; COG1652 423212006938 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 423212006939 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 423212006940 DNA protecting protein DprA; Region: dprA; TIGR00732 423212006941 Protein of unknown function (DUF494); Region: DUF494; pfam04361 423212006942 DNA topoisomerase I; Validated; Region: PRK06599 423212006943 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 423212006944 active site 423212006945 metal binding site [ion binding]; metal-binding site 423212006946 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 423212006947 domain I; other site 423212006948 DNA binding groove [nucleotide binding] 423212006949 phosphate binding site [ion binding]; other site 423212006950 domain II; other site 423212006951 domain III; other site 423212006952 nucleotide binding site [chemical binding]; other site 423212006953 catalytic site [active] 423212006954 domain IV; other site 423212006955 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 423212006956 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 423212006957 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 423212006958 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 423212006959 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 423212006960 Bacterial PH domain; Region: DUF304; pfam03703 423212006961 Protein of unknown function (DUF721); Region: DUF721; pfam05258 423212006962 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 423212006963 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 423212006964 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 423212006965 Uncharacterized conserved protein [Function unknown]; Region: COG4278 423212006966 ergothioneine biosynthesis protein EgtC; Region: TIGR03442 423212006967 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 423212006968 putative active site [active] 423212006969 putative dimer interface [polypeptide binding]; other site 423212006970 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 423212006971 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 423212006972 active site 423212006973 Zn binding site [ion binding]; other site 423212006974 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 423212006975 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 423212006976 cell division protein FtsZ; Validated; Region: PRK09330 423212006977 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 423212006978 nucleotide binding site [chemical binding]; other site 423212006979 SulA interaction site; other site 423212006980 cell division protein FtsA; Region: ftsA; TIGR01174 423212006981 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 423212006982 nucleotide binding site [chemical binding]; other site 423212006983 Cell division protein FtsA; Region: FtsA; pfam14450 423212006984 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 423212006985 Cell division protein FtsQ; Region: FtsQ; pfam03799 423212006986 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 423212006987 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 423212006988 ATP-grasp domain; Region: ATP-grasp_4; cl17255 423212006989 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 423212006990 FAD binding domain; Region: FAD_binding_4; pfam01565 423212006991 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 423212006992 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 423212006993 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 423212006994 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 423212006995 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 423212006996 cell division protein FtsW; Region: ftsW; TIGR02614 423212006997 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03803 423212006998 TrkA-N domain; Region: TrkA_N; pfam02254 423212006999 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 423212007000 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 423212007001 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 423212007002 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 423212007003 Mg++ binding site [ion binding]; other site 423212007004 putative catalytic motif [active] 423212007005 putative substrate binding site [chemical binding]; other site 423212007006 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 423212007007 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 423212007008 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 423212007009 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 423212007010 ZipA, C-terminal FtsZ-binding domain; Region: ZipA_C; pfam04354 423212007011 FtsZ protein binding site [polypeptide binding]; other site 423212007012 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 423212007013 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 423212007014 Walker A/P-loop; other site 423212007015 ATP binding site [chemical binding]; other site 423212007016 Q-loop/lid; other site 423212007017 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; cl05797 423212007018 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 423212007019 Q-loop/lid; other site 423212007020 ABC transporter signature motif; other site 423212007021 Walker B; other site 423212007022 D-loop; other site 423212007023 H-loop/switch region; other site 423212007024 HAD superfamily, subfamily IIIB (Acid phosphatase); Region: Acid_phosphat_B; pfam03767 423212007025 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some...; Region: Peptidase_C1; cd02619 423212007026 active site 423212007027 Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane; Region: Tim44; smart00978 423212007028 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 423212007029 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 423212007030 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 423212007031 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 423212007032 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 423212007033 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 423212007034 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 423212007035 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 423212007036 ATP-grasp domain; Region: ATP-grasp_4; cl17255 423212007037 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 423212007038 IMP binding site; other site 423212007039 dimer interface [polypeptide binding]; other site 423212007040 interdomain contacts; other site 423212007041 partial ornithine binding site; other site 423212007042 Predicted flavoproteins [General function prediction only]; Region: COG2081 423212007043 putative FAD-binding dehydrogenase; Reviewed; Region: PRK12834 423212007044 Uncharacterized conserved protein [Function unknown]; Region: COG1434 423212007045 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 423212007046 putative active site [active] 423212007047 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 423212007048 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 423212007049 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 423212007050 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 423212007051 multifunctional aminopeptidase A; Provisional; Region: PRK00913 423212007052 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 423212007053 interface (dimer of trimers) [polypeptide binding]; other site 423212007054 Substrate-binding/catalytic site; other site 423212007055 Zn-binding sites [ion binding]; other site 423212007056 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 423212007057 Domain of unknown function (DUF1840); Region: DUF1840; pfam08895 423212007058 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 423212007059 interface (dimer of trimers) [polypeptide binding]; other site 423212007060 Leucyl aminopeptidase [Amino acid transport and metabolism]; Region: PepB; COG0260 423212007061 Substrate-binding/catalytic site; other site 423212007062 Zn-binding sites [ion binding]; other site 423212007063 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 423212007064 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 423212007065 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 423212007066 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 423212007067 Sel1-like repeats; Region: SEL1; smart00671 423212007068 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 423212007069 Sel1-like repeats; Region: SEL1; smart00671 423212007070 Sel1-like repeats; Region: SEL1; smart00671 423212007071 Sel1-like repeats; Region: SEL1; smart00671 423212007072 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 423212007073 Sel1-like repeats; Region: SEL1; smart00671 423212007074 Sel1-like repeats; Region: SEL1; smart00671 423212007075 Sel1-like repeats; Region: SEL1; smart00671 423212007076 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 423212007077 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 423212007078 putative active site [active] 423212007079 GAF domain; Region: GAF; pfam01590 423212007080 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212007081 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212007082 metal binding site [ion binding]; metal-binding site 423212007083 active site 423212007084 I-site; other site 423212007085 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 423212007086 Collagen triple helix repeat (20 copies); Region: Collagen; pfam01391 423212007087 Collagen triple helix repeat (20 copies); Region: Collagen; pfam01391 423212007088 Collagen triple helix repeat (20 copies); Region: Collagen; pfam01391 423212007089 Collagen triple helix repeat (20 copies); Region: Collagen; pfam01391 423212007090 Collagen triple helix repeat (20 copies); Region: Collagen; pfam01391 423212007091 Collagen triple helix repeat (20 copies); Region: Collagen; pfam01391 423212007092 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 423212007093 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 423212007094 active site 423212007095 catalytic site [active] 423212007096 putative DNA binding site [nucleotide binding]; other site 423212007097 GIY-YIG motif/motif A; other site 423212007098 metal binding site [ion binding]; metal-binding site 423212007099 UvrB/uvrC motif; Region: UVR; pfam02151 423212007100 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 423212007101 response regulator; Provisional; Region: PRK09483 423212007102 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 423212007103 active site 423212007104 phosphorylation site [posttranslational modification] 423212007105 intermolecular recognition site; other site 423212007106 dimerization interface [polypeptide binding]; other site 423212007107 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 423212007108 DNA binding residues [nucleotide binding] 423212007109 dimerization interface [polypeptide binding]; other site 423212007110 Prokaryotic phenylalanine-4-hydroxylase (pro_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes the eukaryotic proteins, phenylalanine-4-hydroxylase (eu_PheOH); Region: pro_PheOH; cd03348 423212007111 cofactor binding site; other site 423212007112 metal binding site [ion binding]; metal-binding site 423212007113 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 423212007114 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 423212007115 putative MPT binding site; other site 423212007116 GTPase CgtA; Reviewed; Region: obgE; PRK12299 423212007117 GTP1/OBG; Region: GTP1_OBG; pfam01018 423212007118 Obg GTPase; Region: Obg; cd01898 423212007119 G1 box; other site 423212007120 GTP/Mg2+ binding site [chemical binding]; other site 423212007121 Switch I region; other site 423212007122 G2 box; other site 423212007123 G3 box; other site 423212007124 Switch II region; other site 423212007125 G4 box; other site 423212007126 G5 box; other site 423212007127 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 423212007128 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 423212007129 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 423212007130 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 423212007131 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 423212007132 5S rRNA interface [nucleotide binding]; other site 423212007133 CTC domain interface [polypeptide binding]; other site 423212007134 L16 interface [polypeptide binding]; other site 423212007135 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 423212007136 putative active site [active] 423212007137 catalytic residue [active] 423212007138 GTP-binding protein YchF; Reviewed; Region: PRK09601 423212007139 YchF GTPase; Region: YchF; cd01900 423212007140 G1 box; other site 423212007141 GTP/Mg2+ binding site [chemical binding]; other site 423212007142 Switch I region; other site 423212007143 G2 box; other site 423212007144 Switch II region; other site 423212007145 G3 box; other site 423212007146 G4 box; other site 423212007147 G5 box; other site 423212007148 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 423212007149 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 423212007150 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 423212007151 metal binding site [ion binding]; metal-binding site 423212007152 active site 423212007153 I-site; other site 423212007154 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 423212007155 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 423212007156 substrate binding pocket [chemical binding]; other site 423212007157 chain length determination region; other site 423212007158 substrate-Mg2+ binding site; other site 423212007159 catalytic residues [active] 423212007160 aspartate-rich region 1; other site 423212007161 active site lid residues [active] 423212007162 aspartate-rich region 2; other site 423212007163 FeoC like transcriptional regulator; Region: FeoC; pfam09012 423212007164 ferrous iron transport protein B; Reviewed; Region: feoB; PRK09554 423212007165 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 423212007166 G1 box; other site 423212007167 GTP/Mg2+ binding site [chemical binding]; other site 423212007168 Switch I region; other site 423212007169 G2 box; other site 423212007170 G3 box; other site 423212007171 Switch II region; other site 423212007172 G4 box; other site 423212007173 G5 box; other site 423212007174 Nucleoside recognition; Region: Gate; pfam07670 423212007175 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 423212007176 Nucleoside recognition; Region: Gate; pfam07670 423212007177 FeoA domain; Region: FeoA; pfam04023 423212007178 Predicted ATPase [General function prediction only]; Region: COG1485 423212007179 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 423212007180 Walker A motif; other site 423212007181 ATP binding site [chemical binding]; other site 423212007182 Walker B motif; other site 423212007183 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 423212007184 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 423212007185 oligomerization interface [polypeptide binding]; other site 423212007186 active site 423212007187 metal binding site [ion binding]; metal-binding site 423212007188 pantoate--beta-alanine ligase; Region: panC; TIGR00018 423212007189 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 423212007190 active site 423212007191 nucleotide binding site [chemical binding]; other site 423212007192 HIGH motif; other site 423212007193 KMSKS motif; other site 423212007194 AAA domain; Region: AAA_28; pfam13521 423212007195 Predicted ATPase [General function prediction only]; Region: COG3911 423212007196 pyruvate carboxylase subunit A; Validated; Region: PRK07178 423212007197 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 423212007198 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 423212007199 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 423212007200 Dienelactone hydrolase family; Region: DLH; pfam01738 423212007201 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 423212007202 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 423212007203 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 423212007204 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 423212007205 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 423212007206 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 423212007207 DNA binding residues [nucleotide binding] 423212007208 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 423212007209 putative protein insertion permease FtsX; Region: ftsX; TIGR00439 423212007210 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 423212007211 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 423212007212 Walker A/P-loop; other site 423212007213 ATP binding site [chemical binding]; other site 423212007214 Q-loop/lid; other site 423212007215 ABC transporter signature motif; other site 423212007216 Walker B; other site 423212007217 D-loop; other site 423212007218 H-loop/switch region; other site 423212007219 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 423212007220 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 423212007221 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 423212007222 P loop; other site 423212007223 GTP binding site [chemical binding]; other site 423212007224 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 423212007225 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 423212007226 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 423212007227 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 423212007228 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 423212007229 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 423212007230 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 423212007231 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 423212007232 S-adenosylmethionine binding site [chemical binding]; other site 423212007233 Dot/Icm secretion system ATPase DotB; Region: dot_icm_DotB; TIGR02524 423212007234 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 423212007235 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 423212007236 Walker A motif; other site 423212007237 Walker A/P-loop; other site 423212007238 ATP binding site [chemical binding]; other site 423212007239 ATP binding site [chemical binding]; other site 423212007240 Walker B motif; other site 423212007241 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 423212007242 Bacillus subtilis YhcR endonuclease and related proteins, N-terminal metallophosphatase domain; Region: MPP_YhcR_N; cd07412 423212007243 putative active site [active] 423212007244 putative metal binding site [ion binding]; other site 423212007245 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 423212007246 Putative methyltransferase; Region: Methyltransf_4; cl17290 423212007247 Methyltransferase domain; Region: Methyltransf_23; pfam13489 423212007248 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 423212007249 S-adenosylmethionine binding site [chemical binding]; other site 423212007250 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 423212007251 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 423212007252 NAD binding site [chemical binding]; other site 423212007253 ATP-grasp domain; Region: ATP-grasp_4; cl17255 423212007254 4-hydroxy-2-oxovalerate aldolase-like, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA_like; cd07944 423212007255 active site 423212007256 catalytic residues [active] 423212007257 metal binding site [ion binding]; metal-binding site 423212007258 tartrate dehydrogenase; Provisional; Region: PRK08194 423212007259 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 423212007260 Demethylmenaquinone methyltransferase [Coenzyme metabolism]; Region: MenG; COG0684 423212007261 Dienelactone hydrolase family; Region: DLH; pfam01738 423212007262 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 423212007263 conjugal transfer/type IV secretion protein DotA/TraY; Region: DotA_TraY; TIGR04346 423212007264 Phagosome trafficking protein DotA; Region: DotA; pfam11388 423212007265 conjugal transfer/type IV secretion protein DotA/TraY; Region: DotA_TraY; TIGR04346 423212007266 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 423212007267 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 423212007268 metal-binding site [ion binding] 423212007269 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 423212007270 Methyltransferase domain; Region: Methyltransf_31; pfam13847 423212007271 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 423212007272 S-adenosylmethionine binding site [chemical binding]; other site 423212007273 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; pfam05721 423212007274 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 423212007275 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 423212007276 putative active site [active] 423212007277 Zinc-finger domain; Region: zf-CHCC; cl01821 423212007278 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 423212007279 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 423212007280 DNA mismatch repair enzyme (predicted ATPase) [DNA replication, recombination, and repair]; Region: MutL; COG0323 423212007281 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 423212007282 ATP binding site [chemical binding]; other site 423212007283 Mg2+ binding site [ion binding]; other site 423212007284 G-X-G motif; other site 423212007285 MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second...; Region: MutL_Trans_MutL; cd03482 423212007286 ATP binding site [chemical binding]; other site 423212007287 MutL C terminal dimerisation domain; Region: MutL_C; smart00853 423212007288 N-acetylmuramoyl-l-alanine amidase II; Provisional; Region: PRK10431 423212007289 AMIN domain; Region: AMIN; pfam11741 423212007290 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 423212007291 active site 423212007292 metal binding site [ion binding]; metal-binding site 423212007293 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 423212007294 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 423212007295 putative carbohydrate kinase; Provisional; Region: PRK10565 423212007296 Uncharacterized conserved protein [Function unknown]; Region: COG0062 423212007297 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 423212007298 putative substrate binding site [chemical binding]; other site 423212007299 putative ATP binding site [chemical binding]; other site 423212007300 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 423212007301 stringent starvation protein A; Provisional; Region: sspA; PRK09481 423212007302 GST_N family, Stringent starvation protein A (SspA) subfamily; SspA is a RNA polymerase (RNAP)-associated protein required for the lytic development of phage P1 and for stationary phase-induced acid tolerance of E. coli. It is implicated in survival...; Region: GST_N_SspA; cd03059 423212007303 C-terminal domain interface [polypeptide binding]; other site 423212007304 putative GSH binding site (G-site) [chemical binding]; other site 423212007305 dimer interface [polypeptide binding]; other site 423212007306 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 423212007307 dimer interface [polypeptide binding]; other site 423212007308 N-terminal domain interface [polypeptide binding]; other site 423212007309 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 423212007310 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 423212007311 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 423212007312 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 423212007313 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 423212007314 cytochrome b; Provisional; Region: CYTB; MTH00145 423212007315 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cd00284 423212007316 Qi binding site; other site 423212007317 intrachain domain interface; other site 423212007318 interchain domain interface [polypeptide binding]; other site 423212007319 heme bH binding site [chemical binding]; other site 423212007320 heme bL binding site [chemical binding]; other site 423212007321 Qo binding site; other site 423212007322 Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: cytochrome_b_C; cd00290 423212007323 interchain domain interface [polypeptide binding]; other site 423212007324 intrachain domain interface; other site 423212007325 Qi binding site; other site 423212007326 Qo binding site; other site 423212007327 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 423212007328 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 423212007329 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including...; Region: Rieske_cytochrome_bc1; cd03470 423212007330 [2Fe-2S] cluster binding site [ion binding]; other site 423212007331 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 423212007332 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 423212007333 23S rRNA interface [nucleotide binding]; other site 423212007334 L3 interface [polypeptide binding]; other site 423212007335 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 423212007336 dimer interface [polypeptide binding]; other site 423212007337 [2Fe-2S] cluster binding site [ion binding]; other site 423212007338 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 423212007339 IHF - DNA interface [nucleotide binding]; other site 423212007340 IHF dimer interface [polypeptide binding]; other site 423212007341 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 423212007342 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 423212007343 putative tRNA-binding site [nucleotide binding]; other site 423212007344 B3/4 domain; Region: B3_4; pfam03483 423212007345 tRNA synthetase B5 domain; Region: B5; pfam03484 423212007346 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 423212007347 dimer interface [polypeptide binding]; other site 423212007348 motif 1; other site 423212007349 motif 3; other site 423212007350 motif 2; other site 423212007351 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 423212007352 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 423212007353 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 423212007354 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 423212007355 dimer interface [polypeptide binding]; other site 423212007356 motif 1; other site 423212007357 active site 423212007358 motif 2; other site 423212007359 motif 3; other site 423212007360 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 423212007361 23S rRNA binding site [nucleotide binding]; other site 423212007362 L21 binding site [polypeptide binding]; other site 423212007363 L13 binding site [polypeptide binding]; other site 423212007364 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 423212007365 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 423212007366 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 423212007367 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 423212007368 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 423212007369 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 423212007370 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 423212007371 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 423212007372 active site 423212007373 dimer interface [polypeptide binding]; other site 423212007374 motif 1; other site 423212007375 motif 2; other site 423212007376 motif 3; other site 423212007377 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 423212007378 anticodon binding site; other site 423212007379 Uncharacterized ACR, YggU family COG1872; Region: DUF167; pfam02594 423212007380 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 423212007381 non-specific DNA binding site [nucleotide binding]; other site 423212007382 salt bridge; other site 423212007383 sequence-specific DNA binding site [nucleotide binding]; other site 423212007384 gamma-glutamyl:cysteine ligase; Provisional; Region: PRK13516 423212007385 carboxylate-amine ligase, YbdK family; Region: gshA_cyan_rel; TIGR02050 423212007386 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 423212007387 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 423212007388 ligand binding site [chemical binding]; other site 423212007389 flexible hinge region; other site 423212007390 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 423212007391 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 423212007392 ligand binding site [chemical binding]; other site 423212007393 flexible hinge region; other site 423212007394 ergothioneine biosynthesis protein EgtC; Region: TIGR03442 423212007395 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 423212007396 putative active site [active] 423212007397 putative dimer interface [polypeptide binding]; other site 423212007398 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 423212007399 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN; cd02933 423212007400 FMN binding site [chemical binding]; other site 423212007401 active site 423212007402 substrate binding site [chemical binding]; other site 423212007403 catalytic residue [active] 423212007404 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 423212007405 putative DNA binding site [nucleotide binding]; other site 423212007406 putative Zn2+ binding site [ion binding]; other site 423212007407 Protein of unknown function (DUF3775); Region: DUF3775; pfam12616 423212007408 Predicted membrane protein [Function unknown]; Region: COG2860 423212007409 UPF0126 domain; Region: UPF0126; pfam03458 423212007410 UPF0126 domain; Region: UPF0126; pfam03458 423212007411 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 423212007412 substrate binding site [chemical binding]; other site 423212007413 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 423212007414 Queuine tRNA-ribosyltransferase; Region: TGT; pfam01702 423212007415 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 423212007416 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 423212007417 hypothetical protein; Provisional; Region: PRK07179 423212007418 Aminotransferase class I and II; Region: Aminotran_1_2; pfam00155 423212007419 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 423212007420 catalytic residue [active] 423212007421 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 423212007422 active site 423212007423 phosphorylation site [posttranslational modification] 423212007424 intermolecular recognition site; other site 423212007425 Uncharacterized conserved protein [Function unknown]; Region: HdeD; COG3247 423212007426 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 423212007427 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 423212007428 ATP binding site [chemical binding]; other site 423212007429 Mg2+ binding site [ion binding]; other site 423212007430 G-X-G motif; other site 423212007431 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 423212007432 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 423212007433 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cl17708 423212007434 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 423212007435 active site 423212007436 domain interfaces; other site 423212007437 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 423212007438 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 423212007439 active site 423212007440 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 423212007441 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 423212007442 HemY protein N-terminus; Region: HemY_N; pfam07219 423212007443 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 423212007444 TPR motif; other site 423212007445 binding surface 423212007446 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 423212007447 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 423212007448 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 423212007449 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 423212007450 catalytic site [active] 423212007451 putative active site [active] 423212007452 putative substrate binding site [chemical binding]; other site 423212007453 dimer interface [polypeptide binding]; other site 423212007454 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 423212007455 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 423212007456 active site 423212007457 NTP binding site [chemical binding]; other site 423212007458 metal binding triad [ion binding]; metal-binding site 423212007459 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 423212007460 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 423212007461 Zn2+ binding site [ion binding]; other site 423212007462 Mg2+ binding site [ion binding]; other site 423212007463 GTPase RsgA; Reviewed; Region: PRK12288 423212007464 S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of...; Region: S1_YloQ_GTPase; cd04466 423212007465 RNA binding site [nucleotide binding]; other site 423212007466 homodimer interface [polypeptide binding]; other site 423212007467 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 423212007468 GTPase/Zn-binding domain interface [polypeptide binding]; other site 423212007469 GTP/Mg2+ binding site [chemical binding]; other site 423212007470 G4 box; other site 423212007471 G5 box; other site 423212007472 G1 box; other site 423212007473 Switch I region; other site 423212007474 G2 box; other site 423212007475 G3 box; other site 423212007476 Switch II region; other site 423212007477 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14969 423212007478 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 423212007479 Walker A motif; other site 423212007480 ATP binding site [chemical binding]; other site 423212007481 Walker B motif; other site 423212007482 arginine finger; other site 423212007483 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 423212007484 hypothetical protein; Validated; Region: PRK00153 423212007485 recombination protein RecR; Reviewed; Region: recR; PRK00076 423212007486 RecR protein; Region: RecR; pfam02132 423212007487 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 423212007488 putative active site [active] 423212007489 putative metal-binding site [ion binding]; other site 423212007490 tetramer interface [polypeptide binding]; other site 423212007491 Protein of unknown function, DUF547; Region: DUF547; pfam04784 423212007492 Sulfatase; Region: Sulfatase; cl17466 423212007493 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 423212007494 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 423212007495 active site 423212007496 dimerization interface [polypeptide binding]; other site 423212007497 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 423212007498 DNA binding site [nucleotide binding] 423212007499 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 423212007500 Domain of unknown function DUF21; Region: DUF21; pfam01595 423212007501 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 423212007502 Transporter associated domain; Region: CorC_HlyC; smart01091 423212007503 Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers; Region: pyrophosphatase; cd00412 423212007504 dimer interface [polypeptide binding]; other site 423212007505 substrate binding site [chemical binding]; other site 423212007506 metal binding sites [ion binding]; metal-binding site 423212007507 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 423212007508 nucleotide binding site/active site [active] 423212007509 HIT family signature motif; other site 423212007510 catalytic residue [active] 423212007511 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In...; Region: GTP_cyclohydro1; cd00642 423212007512 GTP cyclohydrolase I; Provisional; Region: PLN03044 423212007513 homodecamer interface [polypeptide binding]; other site 423212007514 active site 423212007515 putative catalytic site residues [active] 423212007516 zinc binding site [ion binding]; other site 423212007517 GTP-CH-I/GFRP interaction surface; other site 423212007518 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 423212007519 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 423212007520 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 423212007521 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 423212007522 RNase E interface [polypeptide binding]; other site 423212007523 trimer interface [polypeptide binding]; other site 423212007524 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 423212007525 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 423212007526 RNase E interface [polypeptide binding]; other site 423212007527 trimer interface [polypeptide binding]; other site 423212007528 active site 423212007529 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 423212007530 putative nucleic acid binding region [nucleotide binding]; other site 423212007531 G-X-X-G motif; other site 423212007532 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 423212007533 RNA binding site [nucleotide binding]; other site 423212007534 domain interface; other site 423212007535 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 423212007536 16S/18S rRNA binding site [nucleotide binding]; other site 423212007537 S13e-L30e interaction site [polypeptide binding]; other site 423212007538 25S rRNA binding site [nucleotide binding]; other site 423212007539 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 423212007540 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 423212007541 RNA binding site [nucleotide binding]; other site 423212007542 active site 423212007543 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 423212007544 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 423212007545 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 423212007546 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 423212007547 translation initiation factor IF-2; Region: IF-2; TIGR00487 423212007548 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 423212007549 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 423212007550 G1 box; other site 423212007551 putative GEF interaction site [polypeptide binding]; other site 423212007552 GTP/Mg2+ binding site [chemical binding]; other site 423212007553 Switch I region; other site 423212007554 G2 box; other site 423212007555 G3 box; other site 423212007556 Switch II region; other site 423212007557 G4 box; other site 423212007558 G5 box; other site 423212007559 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 423212007560 Translation-initiation factor 2; Region: IF-2; pfam11987 423212007561 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 423212007562 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 423212007563 NusA N-terminal domain; Region: NusA_N; pfam08529 423212007564 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 423212007565 RNA binding site [nucleotide binding]; other site 423212007566 homodimer interface [polypeptide binding]; other site 423212007567 NusA-like KH domain; Region: KH_5; pfam13184 423212007568 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 423212007569 G-X-X-G motif; other site 423212007570 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 423212007571 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 423212007572 Uncharacterized BCR, YhbC family COG0779; Region: DUF150; pfam02576 423212007573 Sm and related proteins; Region: Sm_like; cl00259 423212007574 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 423212007575 putative oligomer interface [polypeptide binding]; other site 423212007576 putative RNA binding site [nucleotide binding]; other site 423212007577 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 423212007578 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 423212007579 proton-translocating NADH-quinone oxidoreductase, chain M; Region: NDH_I_M; TIGR01972 423212007580 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 423212007581 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 423212007582 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 423212007583 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 423212007584 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 423212007585 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 423212007586 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 423212007587 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 423212007588 4Fe-4S binding domain; Region: Fer4; cl02805 423212007589 4Fe-4S binding domain; Region: Fer4; pfam00037 423212007590 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 423212007591 NADH dehydrogenase subunit G; Validated; Region: PRK09129 423212007592 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 423212007593 catalytic loop [active] 423212007594 iron binding site [ion binding]; other site 423212007595 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 423212007596 MopB_NDH-1_NuoG2: The second domain of the NuoG subunit of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1), found in beta- and gammaproteobacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as...; Region: MopB_NDH-1_NuoG2; cd02772 423212007597 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 423212007598 NADH-quinone oxidoreductase, F subunit; Region: nuoF_fam; TIGR01959 423212007599 SLBB domain; Region: SLBB; pfam10531 423212007600 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 423212007601 NADH dehydrogenase subunit E; Validated; Region: PRK07539 423212007602 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 423212007603 putative dimer interface [polypeptide binding]; other site 423212007604 [2Fe-2S] cluster binding site [ion binding]; other site 423212007605 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 423212007606 NADH dehydrogenase subunit D; Validated; Region: PRK06075 423212007607 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 423212007608 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 423212007609 NADH dehydrogenase subunit B; Validated; Region: PRK06411 423212007610 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 423212007611 Preprotein translocase SecG subunit; Region: SecG; pfam03840 423212007612 triosephosphate isomerase; Provisional; Region: PRK14567 423212007613 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 423212007614 substrate binding site [chemical binding]; other site 423212007615 dimer interface [polypeptide binding]; other site 423212007616 catalytic triad [active] 423212007617 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 423212007618 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 423212007619 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 423212007620 active site 423212007621 substrate binding site [chemical binding]; other site 423212007622 metal binding site [ion binding]; metal-binding site 423212007623 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 423212007624 dihydropteroate synthase; Region: DHPS; TIGR01496 423212007625 substrate binding pocket [chemical binding]; other site 423212007626 dimer interface [polypeptide binding]; other site 423212007627 inhibitor binding site; inhibition site 423212007628 ATP-dependent metalloprotease; Reviewed; Region: hflB; PRK10733 423212007629 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 423212007630 Walker A motif; other site 423212007631 ATP binding site [chemical binding]; other site 423212007632 Walker B motif; other site 423212007633 arginine finger; other site 423212007634 Peptidase family M41; Region: Peptidase_M41; pfam01434 423212007635 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 423212007636 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 423212007637 S-adenosylmethionine binding site [chemical binding]; other site 423212007638 Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; Region: CRS1_YhbY; smart01103 423212007639 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 423212007640 IucA / IucC family; Region: IucA_IucC; pfam04183 423212007641 Ferric iron reductase FhuF-like transporter; Region: FhuF; pfam06276 423212007642 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 423212007643 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 423212007644 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 423212007645 Walker A motif; other site 423212007646 ATP binding site [chemical binding]; other site 423212007647 Walker B motif; other site 423212007648 arginine finger; other site 423212007649 dipeptide/tripeptide permease B; Provisional; Region: PRK10207 423212007650 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 423212007651 putative substrate translocation pore; other site 423212007652 POT family; Region: PTR2; cl17359 423212007653 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 423212007654 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 423212007655 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 423212007656 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 423212007657 shikimate binding site; other site 423212007658 NAD(P) binding site [chemical binding]; other site 423212007659 aminopeptidase N; Provisional; Region: pepN; PRK14015 423212007660 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 423212007661 active site 423212007662 Zn binding site [ion binding]; other site 423212007663 PrkA family serine protein kinase; Provisional; Region: PRK15455 423212007664 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 423212007665 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 423212007666 hypothetical protein; Provisional; Region: PRK05325 423212007667 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 423212007668 SpoVR family protein; Provisional; Region: PRK11767 423212007669 M28 Zn-Peptidase Aeromonas (Vibrio) proteolytica aminopeptidase; Region: M28_AAP; cd03879 423212007670 Peptidase family M28; Region: Peptidase_M28; pfam04389 423212007671 active site 423212007672 metal binding site [ion binding]; metal-binding site 423212007673 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 423212007674 Part of AAA domain; Region: AAA_19; pfam13245 423212007675 Family description; Region: UvrD_C_2; pfam13538 423212007676 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 423212007677 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 423212007678 dimerization interface [polypeptide binding]; other site 423212007679 domain crossover interface; other site 423212007680 redox-dependent activation switch; other site 423212007681 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 423212007682 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 423212007683 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 423212007684 active site 423212007685 catalytic tetrad [active] 423212007686 YjeF-related protein N-terminus; Region: YjeF_N; pfam03853 423212007687 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 423212007688 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 423212007689 G1 box; other site 423212007690 putative GEF interaction site [polypeptide binding]; other site 423212007691 GTP/Mg2+ binding site [chemical binding]; other site 423212007692 Switch I region; other site 423212007693 G2 box; other site 423212007694 G3 box; other site 423212007695 Switch II region; other site 423212007696 G4 box; other site 423212007697 G5 box; other site 423212007698 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 423212007699 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 423212007700 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK01231 423212007701 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 423212007702 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 423212007703 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 423212007704 Walker A/P-loop; other site 423212007705 ATP binding site [chemical binding]; other site 423212007706 Q-loop/lid; other site 423212007707 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 423212007708 ABC transporter signature motif; other site 423212007709 Walker B; other site 423212007710 D-loop; other site 423212007711 H-loop/switch region; other site 423212007712 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 423212007713 DNA-binding site [nucleotide binding]; DNA binding site 423212007714 RNA-binding motif; other site 423212007715 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 423212007716 conserved cys residue [active] 423212007717 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 423212007718 Integrase core domain; Region: rve; pfam00665 423212007719 multidrug efflux protein; Reviewed; Region: PRK09579 423212007720 Amidinotransferase; Region: Amidinotransf; pfam02274 423212007721 Uncharacterized protein conserved in bacteria containing a pentein-type domain [Function unknown]; Region: COG4874 423212007722 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 423212007723 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 423212007724 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 423212007725 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 423212007726 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 423212007727 RNA binding site [nucleotide binding]; other site 423212007728 thiopurine S-methyltransferase; Reviewed; Region: PRK13255 423212007729 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 423212007730 S-adenosylmethionine binding site [chemical binding]; other site 423212007731 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 423212007732 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 423212007733 glutaminase active site [active] 423212007734 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 423212007735 dimer interface [polypeptide binding]; other site 423212007736 active site 423212007737 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 423212007738 dimer interface [polypeptide binding]; other site 423212007739 active site 423212007740 Phospholipase/lecithinase/hemolysin [Lipid metabolism / General function prediction only]; Region: COG3240 423212007741 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 423212007742 Fatty acyltransferase-like subfamily of the SGNH hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its...; Region: fatty_acyltransferase_like; cd01846 423212007743 active site 423212007744 oxyanion hole [active] 423212007745 catalytic triad [active] 423212007746 rhodanese superfamily protein; Provisional; Region: PRK05320 423212007747 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 423212007748 active site residue [active] 423212007749 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 423212007750 SmpB-tmRNA interface; other site 423212007751 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 423212007752 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 423212007753 catalytic triad [active] 423212007754 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 423212007755 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 423212007756 putative substrate translocation pore; other site 423212007757 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 423212007758 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 423212007759 putative active site [active] 423212007760 PhoH-like protein; Region: PhoH; pfam02562 423212007761 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 423212007762 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05096 423212007763 active site 423212007764 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 423212007765 Domain of unknown function (DUF4372); Region: DUF4372; pfam14294 423212007766 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 423212007767 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 423212007768 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 423212007769 Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far. This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases). Plant T2 RNases are expressed during leaf...; Region: RNase_T2_prok; cd01062 423212007770 B1 nucleotide binding pocket [chemical binding]; other site 423212007771 B2 nucleotide binding pocket [chemical binding]; other site 423212007772 CAS motifs; other site 423212007773 active site 423212007774 TPR repeat; Region: TPR_11; pfam13414 423212007775 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 423212007776 TPR motif; other site 423212007777 Anaphase-promoting complex, cyclosome, subunit 3; Region: Apc3; pfam12895 423212007778 Methyltransferase domain; Region: Methyltransf_24; pfam13578 423212007779 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 423212007780 DNA-binding site [nucleotide binding]; DNA binding site 423212007781 RNA-binding motif; other site 423212007782 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 423212007783 Flavin containing amine oxidoreductase; Region: Amino_oxidase; pfam01593 423212007784 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 423212007785 Amidase; Region: Amidase; cl11426 423212007786 Oxygen tolerance; Region: BatD; pfam13584 423212007787 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 423212007788 binding surface 423212007789 TPR motif; other site 423212007790 Tetratricopeptide repeat; Region: TPR_16; pfam13432 423212007791 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 423212007792 metal ion-dependent adhesion site (MIDAS); other site 423212007793 Aerotolerance regulator N-terminal; Region: BatA; cl06567 423212007794 VWA BatA type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b...; Region: vWA_BatA_type; cd01467 423212007795 metal ion-dependent adhesion site (MIDAS); other site 423212007796 Domain of unknown function (DUF4381); Region: DUF4381; pfam14316 423212007797 Protein of unknown function DUF58; Region: DUF58; pfam01882 423212007798 MoxR-like ATPases [General function prediction only]; Region: COG0714 423212007799 ATPase family associated with various cellular activities (AAA); Region: AAA_3; pfam07726 423212007800 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 423212007801 FMN binding site [chemical binding]; other site 423212007802 active site 423212007803 catalytic residues [active] 423212007804 substrate binding site [chemical binding]; other site 423212007805 pteridine reductase; Provisional; Region: PRK09135 423212007806 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 423212007807 NAD(P) binding site [chemical binding]; other site 423212007808 active site 423212007809 Uncharacterized conserved protein [Function unknown]; Region: COG1565 423212007810 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 423212007811 primosome assembly protein PriA; Validated; Region: PRK05580 423212007812 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 423212007813 ATP binding site [chemical binding]; other site 423212007814 putative Mg++ binding site [ion binding]; other site 423212007815 helicase superfamily c-terminal domain; Region: HELICc; smart00490 423212007816 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 423212007817 active site 423212007818 thymidylate synthase; Reviewed; Region: thyA; PRK01827 423212007819 Thymidylate synthase and pyrimidine hydroxymethylase: Thymidylate synthase (TS) and deoxycytidylate hydroxymethylase (dCMP-HMase) are homologs that catalyze analogous alkylation of C5 of pyrimidine nucleotides. Both enzymes are involved in the...; Region: TS_Pyrimidine_HMase; cd00351 423212007820 dimerization interface [polypeptide binding]; other site 423212007821 active site 423212007822 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 423212007823 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 423212007824 Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms]; Region: PtsP; COG3605 423212007825 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 423212007826 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 423212007827 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 423212007828 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 423212007829 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 423212007830 putative active site [active] 423212007831 Ap4A binding site [chemical binding]; other site 423212007832 nudix motif; other site 423212007833 putative metal binding site [ion binding]; other site 423212007834 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 423212007835 active site 423212007836 homodimer interface [polypeptide binding]; other site 423212007837 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 423212007838 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 423212007839 Substrate binding site; other site 423212007840 Mg++ binding site; other site 423212007841 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 423212007842 active site 423212007843 substrate binding site [chemical binding]; other site 423212007844 CoA binding site [chemical binding]; other site 423212007845 Putative anion permease YbiR. Based on sequence similarity, YbiR proteins are predicted to function as anion translocating permeases in eubacteria, archaea and plants. They belong to ArsB/NhaD superfamily of permeases that have been shown to translocate...; Region: YbiR_permease; cd01117 423212007846 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 423212007847 transmembrane helices; other site 423212007848 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 423212007849 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 423212007850 Thermotoga maritima CorA_like subfamily; Region: TmCorA-like_1; cd12828 423212007851 oligomer interface [polypeptide binding]; other site 423212007852 metal binding site [ion binding]; metal-binding site 423212007853 metal binding site [ion binding]; metal-binding site 423212007854 Cl binding site [ion binding]; other site 423212007855 aspartate ring; other site 423212007856 basic sphincter; other site 423212007857 putative hydrophobic gate; other site 423212007858 periplasmic entrance; other site 423212007859 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 423212007860 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 423212007861 minor groove reading motif; other site 423212007862 helix-hairpin-helix signature motif; other site 423212007863 substrate binding pocket [chemical binding]; other site 423212007864 active site 423212007865 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 423212007866 ferredoxin; Provisional; Region: PRK08764 423212007867 Putative Fe-S cluster; Region: FeS; pfam04060 423212007868 4Fe-4S binding domain; Region: Fer4; pfam00037 423212007869 4Fe-4S binding domain; Region: Fer4; cl02805 423212007870 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 423212007871 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 423212007872 active site 423212007873 HIGH motif; other site 423212007874 KMSKS motif; other site 423212007875 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 423212007876 anticodon binding site; other site 423212007877 tRNA binding surface [nucleotide binding]; other site 423212007878 tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine...; Region: tRNA_bind_EcMetRS_like; cd02800 423212007879 dimer interface [polypeptide binding]; other site 423212007880 putative tRNA-binding site [nucleotide binding]; other site 423212007881 polyprenyl P-hydroxybenzoate and phenylacrylic acid decarboxylases; Region: ubiX_pad; TIGR00421 423212007882 Flavoprotein; Region: Flavoprotein; pfam02441 423212007883 Protein of unknown function (DUF1049); Region: DUF1049; cl01539 423212007884 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 423212007885 Ligand Binding Site [chemical binding]; other site 423212007886 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 423212007887 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 423212007888 Substrate binding site; other site 423212007889 Cupin domain; Region: Cupin_2; cl17218 423212007890 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 423212007891 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 423212007892 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 423212007893 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 423212007894 rRNA small subunit methyltransferase G; Region: GidB; pfam02527 423212007895 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 423212007896 S-adenosylmethionine binding site [chemical binding]; other site 423212007897 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 423212007898 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 423212007899 P-loop; other site 423212007900 Magnesium ion binding site [ion binding]; other site 423212007901 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 423212007902 Magnesium ion binding site [ion binding]; other site 423212007903 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 423212007904 ParB-like nuclease domain; Region: ParBc; pfam02195 423212007905 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 423212007906 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; cl17722 423212007907 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 423212007908 Predicted transcriptional regulator [Transcription]; Region: COG3655 423212007909 salt bridge; other site 423212007910 non-specific DNA binding site [nucleotide binding]; other site 423212007911 sequence-specific DNA binding site [nucleotide binding]; other site 423212007912 Protein of unknown function (DUF2975); Region: DUF2975; pfam11188 423212007913 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 423212007914 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 423212007915 Coenzyme A binding pocket [chemical binding]; other site 423212007916 Cytochrome c oxidase subunit III. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_III; cd01665 423212007917 Subunit III/VIIa interface [polypeptide binding]; other site 423212007918 Phospholipid binding site [chemical binding]; other site 423212007919 Subunit I/III interface [polypeptide binding]; other site 423212007920 Subunit III/VIb interface [polypeptide binding]; other site 423212007921 Subunit III/VIa interface; other site 423212007922 Subunit III/Vb interface [polypeptide binding]; other site 423212007923 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 423212007924 Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_I; cd01663 423212007925 Subunit I/III interface [polypeptide binding]; other site 423212007926 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 423212007927 D-pathway; other site 423212007928 Subunit I/VIIc interface [polypeptide binding]; other site 423212007929 Subunit I/IV interface [polypeptide binding]; other site 423212007930 Subunit I/II interface [polypeptide binding]; other site 423212007931 Low-spin heme (heme a) binding site [chemical binding]; other site 423212007932 Subunit I/VIIa interface [polypeptide binding]; other site 423212007933 Subunit I/VIa interface [polypeptide binding]; other site 423212007934 Dimer interface; other site 423212007935 Putative water exit pathway; other site 423212007936 Binuclear center (heme a3/CuB) [ion binding]; other site 423212007937 K-pathway; other site 423212007938 Subunit I/Vb interface [polypeptide binding]; other site 423212007939 Putative proton exit pathway; other site 423212007940 Subunit I/VIb interface; other site 423212007941 Subunit I/VIc interface [polypeptide binding]; other site 423212007942 Electron transfer pathway; other site 423212007943 Subunit I/VIIIb interface [polypeptide binding]; other site 423212007944 Subunit I/VIIb interface [polypeptide binding]; other site 423212007945 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 423212007946 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00168 423212007947 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 423212007948 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 423212007949 Cytochrome c; Region: Cytochrom_C; pfam00034 423212007950 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 423212007951 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 423212007952 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 423212007953 Ferredoxin subunits of nitrite reductase and ring-hydroxylating dioxygenases [Inorganic ion transport and metabolism / General function prediction only]; Region: {NirD}; COG2146 423212007954 iron-sulfur cluster [ion binding]; other site 423212007955 [2Fe-2S] cluster binding site [ion binding]; other site 423212007956 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 423212007957 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 423212007958 Lysine efflux permease [General function prediction only]; Region: COG1279 423212007959 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 423212007960 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 423212007961 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 423212007962 S-adenosylmethionine binding site [chemical binding]; other site 423212007963 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 423212007964 SCP-2 sterol transfer family; Region: SCP2; pfam02036 423212007965 SCP-2 sterol transfer family; Region: SCP2; cl01225 423212007966 putative ubiquinone biosynthesis protein UbiB; Reviewed; Region: ubiB; PRK04750 423212007967 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 423212007968 twin arginine-targeting protein translocase, TatA/E family; Region: tatAE; TIGR01411 423212007969 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 423212007970 bifunctional methionine sulfoxide reductase B/A protein; Provisional; Region: PRK05550 423212007971 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229; cl15841 423212007972 methionine sulfoxide reductase A; Provisional; Region: PRK14054 423212007973 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional; Region: PRK11760 423212007974 Domain of unknown function (DUF4169); Region: DUF4169; pfam13770 423212007975 tyramine oxidase; Provisional; Region: tynA; PRK11504 423212007976 Copper amine oxidase, N2 domain; Region: Cu_amine_oxidN2; pfam02727 423212007977 Copper amine oxidase, N3 domain; Region: Cu_amine_oxidN3; pfam02728 423212007978 Copper amine oxidase, enzyme domain; Region: Cu_amine_oxid; pfam01179 423212007979 lytic murein transglycosylase; Region: MltB_2; TIGR02283 423212007980 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 423212007981 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cl02788 423212007982 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 423212007983 DNA-binding interface [nucleotide binding]; DNA binding site 423212007984 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 423212007985 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cl02788 423212007986 catalytic nucleophile [active] 423212007987 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 423212007988 Transglycosylase SLT domain; Region: SLT_2; pfam13406 423212007989 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 423212007990 N-acetyl-D-glucosamine binding site [chemical binding]; other site 423212007991 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 423212007992 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 423212007993 FtsX-like permease family; Region: FtsX; pfam02687 423212007994 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 423212007995 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 423212007996 Walker A/P-loop; other site 423212007997 ATP binding site [chemical binding]; other site 423212007998 Q-loop/lid; other site 423212007999 ABC transporter signature motif; other site 423212008000 Walker B; other site 423212008001 D-loop; other site 423212008002 H-loop/switch region; other site 423212008003 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 423212008004 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 423212008005 HlyD family secretion protein; Region: HlyD_3; pfam13437 423212008006 Outer membrane efflux protein; Region: OEP; pfam02321 423212008007 Outer membrane efflux protein; Region: OEP; pfam02321 423212008008 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 423212008009 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 423212008010 active site 423212008011 metal binding site [ion binding]; metal-binding site 423212008012 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 423212008013 Protein of unknown function (DUF1528); Region: DUF1528; pfam07515 423212008014 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 423212008015 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 423212008016 S-adenosylmethionine binding site [chemical binding]; other site 423212008017 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 423212008018 tetramerization interface [polypeptide binding]; other site 423212008019 active site 423212008020 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 423212008021 Hemimethylated DNA-binding protein YccV like; Region: YccV-like; pfam08755 423212008022 FMN reductase; Validated; Region: fre; PRK08051 423212008023 NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD, FMN; Region: flavin_oxioreductase; cd06189 423212008024 FAD binding pocket [chemical binding]; other site 423212008025 FAD binding motif [chemical binding]; other site 423212008026 phosphate binding motif [ion binding]; other site 423212008027 beta-alpha-beta structure motif; other site 423212008028 NAD binding pocket [chemical binding]; other site 423212008029 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 423212008030 transcription termination factor Rho; Provisional; Region: rho; PRK09376 423212008031 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 423212008032 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 423212008033 RNA binding site [nucleotide binding]; other site 423212008034 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 423212008035 multimer interface [polypeptide binding]; other site 423212008036 Walker A motif; other site 423212008037 ATP binding site [chemical binding]; other site 423212008038 Walker B motif; other site 423212008039 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 423212008040 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 423212008041 catalytic residues [active] 423212008042 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 423212008043 RNA methyltransferase, RsmE family; Region: TIGR00046 423212008044 fumarate hydratase; Reviewed; Region: fumC; PRK00485 423212008045 Class II fumarases; Region: Fumarase_classII; cd01362 423212008046 active site 423212008047 tetramer interface [polypeptide binding]; other site 423212008048 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 423212008049 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 423212008050 putative acyl-acceptor binding pocket; other site 423212008051 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 423212008052 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 423212008053 putative acyl-acceptor binding pocket; other site 423212008054 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 423212008055 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 423212008056 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 423212008057 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 423212008058 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 423212008059 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 423212008060 active site 423212008061 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 423212008062 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 423212008063 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 423212008064 trimer interface [polypeptide binding]; other site 423212008065 active site 423212008066 UDP-GlcNAc binding site [chemical binding]; other site 423212008067 lipid binding site [chemical binding]; lipid-binding site 423212008068 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 423212008069 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 423212008070 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_HprK; cl00270 423212008071 active site 423212008072 nucleotide-binding site [chemical binding]; other site 423212008073 metal-binding site [ion binding] 423212008074 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 423212008075 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 423212008076 Walker A/P-loop; other site 423212008077 ATP binding site [chemical binding]; other site 423212008078 Q-loop/lid; other site 423212008079 ABC transporter signature motif; other site 423212008080 Walker B; other site 423212008081 D-loop; other site 423212008082 H-loop/switch region; other site 423212008083 Transglutaminase-like superfamily; Region: Transglut_core3; pfam13471 423212008084 Coenzyme PQQ synthesis protein D (PqqD); Region: PqqD; cl05126 423212008085 Glutamine amidotransferase domain; Region: GATase_6; pfam13522 423212008086 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 423212008087 active site 423212008088 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 423212008089 Ligand Binding Site [chemical binding]; other site 423212008090 Molecular Tunnel; other site 423212008091 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 423212008092 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 423212008093 dimer interface [polypeptide binding]; other site 423212008094 pyridoxal 5'-phosphate binding site [chemical binding]; other site 423212008095 catalytic residue [active] 423212008096 Histone methylation protein DOT1; Region: DOT1; pfam08123 423212008097 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 423212008098 IHF dimer interface [polypeptide binding]; other site 423212008099 IHF - DNA interface [nucleotide binding]; other site 423212008100 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 423212008101 trimer interface [polypeptide binding]; other site 423212008102 active site 423212008103 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 423212008104 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 423212008105 Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]; Region: NfeD; COG1030 423212008106 Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Region: Clp_protease_NfeD_1; cd07020 423212008107 dimer interface [polypeptide binding]; other site 423212008108 active site residues [active] 423212008109 NfeD-like C-terminal, partner-binding; Region: NfeD; pfam01957 423212008110 Legionella pneumophila major outer membrane protein precursor; Region: Legionella_OMP; pfam05150 423212008111 Legionella pneumophila major outer membrane protein precursor; Region: Legionella_OMP; pfam05150 423212008112 Legionella pneumophila major outer membrane protein precursor; Region: Legionella_OMP; pfam05150 423212008113 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 423212008114 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 423212008115 ligand binding site [chemical binding]; other site 423212008116 Dihydroorotase (DHOase) catalyzes the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in the pyrimidine biosynthesis. In contrast to the large polyfunctional CAD proteins of higher organisms, this group of DHOases is...; Region: DHOase; cd01294 423212008117 active site 423212008118 substrate binding pocket [chemical binding]; other site 423212008119 dimer interface [polypeptide binding]; other site 423212008120 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 423212008121 DEDDh 3'-5' exonuclease domain of RNase T; Region: RNaseT; cd06134 423212008122 dimer interface [polypeptide binding]; other site 423212008123 catalytic site [active] 423212008124 putative active site [active] 423212008125 putative substrate binding site [chemical binding]; other site 423212008126 peroxidase; Provisional; Region: PRK15000 423212008127 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 423212008128 dimer interface [polypeptide binding]; other site 423212008129 decamer (pentamer of dimers) interface [polypeptide binding]; other site 423212008130 catalytic triad [active] 423212008131 peroxidatic and resolving cysteines [active] 423212008132 Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain...; Region: GRX_PICOT_like; cd03028 423212008133 putative GSH binding site [chemical binding]; other site 423212008134 catalytic residues [active] 423212008135 superoxide dismutase; Provisional; Region: PRK10543 423212008136 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 423212008137 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 423212008138 acetylornithine aminotransferase; Provisional; Region: PRK02627 423212008139 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 423212008140 inhibitor-cofactor binding pocket; inhibition site 423212008141 pyridoxal 5'-phosphate binding site [chemical binding]; other site 423212008142 catalytic residue [active] 423212008143 Metal-dependent hydrolases of the beta-lactamase superfamily III [General function prediction only]; Region: ElaC; COG1234 423212008144 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 423212008145 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 423212008146 active site 423212008147 catalytic site [active] 423212008148 malate dehydrogenase; Provisional; Region: PRK13529 423212008149 Malic enzyme, N-terminal domain; Region: malic; pfam00390 423212008150 NAD(P) binding domain of malic enzyme (ME), subgroup 1; Region: NAD_bind_1_malic_enz; cd05312 423212008151 NAD(P) binding site [chemical binding]; other site 423212008152 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 423212008153 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 423212008154 phosphatidylserine decarboxylase; Reviewed; Region: psd; PRK00044 423212008155 potential frameshift: common BLAST hit: gi|148361317|ref|YP_001252524.1| virulence metalloprotease 423212008156 Peptidase M4 family includes thermolysin, protealysin, aureolysin and neutral protease; Region: M4_neutral_protease; cd09597 423212008157 active site 423212008158 Zn binding site [ion binding]; other site 423212008159 Zinc metalloprotease (elastase) [Amino acid transport and metabolism]; Region: LasB; COG3227 423212008160 Fungalysin/Thermolysin Propeptide Motif; Region: FTP; pfam07504 423212008161 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 423212008162 Rossmann-like domain; Region: Rossmann-like; pfam10727 423212008163 Domain of unknown function (DUF2520); Region: DUF2520; pfam10728 423212008164 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 423212008165 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 423212008166 CAP-like domain; other site 423212008167 active site 423212008168 primary dimer interface [polypeptide binding]; other site 423212008169 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 423212008170 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 423212008171 gamma subunit interface [polypeptide binding]; other site 423212008172 LBP interface [polypeptide binding]; other site 423212008173 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 423212008174 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 423212008175 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 423212008176 alpha subunit interaction interface [polypeptide binding]; other site 423212008177 Walker A motif; other site 423212008178 ATP binding site [chemical binding]; other site 423212008179 Walker B motif; other site 423212008180 inhibitor binding site; inhibition site 423212008181 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 423212008182 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 423212008183 core domain interface [polypeptide binding]; other site 423212008184 delta subunit interface [polypeptide binding]; other site 423212008185 epsilon subunit interface [polypeptide binding]; other site 423212008186 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 423212008187 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 423212008188 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 423212008189 beta subunit interaction interface [polypeptide binding]; other site 423212008190 Walker A motif; other site 423212008191 ATP binding site [chemical binding]; other site 423212008192 Walker B motif; other site 423212008193 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 423212008194 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 423212008195 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 423212008196 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 423212008197 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 423212008198 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 423212008199 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 423212008200 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 423212008201 F0F1 ATP synthase subunit I; Validated; Region: PRK05760 423212008202 outer membrane lipoprotein; Provisional; Region: PRK11023 423212008203 BON domain; Region: BON; pfam04972 423212008204 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 423212008205 BON domain; Region: BON; pfam04972 423212008206 BON domain; Region: BON; cl02771 423212008207 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 423212008208 dimer interface [polypeptide binding]; other site 423212008209 active site 423212008210 hypothetical protein; Reviewed; Region: PRK12497 423212008211 Putative lipoprotein [General function prediction only]; Region: LppC; COG3107 423212008212 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 423212008213 putative ligand binding site [chemical binding]; other site 423212008214 Predicted methyltransferases [General function prediction only]; Region: COG0313 423212008215 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 423212008216 putative SAM binding site [chemical binding]; other site 423212008217 putative homodimer interface [polypeptide binding]; other site 423212008218 Alkane hydroxylase is a bacterial, integral-membrane di-iron enzyme that shares a requirement for iron and oxygen for activity similar to that of the non-heme integral-membrane acyl coenzyme A (CoA) desaturases and acyl lipid desaturases. The alk genes...; Region: Alkane-hydroxylase; cd03512 423212008219 Fatty acid desaturase; Region: FA_desaturase; pfam00487 423212008220 Di-iron ligands [ion binding]; other site 423212008221 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 423212008222 Sulfate transporter family; Region: Sulfate_transp; pfam00916 423212008223 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 423212008224 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 423212008225 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 423212008226 ligand binding site [chemical binding]; other site 423212008227 flexible hinge region; other site 423212008228 Astacin (Peptidase family M12A); Region: Astacin; pfam01400 423212008229 Zinc-dependent metalloprotease, astacin_like subfamily or peptidase family M12A, a group of zinc-dependent proteolytic enzymes with a HExxH zinc-binding site/active site. Members of this family may have an amino terminal propeptide, which is cleaved to...; Region: ZnMc_astacin_like; cd04280 423212008230 active site 423212008231 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 423212008232 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 423212008233 Circularly permuted YlqF-related GTPases; Region: YlqF_related_GTPase; cl17249 423212008234 GTP/Mg2+ binding site [chemical binding]; other site 423212008235 G4 box; other site 423212008236 G5 box; other site 423212008237 trmE is a tRNA modification GTPase; Region: trmE; cd04164 423212008238 G1 box; other site 423212008239 G1 box; other site 423212008240 GTP/Mg2+ binding site [chemical binding]; other site 423212008241 Switch I region; other site 423212008242 Switch I region; other site 423212008243 G2 box; other site 423212008244 G2 box; other site 423212008245 Switch II region; other site 423212008246 G3 box; other site 423212008247 G4 box; other site 423212008248 G5 box; other site 423212008249 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 423212008250 membrane protein insertase; Provisional; Region: PRK01318 423212008251 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 423212008252 hypothetical protein; Provisional; Region: PRK14380 423212008253 Ribonuclease P; Region: Ribonuclease_P; cl00457 423212008254 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399