-- dump date 20140620_063107 -- class Genbank::misc_feature -- table misc_feature_note -- id note 94122000001 Transposase; Region: DEDD_Tnp_IS110; pfam01548 94122000002 Transposase domain (DUF772); Region: DUF772; pfam05598 94122000003 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 94122000004 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 94122000005 Protein of unknown function (DUF2933); Region: DUF2933; pfam11666 94122000006 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 94122000007 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 94122000008 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 94122000009 metal-binding site [ion binding] 94122000010 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 94122000011 Soluble P-type ATPase [General function prediction only]; Region: COG4087 94122000012 Transcriptional regulators [Transcription]; Region: FadR; COG2186 94122000013 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 94122000014 DNA-binding site [nucleotide binding]; DNA binding site 94122000015 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 94122000016 outer membrane porin, OprD family; Region: OprD; pfam03573 94122000017 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; cl11437 94122000018 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 94122000019 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 94122000020 Probable transposase; Region: OrfB_IS605; pfam01385 94122000021 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 94122000022 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 94122000023 Nitrogen regulatory protein P-II; Region: P-II; cl00412 94122000024 Nitrogen regulatory protein P-II; Region: P-II; smart00938 94122000025 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 94122000026 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 94122000027 E3 interaction surface; other site 94122000028 lipoyl attachment site [posttranslational modification]; other site 94122000029 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 94122000030 Outer membrane efflux protein; Region: OEP; pfam02321 94122000031 Outer membrane efflux protein; Region: OEP; pfam02321 94122000032 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 94122000033 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 94122000034 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 94122000035 DNA binding residues [nucleotide binding] 94122000036 dimer interface [polypeptide binding]; other site 94122000037 putative metal binding site [ion binding]; other site 94122000038 Transposase; Region: HTH_Tnp_1; cl17663 94122000039 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 94122000040 HsdM N-terminal domain; Region: HsdM_N; pfam12161 94122000041 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 94122000042 Methyltransferase domain; Region: Methyltransf_26; pfam13659 94122000043 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 94122000044 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 94122000045 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 94122000046 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 94122000047 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 94122000048 ATP binding site [chemical binding]; other site 94122000049 putative Mg++ binding site [ion binding]; other site 94122000050 Glycoside hydrolase family 15, N-terminal domain; Region: GH15_N; cl07672 94122000051 DNA replication terminus site-binding protein; Provisional; Region: PRK02951 94122000052 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 94122000053 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 94122000054 active site 94122000055 DNA binding site [nucleotide binding] 94122000056 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 94122000057 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 94122000058 Catalytic site [active] 94122000059 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 94122000060 Catalytic site [active] 94122000061 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 94122000062 Protein of unknown function (DUF998); Region: DUF998; pfam06197 94122000063 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 94122000064 RecT family; Region: RecT; cl04285 94122000065 RecT family; Region: RecT; cl04285 94122000066 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 94122000067 N-acetyl-D-glucosamine binding site [chemical binding]; other site 94122000068 catalytic residue [active] 94122000069 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 94122000070 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 94122000071 Probable transposase; Region: OrfB_IS605; pfam01385 94122000072 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 94122000073 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; cl00868 94122000074 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 94122000075 catalytic loop [active] 94122000076 iron binding site [ion binding]; other site 94122000077 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 94122000078 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 94122000079 cofactor binding site; other site 94122000080 DNA binding site [nucleotide binding] 94122000081 substrate interaction site [chemical binding]; other site 94122000082 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 94122000083 active site 94122000084 metal binding site [ion binding]; metal-binding site 94122000085 interdomain interaction site; other site 94122000086 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 94122000087 metal ion-dependent adhesion site (MIDAS); other site 94122000088 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 94122000089 Walker A motif; other site 94122000090 ATP binding site [chemical binding]; other site 94122000091 Walker B motif; other site 94122000092 arginine finger; other site 94122000093 Protein of unknown function (DUF3150); Region: DUF3150; pfam11348 94122000094 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 94122000095 Part of AAA domain; Region: AAA_19; pfam13245 94122000096 Family description; Region: UvrD_C_2; pfam13538 94122000097 Type-1V conjugative transfer system mating pair stabilisation; Region: TraN; pfam06986 94122000098 TraU protein; Region: TraU; pfam06834 94122000099 Type-F conjugative transfer system pilin assembly protein; Region: TrbC_Ftype; pfam09673 94122000100 Sex factor F TraW protein N terminal; Region: TraW_N; cl10149 94122000101 conjugative transfer signal peptidase TraF; Region: TraF_Ti; TIGR02771 94122000102 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 94122000103 RES domain; Region: RES; cl02411 94122000104 Protein of unknown function (DUF2384); Region: DUF2384; cl17718 94122000105 putative toxin-antitoxin system antitoxin component, TIGR02293 family; Region: TAS_TIGR02293 94122000106 Bacterial Ig-like domain (group 3); Region: Big_3_3; pfam13750 94122000107 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 94122000108 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 94122000109 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 94122000110 ATP binding site [chemical binding]; other site 94122000111 putative Mg++ binding site [ion binding]; other site 94122000112 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 94122000113 nucleotide binding region [chemical binding]; other site 94122000114 ATP-binding site [chemical binding]; other site 94122000115 Predicted signal transduction protein [Signal transduction mechanisms]; Region: COG1639 94122000116 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 94122000117 type-IV secretion system protein TraC; Region: TraC-F-type; TIGR02746 94122000118 Type IV conjugative transfer system lipoprotein (TraV); Region: TraV; pfam09676 94122000119 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 94122000120 SAP domain; Region: SAP; pfam02037 94122000121 Abi-like protein; Region: Abi_2; pfam07751 94122000122 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 94122000123 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 94122000124 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 94122000125 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 94122000126 P-loop; other site 94122000127 Magnesium ion binding site [ion binding]; other site 94122000128 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 94122000129 Magnesium ion binding site [ion binding]; other site 94122000130 Initiator Replication protein; Region: Rep_3; pfam01051 94122000131 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 94122000132 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 94122000133 dimer interface [polypeptide binding]; other site 94122000134 ssDNA binding site [nucleotide binding]; other site 94122000135 tetramer (dimer of dimers) interface [polypeptide binding]; other site 94122000136 Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which...; Region: ZnMc; cl00064 94122000137 active site 94122000138 Probable transposase; Region: OrfB_IS605; pfam01385 94122000139 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 94122000140 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 94122000141 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 94122000142 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 94122000143 Transposase IS200 like; Region: Y1_Tnp; pfam01797 94122000144 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 94122000145 non-specific DNA binding site [nucleotide binding]; other site 94122000146 salt bridge; other site 94122000147 sequence-specific DNA binding site [nucleotide binding]; other site 94122000148 AAA domain; Region: AAA_13; pfam13166 94122000149 HsdM N-terminal domain; Region: HsdM_N; pfam12161 94122000150 HsdM N-terminal domain; Region: HsdM_N; pfam12161 94122000151 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 94122000152 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 94122000153 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 94122000154 Protein of unknown function (DUF511); Region: DUF511; cl01114 94122000155 Protein of unknown function (DUF511); Region: DUF511; cl01114 94122000156 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 94122000157 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 94122000158 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 94122000159 ATP binding site [chemical binding]; other site 94122000160 putative Mg++ binding site [ion binding]; other site 94122000161 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 94122000162 mobile mystery protein B; Region: mob_myst_B; TIGR02613 94122000163 Fic/DOC family; Region: Fic; pfam02661 94122000164 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 94122000165 non-specific DNA binding site [nucleotide binding]; other site 94122000166 salt bridge; other site 94122000167 sequence-specific DNA binding site [nucleotide binding]; other site 94122000168 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 94122000169 active site 94122000170 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 94122000171 Predicted P-loop ATPase [General function prediction only]; Region: COG4928 94122000172 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 94122000173 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 94122000174 active site 94122000175 catalytic residues [active] 94122000176 DNA binding site [nucleotide binding] 94122000177 Int/Topo IB signature motif; other site 94122000178 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 94122000179 active site 94122000180 catalytic residues [active] 94122000181 DNA binding site [nucleotide binding] 94122000182 Int/Topo IB signature motif; other site 94122000183 conjugal transfer pilus assembly protein TraB; Provisional; Region: PRK13729 94122000184 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 94122000185 TraE protein; Region: TraE; cl05060 94122000186 Domain of unknown function (DUF4400); Region: DUF4400; pfam14348 94122000187 conjugative coupling factor TraD, SXT/TOL subfamily; Region: SXT_TraD; TIGR03743 94122000188 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 94122000189 Putative helicase; Region: TraI_2; pfam07514 94122000190 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 94122000191 Plasmid segregation protein ParM and similar proteins; Region: ParM_like; cd10227 94122000192 PRTRC system protein D; Region: PRTRC_D; TIGR03739 94122000193 Mg binding site [ion binding]; other site 94122000194 nucleotide binding site [chemical binding]; other site 94122000195 putative protofilament interface [polypeptide binding]; other site 94122000196 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 94122000197 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 94122000198 catalytic residues [active] 94122000199 Conjugative relaxosome accessory transposon protein; Region: TraH; pfam06122 94122000200 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 94122000201 DNA replication terminus site-binding protein (Ter protein); Region: Ter; pfam05472 94122000202 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 94122000203 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 94122000204 ligand binding site [chemical binding]; other site 94122000205 Domain of unknown function (DUF4165); Region: DUF4165; pfam13752 94122000206 Bacterial Ig-like domain (group 3); Region: Big_3_2; pfam12245 94122000207 Bacterial Ig-like domain (group 3); Region: Big_3_3; pfam13750 94122000208 Domain of unknown function (DUF4165); Region: DUF4165; pfam13752 94122000209 Bacterial Ig-like domain (group 3); Region: Big_3_2; pfam12245 94122000210 Bacterial Ig-like domain (group 3); Region: Big_3_3; pfam13750 94122000211 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 94122000212 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 94122000213 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 94122000214 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 94122000215 Integrase core domain; Region: rve; pfam00665 94122000216 Predicted metal-binding protein [General function prediction only]; Region: COG3019 94122000217 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 94122000218 Multicopper oxidase; Region: Cu-oxidase; pfam00394 94122000219 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 94122000220 Copper resistance protein B precursor (CopB); Region: CopB; pfam05275 94122000221 CopC domain; Region: CopC; pfam04234 94122000222 Copper resistance protein D; Region: CopD; cl00563 94122000223 SnoaL-like domain; Region: SnoaL_3; pfam13474 94122000224 Ketosteroid isomerase homolog [Function unknown]; Region: COG4319 94122000225 outer membrane porin, OprD family; Region: OprD; pfam03573 94122000226 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 94122000227 sensor kinase CusS; Provisional; Region: PRK09835 94122000228 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 94122000229 dimerization interface [polypeptide binding]; other site 94122000230 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 94122000231 dimer interface [polypeptide binding]; other site 94122000232 phosphorylation site [posttranslational modification] 94122000233 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 94122000234 ATP binding site [chemical binding]; other site 94122000235 Mg2+ binding site [ion binding]; other site 94122000236 G-X-G motif; other site 94122000237 DNA-binding transcriptional activator CusR; Provisional; Region: PRK09836 94122000238 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122000239 active site 94122000240 phosphorylation site [posttranslational modification] 94122000241 intermolecular recognition site; other site 94122000242 dimerization interface [polypeptide binding]; other site 94122000243 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 94122000244 DNA binding site [nucleotide binding] 94122000245 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 94122000246 periplasmic copper-binding protein; Provisional; Region: PRK09838 94122000247 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 94122000248 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122000249 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 94122000250 Protein of unknown function, DUF; Region: DUF411; cl01142 94122000251 YHS domain; Region: YHS; pfam04945 94122000252 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 94122000253 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 94122000254 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 94122000255 motif II; other site 94122000256 Peptidase family M23; Region: Peptidase_M23; pfam01551 94122000257 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 94122000258 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122000259 dimer interface [polypeptide binding]; other site 94122000260 putative CheW interface [polypeptide binding]; other site 94122000261 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 94122000262 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 94122000263 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 94122000264 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 94122000265 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 94122000266 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 94122000267 DNA binding residues [nucleotide binding] 94122000268 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 94122000269 putative mercuric reductase; Provisional; Region: PRK13748 94122000270 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 94122000271 metal-binding site [ion binding] 94122000272 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 94122000273 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 94122000274 putative mercury transport protein MerC; Provisional; Region: PRK13755 94122000275 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 94122000276 metal-binding site [ion binding] 94122000277 MerT mercuric transport protein; Region: MerT; cl03578 94122000278 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Region: HTH_MerR1; cd04783 94122000279 Hg(II)-responsive transcriptional regulator; Region: MerR; TIGR02051 94122000280 DNA binding residues [nucleotide binding] 94122000281 dimer interface [polypeptide binding]; other site 94122000282 mercury binding site [ion binding]; other site 94122000283 Cre recombinase, C-terminal catalytic domain. Cre-like recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre...; Region: INT_Cre; cd00799 94122000284 DNA binding site [nucleotide binding] 94122000285 dimer interface [polypeptide binding]; other site 94122000286 active site 94122000287 Int/Topo IB signature motif; other site 94122000288 Plasmid replication region DNA-binding N-term; Region: KfrA_N; pfam11740 94122000289 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 94122000290 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 94122000291 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 94122000292 multiple promoter invertase; Provisional; Region: mpi; PRK13413 94122000293 catalytic residues [active] 94122000294 catalytic nucleophile [active] 94122000295 Presynaptic Site I dimer interface [polypeptide binding]; other site 94122000296 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 94122000297 Synaptic Flat tetramer interface [polypeptide binding]; other site 94122000298 Synaptic Site I dimer interface [polypeptide binding]; other site 94122000299 DNA binding site [nucleotide binding] 94122000300 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 94122000301 DNA-binding interface [nucleotide binding]; DNA binding site 94122000302 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; cd01610 94122000303 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 94122000304 active site 94122000305 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 94122000306 lipoprotein signal peptidase; Provisional; Region: PRK14787 94122000307 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 94122000308 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 94122000309 DNA binding residues [nucleotide binding] 94122000310 dimer interface [polypeptide binding]; other site 94122000311 putative metal binding site [ion binding]; other site 94122000312 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 94122000313 methionine sulfoxide reductase A; Provisional; Region: PRK14054 94122000314 methionine sulfoxide reductase B; Provisional; Region: PRK00222 94122000315 SelR domain; Region: SelR; pfam01641 94122000316 Protein of unknown function, DUF417; Region: DUF417; cl01162 94122000317 Uncharacterized conserved protein [Function unknown]; Region: COG2128 94122000318 alkylhydroperoxidase AhpD family core domain; Region: ahpD_dom; TIGR00778 94122000319 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 94122000320 GAF domain; Region: GAF; pfam01590 94122000321 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122000322 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122000323 metal binding site [ion binding]; metal-binding site 94122000324 active site 94122000325 I-site; other site 94122000326 Peptide methionine sulfoxide reductase; Region: PMSR; pfam01625 94122000327 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 94122000328 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229; cl15841 94122000329 SelR domain; Region: SelR; pfam01641 94122000330 Glutaredoxin (GRX) family; composed of GRX, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide...; Region: GRX_family; cd02066 94122000331 GSH binding site [chemical binding]; other site 94122000332 catalytic residues [active] 94122000333 methionine sulfoxide reductase A; Provisional; Region: PRK14054 94122000334 Cupin; Region: Cupin_6; pfam12852 94122000335 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 94122000336 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 94122000337 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 94122000338 Putative FMN-binding domain; Region: FMN_bind_2; cl17803 94122000339 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 94122000340 Helix-turn-helix domain; Region: HTH_38; pfam13936 94122000341 Integrase core domain; Region: rve; pfam00665 94122000342 Electron transfer DM13; Region: DM13; pfam10517 94122000343 putative transcriptional regulator MerR; Provisional; Region: PRK13752 94122000344 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Region: HTH_MerR1; cd04783 94122000345 DNA binding residues [nucleotide binding] 94122000346 dimer interface [polypeptide binding]; other site 94122000347 mercury binding site [ion binding]; other site 94122000348 putative mercuric transport protein; Provisional; Region: PRK13751 94122000349 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 94122000350 metal-binding site [ion binding] 94122000351 putative mercury transport protein MerC; Provisional; Region: PRK13755 94122000352 putative mercuric reductase; Provisional; Region: PRK13748 94122000353 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 94122000354 metal-binding site [ion binding] 94122000355 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 94122000356 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 94122000357 transcriptional regulator MerD; Provisional; Region: PRK13749 94122000358 Helix-Turn-Helix DNA binding domain of the MerD transcription regulator; Region: HTH_MerD; cd01111 94122000359 DNA binding residues [nucleotide binding] 94122000360 putative dimer interface [polypeptide binding]; other site 94122000361 putative mercury resistance protein; Provisional; Region: PRK13747 94122000362 Domain of unknown function (DUF3330); Region: DUF3330; pfam11809 94122000363 Y-family of DNA polymerases; Region: PolY; cl12025 94122000364 DNA binding site [nucleotide binding] 94122000365 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 94122000366 Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme; Region: NT_2-5OAS_ClassI-CCAase; cd05400 94122000367 active site 94122000368 NTP binding site [chemical binding]; other site 94122000369 metal binding triad [ion binding]; metal-binding site 94122000370 Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17; Region: Pat17_PNPLA8_PNPLA9_like; cd07199 94122000371 active site 94122000372 nucleophile elbow; other site 94122000373 Mpr1p, Pad1p N-terminal (MPN) domains; Region: MPN; cl13996 94122000374 Prokaryotic E2 family B; Region: Prok-E2_B; pfam14461 94122000375 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism]; Region: ThiF; COG0476 94122000376 ThiF family; Region: ThiF; pfam00899 94122000377 ATP binding site [chemical binding]; other site 94122000378 substrate interface [chemical binding]; other site 94122000379 Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme; Region: NT_2-5OAS_ClassI-CCAase; cd05400 94122000380 active site 94122000381 NTP binding site [chemical binding]; other site 94122000382 metal binding triad [ion binding]; metal-binding site 94122000383 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 94122000384 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 94122000385 non-specific DNA binding site [nucleotide binding]; other site 94122000386 salt bridge; other site 94122000387 sequence-specific DNA binding site [nucleotide binding]; other site 94122000388 Domain of unknown function (DUF955); Region: DUF955; pfam06114 94122000389 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 94122000390 active site 94122000391 Int/Topo IB signature motif; other site 94122000392 catalytic residues [active] 94122000393 DNA binding site [nucleotide binding] 94122000394 DNA-sulfur modification-associated; Region: DndB; cl17621 94122000395 DGQHR domain; Region: DGQHR; TIGR03187 94122000396 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 94122000397 Ligand Binding Site [chemical binding]; other site 94122000398 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 94122000399 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 94122000400 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 94122000401 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 94122000402 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 94122000403 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 94122000404 Chromate transporter; Region: Chromate_transp; pfam02417 94122000405 Chromate resistance exported protein; Region: Chrome_Resist; pfam09828 94122000406 Cre recombinase, C-terminal catalytic domain. Cre-like recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre...; Region: INT_Cre; cd00799 94122000407 DNA binding site [nucleotide binding] 94122000408 dimer interface [polypeptide binding]; other site 94122000409 active site 94122000410 Int/Topo IB signature motif; other site 94122000411 Plasmid replication region DNA-binding N-term; Region: KfrA_N; pfam11740 94122000412 Birnavirus RNA dependent RNA polymerase (VP1); Region: Birna_RdRp; pfam04197 94122000413 Methyltransferase domain; Region: Methyltransf_26; pfam13659 94122000414 Methyltransferase domain; Region: Methyltransf_27; pfam13708 94122000415 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 94122000416 active site 94122000417 DNA binding site [nucleotide binding] 94122000418 Int/Topo IB signature motif; other site 94122000419 Protein of unknown function (DUF2511); Region: DUF2511; pfam10709 94122000420 HupE / UreJ protein; Region: HupE_UreJ_2; pfam13795 94122000421 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 94122000422 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 94122000423 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122000424 Outer membrane efflux protein; Region: OEP; pfam02321 94122000425 Outer membrane efflux protein; Region: OEP; pfam02321 94122000426 Antirepressor regulating drug resistance, predicted signal transduction N-terminal membrane component [Transcription / Signal transduction mechanisms]; Region: MecR1; COG4219 94122000427 Penicillinase repressor; Region: Pencillinase_R; cl17580 94122000428 hypothetical protein; Provisional; Region: PRK09272 94122000429 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122000430 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122000431 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 94122000432 dimerization interface [polypeptide binding]; other site 94122000433 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 94122000434 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 94122000435 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 94122000436 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 94122000437 S-adenosylmethionine binding site [chemical binding]; other site 94122000438 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 94122000439 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 94122000440 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 94122000441 FMN-binding protein MioC; Provisional; Region: PRK09004 94122000442 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 94122000443 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 94122000444 POT family; Region: PTR2; cl17359 94122000445 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 94122000446 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 94122000447 trmE is a tRNA modification GTPase; Region: trmE; cd04164 94122000448 G1 box; other site 94122000449 GTP/Mg2+ binding site [chemical binding]; other site 94122000450 Switch I region; other site 94122000451 G2 box; other site 94122000452 Switch II region; other site 94122000453 G3 box; other site 94122000454 G4 box; other site 94122000455 G5 box; other site 94122000456 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 94122000457 membrane protein insertase; Provisional; Region: PRK01318 94122000458 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 94122000459 Haemolytic domain; Region: Haemolytic; pfam01809 94122000460 ribonuclease P; Reviewed; Region: rnpA; PRK01732 94122000461 DnaA N-terminal domain; Region: DnaA_N; pfam11638 94122000462 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 94122000463 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 94122000464 Walker A motif; other site 94122000465 ATP binding site [chemical binding]; other site 94122000466 Walker B motif; other site 94122000467 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 94122000468 arginine finger; other site 94122000469 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 94122000470 DnaA box-binding interface [nucleotide binding]; other site 94122000471 DNA polymerase III subunit beta; Validated; Region: PRK05643 94122000472 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 94122000473 putative DNA binding surface [nucleotide binding]; other site 94122000474 dimer interface [polypeptide binding]; other site 94122000475 beta-clamp/clamp loader binding surface; other site 94122000476 beta-clamp/translesion DNA polymerase binding surface; other site 94122000477 recombination protein F; Reviewed; Region: recF; PRK00064 94122000478 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122000479 Walker A/P-loop; other site 94122000480 ATP binding site [chemical binding]; other site 94122000481 Q-loop/lid; other site 94122000482 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122000483 ABC transporter signature motif; other site 94122000484 Walker B; other site 94122000485 D-loop; other site 94122000486 H-loop/switch region; other site 94122000487 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 94122000488 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 94122000489 ATP binding site [chemical binding]; other site 94122000490 Mg2+ binding site [ion binding]; other site 94122000491 G-X-G motif; other site 94122000492 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 94122000493 anchoring element; other site 94122000494 dimer interface [polypeptide binding]; other site 94122000495 ATP binding site [chemical binding]; other site 94122000496 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 94122000497 active site 94122000498 putative metal-binding site [ion binding]; other site 94122000499 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 94122000500 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 94122000501 GST_N family, unknown subfamily 1; composed of uncharacterized proteins, predominantly from bacteria, with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with...; Region: GST_N_1; cd03043 94122000502 putative C-terminal domain interface [polypeptide binding]; other site 94122000503 putative GSH binding site (G-site) [chemical binding]; other site 94122000504 putative dimer interface [polypeptide binding]; other site 94122000505 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 94122000506 putative N-terminal domain interface [polypeptide binding]; other site 94122000507 putative dimer interface [polypeptide binding]; other site 94122000508 putative substrate binding pocket (H-site) [chemical binding]; other site 94122000509 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122000510 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122000511 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 94122000512 dimerization interface [polypeptide binding]; other site 94122000513 HDOD domain; Region: HDOD; pfam08668 94122000514 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 94122000515 Zn2+ binding site [ion binding]; other site 94122000516 Mg2+ binding site [ion binding]; other site 94122000517 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 94122000518 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 94122000519 dimer interface [polypeptide binding]; other site 94122000520 motif 1; other site 94122000521 active site 94122000522 motif 2; other site 94122000523 motif 3; other site 94122000524 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 94122000525 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 94122000526 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 94122000527 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 94122000528 Amidohydrolase; Region: Amidohydro_5; pfam13594 94122000529 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; cd01292 94122000530 active site 94122000531 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 94122000532 MOSC domain; Region: MOSC; pfam03473 94122000533 SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A...; Region: SirA; cd03423 94122000534 CPxP motif; other site 94122000535 Globin domain present in Globin-Coupled-Sensors (GCS). These domains detect changes in intracellular concentrations of oxygen, carbon monoxyde, or nitrous oxide, which result in aerotaxis and/or gene regulation. One subgroup, the HemATs, are aerotactic...; Region: sensor_globin; cd01068 94122000536 heme-binding site [chemical binding]; other site 94122000537 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122000538 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122000539 metal binding site [ion binding]; metal-binding site 94122000540 active site 94122000541 I-site; other site 94122000542 3-ketoacyl-CoA thiolase; Reviewed; Region: fadA; PRK08947 94122000543 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 94122000544 dimer interface [polypeptide binding]; other site 94122000545 active site 94122000546 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadB; PRK11730 94122000547 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 94122000548 substrate binding site [chemical binding]; other site 94122000549 oxyanion hole (OAH) forming residues; other site 94122000550 trimer interface [polypeptide binding]; other site 94122000551 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 94122000552 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 94122000553 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 94122000554 proline dipeptidase; Provisional; Region: PRK13607 94122000555 Aminopeptidase P, N-terminal domain; Region: AMP_N; cl08433 94122000556 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 94122000557 active site 94122000558 hypothetical protein; Provisional; Region: PRK11568 94122000559 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 94122000560 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 94122000561 Cation transport protein; Region: TrkH; cl17365 94122000562 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 94122000563 Flavodoxin domain; Region: Flavodoxin_5; cl17428 94122000564 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 94122000565 dimerization interface [polypeptide binding]; other site 94122000566 putative DNA binding site [nucleotide binding]; other site 94122000567 putative Zn2+ binding site [ion binding]; other site 94122000568 Flavodoxin domain; Region: Flavodoxin_5; cl17428 94122000569 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 94122000570 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 94122000571 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 94122000572 TrkA-N domain; Region: TrkA_N; pfam02254 94122000573 TrkA-C domain; Region: TrkA_C; pfam02080 94122000574 TrkA-N domain; Region: TrkA_N; pfam02254 94122000575 TrkA-C domain; Region: TrkA_C; pfam02080 94122000576 16S rRNA methyltransferase B; Provisional; Region: PRK10901 94122000577 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 94122000578 putative RNA binding site [nucleotide binding]; other site 94122000579 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 94122000580 S-adenosylmethionine binding site [chemical binding]; other site 94122000581 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 94122000582 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 94122000583 putative active site [active] 94122000584 substrate binding site [chemical binding]; other site 94122000585 putative cosubstrate binding site; other site 94122000586 catalytic site [active] 94122000587 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 94122000588 substrate binding site [chemical binding]; other site 94122000589 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 94122000590 active site 94122000591 catalytic residues [active] 94122000592 metal binding site [ion binding]; metal-binding site 94122000593 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 94122000594 DNA protecting protein DprA; Region: dprA; TIGR00732 94122000595 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 94122000596 Protein of unknown function (DUF494); Region: DUF494; pfam04361 94122000597 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 94122000598 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 94122000599 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 94122000600 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 94122000601 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 94122000602 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 94122000603 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 94122000604 apolar tunnel; other site 94122000605 heme binding site [chemical binding]; other site 94122000606 dimerization interface [polypeptide binding]; other site 94122000607 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 94122000608 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 94122000609 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 94122000610 shikimate binding site; other site 94122000611 NAD(P) binding site [chemical binding]; other site 94122000612 Protein of unknown function (DUF1488); Region: DUF1488; pfam07369 94122000613 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 94122000614 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 94122000615 trimer interface [polypeptide binding]; other site 94122000616 putative metal binding site [ion binding]; other site 94122000617 Flagellin N-methylase; Region: FliB; cl00497 94122000618 Transcriptional regulator; Region: Rrf2; cl17282 94122000619 Rrf2 family protein; Region: rrf2_super; TIGR00738 94122000620 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 94122000621 NodB motif; other site 94122000622 putative active site [active] 94122000623 putative catalytic site [active] 94122000624 Zn binding site [ion binding]; other site 94122000625 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 94122000626 C-terminal peptidase (prc); Region: prc; TIGR00225 94122000627 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 94122000628 protein binding site [polypeptide binding]; other site 94122000629 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 94122000630 Catalytic dyad [active] 94122000631 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 94122000632 Peptidase family M23; Region: Peptidase_M23; pfam01551 94122000633 phosphoglyceromutase; Provisional; Region: PRK05434 94122000634 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 94122000635 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 94122000636 active site residue [active] 94122000637 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cd00557 94122000638 SecA binding site; other site 94122000639 Preprotein binding site; other site 94122000640 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 94122000641 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 94122000642 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 94122000643 HI0933-like protein; Region: HI0933_like; pfam03486 94122000644 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 94122000645 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 94122000646 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 94122000647 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 94122000648 TrkA-N domain; Region: TrkA_N; pfam02254 94122000649 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 94122000650 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122000651 active site 94122000652 phosphorylation site [posttranslational modification] 94122000653 intermolecular recognition site; other site 94122000654 dimerization interface [polypeptide binding]; other site 94122000655 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 94122000656 DNA binding site [nucleotide binding] 94122000657 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 94122000658 dimer interface [polypeptide binding]; other site 94122000659 phosphorylation site [posttranslational modification] 94122000660 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 94122000661 ATP binding site [chemical binding]; other site 94122000662 Mg2+ binding site [ion binding]; other site 94122000663 G-X-G motif; other site 94122000664 Pirin-related protein [General function prediction only]; Region: COG1741 94122000665 Pirin; Region: Pirin; pfam02678 94122000666 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 94122000667 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 94122000668 NlpC/P60 family; Region: NLPC_P60; pfam00877 94122000669 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 94122000670 putative substrate translocation pore; other site 94122000671 Transcriptional regulators [Transcription]; Region: PurR; COG1609 94122000672 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 94122000673 DNA binding site [nucleotide binding] 94122000674 domain linker motif; other site 94122000675 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; Region: PBP1_LacI_like_3; cd06279 94122000676 putative dimerization interface [polypeptide binding]; other site 94122000677 putative ligand binding site [chemical binding]; other site 94122000678 sucrose phosphorylase; Provisional; Region: PRK13840 94122000679 Alpha amylase catalytic domain found in sucrose phosphorylase (also called sucrose glucosyltransferase, disaccharide glucosyltransferase, and sucrose-phosphate alpha-D glucosyltransferase); Region: AmyAc_Sucrose_phosphorylase; cd11355 94122000680 active site 94122000681 homodimer interface [polypeptide binding]; other site 94122000682 catalytic site [active] 94122000683 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 94122000684 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 94122000685 putative substrate translocation pore; other site 94122000686 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 94122000687 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122000688 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122000689 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 94122000690 Fructokinases (FRKs) mainly from bacteria and plants are enzymes with high specificity for fructose, as are all FRKs, but they catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into...; Region: bac_FRK; cd01167 94122000691 putative substrate binding site [chemical binding]; other site 94122000692 putative ATP binding site [chemical binding]; other site 94122000693 MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea; Region: MogA_MoaB; cd00886 94122000694 MPT binding site; other site 94122000695 trimer interface [polypeptide binding]; other site 94122000696 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 94122000697 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_2; cd03138 94122000698 conserved cys residue [active] 94122000699 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 94122000700 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 94122000701 Phage shock protein B; Region: PspB; cl05946 94122000702 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 94122000703 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 94122000704 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 94122000705 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122000706 Walker A/P-loop; other site 94122000707 ATP binding site [chemical binding]; other site 94122000708 Q-loop/lid; other site 94122000709 ABC transporter signature motif; other site 94122000710 Walker B; other site 94122000711 D-loop; other site 94122000712 H-loop/switch region; other site 94122000713 TAP-like protein; Region: Abhydrolase_4; pfam08386 94122000714 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 94122000715 DNA-binding site [nucleotide binding]; DNA binding site 94122000716 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 94122000717 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 94122000718 Walker A/P-loop; other site 94122000719 ATP binding site [chemical binding]; other site 94122000720 Q-loop/lid; other site 94122000721 ABC transporter signature motif; other site 94122000722 Walker B; other site 94122000723 D-loop; other site 94122000724 H-loop/switch region; other site 94122000725 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 94122000726 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 94122000727 acyl-activating enzyme (AAE) consensus motif; other site 94122000728 putative AMP binding site [chemical binding]; other site 94122000729 putative active site [active] 94122000730 putative CoA binding site [chemical binding]; other site 94122000731 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 94122000732 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 94122000733 active site 94122000734 HPP family; Region: HPP; pfam04982 94122000735 Predicted acetyltransferase [General function prediction only]; Region: COG2388 94122000736 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 94122000737 active site 94122000738 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators; Region: HTH_MerR2; cd04769 94122000739 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 94122000740 DNA binding residues [nucleotide binding] 94122000741 putative dimer interface [polypeptide binding]; other site 94122000742 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 94122000743 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 94122000744 Uncharacterized conserved protein [Function unknown]; Region: COG3791 94122000745 Predicted enolase-phosphatase [Energy production and conversion]; Region: COG4229 94122000746 Protein of unknown function (DUF3137); Region: DUF3137; pfam11335 94122000747 putative transposase OrfB; Reviewed; Region: PHA02517 94122000748 Integrase core domain; Region: rve; pfam00665 94122000749 Integrase core domain; Region: rve_3; pfam13683 94122000750 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 94122000751 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 94122000752 Transcriptional regulators [Transcription]; Region: MarR; COG1846 94122000753 MarR family; Region: MarR_2; pfam12802 94122000754 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 94122000755 Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from...; Region: siderophore_interacting; cd06193 94122000756 FAD binding pocket [chemical binding]; other site 94122000757 FAD binding motif [chemical binding]; other site 94122000758 phosphate binding motif [ion binding]; other site 94122000759 NAD binding pocket [chemical binding]; other site 94122000760 imidazolonepropionase; Validated; Region: PRK09356 94122000761 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 94122000762 active site 94122000763 histidine utilization repressor, proteobacterial; Region: his_ut_repres; TIGR02018 94122000764 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 94122000765 DNA-binding site [nucleotide binding]; DNA binding site 94122000766 UTRA domain; Region: UTRA; pfam07702 94122000767 urocanate hydratase; Provisional; Region: PRK05414 94122000768 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 94122000769 active sites [active] 94122000770 tetramer interface [polypeptide binding]; other site 94122000771 formate dehydrogenase, beta subunit, Fe-S containing; Region: FDH-beta; TIGR01582 94122000772 4Fe-4S binding domain; Region: Fer4; pfam00037 94122000773 Formate dehydrogenase N, transmembrane; Region: Form-deh_trans; pfam09163 94122000774 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 94122000775 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 94122000776 formate dehydrogenase accessory protein FdhE; Region: FdhE; TIGR01562 94122000777 Protein involved in formate dehydrogenase formation; Region: FdhE; pfam04216 94122000778 seryl-tRNA(sec) selenium transferase; Region: selA; TIGR00474 94122000779 Selenocysteine synthase N terminal; Region: Se-cys_synth_N; pfam12390 94122000780 Selenocysteine synthase [seryl-tRNASer selenium transferase] [Amino acid transport and metabolism]; Region: SelA; COG1921 94122000781 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 94122000782 catalytic residue [active] 94122000783 selenocysteinyl-tRNA-specific translation factor; Provisional; Region: PRK10512 94122000784 SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; Region: SelB; cd04171 94122000785 G1 box; other site 94122000786 putative GEF interaction site [polypeptide binding]; other site 94122000787 GTP/Mg2+ binding site [chemical binding]; other site 94122000788 Switch I region; other site 94122000789 G2 box; other site 94122000790 G3 box; other site 94122000791 Switch II region; other site 94122000792 G4 box; other site 94122000793 G5 box; other site 94122000794 selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several...; Region: selB_II; cd03696 94122000795 This family represents the domain of elongation factor SelB, homologous to domain III of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements:...; Region: selB_III; cd04094 94122000796 Elongation factor SelB, winged helix; Region: SelB-wing_2; pfam09106 94122000797 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 94122000798 formate dehydrogenase accessory protein; Reviewed; Region: PRK00724 94122000799 putative inner membrane protein; Provisional; Region: PRK11099 94122000800 YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system...; Region: YedF; cd03422 94122000801 CPxP motif; other site 94122000802 Peptidase family M48; Region: Peptidase_M48; cl12018 94122000803 Pilin (bacterial filament); Region: Pilin; pfam00114 94122000804 Protein of unknown function (DUF1311); Region: DUF1311; pfam07007 94122000805 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; pfam09864 94122000806 Protein of unknown function, DUF481; Region: DUF481; cl01213 94122000807 Protein of unknown function (DUF3157); Region: DUF3157; pfam11355 94122000808 Protein of unknown function (DUF1090); Region: DUF1090; pfam06476 94122000809 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 94122000810 Mechanosensitive ion channel; Region: MS_channel; pfam00924 94122000811 LysE type translocator; Region: LysE; cl00565 94122000812 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 94122000813 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ABO13168; Region: LPLAT_ABO13168-like; cd07988 94122000814 putative acyl-acceptor binding pocket; other site 94122000815 Calcium/calmodulin dependent protein kinase II Association; Region: CaMKII_AD; cl17504 94122000816 SnoaL-like domain; Region: SnoaL_3; pfam13474 94122000817 NRDE protein; Region: NRDE; cl01315 94122000818 putative antibiotic transporter; Provisional; Region: PRK10739 94122000819 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4412 94122000820 Immune inhibitor A peptidase M6; Region: Peptidase_M6; cl11525 94122000821 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cd00146 94122000822 Chorismate lyase; Region: Chor_lyase; cl01230 94122000823 flagellar basal body-associated protein FliL-like protein; Validated; Region: PRK05697 94122000824 23S rRNA mA1618 methyltransferase; Provisional; Region: PRK11727 94122000825 Protein of unknown function (DUF890); Region: Methyltransf_10; pfam05971 94122000826 Putative hemolysin [General function prediction only]; Region: Hlx; COG3042 94122000827 Domain of unknown function (DUF333); Region: DUF333; pfam03891 94122000828 Inhibitor of apoptosis-promoting Bax1; Region: Bax1-I; pfam01027 94122000829 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 94122000830 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 94122000831 ATP binding site [chemical binding]; other site 94122000832 substrate interface [chemical binding]; other site 94122000833 molybdopterin biosynthesis protein MoeA; Provisional; Region: PRK10680 94122000834 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 94122000835 dimer interface [polypeptide binding]; other site 94122000836 putative functional site; other site 94122000837 putative MPT binding site; other site 94122000838 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 94122000839 Ferritin-like domain; Region: Ferritin; pfam00210 94122000840 ferroxidase diiron center [ion binding]; other site 94122000841 Nitrate and nitrite sensing; Region: NIT; pfam08376 94122000842 HAMP domain; Region: HAMP; pfam00672 94122000843 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 94122000844 PAS domain; Region: PAS_9; pfam13426 94122000845 putative active site [active] 94122000846 heme pocket [chemical binding]; other site 94122000847 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122000848 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122000849 metal binding site [ion binding]; metal-binding site 94122000850 active site 94122000851 I-site; other site 94122000852 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 94122000853 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional; Region: ribB; PRK03353 94122000854 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]; Region: RibB; COG0108 94122000855 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 94122000856 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 94122000857 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 94122000858 GIY-YIG motif/motif A; other site 94122000859 putative active site [active] 94122000860 putative metal binding site [ion binding]; other site 94122000861 Protein of unknown function (DUF3800); Region: DUF3800; pfam12686 94122000862 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 94122000863 S-adenosylmethionine binding site [chemical binding]; other site 94122000864 Peptidase M14-like domain; uncharacterized subgroup; Region: M14-like_1_4; cd06241 94122000865 putative active site [active] 94122000866 Zn binding site [ion binding]; other site 94122000867 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 94122000868 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 94122000869 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 94122000870 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 94122000871 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 94122000872 ligand binding site [chemical binding]; other site 94122000873 Putative p-aminobenzoyl-glutamate transporter [Coenzyme metabolism]; Region: AbgT; COG2978 94122000874 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 94122000875 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 94122000876 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_ATP; cd00484 94122000877 active site 94122000878 substrate-binding site [chemical binding]; other site 94122000879 metal-binding site [ion binding] 94122000880 ATP binding site [chemical binding]; other site 94122000881 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 94122000882 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 94122000883 dimerization interface [polypeptide binding]; other site 94122000884 domain crossover interface; other site 94122000885 redox-dependent activation switch; other site 94122000886 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 94122000887 RNA binding surface [nucleotide binding]; other site 94122000888 Type IV pilus biogenesis; Region: Pilus_PilP; pfam11356 94122000889 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 94122000890 type II secretion system protein D; Region: type_II_gspD; TIGR02517 94122000891 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 94122000892 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 94122000893 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 94122000894 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 94122000895 type II secretion system protein E; Region: type_II_gspE; TIGR02533 94122000896 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 94122000897 Walker A motif; other site 94122000898 ATP binding site [chemical binding]; other site 94122000899 Walker B motif; other site 94122000900 type II secretion system protein F; Region: GspF; TIGR02120 94122000901 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 94122000902 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 94122000903 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 94122000904 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 94122000905 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 94122000906 type II secretion system protein H; Region: typeII_sec_gspH; TIGR01708 94122000907 Type II transport protein GspH; Region: GspH; pfam12019 94122000908 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 94122000909 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 94122000910 type II secretion system protein J; Region: gspJ; TIGR01711 94122000911 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 94122000912 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 94122000913 type II secretion system protein L; Region: typeII_sec_gspL; TIGR01709 94122000914 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 94122000915 GspL periplasmic domain; Region: GspL_C; pfam12693 94122000916 Type II secretion system (T2SS), protein M; Region: T2SM; pfam04612 94122000917 Type II secretion system (T2SS), protein N; Region: T2SN; pfam01203 94122000918 haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; Region: HAD-SF-IA-v3; TIGR01509 94122000919 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 94122000920 motif II; other site 94122000921 Aspartyl/Asparaginyl beta-hydroxylase; Region: Asp_Arg_Hydrox; cl17820 94122000922 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 94122000923 S-adenosylmethionine binding site [chemical binding]; other site 94122000924 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; cl17312 94122000925 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 94122000926 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122000927 Coenzyme A binding pocket [chemical binding]; other site 94122000928 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 94122000929 Microcystin-dependent protein [Function unknown]; Region: MdpB; COG4675 94122000930 Phage Tail Collar Domain; Region: Collar; pfam07484 94122000931 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 94122000932 Interdomain contacts; other site 94122000933 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 94122000934 Interdomain contacts; other site 94122000935 Cytokine receptor motif; other site 94122000936 Cadherin repeat-like domain; Region: CA_like; cl15786 94122000937 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 94122000938 Ca2+ binding site [ion binding]; other site 94122000939 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 94122000940 Cadherin repeat-like domain; Region: CA_like; cl15786 94122000941 Ca2+ binding site [ion binding]; other site 94122000942 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 94122000943 Cadherin repeat-like domain; Region: CA_like; cl15786 94122000944 Ca2+ binding site [ion binding]; other site 94122000945 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 94122000946 Cadherin repeat-like domain; Region: CA_like; cl15786 94122000947 Ca2+ binding site [ion binding]; other site 94122000948 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 94122000949 Cadherin repeat-like domain; Region: CA_like; cl15786 94122000950 Ca2+ binding site [ion binding]; other site 94122000951 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 94122000952 Cadherin repeat-like domain; Region: CA_like; cl15786 94122000953 Ca2+ binding site [ion binding]; other site 94122000954 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 94122000955 Cadherin repeat-like domain; Region: CA_like; cl15786 94122000956 Ca2+ binding site [ion binding]; other site 94122000957 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 94122000958 Cadherin repeat-like domain; Region: CA_like; cl15786 94122000959 Ca2+ binding site [ion binding]; other site 94122000960 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 94122000961 Cadherin repeat-like domain; Region: CA_like; cl15786 94122000962 Ca2+ binding site [ion binding]; other site 94122000963 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 94122000964 Cadherin repeat-like domain; Region: CA_like; cl15786 94122000965 Ca2+ binding site [ion binding]; other site 94122000966 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 94122000967 Cadherin repeat-like domain; Region: CA_like; cl15786 94122000968 Ca2+ binding site [ion binding]; other site 94122000969 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 94122000970 Cadherin repeat-like domain; Region: CA_like; cl15786 94122000971 Ca2+ binding site [ion binding]; other site 94122000972 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 94122000973 Cadherin repeat-like domain; Region: CA_like; cl15786 94122000974 Ca2+ binding site [ion binding]; other site 94122000975 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 94122000976 Cadherin repeat-like domain; Region: CA_like; cl15786 94122000977 Ca2+ binding site [ion binding]; other site 94122000978 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 94122000979 adenosine nucleotide hydrolase NudE; Provisional; Region: nudE; PRK11762 94122000980 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 94122000981 dimer interface [polypeptide binding]; other site 94122000982 ADP-ribose binding site [chemical binding]; other site 94122000983 active site 94122000984 nudix motif; other site 94122000985 metal binding site [ion binding]; metal-binding site 94122000986 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 94122000987 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 94122000988 active site 94122000989 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 94122000990 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122000991 Coenzyme A binding pocket [chemical binding]; other site 94122000992 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 94122000993 WHG domain; Region: WHG; pfam13305 94122000994 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 94122000995 putative substrate translocation pore; other site 94122000996 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 94122000997 putative acyl-acceptor binding pocket; other site 94122000998 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 94122000999 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 94122001000 active site residue [active] 94122001001 selenophosphate synthetase; Provisional; Region: PRK00943 94122001002 Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The...; Region: SelD; cd02195 94122001003 dimerization interface [polypeptide binding]; other site 94122001004 putative ATP binding site [chemical binding]; other site 94122001005 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 94122001006 Di-iron ligands [ion binding]; other site 94122001007 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 94122001008 DNA-binding transcriptional repressor FabR; Provisional; Region: PRK11202 94122001009 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 94122001010 tRNA (uracil-5-)-methyltransferase; Validated; Region: PRK05031 94122001011 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 94122001012 S-adenosylmethionine binding site [chemical binding]; other site 94122001013 glutamate racemase; Provisional; Region: PRK00865 94122001014 RNA-binding proteins (RRM domain) [General function prediction only]; Region: COG0724 94122001015 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 94122001016 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 94122001017 FAD binding domain; Region: FAD_binding_4; pfam01565 94122001018 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 94122001019 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 94122001020 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 94122001021 dimerization interface [polypeptide binding]; other site 94122001022 putative Zn2+ binding site [ion binding]; other site 94122001023 putative DNA binding site [nucleotide binding]; other site 94122001024 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 94122001025 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 94122001026 pantothenate kinase; Provisional; Region: PRK05439 94122001027 Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point...; Region: PanK; cd02025 94122001028 ATP-binding site [chemical binding]; other site 94122001029 CoA-binding site [chemical binding]; other site 94122001030 Mg2+-binding site [ion binding]; other site 94122001031 elongation factor Tu; Reviewed; Region: PRK00049 94122001032 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 94122001033 G1 box; other site 94122001034 GEF interaction site [polypeptide binding]; other site 94122001035 GTP/Mg2+ binding site [chemical binding]; other site 94122001036 Switch I region; other site 94122001037 G2 box; other site 94122001038 G3 box; other site 94122001039 Switch II region; other site 94122001040 G4 box; other site 94122001041 G5 box; other site 94122001042 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 94122001043 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 94122001044 Antibiotic Binding Site [chemical binding]; other site 94122001045 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 94122001046 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 94122001047 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 94122001048 putative homodimer interface [polypeptide binding]; other site 94122001049 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 94122001050 heterodimer interface [polypeptide binding]; other site 94122001051 homodimer interface [polypeptide binding]; other site 94122001052 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 94122001053 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 94122001054 23S rRNA interface [nucleotide binding]; other site 94122001055 L7/L12 interface [polypeptide binding]; other site 94122001056 putative thiostrepton binding site; other site 94122001057 L25 interface [polypeptide binding]; other site 94122001058 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 94122001059 mRNA/rRNA interface [nucleotide binding]; other site 94122001060 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 94122001061 23S rRNA interface [nucleotide binding]; other site 94122001062 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 94122001063 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 94122001064 core dimer interface [polypeptide binding]; other site 94122001065 peripheral dimer interface [polypeptide binding]; other site 94122001066 L10 interface [polypeptide binding]; other site 94122001067 L11 interface [polypeptide binding]; other site 94122001068 putative EF-Tu interaction site [polypeptide binding]; other site 94122001069 putative EF-G interaction site [polypeptide binding]; other site 94122001070 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 94122001071 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 94122001072 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 94122001073 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 94122001074 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 94122001075 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 94122001076 RPB3 interaction site [polypeptide binding]; other site 94122001077 RPB1 interaction site [polypeptide binding]; other site 94122001078 RPB11 interaction site [polypeptide binding]; other site 94122001079 RPB10 interaction site [polypeptide binding]; other site 94122001080 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 94122001081 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 94122001082 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 94122001083 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 94122001084 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 94122001085 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 94122001086 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 94122001087 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 94122001088 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 94122001089 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 94122001090 DNA binding site [nucleotide binding] 94122001091 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 94122001092 S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit...; Region: Ribosomal_S12; cd03368 94122001093 S17 interaction site [polypeptide binding]; other site 94122001094 S8 interaction site; other site 94122001095 16S rRNA interaction site [nucleotide binding]; other site 94122001096 streptomycin interaction site [chemical binding]; other site 94122001097 23S rRNA interaction site [nucleotide binding]; other site 94122001098 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 94122001099 30S ribosomal protein S7; Validated; Region: PRK05302 94122001100 elongation factor G; Reviewed; Region: PRK00007 94122001101 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 94122001102 G1 box; other site 94122001103 putative GEF interaction site [polypeptide binding]; other site 94122001104 GTP/Mg2+ binding site [chemical binding]; other site 94122001105 Switch I region; other site 94122001106 G2 box; other site 94122001107 G3 box; other site 94122001108 Switch II region; other site 94122001109 G4 box; other site 94122001110 G5 box; other site 94122001111 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 94122001112 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 94122001113 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 94122001114 elongation factor Tu; Reviewed; Region: PRK00049 94122001115 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 94122001116 G1 box; other site 94122001117 GEF interaction site [polypeptide binding]; other site 94122001118 GTP/Mg2+ binding site [chemical binding]; other site 94122001119 Switch I region; other site 94122001120 G2 box; other site 94122001121 G3 box; other site 94122001122 Switch II region; other site 94122001123 G4 box; other site 94122001124 G5 box; other site 94122001125 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 94122001126 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 94122001127 Antibiotic Binding Site [chemical binding]; other site 94122001128 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 94122001129 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 94122001130 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 94122001131 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 94122001132 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 94122001133 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 94122001134 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 94122001135 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 94122001136 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 94122001137 putative translocon binding site; other site 94122001138 protein-rRNA interface [nucleotide binding]; other site 94122001139 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 94122001140 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 94122001141 G-X-X-G motif; other site 94122001142 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 94122001143 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 94122001144 23S rRNA interface [nucleotide binding]; other site 94122001145 5S rRNA interface [nucleotide binding]; other site 94122001146 putative antibiotic binding site [chemical binding]; other site 94122001147 L25 interface [polypeptide binding]; other site 94122001148 L27 interface [polypeptide binding]; other site 94122001149 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 94122001150 23S rRNA interface [nucleotide binding]; other site 94122001151 putative translocon interaction site; other site 94122001152 signal recognition particle (SRP54) interaction site; other site 94122001153 L23 interface [polypeptide binding]; other site 94122001154 trigger factor interaction site; other site 94122001155 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 94122001156 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 94122001157 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 94122001158 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 94122001159 RNA binding site [nucleotide binding]; other site 94122001160 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 94122001161 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 94122001162 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 94122001163 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 94122001164 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 94122001165 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 94122001166 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 94122001167 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 94122001168 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 94122001169 5S rRNA interface [nucleotide binding]; other site 94122001170 23S rRNA interface [nucleotide binding]; other site 94122001171 L5 interface [polypeptide binding]; other site 94122001172 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 94122001173 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 94122001174 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 94122001175 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 94122001176 23S rRNA binding site [nucleotide binding]; other site 94122001177 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 94122001178 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 94122001179 SecY translocase; Region: SecY; pfam00344 94122001180 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 94122001181 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 94122001182 30S ribosomal protein S13; Region: bact_S13; TIGR03631 94122001183 30S ribosomal protein S11; Validated; Region: PRK05309 94122001184 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 94122001185 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 94122001186 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 94122001187 RNA binding surface [nucleotide binding]; other site 94122001188 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 94122001189 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 94122001190 alphaNTD homodimer interface [polypeptide binding]; other site 94122001191 alphaNTD - beta interaction site [polypeptide binding]; other site 94122001192 alphaNTD - beta' interaction site [polypeptide binding]; other site 94122001193 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 94122001194 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 94122001195 ABC transporter substrate binding protein; Region: ABC_sub_bind; cl17301 94122001196 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13165 94122001197 Heme exporter protein D [Intracellular trafficking and secretion]; Region: CcmD; COG3114 94122001198 heme exporter protein CcmC; Region: ccmC; TIGR01191 94122001199 CcmB protein; Region: CcmB; pfam03379 94122001200 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 94122001201 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122001202 Walker A/P-loop; other site 94122001203 ATP binding site [chemical binding]; other site 94122001204 Q-loop/lid; other site 94122001205 ABC transporter signature motif; other site 94122001206 Walker B; other site 94122001207 D-loop; other site 94122001208 H-loop/switch region; other site 94122001209 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 94122001210 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 94122001211 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 94122001212 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 94122001213 TPR motif; other site 94122001214 binding surface 94122001215 cytochrome c nitrate reductase biogenesis protein NrfE; Region: cyt_nit_nrfE; TIGR03145 94122001216 periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily; Region: dsbE; TIGR00385 94122001217 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 94122001218 catalytic residues [active] 94122001219 central insert; other site 94122001220 Cytochrome C biogenesis protein; Region: CcmH; cl01179 94122001221 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 94122001222 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 94122001223 catalytic residues [active] 94122001224 Domain of unknown function (DUF1993); Region: DUF1993; pfam09351 94122001225 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 94122001226 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 94122001227 dimer interface [polypeptide binding]; other site 94122001228 phosphorylation site [posttranslational modification] 94122001229 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 94122001230 ATP binding site [chemical binding]; other site 94122001231 Mg2+ binding site [ion binding]; other site 94122001232 G-X-G motif; other site 94122001233 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 94122001234 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122001235 active site 94122001236 phosphorylation site [posttranslational modification] 94122001237 intermolecular recognition site; other site 94122001238 dimerization interface [polypeptide binding]; other site 94122001239 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 94122001240 DNA binding site [nucleotide binding] 94122001241 Predicted membrane protein [Function unknown]; Region: COG3212 94122001242 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 94122001243 Dihaem cytochrome c; Region: DHC; pfam09626 94122001244 Domain of unknown function (DUF1924); Region: DUF1924; pfam09086 94122001245 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 94122001246 Protein of unknown function (DUF2809); Region: DUF2809; pfam10990 94122001247 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122001248 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122001249 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 94122001250 putative effector binding pocket; other site 94122001251 putative dimerization interface [polypeptide binding]; other site 94122001252 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 94122001253 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 94122001254 NAD(P) binding site [chemical binding]; other site 94122001255 active site 94122001256 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 94122001257 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 94122001258 NAD(P) binding site [chemical binding]; other site 94122001259 catalytic residues [active] 94122001260 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 94122001261 GAF domain; Region: GAF; pfam01590 94122001262 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 94122001263 Walker A motif; other site 94122001264 ATP binding site [chemical binding]; other site 94122001265 Walker B motif; other site 94122001266 arginine finger; other site 94122001267 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 94122001268 two-component sensor protein; Provisional; Region: cpxA; PRK09470 94122001269 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 94122001270 dimerization interface [polypeptide binding]; other site 94122001271 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 94122001272 dimer interface [polypeptide binding]; other site 94122001273 phosphorylation site [posttranslational modification] 94122001274 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 94122001275 ATP binding site [chemical binding]; other site 94122001276 Mg2+ binding site [ion binding]; other site 94122001277 G-X-G motif; other site 94122001278 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122001279 active site 94122001280 phosphorylation site [posttranslational modification] 94122001281 intermolecular recognition site; other site 94122001282 dimerization interface [polypeptide binding]; other site 94122001283 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 94122001284 DNA binding site [nucleotide binding] 94122001285 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 94122001286 dimer interface [polypeptide binding]; other site 94122001287 Cation efflux family; Region: Cation_efflux; cl00316 94122001288 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 94122001289 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 94122001290 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 94122001291 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122001292 active site 94122001293 phosphorylation site [posttranslational modification] 94122001294 intermolecular recognition site; other site 94122001295 dimerization interface [polypeptide binding]; other site 94122001296 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 94122001297 Walker A motif; other site 94122001298 ATP binding site [chemical binding]; other site 94122001299 Walker B motif; other site 94122001300 arginine finger; other site 94122001301 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 94122001302 nitrogen regulation protein NR(II); Provisional; Region: glnL; PRK11073 94122001303 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 94122001304 dimer interface [polypeptide binding]; other site 94122001305 phosphorylation site [posttranslational modification] 94122001306 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 94122001307 ATP binding site [chemical binding]; other site 94122001308 Mg2+ binding site [ion binding]; other site 94122001309 G-X-G motif; other site 94122001310 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 94122001311 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 94122001312 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 94122001313 dimer interface [polypeptide binding]; other site 94122001314 active site 94122001315 metal binding site [ion binding]; metal-binding site 94122001316 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 94122001317 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 94122001318 Protein of unknown function (DUF1255); Region: DUF1255; pfam06865 94122001319 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 94122001320 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122001321 dimer interface [polypeptide binding]; other site 94122001322 putative CheW interface [polypeptide binding]; other site 94122001323 5-histidylcysteine sulfoxide synthase; Region: ovoA_Nterm; TIGR04344 94122001324 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 94122001325 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 94122001326 S-adenosylmethionine binding site [chemical binding]; other site 94122001327 Prolyl 4-hydroxylase alpha subunit homologues; Region: P4Hc; smart00702 94122001328 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase; Region: ribokinase_pfkB_like; cl00192 94122001329 substrate binding site [chemical binding]; other site 94122001330 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 94122001331 ATP binding site [chemical binding]; other site 94122001332 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122001333 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122001334 metal binding site [ion binding]; metal-binding site 94122001335 active site 94122001336 I-site; other site 94122001337 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 94122001338 MOSC domain; Region: MOSC; pfam03473 94122001339 3-alpha domain; Region: 3-alpha; pfam03475 94122001340 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3296 94122001341 Cache domain; Region: Cache_1; pfam02743 94122001342 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 94122001343 dimerization interface [polypeptide binding]; other site 94122001344 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 94122001345 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122001346 dimer interface [polypeptide binding]; other site 94122001347 putative CheW interface [polypeptide binding]; other site 94122001348 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 94122001349 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 94122001350 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 94122001351 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 94122001352 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 94122001353 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 94122001354 FeS/SAM binding site; other site 94122001355 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 94122001356 MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine...; Region: MoaC_PE; cd01420 94122001357 trimer interface [polypeptide binding]; other site 94122001358 dimer interface [polypeptide binding]; other site 94122001359 putative active site [active] 94122001360 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 94122001361 MoaE interaction surface [polypeptide binding]; other site 94122001362 MoeB interaction surface [polypeptide binding]; other site 94122001363 thiocarboxylated glycine; other site 94122001364 MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoaE; cd00756 94122001365 MoaE homodimer interface [polypeptide binding]; other site 94122001366 MoaD interaction [polypeptide binding]; other site 94122001367 active site residues [active] 94122001368 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 94122001369 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 94122001370 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 94122001371 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 94122001372 dimer interface [polypeptide binding]; other site 94122001373 conserved gate region; other site 94122001374 putative PBP binding loops; other site 94122001375 ABC-ATPase subunit interface; other site 94122001376 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 94122001377 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122001378 Walker A/P-loop; other site 94122001379 ATP binding site [chemical binding]; other site 94122001380 Q-loop/lid; other site 94122001381 ABC transporter signature motif; other site 94122001382 Walker B; other site 94122001383 D-loop; other site 94122001384 H-loop/switch region; other site 94122001385 alkaline phosphatase isozyme conversion aminopeptidase; Provisional; Region: PRK10199 94122001386 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 94122001387 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122001388 active site 94122001389 phosphorylation site [posttranslational modification] 94122001390 intermolecular recognition site; other site 94122001391 dimerization interface [polypeptide binding]; other site 94122001392 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 94122001393 DNA binding site [nucleotide binding] 94122001394 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 94122001395 HAMP domain; Region: HAMP; pfam00672 94122001396 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 94122001397 dimer interface [polypeptide binding]; other site 94122001398 phosphorylation site [posttranslational modification] 94122001399 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 94122001400 ATP binding site [chemical binding]; other site 94122001401 Mg2+ binding site [ion binding]; other site 94122001402 G-X-G motif; other site 94122001403 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 94122001404 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 94122001405 active site 94122001406 Proteolipid membrane potential modulator; Region: Pmp3; pfam01679 94122001407 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 94122001408 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122001409 N-terminal plug; other site 94122001410 ligand-binding site [chemical binding]; other site 94122001411 Protein of unknown function (DUF2986); Region: DUF2986; pfam11661 94122001412 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 94122001413 Peptidase family M23; Region: Peptidase_M23; pfam01551 94122001414 CHAP domain; Region: CHAP; pfam05257 94122001415 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 94122001416 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 94122001417 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 94122001418 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 94122001419 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 94122001420 Anaerobic C4-dicarboxylate transporter [General function prediction only]; Region: DcuB; COG2704 94122001421 anaerobic C4-dicarboxylate transporter; Reviewed; Region: PRK12489 94122001422 Domain of unknown function (DUF1864); Region: DUF1864; pfam08933 94122001423 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 94122001424 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 94122001425 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 94122001426 catalytic residue [active] 94122001427 Protein of unknown function (DUF1375); Region: DUF1375; cl11456 94122001428 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 94122001429 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 94122001430 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 94122001431 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122001432 N-terminal plug; other site 94122001433 ligand-binding site [chemical binding]; other site 94122001434 glutamine synthetase; Provisional; Region: glnA; PRK09469 94122001435 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 94122001436 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 94122001437 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 94122001438 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 94122001439 G1 box; other site 94122001440 putative GEF interaction site [polypeptide binding]; other site 94122001441 GTP/Mg2+ binding site [chemical binding]; other site 94122001442 Switch I region; other site 94122001443 G2 box; other site 94122001444 G3 box; other site 94122001445 Switch II region; other site 94122001446 G4 box; other site 94122001447 G5 box; other site 94122001448 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 94122001449 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 94122001450 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 94122001451 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 94122001452 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 94122001453 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 94122001454 classical (c) SDRs; Region: SDR_c; cd05233 94122001455 NAD(P) binding site [chemical binding]; other site 94122001456 active site 94122001457 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 94122001458 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 94122001459 Alcohol dehydrogenases of the MDR family; Region: Zn_ADH8; cd08262 94122001460 putative NAD(P) binding site [chemical binding]; other site 94122001461 catalytic Zn binding site [ion binding]; other site 94122001462 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 94122001463 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 94122001464 dimer interface [polypeptide binding]; other site 94122001465 active site 94122001466 heme binding site [chemical binding]; other site 94122001467 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 94122001468 4Fe-4S binding domain; Region: Fer4_5; pfam12801 94122001469 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 94122001470 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 94122001471 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 94122001472 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122001473 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122001474 metal binding site [ion binding]; metal-binding site 94122001475 active site 94122001476 I-site; other site 94122001477 Protein of unknown function (DUF2959); Region: DUF2959; pfam11172 94122001478 hypothetical protein; Reviewed; Region: PRK01637 94122001479 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 94122001480 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 94122001481 putative active site [active] 94122001482 dimerization interface [polypeptide binding]; other site 94122001483 putative tRNAtyr binding site [nucleotide binding]; other site 94122001484 Putative thioesterase (yiiD_Cterm); Region: YiiD_Cterm; pfam09500 94122001485 azoreductase; Reviewed; Region: PRK00170 94122001486 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 94122001487 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 94122001488 active site residue [active] 94122001489 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 94122001490 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 94122001491 non-specific DNA binding site [nucleotide binding]; other site 94122001492 salt bridge; other site 94122001493 sequence-specific DNA binding site [nucleotide binding]; other site 94122001494 Cupin domain; Region: Cupin_2; pfam07883 94122001495 Benzoate membrane transport protein; Region: BenE; pfam03594 94122001496 benzoate transporter; Region: benE; TIGR00843 94122001497 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122001498 Coenzyme A binding pocket [chemical binding]; other site 94122001499 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 94122001500 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 94122001501 trimer interface [polypeptide binding]; other site 94122001502 active site 94122001503 substrate binding site [chemical binding]; other site 94122001504 CoA binding site [chemical binding]; other site 94122001505 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK09116 94122001506 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 94122001507 dimer interface [polypeptide binding]; other site 94122001508 active site 94122001509 3-oxoacyl-(acyl-carrier-protein) reductase, putative; Region: fabG_rel; TIGR01831 94122001510 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 94122001511 NAD(P) binding site [chemical binding]; other site 94122001512 active site 94122001513 Domain of unknown function, appears to be related to a diverse group of beta-hydroxydecanoyl ACP dehydratases (FabA) and beta-hydroxyacyl ACP dehydratases (FabZ). This group appears to lack the conserved active site histidine of FabA and FabZ; Region: FabA_like; cd01289 94122001514 putative active site 1 [active] 94122001515 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK09185 94122001516 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 94122001517 dimer interface [polypeptide binding]; other site 94122001518 active site 94122001519 Protein of unknown function (DUF3261); Region: DUF3261; pfam11659 94122001520 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 94122001521 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 94122001522 Predicted exporter [General function prediction only]; Region: COG4258 94122001523 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 94122001524 active site 94122001525 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 94122001526 active sites [active] 94122001527 tetramer interface [polypeptide binding]; other site 94122001528 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 94122001529 Ligand binding site; other site 94122001530 Putative Catalytic site; other site 94122001531 DXD motif; other site 94122001532 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 94122001533 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 94122001534 putative acyl-acceptor binding pocket; other site 94122001535 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 94122001536 active site 2 [active] 94122001537 active site 1 [active] 94122001538 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 94122001539 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 94122001540 acyl-activating enzyme (AAE) consensus motif; other site 94122001541 AMP binding site [chemical binding]; other site 94122001542 active site 94122001543 CoA binding site [chemical binding]; other site 94122001544 Predicted membrane protein [Function unknown]; Region: COG4648 94122001545 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 94122001546 putative transposase OrfB; Reviewed; Region: PHA02517 94122001547 Integrase core domain; Region: rve; pfam00665 94122001548 Integrase core domain; Region: rve_3; pfam13683 94122001549 Predicted membrane protein [Function unknown]; Region: COG4648 94122001550 acyl carrier protein; Provisional; Region: PRK05350 94122001551 Phosphopantetheine attachment site; Region: PP-binding; cl09936 94122001552 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 94122001553 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 94122001554 putative acyl-acceptor binding pocket; other site 94122001555 Beta-ketoacyl synthase, N-terminal domain; Region: Ketoacyl-synt_2; pfam13723 94122001556 Protein of unknown function (DUF3014); Region: DUF3014; pfam11219 94122001557 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 94122001558 Y-family of DNA polymerases; Region: PolY; cl12025 94122001559 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 94122001560 generic binding surface II; other site 94122001561 ssDNA binding site; other site 94122001562 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 94122001563 ATP binding site [chemical binding]; other site 94122001564 putative Mg++ binding site [ion binding]; other site 94122001565 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 94122001566 nucleotide binding region [chemical binding]; other site 94122001567 ATP-binding site [chemical binding]; other site 94122001568 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 94122001569 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 94122001570 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122001571 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122001572 metal binding site [ion binding]; metal-binding site 94122001573 active site 94122001574 I-site; other site 94122001575 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 94122001576 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 94122001577 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 94122001578 substrate binding pocket [chemical binding]; other site 94122001579 membrane-bound complex binding site; other site 94122001580 hinge residues; other site 94122001581 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 94122001582 Domain of unknown function DUF21; Region: DUF21; pfam01595 94122001583 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 94122001584 Transporter associated domain; Region: CorC_HlyC; smart01091 94122001585 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122001586 DNA-binding transcriptional regulator IlvY; Provisional; Region: PRK11716 94122001587 The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic bindin; Region: PBP2_IlvY; cd08430 94122001588 putative dimerization interface [polypeptide binding]; other site 94122001589 ketol-acid reductoisomerase; Validated; Region: PRK05225 94122001590 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 94122001591 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 94122001592 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 94122001593 acetolactate synthase 2 catalytic subunit; Reviewed; Region: PRK08978 94122001594 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 94122001595 PYR/PP interface [polypeptide binding]; other site 94122001596 dimer interface [polypeptide binding]; other site 94122001597 TPP binding site [chemical binding]; other site 94122001598 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 94122001599 Thiamine pyrophosphate (TPP) family, Acetohydroxyacid synthase (AHAS) subfamily, TPP-binding module; composed of proteins similar to the large catalytic subunit of AHAS. AHAS catalyzes the condensation of two molecules of pyruvate to give the...; Region: TPP_AHAS; cd02015 94122001600 TPP-binding site [chemical binding]; other site 94122001601 dimer interface [polypeptide binding]; other site 94122001602 acetolactate synthase 2 regulatory subunit; Provisional; Region: ilvM; PRK11152 94122001603 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 94122001604 threonine dehydratase; Reviewed; Region: PRK09224 94122001605 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 94122001606 tetramer interface [polypeptide binding]; other site 94122001607 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122001608 catalytic residue [active] 94122001609 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 94122001610 putative Ile/Val binding site [chemical binding]; other site 94122001611 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 94122001612 putative Ile/Val binding site [chemical binding]; other site 94122001613 Alanine-glyoxylate aminotransferase (AGAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to alanine-glyoxylate aminotransferase (AGAT); Region: AGAT_like; cd06451 94122001614 homodimer interface [polypeptide binding]; other site 94122001615 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122001616 catalytic residue [active] 94122001617 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; cd01610 94122001618 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 94122001619 active site 94122001620 inner membrane protein; Provisional; Region: PRK11715 94122001621 Protein of unknown function (DUF1006); Region: DUF1006; pfam06224 94122001622 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3214 94122001623 Membrane fusogenic activity; Region: BMFP; pfam04380 94122001624 multidrug efflux protein; Reviewed; Region: PRK09579 94122001625 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 94122001626 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 94122001627 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122001628 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 94122001629 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 94122001630 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 94122001631 Part of AAA domain; Region: AAA_19; pfam13245 94122001632 Family description; Region: UvrD_C_2; pfam13538 94122001633 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 94122001634 GAF domain; Region: GAF; pfam01590 94122001635 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 94122001636 GAF domain; Region: GAF_3; pfam13492 94122001637 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122001638 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122001639 metal binding site [ion binding]; metal-binding site 94122001640 active site 94122001641 I-site; other site 94122001642 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 94122001643 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 94122001644 dimerization interface [polypeptide binding]; other site 94122001645 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122001646 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122001647 metal binding site [ion binding]; metal-binding site 94122001648 active site 94122001649 I-site; other site 94122001650 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 94122001651 Bacterial transglutaminase-like cysteine proteinase BTLCP; Region: BTLCP; cl17596 94122001652 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 94122001653 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 94122001654 ligand binding site [chemical binding]; other site 94122001655 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 94122001656 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 94122001657 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 94122001658 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122001659 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 94122001660 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 94122001661 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 94122001662 ATP-binding cassette domain of bacteriocin exporters, subfamily C; Region: ABCC_bacteriocin_exporters; cd03245 94122001663 Walker A/P-loop; other site 94122001664 ATP binding site [chemical binding]; other site 94122001665 Q-loop/lid; other site 94122001666 ABC transporter signature motif; other site 94122001667 Walker B; other site 94122001668 D-loop; other site 94122001669 H-loop/switch region; other site 94122001670 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 94122001671 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 94122001672 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 94122001673 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 94122001674 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 94122001675 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 94122001676 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 94122001677 metal ion-dependent adhesion site (MIDAS); other site 94122001678 type I secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 94122001679 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 94122001680 HemY protein N-terminus; Region: HemY_N; pfam07219 94122001681 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 94122001682 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 94122001683 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 94122001684 active site 94122001685 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 94122001686 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cd00494 94122001687 domain interfaces; other site 94122001688 active site 94122001689 Adenylate cyclase NT domain; Region: Adenyl_cycl_N; pfam12633 94122001690 adenylate cyclase; Provisional; Region: cyaA; PRK09450 94122001691 Adenylate cyclase, class-I; Region: Adenylate_cycl; pfam01295 94122001692 Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate...; Region: Frataxin; cd00503 94122001693 putative iron binding site [ion binding]; other site 94122001694 Prokaryotic lipoprotein-attachment site; Region: LPAM_2; cl02361 94122001695 diaminopimelate decarboxylase; Region: lysA; TIGR01048 94122001696 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 94122001697 active site 94122001698 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 94122001699 substrate binding site [chemical binding]; other site 94122001700 catalytic residues [active] 94122001701 dimer interface [polypeptide binding]; other site 94122001702 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 94122001703 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 94122001704 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 94122001705 Protein of unknown function, DUF484; Region: DUF484; cl17449 94122001706 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 94122001707 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 94122001708 active site 94122001709 Int/Topo IB signature motif; other site 94122001710 flavin mononucleotide phosphatase; Provisional; Region: PRK10748 94122001711 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 94122001712 motif II; other site 94122001713 HupE / UreJ protein; Region: HupE_UreJ; pfam04955 94122001714 Divergent AAA domain; Region: AAA_4; pfam04326 94122001715 Domain of Unknown function (DUF542); Region: ScdA_N; pfam04405 94122001716 iron-sulfur cluster repair di-iron protein; Region: FeS_repair_RIC; TIGR03652 94122001717 Hemerythrin-like domain; Region: Hr-like; cd12108 94122001718 Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]; Region: Fis; COG2901 94122001719 global DNA-binding transcriptional dual regulator Fis; Provisional; Region: fis; PRK00430 94122001720 tRNA-dihydrouridine synthase B; Provisional; Region: PRK10415 94122001721 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 94122001722 FMN binding site [chemical binding]; other site 94122001723 active site 94122001724 catalytic residues [active] 94122001725 substrate binding site [chemical binding]; other site 94122001726 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 94122001727 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 94122001728 fumarate reductase cytochrome b-556 subunit; Provisional; Region: PRK13554 94122001729 Quinol:fumarate reductase (QFR) Type B subfamily, transmembrane subunit; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinone...; Region: QFR_TypeB_TM; cd00581 94122001730 Iron-sulfur protein interface; other site 94122001731 proximal heme binding site [chemical binding]; other site 94122001732 distal heme binding site [chemical binding]; other site 94122001733 dimer interface [polypeptide binding]; other site 94122001734 Quinol:fumarate reductase (QFR) Type B subfamily, transmembrane subunit; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinone...; Region: QFR_TypeB_TM; cd00581 94122001735 Iron-sulfur protein interface; other site 94122001736 proximal heme binding site [chemical binding]; other site 94122001737 distal heme binding site [chemical binding]; other site 94122001738 dimer interface [polypeptide binding]; other site 94122001739 fumarate reductase flavoprotein subunit; Provisional; Region: PRK08626 94122001740 L-aspartate oxidase; Provisional; Region: PRK06175 94122001741 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 94122001742 fumarate reductase iron-sulfur subunit; Provisional; Region: frdB; PRK13552 94122001743 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 94122001744 Uncharacterized conserved protein [Function unknown]; Region: COG1359 94122001745 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 94122001746 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 94122001747 putative NAD(P) binding site [chemical binding]; other site 94122001748 dimer interface [polypeptide binding]; other site 94122001749 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122001750 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122001751 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 94122001752 putative effector binding pocket; other site 94122001753 dimerization interface [polypeptide binding]; other site 94122001754 transcription termination factor Rho; Provisional; Region: rho; PRK09376 94122001755 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 94122001756 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 94122001757 RNA binding site [nucleotide binding]; other site 94122001758 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 94122001759 multimer interface [polypeptide binding]; other site 94122001760 Walker A motif; other site 94122001761 ATP binding site [chemical binding]; other site 94122001762 Walker B motif; other site 94122001763 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 94122001764 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 94122001765 catalytic residues [active] 94122001766 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 94122001767 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 94122001768 ATP binding site [chemical binding]; other site 94122001769 Mg++ binding site [ion binding]; other site 94122001770 motif III; other site 94122001771 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 94122001772 nucleotide binding region [chemical binding]; other site 94122001773 ATP-binding site [chemical binding]; other site 94122001774 exopolyphosphatase; Region: exo_poly_only; TIGR03706 94122001775 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 94122001776 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 94122001777 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 94122001778 catalytic residues [active] 94122001779 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 94122001780 active site 94122001781 8-oxo-dGMP binding site [chemical binding]; other site 94122001782 nudix motif; other site 94122001783 metal binding site [ion binding]; metal-binding site 94122001784 Domain of unknown function (DUF329); Region: DUF329; pfam03884 94122001785 hypothetical protein; Provisional; Region: PRK05287 94122001786 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 94122001787 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 94122001788 CoA-binding site [chemical binding]; other site 94122001789 ATP-binding [chemical binding]; other site 94122001790 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 94122001791 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 94122001792 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 94122001793 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 94122001794 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 94122001795 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 94122001796 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 94122001797 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 94122001798 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 94122001799 Walker A motif; other site 94122001800 ATP binding site [chemical binding]; other site 94122001801 Walker B motif; other site 94122001802 O-Antigen ligase; Region: Wzy_C; pfam04932 94122001803 quinolinate phosphoribosyltransferase; Validated; Region: PRK09016 94122001804 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 94122001805 dimerization interface [polypeptide binding]; other site 94122001806 active site 94122001807 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 94122001808 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 94122001809 amidase catalytic site [active] 94122001810 Zn binding residues [ion binding]; other site 94122001811 substrate binding site [chemical binding]; other site 94122001812 regulatory protein AmpE; Provisional; Region: PRK10987 94122001813 transcriptional regulator PdhR; Reviewed; Region: pdhR; PRK09464 94122001814 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 94122001815 DNA-binding site [nucleotide binding]; DNA binding site 94122001816 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 94122001817 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 94122001818 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 94122001819 dimer interface [polypeptide binding]; other site 94122001820 TPP-binding site [chemical binding]; other site 94122001821 pyruvate dehydrogenase dihydrolipoyltransacetylase; Validated; Region: aceF; PRK11854 94122001822 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 94122001823 E3 interaction surface; other site 94122001824 lipoyl attachment site [posttranslational modification]; other site 94122001825 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 94122001826 E3 interaction surface; other site 94122001827 lipoyl attachment site [posttranslational modification]; other site 94122001828 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 94122001829 E3 interaction surface; other site 94122001830 lipoyl attachment site [posttranslational modification]; other site 94122001831 e3 binding domain; Region: E3_binding; pfam02817 94122001832 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 94122001833 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 94122001834 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 94122001835 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 94122001836 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 94122001837 PAS fold; Region: PAS_3; pfam08447 94122001838 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 94122001839 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 94122001840 PAS domain; Region: PAS_9; pfam13426 94122001841 putative active site [active] 94122001842 heme pocket [chemical binding]; other site 94122001843 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122001844 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122001845 metal binding site [ion binding]; metal-binding site 94122001846 active site 94122001847 I-site; other site 94122001848 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 94122001849 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 94122001850 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 94122001851 active site 94122001852 nucleophile elbow; other site 94122001853 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 94122001854 Surface antigen; Region: Bac_surface_Ag; pfam01103 94122001855 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 94122001856 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 94122001857 active site 94122001858 Zn binding site [ion binding]; other site 94122001859 2-deoxyglucose-6-phosphatase; Provisional; Region: PRK10826 94122001860 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 94122001861 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 94122001862 motif II; other site 94122001863 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 94122001864 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change in...; Region: AcnB_Swivel; cd01576 94122001865 substrate binding site [chemical binding]; other site 94122001866 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 94122001867 substrate binding site [chemical binding]; other site 94122001868 ligand binding site [chemical binding]; other site 94122001869 anti-RNA polymerase sigma 70 factor; Provisional; Region: PRK11718 94122001870 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 94122001871 substrate binding site [chemical binding]; other site 94122001872 active site 94122001873 PAS fold; Region: PAS_4; pfam08448 94122001874 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 94122001875 putative active site [active] 94122001876 heme pocket [chemical binding]; other site 94122001877 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122001878 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122001879 metal binding site [ion binding]; metal-binding site 94122001880 active site 94122001881 I-site; other site 94122001882 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 94122001883 11beta-hydroxysteroid dehydrogenase type 1 (11beta-HSD1)-like, classical (c) SDRs; Region: 11beta-HSD1_like_SDR_c; cd05332 94122001884 short chain dehydrogenase; Provisional; Region: PRK06181 94122001885 NADP binding site [chemical binding]; other site 94122001886 homodimer interface [polypeptide binding]; other site 94122001887 substrate binding site [chemical binding]; other site 94122001888 active site 94122001889 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 94122001890 Peptidase M60-like family; Region: M60-like; pfam13402 94122001891 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 94122001892 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 94122001893 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 94122001894 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 94122001895 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 94122001896 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 94122001897 purine monophosphate binding site [chemical binding]; other site 94122001898 dimer interface [polypeptide binding]; other site 94122001899 putative catalytic residues [active] 94122001900 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 94122001901 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 94122001902 zinc-responsive transcriptional regulator; Provisional; Region: zntR; PRK09514 94122001903 Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; Region: HTH_HMRTR; cd04770 94122001904 DNA binding residues [nucleotide binding] 94122001905 dimer interface [polypeptide binding]; other site 94122001906 metal binding site [ion binding]; metal-binding site 94122001907 Predicted permease; Region: DUF318; cl17795 94122001908 Predicted permease; Region: DUF318; cl17795 94122001909 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 94122001910 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 94122001911 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 94122001912 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 94122001913 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 94122001914 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 94122001915 putative MFS family transporter protein; Provisional; Region: PRK03633 94122001916 putative substrate translocation pore; other site 94122001917 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 94122001918 GAF domain; Region: GAF; pfam01590 94122001919 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122001920 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122001921 metal binding site [ion binding]; metal-binding site 94122001922 active site 94122001923 I-site; other site 94122001924 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 94122001925 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 94122001926 transmembrane helices; other site 94122001927 thioredoxin 2; Provisional; Region: PRK10996 94122001928 zinc-ribbon domain; Region: zinc_ribbon_5; cl11777 94122001929 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 94122001930 catalytic residues [active] 94122001931 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 94122001932 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 94122001933 putative active site [active] 94122001934 PAS fold; Region: PAS_3; pfam08447 94122001935 heme pocket [chemical binding]; other site 94122001936 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122001937 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122001938 metal binding site [ion binding]; metal-binding site 94122001939 active site 94122001940 I-site; other site 94122001941 Domain of unknown function (DUF1850); Region: DUF1850; pfam08905 94122001942 TRAP transporter, 4TM/12TM fusion protein; Region: TRAP_fused; TIGR02123 94122001943 DctM-like transporters; Region: DctM; pfam06808 94122001944 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 94122001945 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 94122001946 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 94122001947 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 94122001948 Predicted metalloprotease [General function prediction only]; Region: COG2321 94122001949 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; pfam04228 94122001950 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 94122001951 nudix motif; other site 94122001952 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cl17355 94122001953 DNA binding site [nucleotide binding] 94122001954 Response regulator receiver domain; Region: Response_reg; pfam00072 94122001955 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122001956 active site 94122001957 phosphorylation site [posttranslational modification] 94122001958 intermolecular recognition site; other site 94122001959 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 94122001960 Part of AAA domain; Region: AAA_19; pfam13245 94122001961 Family description; Region: UvrD_C_2; pfam13538 94122001962 4-hydroxybenzoate octaprenyltransferase; Reviewed; Region: ubiA; PRK12848 94122001963 UbiA prenyltransferase family; Region: UbiA; pfam01040 94122001964 Domain of unknown function (DUF4156); Region: DUF4156; pfam13698 94122001965 Domain of unknown function (DUF4277); Region: DUF4277; pfam14104 94122001966 Transposase [DNA replication, recombination, and repair]; Region: COG5421 94122001967 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 94122001968 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 94122001969 FMN binding site [chemical binding]; other site 94122001970 substrate binding site [chemical binding]; other site 94122001971 putative catalytic residue [active] 94122001972 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 94122001973 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 94122001974 catalytic residues [active] 94122001975 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 94122001976 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 94122001977 catalytic residues [active] 94122001978 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 94122001979 Domain of unknown function DUF20; Region: UPF0118; pfam01594 94122001980 Pathogenicity locus; Region: Cdd1; pfam11731 94122001981 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 94122001982 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122001983 active site 94122001984 phosphorylation site [posttranslational modification] 94122001985 intermolecular recognition site; other site 94122001986 dimerization interface [polypeptide binding]; other site 94122001987 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 94122001988 Zn2+ binding site [ion binding]; other site 94122001989 Mg2+ binding site [ion binding]; other site 94122001990 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 94122001991 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 94122001992 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 94122001993 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 94122001994 substrate binding pocket [chemical binding]; other site 94122001995 membrane-bound complex binding site; other site 94122001996 hinge residues; other site 94122001997 PAS domain S-box; Region: sensory_box; TIGR00229 94122001998 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 94122001999 putative active site [active] 94122002000 heme pocket [chemical binding]; other site 94122002001 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 94122002002 dimer interface [polypeptide binding]; other site 94122002003 phosphorylation site [posttranslational modification] 94122002004 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 94122002005 ATP binding site [chemical binding]; other site 94122002006 Mg2+ binding site [ion binding]; other site 94122002007 G-X-G motif; other site 94122002008 Response regulator receiver domain; Region: Response_reg; pfam00072 94122002009 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122002010 active site 94122002011 phosphorylation site [posttranslational modification] 94122002012 intermolecular recognition site; other site 94122002013 dimerization interface [polypeptide binding]; other site 94122002014 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 94122002015 putative binding surface; other site 94122002016 active site 94122002017 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122002018 Response regulator receiver domain; Region: Response_reg; pfam00072 94122002019 active site 94122002020 phosphorylation site [posttranslational modification] 94122002021 intermolecular recognition site; other site 94122002022 dimerization interface [polypeptide binding]; other site 94122002023 Response regulator receiver domain; Region: Response_reg; pfam00072 94122002024 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122002025 active site 94122002026 phosphorylation site [posttranslational modification] 94122002027 intermolecular recognition site; other site 94122002028 dimerization interface [polypeptide binding]; other site 94122002029 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 94122002030 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 94122002031 ATP binding site [chemical binding]; other site 94122002032 Mg2+ binding site [ion binding]; other site 94122002033 G-X-G motif; other site 94122002034 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 94122002035 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 94122002036 Predicted transcriptional regulator [Transcription]; Region: COG3655 94122002037 salt bridge; other site 94122002038 non-specific DNA binding site [nucleotide binding]; other site 94122002039 sequence-specific DNA binding site [nucleotide binding]; other site 94122002040 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Deinococcus radiodurans DR2231 protein and its bacterial homologs; Region: NTP-PPase_DR2231_like; cd11530 94122002041 metal binding site [ion binding]; metal-binding site 94122002042 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 94122002043 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 94122002044 catalytic residues [active] 94122002045 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 94122002046 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 94122002047 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 94122002048 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 94122002049 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 94122002050 active site residue [active] 94122002051 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 94122002052 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 94122002053 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 94122002054 formate-dependent nitrite reductase complex subunit NrfG; Provisional; Region: PRK10370 94122002055 cytochrome c nitrite reductase, Fe-S protein; Region: cyt_nit_nrfC; TIGR03149 94122002056 Polysulphide reductase, NrfD; Region: NrfD; pfam03916 94122002057 cytochrome c nitrite reductase, NrfD subunit; Region: cyt_nit_nrfD; TIGR03148 94122002058 nitrous oxide reductase family maturation protein NosD; Region: NosD_copper_fam; TIGR04247 94122002059 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 94122002060 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 94122002061 Walker A/P-loop; other site 94122002062 ATP binding site [chemical binding]; other site 94122002063 Q-loop/lid; other site 94122002064 ABC transporter signature motif; other site 94122002065 Walker B; other site 94122002066 D-loop; other site 94122002067 H-loop/switch region; other site 94122002068 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 94122002069 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 94122002070 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 94122002071 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 94122002072 DNA binding site [nucleotide binding] 94122002073 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 94122002074 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 94122002075 active site 94122002076 Zn binding site [ion binding]; other site 94122002077 Fatty acid cis/trans isomerase (CTI); Region: CTI; pfam06934 94122002078 Peptidase S8 family domain, uncharacterized subfamily 3; Region: Peptidases_S8_3; cd04852 94122002079 Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones]; Region: AprE; COG1404 94122002080 active site 94122002081 catalytic triad [active] 94122002082 PA_subtilisin_like: Protease-associated domain containing subtilisin-like proteases. This group contains various PA domain-containing subtilisin-like proteases including melon cucumisin, Arabidopsis thaliana Ara12, a nodule specific serine protease from...; Region: PA_subtilisin_like; cd02120 94122002083 PA/protease or protease-like domain interface [polypeptide binding]; other site 94122002084 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 94122002085 catalytic residues [active] 94122002086 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 94122002087 FMN reductase; Validated; Region: fre; PRK08051 94122002088 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 94122002089 FAD binding pocket [chemical binding]; other site 94122002090 FAD binding motif [chemical binding]; other site 94122002091 phosphate binding motif [ion binding]; other site 94122002092 beta-alpha-beta structure motif; other site 94122002093 NAD binding pocket [chemical binding]; other site 94122002094 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 94122002095 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 94122002096 Major Facilitator Superfamily; Region: MFS_1; pfam07690 94122002097 putative substrate translocation pore; other site 94122002098 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 94122002099 short chain dehydrogenase; Provisional; Region: PRK07454 94122002100 NAD(P) binding site [chemical binding]; other site 94122002101 active site 94122002102 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 94122002103 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 94122002104 carboxyltransferase (CT) interaction site; other site 94122002105 biotinylation site [posttranslational modification]; other site 94122002106 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 94122002107 Dehydroquinase class II; Region: DHquinase_II; pfam01220 94122002108 active site 94122002109 trimer interface [polypeptide binding]; other site 94122002110 dimer interface [polypeptide binding]; other site 94122002111 hypothetical protein; Provisional; Region: PRK09256 94122002112 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 94122002113 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 94122002114 Protein of unknown function (DUF3012); Region: DUF3012; pfam11216 94122002115 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 94122002116 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 94122002117 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 94122002118 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122002119 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 94122002120 Protein export membrane protein; Region: SecD_SecF; cl14618 94122002121 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 94122002122 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 94122002123 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 94122002124 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122002125 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122002126 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 94122002127 putative effector binding pocket; other site 94122002128 dimerization interface [polypeptide binding]; other site 94122002129 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 94122002130 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 94122002131 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122002132 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 94122002133 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 94122002134 putative substrate translocation pore; other site 94122002135 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 94122002136 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122002137 Coenzyme A binding pocket [chemical binding]; other site 94122002138 Uncharacterized conserved protein [Function unknown]; Region: COG1359 94122002139 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 94122002140 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 94122002141 Walker A motif; other site 94122002142 ATP binding site [chemical binding]; other site 94122002143 Walker B motif; other site 94122002144 arginine finger; other site 94122002145 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 94122002146 Gametolysin peptidase M11; Region: Peptidase_M11; pfam05548 94122002147 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 94122002148 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122002149 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 94122002150 dimerization interface [polypeptide binding]; other site 94122002151 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 94122002152 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 94122002153 dimerization interface [polypeptide binding]; other site 94122002154 putative DNA binding site [nucleotide binding]; other site 94122002155 putative Zn2+ binding site [ion binding]; other site 94122002156 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 94122002157 arsenical-resistance protein; Region: acr3; TIGR00832 94122002158 glyceraldehyde-3-phosphate dehydrogenase; Validated; Region: PRK08955 94122002159 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 94122002160 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 94122002161 Major Facilitator Superfamily; Region: MFS_1; pfam07690 94122002162 Protein of unknown function (DUF2927); Region: DUF2927; pfam11150 94122002163 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 94122002164 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 94122002165 Beta-Casp domain; Region: Beta-Casp; smart01027 94122002166 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 94122002167 conserved hypothetical protein; Region: QEGLA; TIGR02421 94122002168 CHASE domain; Region: CHASE; pfam03924 94122002169 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 94122002170 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 94122002171 putative active site [active] 94122002172 heme pocket [chemical binding]; other site 94122002173 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 94122002174 dimer interface [polypeptide binding]; other site 94122002175 phosphorylation site [posttranslational modification] 94122002176 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 94122002177 ATP binding site [chemical binding]; other site 94122002178 Mg2+ binding site [ion binding]; other site 94122002179 G-X-G motif; other site 94122002180 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 94122002181 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122002182 active site 94122002183 phosphorylation site [posttranslational modification] 94122002184 intermolecular recognition site; other site 94122002185 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 94122002186 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122002187 active site 94122002188 phosphorylation site [posttranslational modification] 94122002189 intermolecular recognition site; other site 94122002190 dimerization interface [polypeptide binding]; other site 94122002191 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122002192 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122002193 metal binding site [ion binding]; metal-binding site 94122002194 active site 94122002195 I-site; other site 94122002196 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 94122002197 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 94122002198 RimK-like ATP-grasp domain; Region: RimK; pfam08443 94122002199 conserved hypothetical protein, proteobacterial; Region: gcw_chp; TIGR02001 94122002200 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 94122002201 IHF dimer interface [polypeptide binding]; other site 94122002202 IHF - DNA interface [nucleotide binding]; other site 94122002203 Protein of unknown function (DUF4240); Region: DUF4240; pfam14024 94122002204 Protein of unknown function (DUF3016); Region: DUF3016; pfam11454 94122002205 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 94122002206 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and...; Region: CBS_pair_GGDEF_assoc; cd04598 94122002207 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122002208 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122002209 metal binding site [ion binding]; metal-binding site 94122002210 active site 94122002211 I-site; other site 94122002212 TraB family; Region: TraB; pfam01963 94122002213 Methyltransferase domain; Region: Methyltransf_31; pfam13847 94122002214 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 94122002215 S-adenosylmethionine binding site [chemical binding]; other site 94122002216 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 94122002217 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 94122002218 active site 2 [active] 94122002219 active site 1 [active] 94122002220 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 94122002221 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 94122002222 active site 94122002223 catalytic tetrad [active] 94122002224 formate--tetrahydrofolate ligase; Provisional; Region: PRK13506 94122002225 Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2...; Region: FTHFS; cd00477 94122002226 Potassium binding sites [ion binding]; other site 94122002227 Cesium cation binding sites [ion binding]; other site 94122002228 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 94122002229 Mechanosensitive ion channel; Region: MS_channel; pfam00924 94122002230 Periplasmic binding protein TroA_c. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a...; Region: TroA_c; cd01145 94122002231 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 94122002232 putative ligand binding site [chemical binding]; other site 94122002233 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 94122002234 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 94122002235 putative acyl-acceptor binding pocket; other site 94122002236 RNase E inhibitor protein; Provisional; Region: PRK11191 94122002237 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 94122002238 PAS domain; Region: PAS_9; pfam13426 94122002239 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122002240 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122002241 metal binding site [ion binding]; metal-binding site 94122002242 active site 94122002243 I-site; other site 94122002244 Response regulator receiver domain; Region: Response_reg; pfam00072 94122002245 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122002246 active site 94122002247 phosphorylation site [posttranslational modification] 94122002248 intermolecular recognition site; other site 94122002249 dimerization interface [polypeptide binding]; other site 94122002250 Chemotaxis protein CheC, inhibitor of MCP methylation [Cell motility and secretion / Signal transduction mechanisms]; Region: CheC; COG1776 94122002251 enoyl-CoA hydratase; Provisional; Region: PRK07509 94122002252 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 94122002253 substrate binding site [chemical binding]; other site 94122002254 oxyanion hole (OAH) forming residues; other site 94122002255 trimer interface [polypeptide binding]; other site 94122002256 Protein of unknown function (DUF3530); Region: DUF3530; pfam12048 94122002257 ATP-dependent helicase HepA; Validated; Region: PRK04914 94122002258 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 94122002259 ATP binding site [chemical binding]; other site 94122002260 putative Mg++ binding site [ion binding]; other site 94122002261 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 94122002262 nucleotide binding region [chemical binding]; other site 94122002263 ATP-binding site [chemical binding]; other site 94122002264 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 94122002265 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 94122002266 putative active site [active] 94122002267 PhoH-like protein; Region: PhoH; pfam02562 94122002268 Cache domain; Region: Cache_1; pfam02743 94122002269 PAS fold; Region: PAS_4; pfam08448 94122002270 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 94122002271 putative active site [active] 94122002272 heme pocket [chemical binding]; other site 94122002273 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 94122002274 PAS fold; Region: PAS_3; pfam08447 94122002275 putative active site [active] 94122002276 heme pocket [chemical binding]; other site 94122002277 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 94122002278 dimer interface [polypeptide binding]; other site 94122002279 phosphorylation site [posttranslational modification] 94122002280 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 94122002281 ATP binding site [chemical binding]; other site 94122002282 Mg2+ binding site [ion binding]; other site 94122002283 G-X-G motif; other site 94122002284 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 94122002285 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122002286 active site 94122002287 phosphorylation site [posttranslational modification] 94122002288 intermolecular recognition site; other site 94122002289 dimerization interface [polypeptide binding]; other site 94122002290 Response regulator receiver domain; Region: Response_reg; pfam00072 94122002291 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122002292 active site 94122002293 phosphorylation site [posttranslational modification] 94122002294 intermolecular recognition site; other site 94122002295 dimerization interface [polypeptide binding]; other site 94122002296 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin; Region: ZnMc_MMP_like_2; cd04276 94122002297 active site 94122002298 Catalytic domain of Protein Kinases; Region: PKc; cd00180 94122002299 active site 94122002300 ATP binding site [chemical binding]; other site 94122002301 substrate binding site [chemical binding]; other site 94122002302 activation loop (A-loop); other site 94122002303 thiopurine S-methyltransferase; Reviewed; Region: PRK13255 94122002304 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 94122002305 S-adenosylmethionine binding site [chemical binding]; other site 94122002306 Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]; Region: Bfd; COG2906 94122002307 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 94122002308 PAS fold; Region: PAS_3; pfam08447 94122002309 putative active site [active] 94122002310 heme pocket [chemical binding]; other site 94122002311 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 94122002312 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122002313 dimer interface [polypeptide binding]; other site 94122002314 putative CheW interface [polypeptide binding]; other site 94122002315 Putative D-isomer specific 2-hydroxyacid dehydrogenase; Region: 2-Hacid_dh_1; cd05300 94122002316 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 94122002317 NAD binding site [chemical binding]; other site 94122002318 ligand binding site [chemical binding]; other site 94122002319 catalytic site [active] 94122002320 Protein of unknown function (DUF3392); Region: DUF3392; pfam11872 94122002321 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 94122002322 Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins; Region: GDPD; cd08556 94122002323 active site 94122002324 catalytic site [active] 94122002325 metal binding site [ion binding]; metal-binding site 94122002326 putative mechanosensitive channel protein; Provisional; Region: PRK10929 94122002327 Mechanosensitive ion channel inner membrane domain 1; Region: MscS_TM; pfam12794 94122002328 Mechanosensitive ion channel; Region: MS_channel; pfam00924 94122002329 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 94122002330 EamA-like transporter family; Region: EamA; pfam00892 94122002331 phosphatidylserine decarboxylase; Reviewed; Region: psd; PRK00044 94122002332 GTPase RsgA; Reviewed; Region: PRK12288 94122002333 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 94122002334 RNA binding site [nucleotide binding]; other site 94122002335 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 94122002336 GTPase/Zn-binding domain interface [polypeptide binding]; other site 94122002337 GTP/Mg2+ binding site [chemical binding]; other site 94122002338 G4 box; other site 94122002339 G5 box; other site 94122002340 G1 box; other site 94122002341 Switch I region; other site 94122002342 G2 box; other site 94122002343 G3 box; other site 94122002344 Switch II region; other site 94122002345 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 94122002346 catalytic site [active] 94122002347 putative active site [active] 94122002348 putative substrate binding site [chemical binding]; other site 94122002349 dimer interface [polypeptide binding]; other site 94122002350 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 94122002351 dinuclear metal binding motif [ion binding]; other site 94122002352 putative carbohydrate kinase; Provisional; Region: PRK10565 94122002353 YjeF-related protein N-terminus; Region: YjeF_N; pfam03853 94122002354 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 94122002355 putative substrate binding site [chemical binding]; other site 94122002356 putative ATP binding site [chemical binding]; other site 94122002357 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 94122002358 AMIN domain; Region: AMIN; pfam11741 94122002359 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 94122002360 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 94122002361 active site 94122002362 metal binding site [ion binding]; metal-binding site 94122002363 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 94122002364 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 94122002365 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 94122002366 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 94122002367 ATP binding site [chemical binding]; other site 94122002368 Mg2+ binding site [ion binding]; other site 94122002369 G-X-G motif; other site 94122002370 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 94122002371 ATP binding site [chemical binding]; other site 94122002372 MutL C terminal dimerisation domain; Region: MutL_C; smart00853 94122002373 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 94122002374 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 94122002375 bacterial Hfq-like; Region: Hfq; cd01716 94122002376 hexamer interface [polypeptide binding]; other site 94122002377 Sm1 motif; other site 94122002378 RNA binding site [nucleotide binding]; other site 94122002379 Sm2 motif; other site 94122002380 GTPase HflX; Provisional; Region: PRK11058 94122002381 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 94122002382 HflX GTPase family; Region: HflX; cd01878 94122002383 G1 box; other site 94122002384 GTP/Mg2+ binding site [chemical binding]; other site 94122002385 Switch I region; other site 94122002386 G2 box; other site 94122002387 G3 box; other site 94122002388 Switch II region; other site 94122002389 G4 box; other site 94122002390 G5 box; other site 94122002391 FtsH protease regulator HflK; Provisional; Region: PRK10930 94122002392 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 94122002393 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 94122002394 FtsH protease regulator HflC; Provisional; Region: PRK11029 94122002395 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 94122002396 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 94122002397 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 94122002398 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 94122002399 [2Fe-2S] cluster binding site [ion binding]; other site 94122002400 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 94122002401 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 94122002402 Qi binding site; other site 94122002403 intrachain domain interface; other site 94122002404 interchain domain interface [polypeptide binding]; other site 94122002405 heme bH binding site [chemical binding]; other site 94122002406 heme bL binding site [chemical binding]; other site 94122002407 Qo binding site; other site 94122002408 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 94122002409 interchain domain interface [polypeptide binding]; other site 94122002410 intrachain domain interface; other site 94122002411 Qi binding site; other site 94122002412 Qo binding site; other site 94122002413 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 94122002414 stringent starvation protein A; Provisional; Region: sspA; PRK09481 94122002415 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 94122002416 C-terminal domain interface [polypeptide binding]; other site 94122002417 putative GSH binding site (G-site) [chemical binding]; other site 94122002418 dimer interface [polypeptide binding]; other site 94122002419 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 94122002420 dimer interface [polypeptide binding]; other site 94122002421 N-terminal domain interface [polypeptide binding]; other site 94122002422 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 94122002423 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 94122002424 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 94122002425 glutamine binding [chemical binding]; other site 94122002426 catalytic triad [active] 94122002427 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 94122002428 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 94122002429 HDOD domain; Region: HDOD; pfam08668 94122002430 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 94122002431 Protein of unknown function (DUF2424); Region: DUF2424; pfam10340 94122002432 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein; Reviewed; Region: argD; PRK05093 94122002433 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 94122002434 inhibitor-cofactor binding pocket; inhibition site 94122002435 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122002436 catalytic residue [active] 94122002437 Arginine/ornithine N-succinyltransferase beta subunit [Amino acid transport and metabolism]; Region: AstA; COG3138 94122002438 Arginine N-succinyltransferase beta subunit; Region: AstA; pfam04958 94122002439 succinylglutamic semialdehyde dehydrogenase; Reviewed; Region: astD; PRK09457 94122002440 N-succinylglutamate 5-semialdehyde dehydrogenase, AstD-like; Region: ALDH_SGSD_AstD; cd07095 94122002441 NAD(P) binding site [chemical binding]; other site 94122002442 catalytic residues [active] 94122002443 Domain of unknown function (DUF1338); Region: DUF1338; pfam07063 94122002444 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 94122002445 HAMP domain; Region: HAMP; pfam00672 94122002446 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 94122002447 dimer interface [polypeptide binding]; other site 94122002448 phosphorylation site [posttranslational modification] 94122002449 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 94122002450 ATP binding site [chemical binding]; other site 94122002451 Mg2+ binding site [ion binding]; other site 94122002452 G-X-G motif; other site 94122002453 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 94122002454 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122002455 active site 94122002456 phosphorylation site [posttranslational modification] 94122002457 intermolecular recognition site; other site 94122002458 dimerization interface [polypeptide binding]; other site 94122002459 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 94122002460 DNA binding site [nucleotide binding] 94122002461 Predicted membrane protein [Function unknown]; Region: COG3212 94122002462 DNA-binding transcriptional dual regulator Crp; Provisional; Region: PRK11753 94122002463 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 94122002464 ligand binding site [chemical binding]; other site 94122002465 flexible hinge region; other site 94122002466 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 94122002467 putative switch regulator; other site 94122002468 non-specific DNA interactions [nucleotide binding]; other site 94122002469 DNA binding site [nucleotide binding] 94122002470 sequence specific DNA binding site [nucleotide binding]; other site 94122002471 putative cAMP binding site [chemical binding]; other site 94122002472 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 94122002473 Sel1-like repeats; Region: SEL1; smart00671 94122002474 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 94122002475 binding surface 94122002476 TPR motif; other site 94122002477 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 94122002478 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 94122002479 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122002480 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122002481 metal binding site [ion binding]; metal-binding site 94122002482 active site 94122002483 I-site; other site 94122002484 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 94122002485 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 94122002486 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122002487 ATP-dependent helicase HrpB; Region: DEAH_box_HrpB; TIGR01970 94122002488 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 94122002489 ATP binding site [chemical binding]; other site 94122002490 putative Mg++ binding site [ion binding]; other site 94122002491 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 94122002492 nucleotide binding region [chemical binding]; other site 94122002493 Helicase associated domain (HA2) Add an annotation; Region: HA2; smart00847 94122002494 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 94122002495 penicillin-binding protein 1B; Region: PBP_1b; TIGR02071 94122002496 Transglycosylase; Region: Transgly; pfam00912 94122002497 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 94122002498 PPIC-type PPIASE domain; Region: Rotamase_2; cl08278 94122002499 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 94122002500 Regulator of replication initiation timing [Replication, recombination, and repair]; Region: COG4467; cl01853 94122002501 Protein of unknown function (DUF3581); Region: DUF3581; pfam12119 94122002502 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 94122002503 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 94122002504 putative active site [active] 94122002505 heme pocket [chemical binding]; other site 94122002506 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 94122002507 putative active site [active] 94122002508 heme pocket [chemical binding]; other site 94122002509 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122002510 dimer interface [polypeptide binding]; other site 94122002511 putative CheW interface [polypeptide binding]; other site 94122002512 tetrathionate reductase subunit A; Provisional; Region: PRK14991 94122002513 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 94122002514 molybdopterin cofactor binding site; other site 94122002515 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 94122002516 This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins; Region: MopB_CT_Tetrathionate_Arsenate-R; cd02780 94122002517 putative molybdopterin cofactor binding site; other site 94122002518 tetrathionate reductase subunit C; Provisional; Region: PRK14992 94122002519 tetrathionate reductase subunit B; Provisional; Region: PRK14993 94122002520 4Fe-4S binding domain; Region: Fer4; pfam00037 94122002521 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 94122002522 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 94122002523 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 94122002524 dimer interface [polypeptide binding]; other site 94122002525 phosphorylation site [posttranslational modification] 94122002526 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 94122002527 ATP binding site [chemical binding]; other site 94122002528 G-X-G motif; other site 94122002529 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 94122002530 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122002531 active site 94122002532 phosphorylation site [posttranslational modification] 94122002533 intermolecular recognition site; other site 94122002534 dimerization interface [polypeptide binding]; other site 94122002535 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 94122002536 DNA binding residues [nucleotide binding] 94122002537 dimerization interface [polypeptide binding]; other site 94122002538 Protein of unknown function (DUF3584); Region: DUF3584; pfam12128 94122002539 Pleckstrin homology-like domain; Region: PH-like; cl17171 94122002540 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 94122002541 active site 94122002542 metal binding site [ion binding]; metal-binding site 94122002543 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 94122002544 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 94122002545 hypothetical protein; Provisional; Region: PRK05208 94122002546 Protein of unknown function DUF262; Region: DUF262; pfam03235 94122002547 Nuclease-related domain; Region: NERD; pfam08378 94122002548 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1; Region: FBPase; cd00354 94122002549 AMP binding site [chemical binding]; other site 94122002550 metal binding site [ion binding]; metal-binding site 94122002551 active site 94122002552 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 94122002553 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 94122002554 two-component response regulator; Provisional; Region: PRK11173 94122002555 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122002556 active site 94122002557 phosphorylation site [posttranslational modification] 94122002558 intermolecular recognition site; other site 94122002559 dimerization interface [polypeptide binding]; other site 94122002560 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 94122002561 DNA binding site [nucleotide binding] 94122002562 Protein of unknown function (DUF3293); Region: DUF3293; pfam11697 94122002563 aspartate kinase III; Validated; Region: PRK09084 94122002564 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 94122002565 nucleotide binding site [chemical binding]; other site 94122002566 substrate binding site [chemical binding]; other site 94122002567 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC-like_1; cd04912 94122002568 dimer interface [polypeptide binding]; other site 94122002569 allosteric regulatory binding pocket; other site 94122002570 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC_2; cd04917 94122002571 dimer interface [polypeptide binding]; other site 94122002572 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like subfamily; subgroup includes Pseudomonas aeruginosa AotO; Region: M14_PaAOTO_like; cd06250 94122002573 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 94122002574 active site 94122002575 Zn binding site [ion binding]; other site 94122002576 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 94122002577 Salmonella typhimurium Zn2+ transporter ZntB-like subgroup; Region: ZntB-like_1; cd12833 94122002578 Cl binding site [ion binding]; other site 94122002579 oligomer interface [polypeptide binding]; other site 94122002580 Uncharacterized protein family (UPF0231); Region: UPF0231; pfam06062 94122002581 transcriptional regulator NarL; Provisional; Region: PRK10651 94122002582 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122002583 active site 94122002584 phosphorylation site [posttranslational modification] 94122002585 intermolecular recognition site; other site 94122002586 dimerization interface [polypeptide binding]; other site 94122002587 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 94122002588 DNA binding residues [nucleotide binding] 94122002589 dimerization interface [polypeptide binding]; other site 94122002590 nitrate/nitrite sensor protein NarQ; Provisional; Region: PRK10935 94122002591 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 94122002592 HAMP domain; Region: HAMP; pfam00672 94122002593 dimerization interface [polypeptide binding]; other site 94122002594 Histidine kinase; Region: HisKA_3; pfam07730 94122002595 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 94122002596 ATP binding site [chemical binding]; other site 94122002597 Mg2+ binding site [ion binding]; other site 94122002598 G-X-G motif; other site 94122002599 cytochrome c nitrite reductase subunit c552; Provisional; Region: nrfA; PRK11125 94122002600 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 94122002601 GAF domain; Region: GAF; pfam01590 94122002602 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122002603 metal binding site [ion binding]; metal-binding site 94122002604 active site 94122002605 I-site; other site 94122002606 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 94122002607 PAP2_like_6 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which mainly contains bacterial proteins, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_6; cd03396 94122002608 active site 94122002609 lipoprotein; Provisional; Region: PRK11443 94122002610 Protein of unknown function (DUF2799); Region: DUF2799; pfam10973 94122002611 Serine/threonine protein kinase involved in cell cycle control [Signal transduction mechanisms / Cell division and chromosome partitioning]; Region: RIO1; COG1718 94122002612 RIO kinase family; RIO1, RIO3 and similar proteins, catalytic domain. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein...; Region: RIO1_like; cd05145 94122002613 ATP binding site [chemical binding]; other site 94122002614 Transposase; Region: HTH_Tnp_1; cl17663 94122002615 putative outer membrane lipoprotein; Provisional; Region: PRK10510 94122002616 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 94122002617 ligand binding site [chemical binding]; other site 94122002618 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 94122002619 molybdate ABC transporter periplasmic molybdate-binding protein; Provisional; Region: PRK03537 94122002620 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 94122002621 MgtE intracellular N domain; Region: MgtE_N; smart00924 94122002622 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 94122002623 Divalent cation transporter; Region: MgtE; pfam01769 94122002624 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 94122002625 dimerization domain swap beta strand [polypeptide binding]; other site 94122002626 regulatory protein interface [polypeptide binding]; other site 94122002627 active site 94122002628 regulatory phosphorylation site [posttranslational modification]; other site 94122002629 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 94122002630 AAA domain; Region: AAA_18; pfam13238 94122002631 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 94122002632 active site 94122002633 phosphorylation site [posttranslational modification] 94122002634 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 94122002635 30S subunit binding site; other site 94122002636 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 94122002637 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 94122002638 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 94122002639 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 94122002640 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 94122002641 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 94122002642 Walker A/P-loop; other site 94122002643 ATP binding site [chemical binding]; other site 94122002644 Q-loop/lid; other site 94122002645 ABC transporter signature motif; other site 94122002646 Walker B; other site 94122002647 D-loop; other site 94122002648 H-loop/switch region; other site 94122002649 OstA-like protein; Region: OstA; cl00844 94122002650 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 94122002651 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117 94122002652 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 94122002653 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 94122002654 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 94122002655 active site 94122002656 motif I; other site 94122002657 motif II; other site 94122002658 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 94122002659 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 94122002660 putative active site [active] 94122002661 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 94122002662 putative ABC transporter ATP-binding protein YrbF; Provisional; Region: PRK11831 94122002663 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 94122002664 Walker A/P-loop; other site 94122002665 ATP binding site [chemical binding]; other site 94122002666 Q-loop/lid; other site 94122002667 ABC transporter signature motif; other site 94122002668 Walker B; other site 94122002669 D-loop; other site 94122002670 H-loop/switch region; other site 94122002671 Permease; Region: Permease; cl00510 94122002672 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 94122002673 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 94122002674 mce related protein; Region: MCE; pfam02470 94122002675 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 94122002676 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 94122002677 anti sigma factor interaction site; other site 94122002678 regulatory phosphorylation site [posttranslational modification]; other site 94122002679 Predicted transcriptional regulator, BolA superfamily [Transcription]; Region: COG5007 94122002680 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 94122002681 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 94122002682 hinge; other site 94122002683 active site 94122002684 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 94122002685 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 94122002686 Predicted alpha/beta hydrolase [General function prediction only]; Region: COG4757 94122002687 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 94122002688 CoenzymeA binding site [chemical binding]; other site 94122002689 subunit interaction site [polypeptide binding]; other site 94122002690 PHB binding site; other site 94122002691 periplasmic serine pepetdase DegS; Region: protease_degS; TIGR02038 94122002692 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 94122002693 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 94122002694 protein binding site [polypeptide binding]; other site 94122002695 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 94122002696 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 94122002697 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 94122002698 protein binding site [polypeptide binding]; other site 94122002699 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 94122002700 Predicted ATPase [General function prediction only]; Region: COG1485 94122002701 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 94122002702 23S rRNA interface [nucleotide binding]; other site 94122002703 L3 interface [polypeptide binding]; other site 94122002704 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 94122002705 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; pfam09838 94122002706 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 94122002707 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 94122002708 GDP-binding site [chemical binding]; other site 94122002709 ACT binding site; other site 94122002710 IMP binding site; other site 94122002711 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 94122002712 exoribonuclease R; Provisional; Region: PRK11642 94122002713 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 94122002714 RNB domain; Region: RNB; pfam00773 94122002715 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 94122002716 RNA binding site [nucleotide binding]; other site 94122002717 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 94122002718 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 94122002719 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 94122002720 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 94122002721 Major Facilitator Superfamily; Region: MFS_1; pfam07690 94122002722 putative substrate translocation pore; other site 94122002723 Protein of unknown function, DUF481; Region: DUF481; pfam04338 94122002724 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 94122002725 primosomal replication protein N; Provisional; Region: PRK02801 94122002726 generic binding surface II; other site 94122002727 generic binding surface I; other site 94122002728 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 94122002729 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 94122002730 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 94122002731 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 94122002732 [FeFe] hydrogenase H-cluster maturation GTPase HydF; Region: GTP_HydF; TIGR03918 94122002733 E. coli Ras-like protein (Era)-like GTPase; Region: Era_like; cd00880 94122002734 G1 box; other site 94122002735 GTP/Mg2+ binding site [chemical binding]; other site 94122002736 Switch I region; other site 94122002737 G2 box; other site 94122002738 Switch II region; other site 94122002739 G3 box; other site 94122002740 G4 box; other site 94122002741 G5 box; other site 94122002742 biotin synthase; Provisional; Region: PRK07094 94122002743 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 94122002744 FeS/SAM binding site; other site 94122002745 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09613 94122002746 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 94122002747 FeS/SAM binding site; other site 94122002748 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 94122002749 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 94122002750 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 94122002751 Iron hydrogenase small subunit; Region: Fe_hyd_SSU; pfam02256 94122002752 [FeFe] hydrogenase, group A; Region: FeFe_hydrog_A; TIGR02512 94122002753 4Fe-4S binding domain; Region: Fer4; pfam00037 94122002754 4Fe-4S binding domain; Region: Fer4; pfam00037 94122002755 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 94122002756 Peptidase S46; Region: Peptidase_S46; pfam10459 94122002757 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 94122002758 replicative DNA helicase; Provisional; Region: PRK08840 94122002759 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 94122002760 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 94122002761 Walker A motif; other site 94122002762 ATP binding site [chemical binding]; other site 94122002763 Walker B motif; other site 94122002764 DNA binding loops [nucleotide binding] 94122002765 alanine racemase; Reviewed; Region: alr; PRK00053 94122002766 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 94122002767 active site 94122002768 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 94122002769 substrate binding site [chemical binding]; other site 94122002770 catalytic residues [active] 94122002771 dimer interface [polypeptide binding]; other site 94122002772 Predicted inhibitor of MCP methylation, homolog of CheC [Cell motility and secretion]; Region: COG1406 94122002773 Chemotaxis phosphatase CheX; Region: CheX; pfam13690 94122002774 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 94122002775 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122002776 N-terminal plug; other site 94122002777 ligand-binding site [chemical binding]; other site 94122002778 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 94122002779 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 94122002780 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 94122002781 FMN binding site [chemical binding]; other site 94122002782 active site 94122002783 catalytic residues [active] 94122002784 substrate binding site [chemical binding]; other site 94122002785 PspC domain; Region: PspC; pfam04024 94122002786 enoyl-CoA hydratase; Provisional; Region: PRK06688 94122002787 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 94122002788 substrate binding site [chemical binding]; other site 94122002789 oxyanion hole (OAH) forming residues; other site 94122002790 trimer interface [polypeptide binding]; other site 94122002791 Protein of unknown function (DUF461); Region: DUF461; pfam04314 94122002792 Uncharacterized protein conserved in bacteria (DUF2333); Region: DUF2333; pfam10095 94122002793 outer membrane protein; Region: OMP_w_GlyGly; TIGR04219 94122002794 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 94122002795 ADP-ribose pyrophosphatase NudF; Provisional; Region: nudF; PRK10729 94122002796 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 94122002797 dimer interface [polypeptide binding]; other site 94122002798 ADP-ribose binding site [chemical binding]; other site 94122002799 active site 94122002800 nudix motif; other site 94122002801 metal binding site [ion binding]; metal-binding site 94122002802 Protein of unknown function (DUF1249); Region: DUF1249; pfam06853 94122002803 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 94122002804 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 94122002805 active site 94122002806 metal binding site [ion binding]; metal-binding site 94122002807 hexamer interface [polypeptide binding]; other site 94122002808 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 94122002809 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 94122002810 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 94122002811 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 94122002812 ATP binding site [chemical binding]; other site 94122002813 Mg2+ binding site [ion binding]; other site 94122002814 G-X-G motif; other site 94122002815 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 94122002816 anchoring element; other site 94122002817 dimer interface [polypeptide binding]; other site 94122002818 ATP binding site [chemical binding]; other site 94122002819 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 94122002820 active site 94122002821 metal binding site [ion binding]; metal-binding site 94122002822 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 94122002823 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 94122002824 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 94122002825 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 94122002826 CAP-like domain; other site 94122002827 active site 94122002828 primary dimer interface [polypeptide binding]; other site 94122002829 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 94122002830 eyelet of channel; other site 94122002831 trimer interface [polypeptide binding]; other site 94122002832 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 94122002833 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 94122002834 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 94122002835 eyelet of channel; other site 94122002836 trimer interface [polypeptide binding]; other site 94122002837 sulfur acceptor protein CsdL; Provisional; Region: PRK15116 94122002838 Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like...; Region: YgdL_like; cd00755 94122002839 putative ATP binding site [chemical binding]; other site 94122002840 putative substrate interface [chemical binding]; other site 94122002841 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 94122002842 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 94122002843 ATP binding site [chemical binding]; other site 94122002844 Mg2+ binding site [ion binding]; other site 94122002845 G-X-G motif; other site 94122002846 Superinfection exclusion protein B; Region: SieB; pfam14163 94122002847 Protein of unknown function (DUF3149); Region: DUF3149; pfam11346 94122002848 HAMP domain; Region: HAMP; pfam00672 94122002849 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 94122002850 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122002851 dimer interface [polypeptide binding]; other site 94122002852 putative CheW interface [polypeptide binding]; other site 94122002853 Hemerythrin; Region: Hemerythrin; cd12107 94122002854 Fe binding site [ion binding]; other site 94122002855 Domain of unknown function (DUF1508); Region: DUF1508; pfam07411 94122002856 Domain of unknown function (DUF1508); Region: DUF1508; pfam07411 94122002857 molybdate transporter ATP-binding protein; Provisional; Region: modC; PRK11144 94122002858 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122002859 Walker A/P-loop; other site 94122002860 ATP binding site [chemical binding]; other site 94122002861 Q-loop/lid; other site 94122002862 ABC transporter signature motif; other site 94122002863 Walker B; other site 94122002864 D-loop; other site 94122002865 H-loop/switch region; other site 94122002866 TOBE domain; Region: TOBE; cl01440 94122002867 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 94122002868 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 94122002869 dimer interface [polypeptide binding]; other site 94122002870 conserved gate region; other site 94122002871 putative PBP binding loops; other site 94122002872 ABC-ATPase subunit interface; other site 94122002873 molybdate transporter periplasmic protein; Provisional; Region: modA; PRK10677 94122002874 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 94122002875 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 94122002876 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; COG2005 94122002877 TOBE domain; Region: TOBE; cl01440 94122002878 epoxyqueuosine reductase; Region: TIGR00276 94122002879 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 94122002880 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 94122002881 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 94122002882 substrate binding pocket [chemical binding]; other site 94122002883 membrane-bound complex binding site; other site 94122002884 hinge residues; other site 94122002885 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122002886 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122002887 metal binding site [ion binding]; metal-binding site 94122002888 active site 94122002889 I-site; other site 94122002890 PAP2_like_5 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_5; cd03394 94122002891 active site 94122002892 Protein of unknown function (DUF3069); Region: DUF3069; pfam11269 94122002893 malate dehydrogenase; Provisional; Region: PRK13529 94122002894 Malic enzyme, N-terminal domain; Region: malic; pfam00390 94122002895 NAD(P) binding domain of malic enzyme (ME), subgroup 1; Region: NAD_bind_1_malic_enz; cd05312 94122002896 NAD(P) binding site [chemical binding]; other site 94122002897 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4807 94122002898 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 94122002899 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 94122002900 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; COG1914 94122002901 Bacterial PH domain; Region: DUF304; pfam03703 94122002902 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 94122002903 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122002904 N-terminal plug; other site 94122002905 ligand-binding site [chemical binding]; other site 94122002906 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 94122002907 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 94122002908 putative C-terminal domain interface [polypeptide binding]; other site 94122002909 putative GSH binding site (G-site) [chemical binding]; other site 94122002910 putative dimer interface [polypeptide binding]; other site 94122002911 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 94122002912 dimer interface [polypeptide binding]; other site 94122002913 N-terminal domain interface [polypeptide binding]; other site 94122002914 substrate binding pocket (H-site) [chemical binding]; other site 94122002915 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 94122002916 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 94122002917 synthetase active site [active] 94122002918 NTP binding site [chemical binding]; other site 94122002919 metal binding site [ion binding]; metal-binding site 94122002920 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 94122002921 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 94122002922 active site 94122002923 Zn binding site [ion binding]; other site 94122002924 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 94122002925 16S rRNA pseudouridylate synthase A; Provisional; Region: PRK10839 94122002926 RNA binding surface [nucleotide binding]; other site 94122002927 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 94122002928 active site 94122002929 uracil binding [chemical binding]; other site 94122002930 Uncharacterized conserved protein [Function unknown]; Region: COG3595 94122002931 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 94122002932 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 94122002933 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 94122002934 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 94122002935 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 94122002936 DNA binding residues [nucleotide binding] 94122002937 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 94122002938 dimerization interface [polypeptide binding]; other site 94122002939 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 94122002940 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122002941 dimer interface [polypeptide binding]; other site 94122002942 putative CheW interface [polypeptide binding]; other site 94122002943 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 94122002944 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 94122002945 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 94122002946 active site 94122002947 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 94122002948 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 94122002949 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 94122002950 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 94122002951 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 94122002952 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 94122002953 tRNA; other site 94122002954 putative tRNA binding site [nucleotide binding]; other site 94122002955 putative NADP binding site [chemical binding]; other site 94122002956 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 94122002957 peptide chain release factor 1; Validated; Region: prfA; PRK00591 94122002958 This domain is found in peptide chain release factors; Region: PCRF; smart00937 94122002959 RF-1 domain; Region: RF-1; pfam00472 94122002960 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 94122002961 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 94122002962 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122002963 Coenzyme A binding pocket [chemical binding]; other site 94122002964 Invasion gene expression up-regulator, SirB; Region: SirB; pfam04247 94122002965 Transglutaminase-like superfamily; Region: Transglut_core2; pfam13369 94122002966 Tetratricopeptide repeat; Region: TPR_9; pfam13371 94122002967 Protein of unknown function (DUF819); Region: DUF819; cl02317 94122002968 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 94122002969 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 94122002970 CSS motif domain associated with EAL; Region: CSS-motif; pfam12792 94122002971 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 94122002972 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 94122002973 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 94122002974 Nitrogen regulatory protein P-II; Region: P-II; smart00938 94122002975 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 94122002976 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 94122002977 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 94122002978 Predicted integral membrane protein [Function unknown]; Region: COG5652 94122002979 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 94122002980 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 94122002981 AmpG-like permease; Region: 2A0125; TIGR00901 94122002982 muropeptide transporter; Reviewed; Region: ampG; PRK11902 94122002983 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional; Region: PRK10903 94122002984 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 94122002985 substrate binding site [chemical binding]; other site 94122002986 hypothetical protein; Provisional; Region: PRK11627 94122002987 Uncharacterized lipoprotein; Region: Lipoprotein_16; pfam03923 94122002988 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 94122002989 Protein of unknown function (DUF2804); Region: DUF2804; pfam10974 94122002990 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 94122002991 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 94122002992 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 94122002993 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 94122002994 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 94122002995 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 94122002996 aromatic acid decarboxylase; Validated; Region: PRK05920 94122002997 Flavoprotein; Region: Flavoprotein; pfam02441 94122002998 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 94122002999 active site 94122003000 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 94122003001 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 94122003002 Walker A/P-loop; other site 94122003003 ATP binding site [chemical binding]; other site 94122003004 Q-loop/lid; other site 94122003005 ABC transporter signature motif; other site 94122003006 Walker B; other site 94122003007 D-loop; other site 94122003008 H-loop/switch region; other site 94122003009 inner membrane transport permease; Provisional; Region: PRK15066 94122003010 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 94122003011 Fungalysin/Thermolysin Propeptide Motif; Region: FTP; pfam07504 94122003012 Peptidase M36 family also known as fungalysin family; Region: M36; cd09596 94122003013 PA_subtilisin_1: Protease-associated domain containing subtilisin-like proteases, subgroup 1. A subgroup of PA domain-containing subtilisin-like proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined; Region: PA_subtilisin_1; cd04818 94122003014 PA/protease or protease-like domain interface [polypeptide binding]; other site 94122003015 Peptidase M36 family also known as fungalysin family; Region: M36; cd09596 94122003016 Zn binding site [ion binding]; other site 94122003017 GlyGly-CTERM domain; Region: GlyGly_CTERM; TIGR03501 94122003018 DNA-binding transcriptional regulator AsnC; Provisional; Region: PRK11179 94122003019 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 94122003020 putative DNA binding site [nucleotide binding]; other site 94122003021 putative Zn2+ binding site [ion binding]; other site 94122003022 AsnC family; Region: AsnC_trans_reg; pfam01037 94122003023 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 94122003024 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 94122003025 active site 94122003026 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 94122003027 Peptidase family U32; Region: Peptidase_U32; pfam01136 94122003028 Collagenase; Region: DUF3656; pfam12392 94122003029 Pleckstrin homology (PH)-like domains in bacteria (PHb); Region: PH-like_bacteria; cd13225 94122003030 pentamer interface [polypeptide binding]; other site 94122003031 dodecaamer interface [polypeptide binding]; other site 94122003032 CAAX protease self-immunity; Region: Abi; pfam02517 94122003033 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 94122003034 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 94122003035 Cupin domain; Region: Cupin_2; cl17218 94122003036 Predicted ATPase [General function prediction only]; Region: COG4637 94122003037 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122003038 Walker A/P-loop; other site 94122003039 ATP binding site [chemical binding]; other site 94122003040 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 94122003041 active site 94122003042 Fe-S metabolism associated domain; Region: SufE; cl00951 94122003043 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 94122003044 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 94122003045 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 94122003046 catalytic residue [active] 94122003047 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 94122003048 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 94122003049 dimerization interface [polypeptide binding]; other site 94122003050 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122003051 dimer interface [polypeptide binding]; other site 94122003052 putative CheW interface [polypeptide binding]; other site 94122003053 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 94122003054 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 94122003055 ATP binding site [chemical binding]; other site 94122003056 Mg++ binding site [ion binding]; other site 94122003057 motif III; other site 94122003058 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 94122003059 nucleotide binding region [chemical binding]; other site 94122003060 ATP-binding site [chemical binding]; other site 94122003061 Protein of unknown function (DUF3626); Region: DUF3626; pfam12294 94122003062 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11174 94122003063 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 94122003064 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122003065 Walker A/P-loop; other site 94122003066 ATP binding site [chemical binding]; other site 94122003067 Q-loop/lid; other site 94122003068 ABC transporter signature motif; other site 94122003069 Walker B; other site 94122003070 D-loop; other site 94122003071 H-loop/switch region; other site 94122003072 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11160 94122003073 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122003074 Walker A/P-loop; other site 94122003075 ATP binding site [chemical binding]; other site 94122003076 Q-loop/lid; other site 94122003077 ABC transporter signature motif; other site 94122003078 Walker B; other site 94122003079 D-loop; other site 94122003080 H-loop/switch region; other site 94122003081 Adenylyl cyclase (AC) class IV-like, a subgroup of the CYTH-like superfamily; Region: CYTH-like_AC_IV-like; cd07890 94122003082 putative active site [active] 94122003083 putative metal binding residues [ion binding]; other site 94122003084 signature motif; other site 94122003085 putative triphosphate binding site [ion binding]; other site 94122003086 dimer interface [polypeptide binding]; other site 94122003087 Domain of unknown function (DUF4277); Region: DUF4277; pfam14104 94122003088 Transposase [DNA replication, recombination, and repair]; Region: COG5421 94122003089 Helix-turn-helix domain; Region: HTH_17; pfam12728 94122003090 Protein of unknown function, DUF599; Region: DUF599; pfam04654 94122003091 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 94122003092 Proline dehydrogenase; Region: Pro_dh; pfam01619 94122003093 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 94122003094 Glutamate binding site [chemical binding]; other site 94122003095 NAD binding site [chemical binding]; other site 94122003096 catalytic residues [active] 94122003097 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 94122003098 Bacterial SH3 domain homologues; Region: SH3b; smart00287 94122003099 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 94122003100 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 94122003101 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 94122003102 Uncharacterized conserved protein [Function unknown]; Region: COG3025 94122003103 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 94122003104 putative active site [active] 94122003105 putative metal binding residues [ion binding]; other site 94122003106 signature motif; other site 94122003107 putative triphosphate binding site [ion binding]; other site 94122003108 Ion transport protein; Region: Ion_trans; pfam00520 94122003109 Ion channel; Region: Ion_trans_2; pfam07885 94122003110 Domain of unknown function (DUF4178); Region: DUF4178; pfam13785 94122003111 PspA/IM30 family; Region: PspA_IM30; pfam04012 94122003112 Uncharacterized protein conserved in bacteria (DUF2170); Region: DUF2170; pfam09938 94122003113 spermidine synthase; Provisional; Region: PRK03612 94122003114 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 94122003115 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 94122003116 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 94122003117 metal binding triad; other site 94122003118 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 94122003119 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 94122003120 metal binding triad; other site 94122003121 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 94122003122 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 94122003123 GAF domain; Region: GAF; pfam01590 94122003124 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122003125 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122003126 metal binding site [ion binding]; metal-binding site 94122003127 active site 94122003128 I-site; other site 94122003129 Domain of unknown function (DUF897); Region: DUF897; pfam05982 94122003130 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122003131 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 94122003132 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 94122003133 dimerization interface [polypeptide binding]; other site 94122003134 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 94122003135 atypical (a) SDRs, subgroup 3; Region: SDR_a3; cd05229 94122003136 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 94122003137 putative NAD(P) binding site [chemical binding]; other site 94122003138 putative active site [active] 94122003139 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 94122003140 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 94122003141 DNA binding residues [nucleotide binding] 94122003142 Predicted ATPase [General function prediction only]; Region: COG1485 94122003143 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122003144 Walker A/P-loop; other site 94122003145 ATP binding site [chemical binding]; other site 94122003146 ABC transporter signature motif; other site 94122003147 Walker B; other site 94122003148 D-loop; other site 94122003149 H-loop/switch region; other site 94122003150 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 94122003151 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 94122003152 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 94122003153 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 94122003154 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 94122003155 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 94122003156 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_4; cd06231 94122003157 putative active site [active] 94122003158 Zn binding site [ion binding]; other site 94122003159 L,D-transpeptidase; Provisional; Region: PRK10190 94122003160 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 94122003161 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 94122003162 anaerobic nitric oxide reductase transcription regulator; Provisional; Region: PRK05022 94122003163 GAF domain; Region: GAF; pfam01590 94122003164 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 94122003165 Walker A motif; other site 94122003166 ATP binding site [chemical binding]; other site 94122003167 Walker B motif; other site 94122003168 arginine finger; other site 94122003169 Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]; Region: NorB; COG3256 94122003170 potassium/proton antiporter; Reviewed; Region: PRK05326 94122003171 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 94122003172 TrkA-C domain; Region: TrkA_C; pfam02080 94122003173 Transporter associated domain; Region: CorC_HlyC; smart01091 94122003174 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 94122003175 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 94122003176 putative acyl-acceptor binding pocket; other site 94122003177 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional; Region: PRK11316 94122003178 RfaE encodes a bifunctional ADP-heptose synthase involved in the biosynthesis of the lipopolysaccharide (LPS) core precursor ADP-L-glycero-D-manno-heptose. LPS plays an important role in maintaining the structural integrity of the bacterial outer...; Region: RfaE_like; cd01172 94122003179 putative ribose interaction site [chemical binding]; other site 94122003180 putative ADP binding site [chemical binding]; other site 94122003181 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 94122003182 active site 94122003183 HIGH motif; other site 94122003184 nucleotide binding site [chemical binding]; other site 94122003185 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 94122003186 pyridine nucleotide transhydrogenase; Provisional; Region: pntB; PRK09444 94122003187 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 94122003188 NAD(P) transhydrogenase subunit alpha; Provisional; Region: pntA; PRK09424 94122003189 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 94122003190 ligand binding site [chemical binding]; other site 94122003191 homodimer interface [polypeptide binding]; other site 94122003192 NAD(P) binding site [chemical binding]; other site 94122003193 trimer interface B [polypeptide binding]; other site 94122003194 trimer interface A [polypeptide binding]; other site 94122003195 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 94122003196 sulfite reductase [NADPH] flavoprotein, alpha-component; Region: cysJ; TIGR01931 94122003197 Flavodoxin; Region: Flavodoxin_1; pfam00258 94122003198 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ...; Region: SiR; cd06199 94122003199 FAD binding pocket [chemical binding]; other site 94122003200 FAD binding motif [chemical binding]; other site 94122003201 catalytic residues [active] 94122003202 NAD binding pocket [chemical binding]; other site 94122003203 phosphate binding motif [ion binding]; other site 94122003204 beta-alpha-beta structure motif; other site 94122003205 sulfite reductase subunit beta; Provisional; Region: PRK13504 94122003206 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 94122003207 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 94122003208 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 94122003209 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 94122003210 Active Sites [active] 94122003211 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 94122003212 Transglycosylase; Region: Transgly; cl17702 94122003213 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 94122003214 Active site serine [active] 94122003215 The outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of acylester bonds in phospholipids using calcium as a cofactor. The enzyme has a fold of transmembrane beta-barrels and is widespread among...; Region: OMPLA; cd00541 94122003216 dimerization interface [polypeptide binding]; other site 94122003217 substrate binding site [chemical binding]; other site 94122003218 active site 94122003219 calcium binding site [ion binding]; other site 94122003220 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 94122003221 active site 94122003222 SAM binding site [chemical binding]; other site 94122003223 homodimer interface [polypeptide binding]; other site 94122003224 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 94122003225 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 94122003226 Active Sites [active] 94122003227 sulfate adenylyltransferase subunit 1; Provisional; Region: cysN; PRK05124 94122003228 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 94122003229 CysD dimerization site [polypeptide binding]; other site 94122003230 G1 box; other site 94122003231 putative GEF interaction site [polypeptide binding]; other site 94122003232 GTP/Mg2+ binding site [chemical binding]; other site 94122003233 Switch I region; other site 94122003234 G2 box; other site 94122003235 G3 box; other site 94122003236 Switch II region; other site 94122003237 G4 box; other site 94122003238 G5 box; other site 94122003239 CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NodQ_II; cd03695 94122003240 TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NoDQ_III; cd04095 94122003241 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 94122003242 TrkA-C domain; Region: TrkA_C; pfam02080 94122003243 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 94122003244 TrkA-C domain; Region: TrkA_C; pfam02080 94122003245 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 94122003246 Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically "activated" sulfate form...; Region: APSK; cd02027 94122003247 ligand-binding site [chemical binding]; other site 94122003248 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 94122003249 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 94122003250 dimer interface [polypeptide binding]; other site 94122003251 phosphorylation site [posttranslational modification] 94122003252 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 94122003253 ATP binding site [chemical binding]; other site 94122003254 Mg2+ binding site [ion binding]; other site 94122003255 G-X-G motif; other site 94122003256 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 94122003257 Domain of unknown function (DUF3369); Region: DUF3369; pfam11849 94122003258 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122003259 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122003260 metal binding site [ion binding]; metal-binding site 94122003261 active site 94122003262 I-site; other site 94122003263 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 94122003264 TIGR03899 family protein; Region: TIGR03899 94122003265 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 94122003266 Major Facilitator Superfamily; Region: MFS_1; pfam07690 94122003267 putative substrate translocation pore; other site 94122003268 Flavodoxin domain; Region: Flavodoxin_5; cl17428 94122003269 Cytochrome b(N-terminal)/b6/petB; Region: Cytochrom_B_N; pfam00033 94122003270 Domain of unknown function (DUF4382); Region: DUF4382; pfam14321 94122003271 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 94122003272 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 94122003273 catalytic residues [active] 94122003274 hinge region; other site 94122003275 alpha helical domain; other site 94122003276 DNA-J related protein; Region: DNAJ_related; pfam12339 94122003277 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 94122003278 HSP70 interaction site [polypeptide binding]; other site 94122003279 NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family...; Region: NfsB_like_nitroreductase; cd02149 94122003280 dimer interface [polypeptide binding]; other site 94122003281 FMN binding site [chemical binding]; other site 94122003282 Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_sugar_binding_like; cd01536 94122003283 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 94122003284 ligand binding site [chemical binding]; other site 94122003285 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 94122003286 RNA binding site [nucleotide binding]; other site 94122003287 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 94122003288 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 94122003289 Walker A/P-loop; other site 94122003290 ATP binding site [chemical binding]; other site 94122003291 Q-loop/lid; other site 94122003292 ABC transporter signature motif; other site 94122003293 Walker B; other site 94122003294 D-loop; other site 94122003295 H-loop/switch region; other site 94122003296 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 94122003297 dimer interface [polypeptide binding]; other site 94122003298 conserved gate region; other site 94122003299 putative PBP binding loops; other site 94122003300 ABC-ATPase subunit interface; other site 94122003301 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 94122003302 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 94122003303 substrate binding pocket [chemical binding]; other site 94122003304 membrane-bound complex binding site; other site 94122003305 hinge residues; other site 94122003306 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122003307 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122003308 The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; Region: PBP2_CidR; cd08438 94122003309 putative dimerization interface [polypeptide binding]; other site 94122003310 LrgA family; Region: LrgA; pfam03788 94122003311 LrgB-like family; Region: LrgB; pfam04172 94122003312 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 94122003313 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 94122003314 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 94122003315 Carbon starvation protein CstA; Region: CstA; pfam02554 94122003316 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 94122003317 Periplasmic glucans biosynthesis protein [Inorganic ion transport and metabolism]; Region: MdoG; COG3131 94122003318 glucan biosynthesis protein D; Provisional; Region: mdoD; PRK13273 94122003319 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 94122003320 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 94122003321 catalytic triad [active] 94122003322 Cupin domain; Region: Cupin_2; cl17218 94122003323 Helix-turn-helix domain; Region: HTH_18; pfam12833 94122003324 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 94122003325 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 94122003326 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 94122003327 Protein of unknown function DUF72; Region: DUF72; cl00777 94122003328 PAS domain S-box; Region: sensory_box; TIGR00229 94122003329 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 94122003330 putative active site [active] 94122003331 heme pocket [chemical binding]; other site 94122003332 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 94122003333 GAF domain; Region: GAF; pfam01590 94122003334 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122003335 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122003336 metal binding site [ion binding]; metal-binding site 94122003337 active site 94122003338 I-site; other site 94122003339 Cache domain; Region: Cache_1; pfam02743 94122003340 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 94122003341 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 94122003342 dimerization interface [polypeptide binding]; other site 94122003343 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122003344 dimer interface [polypeptide binding]; other site 94122003345 putative CheW interface [polypeptide binding]; other site 94122003346 aminopeptidase N, Streptomyces lividans type; Region: pepN_strep_liv; TIGR02412 94122003347 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_3; cd09602 94122003348 Zn binding site [ion binding]; other site 94122003349 uncharacterized proteobacterial lipoprotein; Region: lp_; TIGR02722 94122003350 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 94122003351 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 94122003352 active site 94122003353 catalytic residues [active] 94122003354 metal binding site [ion binding]; metal-binding site 94122003355 SlyX; Region: SlyX; pfam04102 94122003356 FOG: WD40 repeat [General function prediction only]; Region: COG2319 94122003357 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from...; Region: WD40; cl02567 94122003358 structural tetrad; other site 94122003359 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK10902 94122003360 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 94122003361 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 94122003362 Predicted extracellular nuclease [General function prediction only]; Region: COG2374 94122003363 YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate...; Region: YhcR_OBF_like; cd04486 94122003364 generic binding surface II; other site 94122003365 generic binding surface I; other site 94122003366 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 94122003367 putative catalytic site [active] 94122003368 putative metal binding site [ion binding]; other site 94122003369 putative phosphate binding site [ion binding]; other site 94122003370 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 94122003371 CoenzymeA binding site [chemical binding]; other site 94122003372 subunit interaction site [polypeptide binding]; other site 94122003373 PHB binding site; other site 94122003374 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 94122003375 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 94122003376 tetramer interface [polypeptide binding]; other site 94122003377 heme binding pocket [chemical binding]; other site 94122003378 NADPH binding site [chemical binding]; other site 94122003379 Predicted membrane protein [Function unknown]; Region: COG2119 94122003380 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 94122003381 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 94122003382 yybP-ykoY element as predicted by Rfam (RF00080), score 65.65; riboswitch with unknown function 94122003383 aromatic amino acid transport protein; Region: araaP; TIGR00837 94122003384 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 94122003385 Peptidase S46; Region: Peptidase_S46; pfam10459 94122003386 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]; Region: COG3591 94122003387 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 94122003388 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 94122003389 ligand binding site [chemical binding]; other site 94122003390 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 94122003391 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 94122003392 RNA binding surface [nucleotide binding]; other site 94122003393 Pseudouridine synthase, Escherichia coli RluF like; Region: PseudoU_synth_RluF; cd02554 94122003394 probable active site [active] 94122003395 Na+/H+ antiporter family; Region: Na_H_antiporter; pfam03553 94122003396 FMN-binding domain; Region: FMN_bind; pfam04205 94122003397 ApbE family; Region: ApbE; pfam02424 94122003398 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 94122003399 dimerization interface [polypeptide binding]; other site 94122003400 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 94122003401 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122003402 dimer interface [polypeptide binding]; other site 94122003403 putative CheW interface [polypeptide binding]; other site 94122003404 EamA-like transporter family; Region: EamA; pfam00892 94122003405 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 94122003406 EamA-like transporter family; Region: EamA; pfam00892 94122003407 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 94122003408 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 94122003409 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 94122003410 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 94122003411 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 94122003412 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 94122003413 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 94122003414 DNA-binding site [nucleotide binding]; DNA binding site 94122003415 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 94122003416 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122003417 homodimer interface [polypeptide binding]; other site 94122003418 catalytic residue [active] 94122003419 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 94122003420 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 94122003421 homodimer interface [polypeptide binding]; other site 94122003422 substrate-cofactor binding pocket; other site 94122003423 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122003424 catalytic residue [active] 94122003425 Predicted membrane protein (DUF2339); Region: DUF2339; pfam10101 94122003426 SAM-dependent 23S ribosomal RNA mG1835 methyltransferase; Provisional; Region: PRK15001 94122003427 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 94122003428 S-adenosylmethionine binding site [chemical binding]; other site 94122003429 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_2; pfam13532 94122003430 BolA-like protein; Region: BolA; cl00386 94122003431 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 94122003432 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 94122003433 S-ribosylhomocysteinase; Provisional; Region: PRK02260 94122003434 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 94122003435 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122003436 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 94122003437 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 94122003438 Na(+)-translocating NADH-quinone reductase subunit B; Provisional; Region: PRK05349 94122003439 Na(+)-translocating NADH-quinone reductase subunit C; Provisional; Region: PRK05346 94122003440 NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit; Region: nqrC; TIGR01938 94122003441 Na(+)-translocating NADH-quinone reductase subunit D; Validated; Region: PRK09292 94122003442 Na(+)-translocating NADH-quinone reductase subunit E; Provisional; Region: PRK02830 94122003443 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 94122003444 Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+ oxidoreductase; Region: NADH_quinone_reductase; cd06188 94122003445 FAD binding pocket [chemical binding]; other site 94122003446 FAD binding motif [chemical binding]; other site 94122003447 phosphate binding motif [ion binding]; other site 94122003448 beta-alpha-beta structure motif; other site 94122003449 NAD binding pocket [chemical binding]; other site 94122003450 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 94122003451 ApbE family; Region: ApbE; pfam02424 94122003452 Protein of unknown function (DUF539); Region: DUF539; cl01129 94122003453 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 94122003454 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 94122003455 heme binding site [chemical binding]; other site 94122003456 ferroxidase pore; other site 94122003457 ferroxidase diiron center [ion binding]; other site 94122003458 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 94122003459 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 94122003460 heme binding site [chemical binding]; other site 94122003461 ferroxidase pore; other site 94122003462 ferroxidase diiron center [ion binding]; other site 94122003463 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 94122003464 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 94122003465 dimerization interface [polypeptide binding]; other site 94122003466 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122003467 dimer interface [polypeptide binding]; other site 94122003468 putative CheW interface [polypeptide binding]; other site 94122003469 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 94122003470 active site 94122003471 DNA polymerase IV; Validated; Region: PRK02406 94122003472 DNA binding site [nucleotide binding] 94122003473 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 94122003474 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 94122003475 metal binding site [ion binding]; metal-binding site 94122003476 dimer interface [polypeptide binding]; other site 94122003477 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 94122003478 interface (dimer of trimers) [polypeptide binding]; other site 94122003479 Substrate-binding/catalytic site; other site 94122003480 Zn-binding sites [ion binding]; other site 94122003481 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 94122003482 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122003483 N-terminal plug; other site 94122003484 ligand-binding site [chemical binding]; other site 94122003485 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 94122003486 gamma-glutamyl kinase; Provisional; Region: PRK05429 94122003487 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 94122003488 nucleotide binding site [chemical binding]; other site 94122003489 homotetrameric interface [polypeptide binding]; other site 94122003490 putative phosphate binding site [ion binding]; other site 94122003491 putative allosteric binding site; other site 94122003492 PUA domain; Region: PUA; pfam01472 94122003493 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 94122003494 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 94122003495 putative catalytic cysteine [active] 94122003496 flagellar motor protein MotB; Validated; Region: motB; PRK09041 94122003497 This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS)...; Region: YbaK_deacylase; cd00002 94122003498 putative deacylase active site [active] 94122003499 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 94122003500 EamA-like transporter family; Region: EamA; pfam00892 94122003501 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 94122003502 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 94122003503 nucleotide binding site [chemical binding]; other site 94122003504 chaperone protein DnaJ; Provisional; Region: PRK10767 94122003505 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 94122003506 HSP70 interaction site [polypeptide binding]; other site 94122003507 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 94122003508 substrate binding site [polypeptide binding]; other site 94122003509 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 94122003510 Zn binding sites [ion binding]; other site 94122003511 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 94122003512 dimer interface [polypeptide binding]; other site 94122003513 Uncharacterized conserved protein [Function unknown]; Region: COG4748 94122003514 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 94122003515 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 94122003516 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 94122003517 ATP binding site [chemical binding]; other site 94122003518 Mg++ binding site [ion binding]; other site 94122003519 motif III; other site 94122003520 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 94122003521 nucleotide binding region [chemical binding]; other site 94122003522 ATP-binding site [chemical binding]; other site 94122003523 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 94122003524 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 94122003525 Peptidase family M48; Region: Peptidase_M48; pfam01435 94122003526 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 94122003527 peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK11570 94122003528 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 94122003529 dihydrodipicolinate reductase; Provisional; Region: PRK00048 94122003530 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 94122003531 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 94122003532 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 94122003533 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 94122003534 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 94122003535 catalytic site [active] 94122003536 subunit interface [polypeptide binding]; other site 94122003537 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 94122003538 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 94122003539 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 94122003540 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 94122003541 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 94122003542 ATP-grasp domain; Region: ATP-grasp_4; cl17255 94122003543 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 94122003544 IMP binding site; other site 94122003545 dimer interface [polypeptide binding]; other site 94122003546 interdomain contacts; other site 94122003547 partial ornithine binding site; other site 94122003548 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 94122003549 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 94122003550 substrate binding pocket [chemical binding]; other site 94122003551 membrane-bound complex binding site; other site 94122003552 hinge residues; other site 94122003553 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122003554 dimer interface [polypeptide binding]; other site 94122003555 putative CheW interface [polypeptide binding]; other site 94122003556 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 94122003557 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 94122003558 MgtE intracellular N domain; Region: MgtE_N; pfam03448 94122003559 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 94122003560 Divalent cation transporter; Region: MgtE; pfam01769 94122003561 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 94122003562 putative catalytic site [active] 94122003563 putative metal binding site [ion binding]; other site 94122003564 putative phosphate binding site [ion binding]; other site 94122003565 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; pfam09836 94122003566 hypothetical protein; Provisional; Region: PRK05409 94122003567 Predicted integral membrane protein (DUF2282); Region: DUF2282; cl02366 94122003568 Predicted integral membrane protein (DUF2282); Region: DUF2282; cl02366 94122003569 23S rRNA m(5)C1962 methyltransferase; Provisional; Region: PRK15128 94122003570 Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase; Region: PUA; smart00359 94122003571 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 94122003572 putative RNA binding site [nucleotide binding]; other site 94122003573 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 94122003574 S-adenosylmethionine binding site [chemical binding]; other site 94122003575 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 94122003576 tetramer (dimer of dimers) interface [polypeptide binding]; other site 94122003577 active site 94122003578 dimer interface [polypeptide binding]; other site 94122003579 Protein of unknown function (DUF808); Region: DUF808; pfam05661 94122003580 DEDDy 3'-5' exonuclease domain of WRN and similar proteins; Region: WRN_exo; cd06141 94122003581 catalytic site [active] 94122003582 putative active site [active] 94122003583 putative substrate binding site [chemical binding]; other site 94122003584 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 94122003585 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122003586 N-terminal plug; other site 94122003587 ligand-binding site [chemical binding]; other site 94122003588 Predicted membrane protein [Function unknown]; Region: COG3503 94122003589 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 94122003590 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 94122003591 dimerization interface [polypeptide binding]; other site 94122003592 DPS ferroxidase diiron center [ion binding]; other site 94122003593 ion pore; other site 94122003594 DNA polymerase III psi subunit; Region: DNA_III_psi; cl11436 94122003595 ribosomal-protein-alanine N-acetyltransferase; Provisional; Region: rimI; PRK09491 94122003596 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122003597 Coenzyme A binding pocket [chemical binding]; other site 94122003598 lipoyl synthase; Provisional; Region: PRK05481 94122003599 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 94122003600 FeS/SAM binding site; other site 94122003601 lipoate-protein ligase B; Provisional; Region: PRK14342 94122003602 hypothetical protein; Provisional; Region: PRK04998 94122003603 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 94122003604 D-alanyl-D-alanine carboxypeptidase fraction A; Provisional; Region: PRK10793 94122003605 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 94122003606 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 94122003607 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 94122003608 Sporulation related domain; Region: SPOR; pfam05036 94122003609 Transglycosylase SLT domain; Region: SLT_2; pfam13406 94122003610 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 94122003611 N-acetyl-D-glucosamine binding site [chemical binding]; other site 94122003612 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 94122003613 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 94122003614 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 94122003615 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 94122003616 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 94122003617 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 94122003618 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 94122003619 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 94122003620 active site 94122003621 (T/H)XGH motif; other site 94122003622 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 94122003623 DNA polymerase III, delta subunit; Region: holA; TIGR01128 94122003624 Lipopolysaccharide-assembly; Region: LptE; cl01125 94122003625 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 94122003626 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 94122003627 HIGH motif; other site 94122003628 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 94122003629 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 94122003630 active site 94122003631 KMSKS motif; other site 94122003632 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 94122003633 tRNA binding surface [nucleotide binding]; other site 94122003634 Protein of unknown function (DUF1451); Region: DUF1451; pfam07295 94122003635 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 94122003636 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 94122003637 putative active site [active] 94122003638 catalytic triad [active] 94122003639 putative dimer interface [polypeptide binding]; other site 94122003640 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 94122003641 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 94122003642 Transporter associated domain; Region: CorC_HlyC; smart01091 94122003643 metal-binding heat shock protein; Provisional; Region: PRK00016 94122003644 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 94122003645 PhoH-like protein; Region: PhoH; pfam02562 94122003646 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 94122003647 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 94122003648 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 94122003649 FeS/SAM binding site; other site 94122003650 TRAM domain; Region: TRAM; pfam01938 94122003651 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Provisional; Region: PRK08849 94122003652 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 94122003653 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 94122003654 putative active site [active] 94122003655 catalytic residue [active] 94122003656 GTP-binding protein YchF; Reviewed; Region: PRK09601 94122003657 YchF GTPase; Region: YchF; cd01900 94122003658 G1 box; other site 94122003659 GTP/Mg2+ binding site [chemical binding]; other site 94122003660 Switch I region; other site 94122003661 G2 box; other site 94122003662 Switch II region; other site 94122003663 G3 box; other site 94122003664 G4 box; other site 94122003665 G5 box; other site 94122003666 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 94122003667 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 94122003668 Predicted periplasmic protein (DUF2271); Region: DUF2271; pfam10029 94122003669 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 94122003670 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 94122003671 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 94122003672 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 94122003673 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK12933 94122003674 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 94122003675 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 94122003676 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13021 94122003677 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 94122003678 Protein export membrane protein; Region: SecD_SecF; pfam02355 94122003679 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 94122003680 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 94122003681 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 94122003682 S-adenosylmethionine binding site [chemical binding]; other site 94122003683 ATP-dependent metalloprotease; Reviewed; Region: hflB; PRK10733 94122003684 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 94122003685 Walker A motif; other site 94122003686 ATP binding site [chemical binding]; other site 94122003687 Walker B motif; other site 94122003688 arginine finger; other site 94122003689 Peptidase family M41; Region: Peptidase_M41; pfam01434 94122003690 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 94122003691 dihydropteroate synthase; Region: DHPS; TIGR01496 94122003692 substrate binding pocket [chemical binding]; other site 94122003693 dimer interface [polypeptide binding]; other site 94122003694 inhibitor binding site; inhibition site 94122003695 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 94122003696 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 94122003697 active site 94122003698 substrate binding site [chemical binding]; other site 94122003699 metal binding site [ion binding]; metal-binding site 94122003700 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 94122003701 triosephosphate isomerase; Provisional; Region: PRK14567 94122003702 substrate binding site [chemical binding]; other site 94122003703 dimer interface [polypeptide binding]; other site 94122003704 catalytic triad [active] 94122003705 Preprotein translocase SecG subunit; Region: SecG; pfam03840 94122003706 ribosome maturation protein RimP; Reviewed; Region: PRK00092 94122003707 Sm and related proteins; Region: Sm_like; cl00259 94122003708 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 94122003709 putative oligomer interface [polypeptide binding]; other site 94122003710 putative RNA binding site [nucleotide binding]; other site 94122003711 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 94122003712 NusA N-terminal domain; Region: NusA_N; pfam08529 94122003713 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 94122003714 RNA binding site [nucleotide binding]; other site 94122003715 homodimer interface [polypeptide binding]; other site 94122003716 NusA-like KH domain; Region: KH_5; pfam13184 94122003717 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 94122003718 G-X-X-G motif; other site 94122003719 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 94122003720 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 94122003721 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 94122003722 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 94122003723 translation initiation factor IF-2; Validated; Region: infB; PRK05306 94122003724 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 94122003725 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 94122003726 G1 box; other site 94122003727 putative GEF interaction site [polypeptide binding]; other site 94122003728 GTP/Mg2+ binding site [chemical binding]; other site 94122003729 Switch I region; other site 94122003730 G2 box; other site 94122003731 G3 box; other site 94122003732 Switch II region; other site 94122003733 G4 box; other site 94122003734 G5 box; other site 94122003735 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 94122003736 Translation-initiation factor 2; Region: IF-2; pfam11987 94122003737 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 94122003738 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 94122003739 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 94122003740 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 94122003741 RNA binding site [nucleotide binding]; other site 94122003742 active site 94122003743 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 94122003744 ribosomal S15 leader as predicted by Rfam (RF00114), score 69.59 94122003745 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 94122003746 16S/18S rRNA binding site [nucleotide binding]; other site 94122003747 S13e-L30e interaction site [polypeptide binding]; other site 94122003748 25S rRNA binding site [nucleotide binding]; other site 94122003749 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122003750 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122003751 metal binding site [ion binding]; metal-binding site 94122003752 active site 94122003753 I-site; other site 94122003754 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 94122003755 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 94122003756 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 94122003757 RNase E interface [polypeptide binding]; other site 94122003758 trimer interface [polypeptide binding]; other site 94122003759 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 94122003760 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 94122003761 RNase E interface [polypeptide binding]; other site 94122003762 trimer interface [polypeptide binding]; other site 94122003763 active site 94122003764 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 94122003765 putative nucleic acid binding region [nucleotide binding]; other site 94122003766 G-X-X-G motif; other site 94122003767 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 94122003768 RNA binding site [nucleotide binding]; other site 94122003769 domain interface; other site 94122003770 lipoprotein NlpI; Provisional; Region: PRK11189 94122003771 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 94122003772 TPR motif; other site 94122003773 binding surface 94122003774 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 94122003775 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 94122003776 G1 box; other site 94122003777 putative GEF interaction site [polypeptide binding]; other site 94122003778 GTP/Mg2+ binding site [chemical binding]; other site 94122003779 Switch I region; other site 94122003780 G2 box; other site 94122003781 G3 box; other site 94122003782 Switch II region; other site 94122003783 G4 box; other site 94122003784 G5 box; other site 94122003785 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 94122003786 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 94122003787 active site 94122003788 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 94122003789 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 94122003790 Nucleoside recognition; Region: Gate; pfam07670 94122003791 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 94122003792 Nucleoside-specific channel-forming protein, Tsx; Region: Channel_Tsx; pfam03502 94122003793 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 94122003794 intersubunit interface [polypeptide binding]; other site 94122003795 active site 94122003796 catalytic residue [active] 94122003797 thymidine phosphorylase; Reviewed; Region: deoA; PRK05820 94122003798 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 94122003799 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 94122003800 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; pfam07831 94122003801 phosphopentomutase; Provisional; Region: PRK05362 94122003802 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 94122003803 purine nucleoside phosphorylase; Reviewed; Region: deoD; PRK05819 94122003804 Bacterial virulence factor haemolysin; Region: SMP_2; cl11479 94122003805 phosphoserine phosphatase SerB; Region: serB; TIGR00338 94122003806 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 94122003807 motif II; other site 94122003808 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 94122003809 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 94122003810 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 94122003811 PilZ domain; Region: PilZ; pfam07238 94122003812 PilZ domain; Region: PilZ; pfam07238 94122003813 DNA repair protein RadA; Provisional; Region: PRK11823 94122003814 Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of...; Region: Sms; cd01121 94122003815 Walker A motif/ATP binding site; other site 94122003816 ATP binding site [chemical binding]; other site 94122003817 Walker B motif; other site 94122003818 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 94122003819 PilZ domain; Region: PilZ; pfam07238 94122003820 DNA-binding transcriptional regulator TorR; Provisional; Region: PRK10766 94122003821 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122003822 active site 94122003823 phosphorylation site [posttranslational modification] 94122003824 intermolecular recognition site; other site 94122003825 dimerization interface [polypeptide binding]; other site 94122003826 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 94122003827 DNA binding site [nucleotide binding] 94122003828 TMAO reductase system periplasmic protein TorT; Provisional; Region: PRK10936 94122003829 TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria; Region: PBP1_TorT-like; cd06306 94122003830 putative ligand binding site [chemical binding]; other site 94122003831 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 94122003832 HAMP domain; Region: HAMP; pfam00672 94122003833 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 94122003834 ATP binding site [chemical binding]; other site 94122003835 Mg2+ binding site [ion binding]; other site 94122003836 G-X-G motif; other site 94122003837 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122003838 active site 94122003839 phosphorylation site [posttranslational modification] 94122003840 intermolecular recognition site; other site 94122003841 dimerization interface [polypeptide binding]; other site 94122003842 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 94122003843 putative binding surface; other site 94122003844 active site 94122003845 chaperone protein TorD; Validated; Region: torD; PRK04976 94122003846 trimethylamine N-oxide reductase I catalytic subunit; Provisional; Region: PRK15102 94122003847 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_DMSOR-BSOR-TMAOR; cd02769 94122003848 molybdopterin cofactor binding site [chemical binding]; other site 94122003849 substrate binding site [chemical binding]; other site 94122003850 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_CT_DMSOR-BSOR-TMAOR; cd02793 94122003851 molybdopterin cofactor binding site; other site 94122003852 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 94122003853 trimethylamine-N-oxide reductase c-type cytochrome TorC; Region: torC; TIGR02162 94122003854 Periplasmic nitrate reductase protein NapE; Region: NapE; pfam06796 94122003855 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 94122003856 FOG: CBS domain [General function prediction only]; Region: COG0517 94122003857 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_24; cd04637 94122003858 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 94122003859 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 94122003860 putative acyl-acceptor binding pocket; other site 94122003861 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; pfam13444 94122003862 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 94122003863 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 94122003864 putative active site [active] 94122003865 putative metal binding site [ion binding]; other site 94122003866 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3314 94122003867 Nucleoside recognition; Region: Gate; pfam07670 94122003868 putative protease; Provisional; Region: PRK15447 94122003869 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 94122003870 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 94122003871 Peptidase family U32; Region: Peptidase_U32; pfam01136 94122003872 SCP-2 sterol transfer family; Region: SCP2; cl01225 94122003873 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 94122003874 putative protease; Provisional; Region: PRK15452 94122003875 Peptidase family U32; Region: Peptidase_U32; pfam01136 94122003876 HDOD domain; Region: HDOD; pfam08668 94122003877 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122003878 metal binding site [ion binding]; metal-binding site 94122003879 active site 94122003880 I-site; other site 94122003881 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 94122003882 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 94122003883 active site 94122003884 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 94122003885 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 94122003886 GDP-binding site [chemical binding]; other site 94122003887 ACT binding site; other site 94122003888 IMP binding site; other site 94122003889 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122003890 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122003891 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 94122003892 dimerization interface [polypeptide binding]; other site 94122003893 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 94122003894 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 94122003895 substrate binding pocket [chemical binding]; other site 94122003896 membrane-bound complex binding site; other site 94122003897 hinge residues; other site 94122003898 OsmC-like protein; Region: OsmC; pfam02566 94122003899 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 94122003900 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 94122003901 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 94122003902 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 94122003903 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122003904 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 94122003905 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 94122003906 Zn2+ binding site [ion binding]; other site 94122003907 Mg2+ binding site [ion binding]; other site 94122003908 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 94122003909 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 94122003910 Zn2+ binding site [ion binding]; other site 94122003911 Mg2+ binding site [ion binding]; other site 94122003912 Uncharacterized conserved protein [Function unknown]; Region: COG1432 94122003913 LabA_like proteins; Region: LabA; cd10911 94122003914 putative metal binding site [ion binding]; other site 94122003915 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 94122003916 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 94122003917 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 94122003918 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 94122003919 putative substrate translocation pore; other site 94122003920 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 94122003921 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 94122003922 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 94122003923 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122003924 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 94122003925 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 94122003926 substrate binding pocket [chemical binding]; other site 94122003927 membrane-bound complex binding site; other site 94122003928 hinge residues; other site 94122003929 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 94122003930 Shewanella-like phosphatases, metallophosphatase domain; Region: MPP_Shelphs; cd07425 94122003931 active site 94122003932 metal binding site [ion binding]; metal-binding site 94122003933 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 94122003934 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 94122003935 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: COG3531 94122003936 DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the...; Region: DsbA_FrnE_like; cd03025 94122003937 catalytic residues [active] 94122003938 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 94122003939 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122003940 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122003941 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 94122003942 putative effector binding pocket; other site 94122003943 dimerization interface [polypeptide binding]; other site 94122003944 Domain of unknown function (DUF389); Region: DUF389; pfam04087 94122003945 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 94122003946 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 94122003947 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 94122003948 ABC transporter; Region: ABC_tran_2; pfam12848 94122003949 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 94122003950 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 94122003951 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 94122003952 dimer interface [polypeptide binding]; other site 94122003953 active site 94122003954 glycine-pyridoxal phosphate binding site [chemical binding]; other site 94122003955 folate binding site [chemical binding]; other site 94122003956 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 94122003957 ATP cone domain; Region: ATP-cone; pfam03477 94122003958 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 94122003959 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 94122003960 catalytic motif [active] 94122003961 Zn binding site [ion binding]; other site 94122003962 RibD C-terminal domain; Region: RibD_C; cl17279 94122003963 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 94122003964 Lumazine binding domain; Region: Lum_binding; pfam00677 94122003965 Lumazine binding domain; Region: Lum_binding; pfam00677 94122003966 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 94122003967 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 94122003968 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 94122003969 dimerization interface [polypeptide binding]; other site 94122003970 active site 94122003971 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 94122003972 homopentamer interface [polypeptide binding]; other site 94122003973 active site 94122003974 Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus...; Region: Terminator_NusB; cd00619 94122003975 putative RNA binding site [nucleotide binding]; other site 94122003976 thiamine monophosphate kinase; Provisional; Region: PRK05731 94122003977 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 94122003978 ATP binding site [chemical binding]; other site 94122003979 dimerization interface [polypeptide binding]; other site 94122003980 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 94122003981 tetramer interfaces [polypeptide binding]; other site 94122003982 binuclear metal-binding site [ion binding]; other site 94122003983 universal stress protein UspE; Provisional; Region: PRK11175 94122003984 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 94122003985 Ligand Binding Site [chemical binding]; other site 94122003986 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 94122003987 Ligand Binding Site [chemical binding]; other site 94122003988 recombination and repair protein; Provisional; Region: PRK10869 94122003989 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 94122003990 Walker A/P-loop; other site 94122003991 ATP binding site [chemical binding]; other site 94122003992 Q-loop/lid; other site 94122003993 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 94122003994 ABC transporter signature motif; other site 94122003995 Walker B; other site 94122003996 D-loop; other site 94122003997 H-loop/switch region; other site 94122003998 Predicted permeases [General function prediction only]; Region: COG0679 94122003999 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122004000 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122004001 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 94122004002 putative effector binding pocket; other site 94122004003 dimerization interface [polypeptide binding]; other site 94122004004 Protein of unknown function (DUF3319); Region: DUF3319; pfam11782 94122004005 Protein of unknown function (DUF416); Region: DUF416; pfam04222 94122004006 hybrid sensory histidine kinase BarA; Provisional; Region: PRK11107 94122004007 Uncharacterized signal transduction histidine kinase domain (DUF2222); Region: DUF2222; pfam09984 94122004008 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 94122004009 dimerization interface [polypeptide binding]; other site 94122004010 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 94122004011 dimer interface [polypeptide binding]; other site 94122004012 phosphorylation site [posttranslational modification] 94122004013 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 94122004014 ATP binding site [chemical binding]; other site 94122004015 Mg2+ binding site [ion binding]; other site 94122004016 G-X-G motif; other site 94122004017 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122004018 active site 94122004019 phosphorylation site [posttranslational modification] 94122004020 intermolecular recognition site; other site 94122004021 dimerization interface [polypeptide binding]; other site 94122004022 Hpt domain; Region: Hpt; pfam01627 94122004023 putative binding surface; other site 94122004024 active site 94122004025 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 94122004026 TRAM domain; Region: TRAM; pfam01938 94122004027 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 94122004028 S-adenosylmethionine binding site [chemical binding]; other site 94122004029 (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional; Region: relA; PRK10872 94122004030 HD domain; Region: HD_4; pfam13328 94122004031 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 94122004032 synthetase active site [active] 94122004033 NTP binding site [chemical binding]; other site 94122004034 metal binding site [ion binding]; metal-binding site 94122004035 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 94122004036 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 94122004037 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl17499 94122004038 Winged helix-turn helix; Region: HTH_29; pfam13551 94122004039 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 94122004040 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs; Region: NTP-PPase_MazG_Nterm; cd11528 94122004041 homodimer interface [polypeptide binding]; other site 94122004042 metal binding site [ion binding]; metal-binding site 94122004043 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs' Region: NTP-PPase_MazG_Cterm; cd11529 94122004044 homodimer interface [polypeptide binding]; other site 94122004045 active site 94122004046 putative chemical substrate binding site [chemical binding]; other site 94122004047 metal binding site [ion binding]; metal-binding site 94122004048 CTP synthetase; Validated; Region: pyrG; PRK05380 94122004049 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 94122004050 Catalytic site [active] 94122004051 active site 94122004052 UTP binding site [chemical binding]; other site 94122004053 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 94122004054 active site 94122004055 putative oxyanion hole; other site 94122004056 catalytic triad [active] 94122004057 enolase; Provisional; Region: eno; PRK00077 94122004058 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 94122004059 dimer interface [polypeptide binding]; other site 94122004060 metal binding site [ion binding]; metal-binding site 94122004061 substrate binding pocket [chemical binding]; other site 94122004062 cell division protein FtsB; Reviewed; Region: ftsB; PRK00888 94122004063 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 94122004064 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 94122004065 substrate binding site; other site 94122004066 dimer interface; other site 94122004067 MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis; Region: MECDP_synthase; cd00554 94122004068 homotrimer interaction site [polypeptide binding]; other site 94122004069 zinc binding site [ion binding]; other site 94122004070 CDP-binding sites; other site 94122004071 tRNA pseudouridine synthase D (TruD); Region: TruD; pfam01142 94122004072 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 94122004073 Permutation of conserved domain; other site 94122004074 active site 94122004075 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 94122004076 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 94122004077 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 94122004078 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 94122004079 S-adenosylmethionine binding site [chemical binding]; other site 94122004080 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 94122004081 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 94122004082 Peptidase family M23; Region: Peptidase_M23; pfam01551 94122004083 RNA polymerase sigma factor RpoS; Region: rpoS_proteo; TIGR02394 94122004084 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 94122004085 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 94122004086 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 94122004087 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 94122004088 DNA binding residues [nucleotide binding] 94122004089 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 94122004090 MutS domain I; Region: MutS_I; pfam01624 94122004091 MutS domain II; Region: MutS_II; pfam05188 94122004092 MutS domain III; Region: MutS_III; pfam05192 94122004093 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 94122004094 Walker A/P-loop; other site 94122004095 ATP binding site [chemical binding]; other site 94122004096 Q-loop/lid; other site 94122004097 ABC transporter signature motif; other site 94122004098 Walker B; other site 94122004099 D-loop; other site 94122004100 H-loop/switch region; other site 94122004101 recombinase A; Provisional; Region: recA; PRK09354 94122004102 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 94122004103 hexamer interface [polypeptide binding]; other site 94122004104 Walker A motif; other site 94122004105 ATP binding site [chemical binding]; other site 94122004106 Walker B motif; other site 94122004107 RecX family; Region: RecX; pfam02631 94122004108 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 94122004109 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 94122004110 motif 1; other site 94122004111 active site 94122004112 motif 2; other site 94122004113 motif 3; other site 94122004114 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 94122004115 DHHA1 domain; Region: DHHA1; pfam02272 94122004116 aspartate kinase; Reviewed; Region: PRK06635 94122004117 AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive...; Region: AAK_AKii-LysC-BS; cd04261 94122004118 putative nucleotide binding site [chemical binding]; other site 94122004119 putative catalytic residues [active] 94122004120 putative Mg ion binding site [ion binding]; other site 94122004121 putative aspartate binding site [chemical binding]; other site 94122004122 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AKii-LysC-BS-like_2; cd04936 94122004123 putative allosteric regulatory residue; other site 94122004124 carbon storage regulator; Provisional; Region: PRK01712 94122004125 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 94122004126 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 94122004127 HIGH motif; other site 94122004128 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 94122004129 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 94122004130 active site 94122004131 KMSKS motif; other site 94122004132 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 94122004133 tRNA binding surface [nucleotide binding]; other site 94122004134 anticodon binding site; other site 94122004135 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 94122004136 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 94122004137 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 94122004138 30S subunit binding site; other site 94122004139 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 94122004140 Cytochrome C' Region: Cytochrom_C_2; pfam01322 94122004141 Trp repressor protein; Region: Trp_repressor; pfam01371 94122004142 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 94122004143 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 94122004144 bifunctional aspartokinase I/homoserine dehydrogenase I; Provisional; Region: thrA; PRK09436 94122004145 AAK_AK-HSDH: Amino Acid Kinase Superfamily (AAK), AK-HSDH; this CD includes the N-terminal catalytic domain of aspartokinase (AK) of the bifunctional enzyme AK - homoserine dehydrogenase (HSDH). These aspartokinases are found in bacteria (E. coli...; Region: AAK_AK-HSDH; cd04257 94122004146 putative catalytic residues [active] 94122004147 putative nucleotide binding site [chemical binding]; other site 94122004148 putative aspartate binding site [chemical binding]; other site 94122004149 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA-like_1; cd04921 94122004150 dimer interface [polypeptide binding]; other site 94122004151 putative threonine allosteric regulatory site; other site 94122004152 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA_2; cd04922 94122004153 putative threonine allosteric regulatory site; other site 94122004154 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 94122004155 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 94122004156 homoserine kinase; Provisional; Region: PRK01212 94122004157 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 94122004158 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 94122004159 threonine synthase; Validated; Region: PRK09225 94122004160 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 94122004161 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 94122004162 catalytic residue [active] 94122004163 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 94122004164 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 94122004165 substrate binding pocket [chemical binding]; other site 94122004166 membrane-bound complex binding site; other site 94122004167 hinge residues; other site 94122004168 Uncharacterized protein related to the periplasmic component of the Tol biopolymer transport system [Function unknown]; Region: COG4946 94122004169 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 94122004170 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 94122004171 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 94122004172 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 94122004173 protein binding site [polypeptide binding]; other site 94122004174 Tricorn protease; serine protease family S41; Region: Peptidase_S41_TRI; cd07562 94122004175 Domain interface; other site 94122004176 Peptide binding site; other site 94122004177 Active site tetrad [active] 94122004178 OsmC-like protein; Region: OsmC; cl00767 94122004179 Protein of unknown function (DUF3325); Region: DUF3325; pfam11804 94122004180 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 94122004181 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 94122004182 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 94122004183 PAS domain; Region: PAS_9; pfam13426 94122004184 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 94122004185 putative active site [active] 94122004186 heme pocket [chemical binding]; other site 94122004187 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 94122004188 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122004189 dimer interface [polypeptide binding]; other site 94122004190 putative CheW interface [polypeptide binding]; other site 94122004191 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 94122004192 30S subunit binding site; other site 94122004193 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 94122004194 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122004195 active site 94122004196 phosphorylation site [posttranslational modification] 94122004197 intermolecular recognition site; other site 94122004198 dimerization interface [polypeptide binding]; other site 94122004199 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 94122004200 DNA binding residues [nucleotide binding] 94122004201 dimerization interface [polypeptide binding]; other site 94122004202 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 94122004203 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 94122004204 ATP binding site [chemical binding]; other site 94122004205 Mg2+ binding site [ion binding]; other site 94122004206 G-X-G motif; other site 94122004207 Isochorismatase family; Region: Isochorismatase; pfam00857 94122004208 Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia; Region: nicotinamidase_related; cd01014 94122004209 catalytic triad [active] 94122004210 conserved cis-peptide bond; other site 94122004211 hypothetical protein; Provisional; Region: PRK12378 94122004212 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122004213 dimer interface [polypeptide binding]; other site 94122004214 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 94122004215 putative CheW interface [polypeptide binding]; other site 94122004216 Protein of unknown function (DUF2375); Region: DUF2375; pfam09558 94122004217 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 94122004218 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 94122004219 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 94122004220 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 94122004221 FMN binding site [chemical binding]; other site 94122004222 active site 94122004223 substrate binding site [chemical binding]; other site 94122004224 catalytic residue [active] 94122004225 AAA domain; Region: AAA_32; pfam13654 94122004226 ATP-dependent protease Lon; Provisional; Region: PRK13765 94122004227 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 94122004228 PAS domain; Region: PAS_9; pfam13426 94122004229 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 94122004230 PAS domain; Region: PAS_9; pfam13426 94122004231 putative active site [active] 94122004232 heme pocket [chemical binding]; other site 94122004233 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122004234 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122004235 metal binding site [ion binding]; metal-binding site 94122004236 active site 94122004237 I-site; other site 94122004238 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 94122004239 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 94122004240 DEAD-like helicases superfamily; Region: DEXDc; smart00487 94122004241 ATP binding site [chemical binding]; other site 94122004242 Mg++ binding site [ion binding]; other site 94122004243 motif III; other site 94122004244 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 94122004245 nucleotide binding region [chemical binding]; other site 94122004246 ATP-binding site [chemical binding]; other site 94122004247 Protein of unknown function (DUF523); Region: DUF523; pfam04463 94122004248 Uncharacterized conserved protein [Function unknown]; Region: COG3272 94122004249 Protein of unknown function (DUF1722); Region: DUF1722; pfam08349 94122004250 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 94122004251 DNA binding residues [nucleotide binding] 94122004252 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 94122004253 DNA photolyase; Region: DNA_photolyase; pfam00875 94122004254 deoxyribodipyrimidine photolyase; Provisional; Region: PRK10674 94122004255 SnoaL-like domain; Region: SnoaL_2; pfam12680 94122004256 short chain dehydrogenase; Provisional; Region: PRK06101 94122004257 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 94122004258 NAD(P) binding site [chemical binding]; other site 94122004259 active site 94122004260 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 94122004261 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 94122004262 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 94122004263 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 94122004264 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 94122004265 S-adenosylmethionine binding site [chemical binding]; other site 94122004266 Protein of unknown function (DUF2878); Region: DUF2878; pfam11086 94122004267 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 94122004268 Protein of unknown function (DUF3634); Region: DUF3634; pfam12321 94122004269 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 94122004270 hypothetical protein; Provisional; Region: PRK03757 94122004271 oxidative damage protection protein; Provisional; Region: PRK05408 94122004272 adenine DNA glycosylase; Provisional; Region: PRK10880 94122004273 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 94122004274 minor groove reading motif; other site 94122004275 helix-hairpin-helix signature motif; other site 94122004276 substrate binding pocket [chemical binding]; other site 94122004277 active site 94122004278 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 94122004279 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 94122004280 DNA binding and oxoG recognition site [nucleotide binding] 94122004281 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 94122004282 S-adenosylmethionine binding site [chemical binding]; other site 94122004283 hypothetical protein; Provisional; Region: PRK11702 94122004284 Glutaminase [Amino acid transport and metabolism]; Region: GlsA; COG2066 94122004285 glutaminase; Provisional; Region: PRK00971 94122004286 Protein of unknown function (DUF2884); Region: DUF2884; pfam11101 94122004287 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122004288 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122004289 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 94122004290 putative effector binding pocket; other site 94122004291 dimerization interface [polypeptide binding]; other site 94122004292 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 94122004293 HemN family oxidoreductase; Provisional; Region: PRK05660 94122004294 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 94122004295 FeS/SAM binding site; other site 94122004296 HemN C-terminal domain; Region: HemN_C; pfam06969 94122004297 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 94122004298 active site 94122004299 dimerization interface [polypeptide binding]; other site 94122004300 Domain of unknown function (DUF4426); Region: DUF4426; pfam14467 94122004301 hypothetical protein; Validated; Region: PRK05090 94122004302 YGGT family; Region: YGGT; pfam02325 94122004303 YGGT family; Region: YGGT; pfam02325 94122004304 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 94122004305 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 94122004306 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 94122004307 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 94122004308 catalytic residue [active] 94122004309 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 94122004310 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 94122004311 Walker A motif; other site 94122004312 ATP binding site [chemical binding]; other site 94122004313 Walker B motif; other site 94122004314 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 94122004315 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 94122004316 Walker A motif; other site 94122004317 ATP binding site [chemical binding]; other site 94122004318 Walker B motif; other site 94122004319 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 94122004320 catalytic residues [active] 94122004321 dimer interface [polypeptide binding]; other site 94122004322 ferrochelatase; Reviewed; Region: hemH; PRK00035 94122004323 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 94122004324 C-terminal domain interface [polypeptide binding]; other site 94122004325 active site 94122004326 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 94122004327 active site 94122004328 N-terminal domain interface [polypeptide binding]; other site 94122004329 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 94122004330 hypothetical protein; Validated; Region: PRK00228 94122004331 translation initiation factor Sui1; Validated; Region: PRK06824 94122004332 Homologs of eIF1/SUI1 including Escherichia coli YciH; Region: YciH_like; cd11567 94122004333 putative rRNA binding site [nucleotide binding]; other site 94122004334 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 94122004335 Predicted membrane protein [Function unknown]; Region: COG2860 94122004336 UPF0126 domain; Region: UPF0126; pfam03458 94122004337 UPF0126 domain; Region: UPF0126; pfam03458 94122004338 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 94122004339 dimer interface [polypeptide binding]; other site 94122004340 catalytic triad [active] 94122004341 peroxidatic and resolving cysteines [active] 94122004342 Conserved TM helix; Region: TM_helix; pfam05552 94122004343 mechanosensitive channel MscS; Provisional; Region: PRK10334 94122004344 Mechanosensitive ion channel; Region: MS_channel; pfam00924 94122004345 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 94122004346 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 94122004347 ligand binding site [chemical binding]; other site 94122004348 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 94122004349 Low-specificity threonine aldolase (TA). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). TA catalyzes the conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a...; Region: TA_like; cd06502 94122004350 tetramer interface [polypeptide binding]; other site 94122004351 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122004352 catalytic residue [active] 94122004353 HDOD domain; Region: HDOD; pfam08668 94122004354 GAF domain; Region: GAF_3; pfam13492 94122004355 Calcium/calmodulin dependent protein kinase II Association; Region: CaMKII_AD; cl17504 94122004356 SnoaL-like domain; Region: SnoaL_3; pfam13474 94122004357 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; pfam06167 94122004358 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122004359 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122004360 metal binding site [ion binding]; metal-binding site 94122004361 active site 94122004362 I-site; other site 94122004363 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 94122004364 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 94122004365 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 94122004366 ParA-like protein; Provisional; Region: PHA02518 94122004367 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 94122004368 P-loop; other site 94122004369 Magnesium ion binding site [ion binding]; other site 94122004370 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122004371 Coenzyme A binding pocket [chemical binding]; other site 94122004372 Protein of unknown function (DUF3820); Region: DUF3820; pfam12843 94122004373 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 94122004374 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122004375 Coenzyme A binding pocket [chemical binding]; other site 94122004376 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 94122004377 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122004378 Coenzyme A binding pocket [chemical binding]; other site 94122004379 Pirin-related protein [General function prediction only]; Region: COG1741 94122004380 Pirin; Region: Pirin; pfam02678 94122004381 DoxX; Region: DoxX; pfam07681 94122004382 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122004383 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 94122004384 The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; Region: PBP2_HupR; cd08431 94122004385 putative dimerization interface [polypeptide binding]; other site 94122004386 NAD pyrophosphatase/5'-nucleotidase NadN; Region: nadN; TIGR01530 94122004387 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 94122004388 active site 94122004389 metal binding site [ion binding]; metal-binding site 94122004390 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 94122004391 Domain of unknown function DUF21; Region: DUF21; pfam01595 94122004392 FOG: CBS domain [General function prediction only]; Region: COG0517 94122004393 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 94122004394 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 94122004395 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 94122004396 FeS/SAM binding site; other site 94122004397 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 94122004398 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 94122004399 binding surface 94122004400 TPR motif; other site 94122004401 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 94122004402 binding surface 94122004403 TPR motif; other site 94122004404 cytoskeletal protein RodZ; Provisional; Region: PRK10856 94122004405 Helix-turn-helix domain; Region: HTH_25; pfam13413 94122004406 non-specific DNA binding site [nucleotide binding]; other site 94122004407 salt bridge; other site 94122004408 sequence-specific DNA binding site [nucleotide binding]; other site 94122004409 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 94122004410 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 94122004411 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 94122004412 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 94122004413 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 94122004414 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 94122004415 dimer interface [polypeptide binding]; other site 94122004416 motif 1; other site 94122004417 active site 94122004418 motif 2; other site 94122004419 motif 3; other site 94122004420 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 94122004421 anticodon binding site; other site 94122004422 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 94122004423 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 94122004424 outer membrane biogenesis protein BamB; Provisional; Region: PRK11138 94122004425 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 94122004426 Trp docking motif [polypeptide binding]; other site 94122004427 active site 94122004428 GTP-binding protein Der; Reviewed; Region: PRK00093 94122004429 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 94122004430 G1 box; other site 94122004431 GTP/Mg2+ binding site [chemical binding]; other site 94122004432 Switch I region; other site 94122004433 G2 box; other site 94122004434 Switch II region; other site 94122004435 G3 box; other site 94122004436 G4 box; other site 94122004437 G5 box; other site 94122004438 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 94122004439 G1 box; other site 94122004440 GTP/Mg2+ binding site [chemical binding]; other site 94122004441 Switch I region; other site 94122004442 G2 box; other site 94122004443 G3 box; other site 94122004444 Switch II region; other site 94122004445 G4 box; other site 94122004446 G5 box; other site 94122004447 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 94122004448 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 94122004449 generic binding surface II; other site 94122004450 generic binding surface I; other site 94122004451 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 94122004452 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 94122004453 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 94122004454 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 94122004455 active site 94122004456 GMP synthase; Reviewed; Region: guaA; PRK00074 94122004457 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 94122004458 AMP/PPi binding site [chemical binding]; other site 94122004459 candidate oxyanion hole; other site 94122004460 catalytic triad [active] 94122004461 potential glutamine specificity residues [chemical binding]; other site 94122004462 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 94122004463 ATP Binding subdomain [chemical binding]; other site 94122004464 Ligand Binding sites [chemical binding]; other site 94122004465 Dimerization subdomain; other site 94122004466 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 94122004467 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 94122004468 nucleoside/Zn binding site; other site 94122004469 dimer interface [polypeptide binding]; other site 94122004470 catalytic motif [active] 94122004471 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 94122004472 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 94122004473 substrate binding pocket [chemical binding]; other site 94122004474 membrane-bound complex binding site; other site 94122004475 hinge residues; other site 94122004476 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 94122004477 N-acetyl-D-glucosamine binding site [chemical binding]; other site 94122004478 catalytic residue [active] 94122004479 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 94122004480 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 94122004481 dimerization interface [polypeptide binding]; other site 94122004482 ATP binding site [chemical binding]; other site 94122004483 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 94122004484 dimerization interface [polypeptide binding]; other site 94122004485 ATP binding site [chemical binding]; other site 94122004486 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 94122004487 putative active site [active] 94122004488 catalytic triad [active] 94122004489 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 94122004490 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 94122004491 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 94122004492 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 94122004493 Membrane bound YbgT-like protein; Region: YbgT_YccB; cl02039 94122004494 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 94122004495 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 94122004496 active site 94122004497 DNA binding site [nucleotide binding] 94122004498 Int/Topo IB signature motif; other site 94122004499 Protein of unknown function (DUF1044); Region: DUF1044; pfam06296 94122004500 Predicted transcriptional regulator [Transcription]; Region: COG2944 94122004501 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 94122004502 non-specific DNA binding site [nucleotide binding]; other site 94122004503 salt bridge; other site 94122004504 sequence-specific DNA binding site [nucleotide binding]; other site 94122004505 Protein of unknown function (Hypoth_ymh); Region: Hypoth_Ymh; pfam09509 94122004506 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 94122004507 Predicted ATPase [General function prediction only]; Region: COG3911 94122004508 AAA domain; Region: AAA_28; pfam13521 94122004509 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 94122004510 Integrase core domain; Region: rve; pfam00665 94122004511 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 94122004512 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 94122004513 Walker A motif; other site 94122004514 ATP binding site [chemical binding]; other site 94122004515 Walker B motif; other site 94122004516 hypothetical protein; Reviewed; Region: PRK00024 94122004517 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 94122004518 MPN+ (JAMM) motif; other site 94122004519 Zinc-binding site [ion binding]; other site 94122004520 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 94122004521 AAA domain; Region: AAA_12; pfam13087 94122004522 Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme; Region: NT_2-5OAS_ClassI-CCAase; cd05400 94122004523 active site 94122004524 NTP binding site [chemical binding]; other site 94122004525 metal binding triad [ion binding]; metal-binding site 94122004526 Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17; Region: Pat17_PNPLA8_PNPLA9_like; cd07199 94122004527 active site 94122004528 nucleophile elbow; other site 94122004529 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 94122004530 sequence-specific DNA binding site [nucleotide binding]; other site 94122004531 salt bridge; other site 94122004532 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 94122004533 Uncharacterized conserved protein (DUF2285); Region: DUF2285; pfam10074 94122004534 Helix-turn-helix domain; Region: HTH_17; cl17695 94122004535 Replication initiator protein A; Region: RPA; pfam10134 94122004536 ParA-like protein; Provisional; Region: PHA02518 94122004537 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 94122004538 P-loop; other site 94122004539 Magnesium ion binding site [ion binding]; other site 94122004540 Protein of unknown function (DUF2840); Region: DUF2840; pfam11000 94122004541 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 94122004542 Signal peptidase, peptidase S26; Region: Peptidase_S26; pfam10502 94122004543 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 94122004544 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 94122004545 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 94122004546 salt bridge; other site 94122004547 non-specific DNA binding site [nucleotide binding]; other site 94122004548 sequence-specific DNA binding site [nucleotide binding]; other site 94122004549 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 94122004550 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 94122004551 putative substrate translocation pore; other site 94122004552 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122004553 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 94122004554 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 94122004555 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 94122004556 Transcriptional regulator [Transcription]; Region: IclR; COG1414 94122004557 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 94122004558 Bacterial transcriptional regulator; Region: IclR; pfam01614 94122004559 Domain of unknown function (DUF336); Region: DUF336; cl01249 94122004560 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 94122004561 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 94122004562 putative substrate translocation pore; other site 94122004563 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 94122004564 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122004565 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 94122004566 dimerization interface [polypeptide binding]; other site 94122004567 substrate binding pocket [chemical binding]; other site 94122004568 conjugal transfer coupling protein TraG; Provisional; Region: PRK13876 94122004569 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 94122004570 Walker A motif; other site 94122004571 ATP binding site [chemical binding]; other site 94122004572 Walker B motif; other site 94122004573 P-type conjugative transfer ATPase TrbB; Region: TrbB_P; TIGR02782 94122004574 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 94122004575 ATP binding site [chemical binding]; other site 94122004576 Walker A motif; other site 94122004577 hexamer interface [polypeptide binding]; other site 94122004578 Walker B motif; other site 94122004579 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 94122004580 Type IV secretory pathway, TrbD component [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TrbD; COG5268 94122004581 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 94122004582 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 94122004583 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 94122004584 Walker A motif; other site 94122004585 ATP binding site [chemical binding]; other site 94122004586 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 94122004587 Conjugal transfer/entry exclusion protein [Intracellular trafficking and secretion]; Region: COG5314 94122004588 conjugal transfer protein TrbJ; Provisional; Region: PRK13874 94122004589 conjugal transfer protein TrbL; Provisional; Region: PRK13875 94122004590 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 94122004591 conjugal transfer protein TrbF; Provisional; Region: PRK13872 94122004592 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 94122004593 VirB7 interaction site; other site 94122004594 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 94122004595 Protein of unknown function (DUF2274); Region: DUF2274; pfam10038 94122004596 HAMP domain; Region: HAMP; pfam00672 94122004597 dimerization interface [polypeptide binding]; other site 94122004598 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 94122004599 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122004600 dimer interface [polypeptide binding]; other site 94122004601 putative CheW interface [polypeptide binding]; other site 94122004602 Protein of unknown function (DUF465); Region: DUF465; pfam04325 94122004603 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 94122004604 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 94122004605 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 94122004606 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122004607 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 94122004608 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 94122004609 Chalcone-flavanone isomerase; Region: Chalcone; cl03589 94122004610 Protein of unknown function (DUF2947); Region: DUF2947; pfam11163 94122004611 Protein of unknown function DUF115; Region: MAF_flag10; pfam01973 94122004612 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 94122004613 binding surface 94122004614 TPR motif; other site 94122004615 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 94122004616 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 94122004617 NAD(P) binding site [chemical binding]; other site 94122004618 homodimer interface [polypeptide binding]; other site 94122004619 substrate binding site [chemical binding]; other site 94122004620 active site 94122004621 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 94122004622 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 94122004623 inhibitor-cofactor binding pocket; inhibition site 94122004624 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122004625 catalytic residue [active] 94122004626 pseudaminic acid synthase; Region: PseI; TIGR03586 94122004627 NeuB family; Region: NeuB; pfam03102 94122004628 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 94122004629 NeuB binding interface [polypeptide binding]; other site 94122004630 putative substrate binding site [chemical binding]; other site 94122004631 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; pfam05721 94122004632 Methyltransferase domain; Region: Methyltransf_23; pfam13489 94122004633 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 94122004634 S-adenosylmethionine binding site [chemical binding]; other site 94122004635 WbqC-like protein family; Region: WbqC; pfam08889 94122004636 pseudaminic acid biosynthesis-associated protein PseG; Region: PseG; TIGR03590 94122004637 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 94122004638 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 94122004639 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 94122004640 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 94122004641 ligand binding site; other site 94122004642 tetramer interface; other site 94122004643 Protein of unknown function DUF115; Region: MAF_flag10; pfam01973 94122004644 Integrase core domain; Region: rve_3; cl15866 94122004645 LPP20 lipoprotein; Region: LPP20; pfam02169 94122004646 FlgN protein; Region: FlgN; pfam05130 94122004647 Anti-sigma-28 factor, FlgM; Region: FlgM; pfam04316 94122004648 flagellar basal body P-ring biosynthesis protein FlgA; Reviewed; Region: flgA; PRK07018 94122004649 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 94122004650 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 94122004651 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 94122004652 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122004653 active site 94122004654 phosphorylation site [posttranslational modification] 94122004655 intermolecular recognition site; other site 94122004656 dimerization interface [polypeptide binding]; other site 94122004657 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 94122004658 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 94122004659 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 94122004660 flagellar basal body rod protein FlgB; Provisional; Region: flgB; PRK12625 94122004661 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 94122004662 flagellar basal body rod protein FlgC; Provisional; Region: flgC; PRK12631 94122004663 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 94122004664 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 94122004665 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK06655 94122004666 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 94122004667 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 94122004668 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 94122004669 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 94122004670 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 94122004671 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 94122004672 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 94122004673 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 94122004674 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 94122004675 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 94122004676 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK12698 94122004677 Flagellar L-ring protein; Region: FlgH; pfam02107 94122004678 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 94122004679 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 94122004680 Rod binding protein [Cell envelope biogenesis, outer membrane / Cell motility and secretion / Posttranslational modification, protein turnover, chaperones]; Region: COG3951 94122004681 flagellar rod assembly protein/muramidase FlgJ; Region: flagell_FlgJ; TIGR02541 94122004682 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 94122004683 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK08871 94122004684 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 94122004685 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 94122004686 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 94122004687 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 94122004688 flagellin; Provisional; Region: PRK12802 94122004689 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 94122004690 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 94122004691 flagellin; Provisional; Region: PRK12802 94122004692 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 94122004693 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 94122004694 FlaG protein; Region: FlaG; pfam03646 94122004695 Flagellar capping protein [Cell motility and secretion]; Region: FliD; COG1345 94122004696 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 94122004697 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 94122004698 flagellar protein FliS; Validated; Region: fliS; PRK05685 94122004699 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 94122004700 Flagellar regulatory protein FleQ; Region: FleQ; pfam06490 94122004701 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 94122004702 Walker A motif; other site 94122004703 ATP binding site [chemical binding]; other site 94122004704 Walker B motif; other site 94122004705 arginine finger; other site 94122004706 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 94122004707 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 94122004708 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 94122004709 putative active site [active] 94122004710 heme pocket [chemical binding]; other site 94122004711 His Kinase A (phosphoacceptor) domain; Region: HisKA; smart00388 94122004712 dimer interface [polypeptide binding]; other site 94122004713 phosphorylation site [posttranslational modification] 94122004714 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 94122004715 ATP binding site [chemical binding]; other site 94122004716 Mg2+ binding site [ion binding]; other site 94122004717 G-X-G motif; other site 94122004718 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 94122004719 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122004720 active site 94122004721 phosphorylation site [posttranslational modification] 94122004722 intermolecular recognition site; other site 94122004723 dimerization interface [polypeptide binding]; other site 94122004724 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 94122004725 Walker A motif; other site 94122004726 ATP binding site [chemical binding]; other site 94122004727 Walker B motif; other site 94122004728 arginine finger; other site 94122004729 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 94122004730 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK00253 94122004731 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 94122004732 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 94122004733 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 94122004734 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 94122004735 MgtE intracellular N domain; Region: MgtE_N; smart00924 94122004736 FliG C-terminal domain; Region: FliG_C; pfam01706 94122004737 flagellar assembly protein H; Validated; Region: fliH; PRK05687 94122004738 Flagellar assembly protein FliH; Region: FliH; pfam02108 94122004739 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08972 94122004740 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 94122004741 Walker A motif/ATP binding site; other site 94122004742 Walker B motif; other site 94122004743 Flagellar FliJ protein; Region: FliJ; pfam02050 94122004744 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 94122004745 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 94122004746 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK05696 94122004747 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 94122004748 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 94122004749 flagellar motor switch protein; Validated; Region: fliN; PRK08983 94122004750 Flagellar biosynthesis protein, FliO; Region: FliO; pfam04347 94122004751 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 94122004752 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 94122004753 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 94122004754 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 94122004755 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 94122004756 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 94122004757 FHIPEP family; Region: FHIPEP; pfam00771 94122004758 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 94122004759 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 94122004760 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 94122004761 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 94122004762 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 94122004763 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 94122004764 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 94122004765 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 94122004766 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 94122004767 DNA binding residues [nucleotide binding] 94122004768 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 94122004769 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122004770 active site 94122004771 phosphorylation site [posttranslational modification] 94122004772 intermolecular recognition site; other site 94122004773 dimerization interface [polypeptide binding]; other site 94122004774 Chemotaxis phosphatase, CheZ; Region: CheZ; pfam04344 94122004775 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 94122004776 putative binding surface; other site 94122004777 active site 94122004778 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 94122004779 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 94122004780 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 94122004781 ATP binding site [chemical binding]; other site 94122004782 Mg2+ binding site [ion binding]; other site 94122004783 G-X-G motif; other site 94122004784 CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling...; Region: CheA_reg; cd00731 94122004785 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 94122004786 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122004787 active site 94122004788 phosphorylation site [posttranslational modification] 94122004789 intermolecular recognition site; other site 94122004790 CheB methylesterase; Region: CheB_methylest; pfam01339 94122004791 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 94122004792 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 94122004793 P-loop; other site 94122004794 Magnesium ion binding site [ion binding]; other site 94122004795 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 94122004796 Magnesium ion binding site [ion binding]; other site 94122004797 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cd00588 94122004798 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 94122004799 putative CheA interaction surface; other site 94122004800 Protein of unknown function (DUF2802); Region: DUF2802; pfam10975 94122004801 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 94122004802 Flagellar hook-length control protein FliK; Region: Flg_hook; cl17777 94122004803 VacJ like lipoprotein; Region: VacJ; cl01073 94122004804 Response regulator receiver domain; Region: Response_reg; pfam00072 94122004805 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122004806 active site 94122004807 phosphorylation site [posttranslational modification] 94122004808 intermolecular recognition site; other site 94122004809 dimerization interface [polypeptide binding]; other site 94122004810 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 94122004811 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 94122004812 putative substrate translocation pore; other site 94122004813 POT family; Region: PTR2; cl17359 94122004814 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; Region: NGN_SP_RfaH; cd09892 94122004815 transcriptional activator RfaH; Region: RfaH; TIGR01955 94122004816 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 94122004817 heterodimer interface [polypeptide binding]; other site 94122004818 homodimer interface [polypeptide binding]; other site 94122004819 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 94122004820 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 94122004821 SLBB domain; Region: SLBB; pfam10531 94122004822 SLBB domain; Region: SLBB; pfam10531 94122004823 SLBB domain; Region: SLBB; pfam10531 94122004824 Capsule biosynthesis GfcC; Region: Caps_synth_GfcC; pfam06251 94122004825 SLBB domain; Region: SLBB; pfam10531 94122004826 Chain length determinant protein; Region: Wzz; pfam02706 94122004827 exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase; Region: EPS_sugtrans; TIGR03025 94122004828 Bacterial sugar transferase; Region: Bac_transf; pfam02397 94122004829 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 94122004830 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 94122004831 active site 94122004832 dTDP-glucose 4,6 dehydratase; Provisional; Region: PRK10084 94122004833 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 94122004834 NAD binding site [chemical binding]; other site 94122004835 substrate binding site [chemical binding]; other site 94122004836 homodimer interface [polypeptide binding]; other site 94122004837 active site 94122004838 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 94122004839 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 94122004840 substrate binding site; other site 94122004841 tetramer interface; other site 94122004842 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 94122004843 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 94122004844 NADP binding site [chemical binding]; other site 94122004845 active site 94122004846 putative substrate binding site [chemical binding]; other site 94122004847 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: rmlC; TIGR01221 94122004848 GDP-fucose protein O-fucosyltransferase and related proteins; Region: O-FucT_like; cl16914 94122004849 GDP-Fucose binding site [chemical binding]; other site 94122004850 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 94122004851 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 94122004852 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 94122004853 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 94122004854 HutD; Region: HutD; pfam05962 94122004855 NlpE N-terminal domain; Region: NlpE; pfam04170 94122004856 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 94122004857 GAF domain; Region: GAF; pfam01590 94122004858 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 94122004859 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 94122004860 ATP binding site [chemical binding]; other site 94122004861 Mg2+ binding site [ion binding]; other site 94122004862 G-X-G motif; other site 94122004863 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 94122004864 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 94122004865 substrate binding site; other site 94122004866 tetramer interface; other site 94122004867 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; cl17405 94122004868 Bacterial putative lipoprotein (DUF940); Region: DUF940; pfam06082 94122004869 Capsule biosynthesis GfcC; Region: Caps_synth_GfcC; pfam06251 94122004870 Protein of unknown function (DUF2886); Region: DUF2886; pfam11102 94122004871 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 94122004872 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 94122004873 nucleophile elbow; other site 94122004874 prolyl-tRNA synthetase; Provisional; Region: PRK09194 94122004875 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 94122004876 dimer interface [polypeptide binding]; other site 94122004877 motif 1; other site 94122004878 active site 94122004879 motif 2; other site 94122004880 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 94122004881 putative deacylase active site [active] 94122004882 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 94122004883 active site 94122004884 motif 3; other site 94122004885 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 94122004886 anticodon binding site; other site 94122004887 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 94122004888 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 94122004889 putative CoA binding site [chemical binding]; other site 94122004890 Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the...; Region: LbH_MAT_like; cd04647 94122004891 trimer interface [polypeptide binding]; other site 94122004892 active site 94122004893 substrate binding site [chemical binding]; other site 94122004894 CoA binding site [chemical binding]; other site 94122004895 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 94122004896 homodimer interaction site [polypeptide binding]; other site 94122004897 cofactor binding site; other site 94122004898 outer membrane lipoprotein; Reviewed; Region: rcsF; PRK10781 94122004899 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 94122004900 Metallo-dependent hydrolases, subgroup C 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_C; cd01309 94122004901 active site 94122004902 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 94122004903 active site 94122004904 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 94122004905 Metallo-dependent hydrolases, subgroup C 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_C; cd01309 94122004906 active site 94122004907 Topoisomer_IB_N: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA; Region: Topoisomer_IB_N; cl02774 94122004908 DNA-binding protein H-NS [General function prediction only]; Region: Hns; COG2916 94122004909 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 94122004910 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 94122004911 Ligand binding site [chemical binding]; other site 94122004912 Electron transfer flavoprotein domain; Region: ETF; pfam01012 94122004913 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 94122004914 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 94122004915 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 94122004916 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 94122004917 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 94122004918 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 94122004919 active site 94122004920 Zn binding site [ion binding]; other site 94122004921 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 94122004922 thymidine kinase; Provisional; Region: PRK04296 94122004923 Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane]; Region: MrcB; COG0744 94122004924 Transglycosylase; Region: Transgly; cl17702 94122004925 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 94122004926 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122004927 active site 94122004928 phosphorylation site [posttranslational modification] 94122004929 intermolecular recognition site; other site 94122004930 dimerization interface [polypeptide binding]; other site 94122004931 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 94122004932 Walker A motif; other site 94122004933 ATP binding site [chemical binding]; other site 94122004934 Walker B motif; other site 94122004935 arginine finger; other site 94122004936 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 94122004937 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 94122004938 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 94122004939 dimer interface [polypeptide binding]; other site 94122004940 phosphorylation site [posttranslational modification] 94122004941 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 94122004942 ATP binding site [chemical binding]; other site 94122004943 Mg2+ binding site [ion binding]; other site 94122004944 G-X-G motif; other site 94122004945 DctM-like transporters; Region: DctM; pfam06808 94122004946 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 94122004947 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 94122004948 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 94122004949 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 94122004950 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 94122004951 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 94122004952 active site 94122004953 HIGH motif; other site 94122004954 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 94122004955 active site 94122004956 KMSKS motif; other site 94122004957 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 94122004958 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 94122004959 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 94122004960 Walker A/P-loop; other site 94122004961 ATP binding site [chemical binding]; other site 94122004962 Q-loop/lid; other site 94122004963 ABC transporter signature motif; other site 94122004964 Walker B; other site 94122004965 D-loop; other site 94122004966 H-loop/switch region; other site 94122004967 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 94122004968 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 94122004969 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 94122004970 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 94122004971 AlkA N-terminal domain; Region: AlkA_N; pfam06029 94122004972 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]; Region: AlkA; COG0122 94122004973 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 94122004974 minor groove reading motif; other site 94122004975 helix-hairpin-helix signature motif; other site 94122004976 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 94122004977 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 94122004978 DNA binding site [nucleotide binding] 94122004979 active site 94122004980 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 94122004981 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 94122004982 ATP binding site [chemical binding]; other site 94122004983 putative Mg++ binding site [ion binding]; other site 94122004984 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 94122004985 nucleotide binding region [chemical binding]; other site 94122004986 ATP-binding site [chemical binding]; other site 94122004987 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 94122004988 active site 94122004989 catalytic residues [active] 94122004990 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 94122004991 PLD-like domain; Region: PLDc_2; pfam13091 94122004992 putative active site [active] 94122004993 catalytic site [active] 94122004994 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 94122004995 PLD-like domain; Region: PLDc_2; pfam13091 94122004996 putative active site [active] 94122004997 catalytic site [active] 94122004998 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cd00588 94122004999 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 94122005000 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122005001 active site 94122005002 phosphorylation site [posttranslational modification] 94122005003 intermolecular recognition site; other site 94122005004 dimerization interface [polypeptide binding]; other site 94122005005 serine/threonine transporter SstT; Provisional; Region: PRK13628 94122005006 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 94122005007 Complex I intermediate-associated protein 30 (CIA30); Region: CIA30; pfam08547 94122005008 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 94122005009 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 94122005010 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 94122005011 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 94122005012 active site 94122005013 TlpA-like family, suppressor for copper sensitivity D protein (ScsD) and actinobacterial DsbE homolog subfamily; composed of ScsD, the DsbE homolog of Mycobacterium tuberculosis (MtbDsbE) and similar proteins, all containing a redox-active CXXC motif; Region: TlpA_like_ScsD_MtbDsbE; cd03011 94122005014 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 94122005015 catalytic residues [active] 94122005016 Protein of unknown function, DUF479; Region: DUF479; pfam04336 94122005017 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 94122005018 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 94122005019 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 94122005020 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 94122005021 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 94122005022 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 94122005023 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 94122005024 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 94122005025 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 94122005026 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 94122005027 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 94122005028 Protein export membrane protein; Region: SecD_SecF; pfam02355 94122005029 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 94122005030 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 94122005031 active site residue [active] 94122005032 Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme metabolism]; Region: CysG; COG1648 94122005033 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 94122005034 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 94122005035 YaeQ protein; Region: YaeQ; pfam07152 94122005036 Peptidase inhibitor I9; Region: Inhibitor_I9; pfam05922 94122005037 Peptidase S8 family domain in Subtilisin proteins; Region: Peptidases_S8_Subtilisin_subset; cd07477 94122005038 active site 94122005039 catalytic residues [active] 94122005040 PA_VapT_like: Protease-associated domain containing proteins like VapT from Vibrio metschnikovii strain RH530. This group contains various PA domain-containing proteins similar to V. metschnikovii VapT, including the serine alkaline protease SapSh from...; Region: PA_VapT_like; cd04817 94122005041 PA/subtilisin-like domain interface [polypeptide binding]; other site 94122005042 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 94122005043 catalytic residues [active] 94122005044 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 94122005045 Proprotein convertase P-domain; Region: P_proprotein; pfam01483 94122005046 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 94122005047 active site residue [active] 94122005048 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 94122005049 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 94122005050 Protein export membrane protein; Region: SecD_SecF; cl14618 94122005051 Protein export membrane protein; Region: SecD_SecF; cl14618 94122005052 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 94122005053 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 94122005054 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 94122005055 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2859 94122005056 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 94122005057 active site 94122005058 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; pfam03349 94122005059 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 94122005060 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 94122005061 Na binding site [ion binding]; other site 94122005062 Protein of unknown function (DUF3379); Region: DUF3379; pfam11859 94122005063 RNA polymerase sigma factor; Provisional; Region: PRK12517 94122005064 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 94122005065 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 94122005066 DNA binding residues [nucleotide binding] 94122005067 Oxygen tolerance; Region: BatD; pfam13584 94122005068 von Willebrand factor type A domain; Region: VWA_2; pfam13519 94122005069 metal ion-dependent adhesion site (MIDAS); other site 94122005070 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 94122005071 binding surface 94122005072 TPR motif; other site 94122005073 Tetratricopeptide repeat; Region: TPR_16; pfam13432 94122005074 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG2304 94122005075 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 94122005076 metal ion-dependent adhesion site (MIDAS); other site 94122005077 Domain of unknown function (DUF4381); Region: DUF4381; pfam14316 94122005078 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 94122005079 Protein of unknown function DUF58; Region: DUF58; pfam01882 94122005080 MoxR-like ATPases [General function prediction only]; Region: COG0714 94122005081 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 94122005082 Walker A motif; other site 94122005083 ATP binding site [chemical binding]; other site 94122005084 Walker B motif; other site 94122005085 arginine finger; other site 94122005086 3-ketoacyl-CoA thiolase; Reviewed; Region: fadI; PRK08963 94122005087 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 94122005088 dimer interface [polypeptide binding]; other site 94122005089 active site 94122005090 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 94122005091 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 94122005092 substrate binding site [chemical binding]; other site 94122005093 oxyanion hole (OAH) forming residues; other site 94122005094 trimer interface [polypeptide binding]; other site 94122005095 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 94122005096 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 94122005097 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 94122005098 Two component regulator propeller; Region: Reg_prop; pfam07494 94122005099 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 94122005100 PAS fold; Region: PAS_3; pfam08447 94122005101 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 94122005102 PAS domain; Region: PAS_9; pfam13426 94122005103 putative active site [active] 94122005104 heme pocket [chemical binding]; other site 94122005105 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122005106 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122005107 metal binding site [ion binding]; metal-binding site 94122005108 active site 94122005109 I-site; other site 94122005110 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 94122005111 Secreted/periplasmic Zn-dependent peptidases, insulinase-like [Posttranslational modification, protein turnover, chaperones]; Region: Ptr; COG1025 94122005112 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 94122005113 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 94122005114 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 94122005115 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 94122005116 catalytic core [active] 94122005117 hypothetical protein; Provisional; Region: PRK04946 94122005118 Smr domain; Region: Smr; pfam01713 94122005119 HemK family putative methylases; Region: hemK_fam; TIGR00536 94122005120 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 94122005121 S-adenosylmethionine binding site [chemical binding]; other site 94122005122 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 94122005123 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 94122005124 Tetramer interface [polypeptide binding]; other site 94122005125 active site 94122005126 FMN-binding site [chemical binding]; other site 94122005127 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 94122005128 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 94122005129 putative substrate translocation pore; other site 94122005130 Predicted inorganic polyphosphate/ATP-NAD kinase [General function prediction only]; Region: COG3199 94122005131 ATP-NAD kinase; Region: NAD_kinase; pfam01513 94122005132 YfcL protein; Region: YfcL; pfam08891 94122005133 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 94122005134 S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_30; cl17711 94122005135 tRNA U-34 5-methylaminomethyl-2-thiouridine biosynthesis protein MnmC, C-terminal domain; Region: MnmC_Cterm; TIGR03197 94122005136 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 94122005137 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 94122005138 dimer interface [polypeptide binding]; other site 94122005139 active site 94122005140 erythronate-4-phosphate dehydrogenase; Validated; Region: PRK00257 94122005141 D-Erythronate-4-Phosphate Dehydrogenase NAD-binding and catalytic domains; Region: ErythrP_dh; cd12158 94122005142 ligand binding site [chemical binding]; other site 94122005143 NAD binding site [chemical binding]; other site 94122005144 catalytic site [active] 94122005145 homodimer interface [polypeptide binding]; other site 94122005146 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 94122005147 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 94122005148 FimV N-terminal domain; Region: FimV_core; TIGR03505 94122005149 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 94122005150 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 94122005151 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 94122005152 dimerization interface 3.5A [polypeptide binding]; other site 94122005153 active site 94122005154 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional; Region: PRK10846 94122005155 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 94122005156 cell division protein DedD; Provisional; Region: PRK11633 94122005157 Sporulation related domain; Region: SPOR; pfam05036 94122005158 Colicin V production protein; Region: Colicin_V; cl00567 94122005159 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 94122005160 amidophosphoribosyltransferase; Provisional; Region: PRK09246 94122005161 Glutamine amidotransferases class-II (GN-AT)_GPAT- type. This domain is found at the N-terminus of glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase) . The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the...; Region: GPATase_N; cd00715 94122005162 active site 94122005163 tetramer interface [polypeptide binding]; other site 94122005164 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 94122005165 active site 94122005166 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 94122005167 Sodium:alanine symporter family; Region: Na_Ala_symp; pfam01235 94122005168 DNA topoisomerase III; Provisional; Region: PRK07726 94122005169 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 94122005170 active site 94122005171 putative interdomain interaction site [polypeptide binding]; other site 94122005172 putative metal-binding site [ion binding]; other site 94122005173 putative nucleotide binding site [chemical binding]; other site 94122005174 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 94122005175 domain I; other site 94122005176 DNA binding groove [nucleotide binding] 94122005177 phosphate binding site [ion binding]; other site 94122005178 domain II; other site 94122005179 domain III; other site 94122005180 nucleotide binding site [chemical binding]; other site 94122005181 catalytic site [active] 94122005182 domain IV; other site 94122005183 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 94122005184 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 94122005185 eyelet of channel; other site 94122005186 trimer interface [polypeptide binding]; other site 94122005187 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: PspF; COG1221 94122005188 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 94122005189 Walker A motif; other site 94122005190 ATP binding site [chemical binding]; other site 94122005191 Walker B motif; other site 94122005192 arginine finger; other site 94122005193 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 94122005194 L-aspartate oxidase; Provisional; Region: PRK06175 94122005195 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 94122005196 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 94122005197 active sites [active] 94122005198 tetramer interface [polypeptide binding]; other site 94122005199 chaperone protein DnaJ; Provisional; Region: PRK14280 94122005200 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 94122005201 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 94122005202 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 94122005203 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 94122005204 XdhC Rossmann domain; Region: XdhC_C; pfam13478 94122005205 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 94122005206 Ligand binding site; other site 94122005207 metal-binding site 94122005208 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 94122005209 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 94122005210 catalytic loop [active] 94122005211 iron binding site [ion binding]; other site 94122005212 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 94122005213 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 94122005214 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 94122005215 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 94122005216 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 94122005217 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 94122005218 Protein of unknown function (DUF1097); Region: DUF1097; pfam06496 94122005219 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 94122005220 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 94122005221 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122005222 dimer interface [polypeptide binding]; other site 94122005223 putative CheW interface [polypeptide binding]; other site 94122005224 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 94122005225 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122005226 Coenzyme A binding pocket [chemical binding]; other site 94122005227 SnoaL-like domain; Region: SnoaL_2; pfam12680 94122005228 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 94122005229 putative catalytic site [active] 94122005230 putative phosphate binding site [ion binding]; other site 94122005231 active site 94122005232 metal binding site A [ion binding]; metal-binding site 94122005233 DNA binding site [nucleotide binding] 94122005234 putative AP binding site [nucleotide binding]; other site 94122005235 putative metal binding site B [ion binding]; other site 94122005236 YciI-like protein; Reviewed; Region: PRK11370 94122005237 intracellular septation protein A; Reviewed; Region: PRK00259 94122005238 siderophore-iron reductase FhuF; Region: Fe_III_red_FhuF; TIGR03951 94122005239 Ferric iron reductase FhuF-like transporter; Region: FhuF; pfam06276 94122005240 FhuF 2Fe-2S C-terminal domain; Region: FhuF_C; pfam11575 94122005241 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 94122005242 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122005243 N-terminal plug; other site 94122005244 ligand-binding site [chemical binding]; other site 94122005245 Siderophore synthetase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: RhbC; COG4264 94122005246 IucA / IucC family; Region: IucA_IucC; pfam04183 94122005247 Ferric iron reductase FhuF-like transporter; Region: FhuF; pfam06276 94122005248 Acetyltransferase (GNAT) domain; Region: Acetyltransf_8; pfam13523 94122005249 Siderophore biosynthesis protein domain; Region: AlcB; smart01006 94122005250 Lysine/ornithine N-monooxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: IucD; COG3486 94122005251 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 94122005252 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 94122005253 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 94122005254 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122005255 N-terminal plug; other site 94122005256 ligand-binding site [chemical binding]; other site 94122005257 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819 94122005258 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 94122005259 substrate binding site [chemical binding]; other site 94122005260 active site 94122005261 catalytic residues [active] 94122005262 heterodimer interface [polypeptide binding]; other site 94122005263 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 94122005264 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 94122005265 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122005266 catalytic residue [active] 94122005267 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional; Region: PRK09427 94122005268 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 94122005269 active site 94122005270 ribulose/triose binding site [chemical binding]; other site 94122005271 phosphate binding site [ion binding]; other site 94122005272 substrate (anthranilate) binding pocket [chemical binding]; other site 94122005273 product (indole) binding pocket [chemical binding]; other site 94122005274 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 94122005275 active site 94122005276 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 94122005277 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 94122005278 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 94122005279 Glutamine amidotransferase class-I; Region: GATase; pfam00117 94122005280 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 94122005281 glutamine binding [chemical binding]; other site 94122005282 catalytic triad [active] 94122005283 anthranilate synthase component I; Provisional; Region: PRK13564 94122005284 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 94122005285 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 94122005286 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 94122005287 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 94122005288 active site 94122005289 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 94122005290 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 94122005291 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 94122005292 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 94122005293 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 94122005294 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 94122005295 RNA binding surface [nucleotide binding]; other site 94122005296 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 94122005297 probable active site [active] 94122005298 BNR repeat-like domain; Region: BNR_2; pfam13088 94122005299 Transposase IS200 like; Region: Y1_Tnp; pfam01797 94122005300 putative oxoacyl-(acyl carrier protein) reductase; Provisional; Region: PRK08945 94122005301 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 94122005302 NAD(P) binding site [chemical binding]; other site 94122005303 active site 94122005304 extracellular lipase, Pla-1/cef family; Region: lipase_Pla1_cef; TIGR03502 94122005305 Bacterial virulence factor lipase N-terminal; Region: Lipase_bact_N; pfam12262 94122005306 Peptidase family S49 N-terminal; Region: Peptidase_S49_N; pfam08496 94122005307 putative inner membrane peptidase; Provisional; Region: PRK11778 94122005308 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 94122005309 tandem repeat interface [polypeptide binding]; other site 94122005310 oligomer interface [polypeptide binding]; other site 94122005311 active site residues [active] 94122005312 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 94122005313 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 94122005314 conserved hypothetical protein, HNE_0200 family; Region: chp_HNE_0200; TIGR03806 94122005315 Planctomycete cytochrome C; Region: PSCyt1; pfam07635 94122005316 parallel beta-helix repeat-containing protein; Region: beta_helix_1; TIGR03805 94122005317 conserved hypothetical protein, HNE_0200 family; Region: chp_HNE_0200; TIGR03806 94122005318 Planctomycete cytochrome C; Region: PSCyt1; pfam07635 94122005319 Predicted integral membrane protein [Function unknown]; Region: COG0392 94122005320 Uncharacterized conserved protein [Function unknown]; Region: COG2898 94122005321 Uncharacterized conserved protein (DUF2156); Region: DUF2156; pfam09924 94122005322 Bacterial virulence protein (VirJ); Region: VirJ; pfam06057 94122005323 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 94122005324 Protein of unknown function (DUF3083); Region: DUF3083; pfam11281 94122005325 Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity; Region: Lysophospholipase_L1_like; cd01822 94122005326 active site 94122005327 catalytic triad [active] 94122005328 oxyanion hole [active] 94122005329 switch loop; other site 94122005330 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 94122005331 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 94122005332 Walker A/P-loop; other site 94122005333 ATP binding site [chemical binding]; other site 94122005334 Q-loop/lid; other site 94122005335 ABC transporter signature motif; other site 94122005336 Walker B; other site 94122005337 D-loop; other site 94122005338 H-loop/switch region; other site 94122005339 FtsX-like permease family; Region: FtsX; pfam02687 94122005340 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 94122005341 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 94122005342 Catalytic site [active] 94122005343 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 94122005344 Sodium/glutamate symporter; Region: Glt_symporter; pfam03616 94122005345 atypical (a) SDRs, subgroup 8; Region: SDR_a8; cd05242 94122005346 Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]; Region: COG1090 94122005347 putative NAD(P) binding site [chemical binding]; other site 94122005348 putative active site [active] 94122005349 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 94122005350 homooctamer interface [polypeptide binding]; other site 94122005351 active site 94122005352 Domain of unknown function DUF20; Region: UPF0118; pfam01594 94122005353 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 94122005354 S-adenosylmethionine-dependent methyltransferase; Region: Methyltrans_SAM; pfam10672 94122005355 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 94122005356 S-adenosylmethionine binding site [chemical binding]; other site 94122005357 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 94122005358 putative transposase OrfB; Reviewed; Region: PHA02517 94122005359 Integrase core domain; Region: rve; pfam00665 94122005360 Integrase core domain; Region: rve_3; pfam13683 94122005361 phosphate acetyltransferase; Reviewed; Region: PRK05632 94122005362 DRTGG domain; Region: DRTGG; pfam07085 94122005363 phosphate acetyltransferase; Region: pta; TIGR00651 94122005364 propionate/acetate kinase; Provisional; Region: PRK12379 94122005365 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 94122005366 Protein of unknown function, DUF412; Region: DUF412; pfam04217 94122005367 pyruvate formate lyase-activating enzyme 1; Provisional; Region: pflA; PRK11145 94122005368 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 94122005369 FeS/SAM binding site; other site 94122005370 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 94122005371 Pyruvate formate lyase 1; Region: PFL1; cd01678 94122005372 coenzyme A binding site [chemical binding]; other site 94122005373 active site 94122005374 catalytic residues [active] 94122005375 glycine loop; other site 94122005376 formate transporter FocA; Region: formate_focA; TIGR04060 94122005377 hypothetical protein; Provisional; Region: PRK11588 94122005378 C4-dicarboxylate anaerobic carrier; Region: DcuC; pfam03606 94122005379 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 94122005380 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122005381 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122005382 Tellurite resistance protein and related permeases [Inorganic ion transport and metabolism]; Region: TehA; COG1275 94122005383 C4-dicarboxylate transporters of the Tellurite-resistance/Dicarboxylate Transporter (TDT) family; Region: TDT_C4-dicarb_trans; cd09325 94122005384 gating phenylalanine in ion channel; other site 94122005385 O-methyltransferase; Region: Methyltransf_2; pfam00891 94122005386 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 94122005387 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 94122005388 dimer interface [polypeptide binding]; other site 94122005389 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122005390 catalytic residue [active] 94122005391 RDD family; Region: RDD; pfam06271 94122005392 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK07515 94122005393 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 94122005394 dimer interface [polypeptide binding]; other site 94122005395 active site 94122005396 CoA binding pocket [chemical binding]; other site 94122005397 DOMON-like type 9 carbohydrate binding module; Region: CBM9_like_2; cd09618 94122005398 putative ligand binding site [chemical binding]; other site 94122005399 putative sulfate transport protein CysZ; Validated; Region: PRK04949 94122005400 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 94122005401 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 94122005402 Walker A/P-loop; other site 94122005403 ATP binding site [chemical binding]; other site 94122005404 Q-loop/lid; other site 94122005405 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 94122005406 ABC transporter signature motif; other site 94122005407 Walker B; other site 94122005408 D-loop; other site 94122005409 H-loop/switch region; other site 94122005410 cell division protein ZipA; Provisional; Region: PRK03427 94122005411 ZipA, C-terminal FtsZ-binding domain; Region: ZipA_C; pfam04354 94122005412 FtsZ protein binding site [polypeptide binding]; other site 94122005413 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 94122005414 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 94122005415 nucleotide binding pocket [chemical binding]; other site 94122005416 K-X-D-G motif; other site 94122005417 catalytic site [active] 94122005418 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 94122005419 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 94122005420 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 94122005421 Dimer interface [polypeptide binding]; other site 94122005422 BRCT sequence motif; other site 94122005423 Protein of unknown function (DUF2919); Region: DUF2919; pfam11143 94122005424 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 94122005425 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 94122005426 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 94122005427 Zn2+ binding site [ion binding]; other site 94122005428 Mg2+ binding site [ion binding]; other site 94122005429 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 94122005430 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 94122005431 putative NAD(P) binding site [chemical binding]; other site 94122005432 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 94122005433 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 94122005434 catalytic residues [active] 94122005435 hinge region; other site 94122005436 alpha helical domain; other site 94122005437 Domain of unknown function (DUF4212); Region: DUF4212; pfam13937 94122005438 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 94122005439 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 94122005440 Na binding site [ion binding]; other site 94122005441 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 94122005442 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 94122005443 ligand binding site [chemical binding]; other site 94122005444 flexible hinge region; other site 94122005445 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain; Region: CBS_pair_CAP-ED_DUF294_PBI_assoc2; cd04800 94122005446 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 94122005447 metal binding triad; other site 94122005448 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 94122005449 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 94122005450 active site 94122005451 catalytic site [active] 94122005452 substrate binding site [chemical binding]; other site 94122005453 MarR family; Region: MarR_2; cl17246 94122005454 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 94122005455 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 94122005456 Prostaglandin dehydrogenases; Region: PGDH; cd05288 94122005457 NAD(P) binding site [chemical binding]; other site 94122005458 substrate binding site [chemical binding]; other site 94122005459 dimer interface [polypeptide binding]; other site 94122005460 Lecithin retinol acyltransferase; Region: LRAT; pfam04970 94122005461 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK12879 94122005462 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 94122005463 dimer interface [polypeptide binding]; other site 94122005464 active site 94122005465 CoA binding pocket [chemical binding]; other site 94122005466 Transcriptional regulators [Transcription]; Region: GntR; COG1802 94122005467 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 94122005468 DNA-binding site [nucleotide binding]; DNA binding site 94122005469 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 94122005470 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 94122005471 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 94122005472 active site 94122005473 motif I; other site 94122005474 motif II; other site 94122005475 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 94122005476 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; pfam09829 94122005477 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein; Reviewed; Region: cpdB; PRK09420 94122005478 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 94122005479 active site 94122005480 metal binding site [ion binding]; metal-binding site 94122005481 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 94122005482 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 94122005483 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 94122005484 active site 94122005485 Zn binding site [ion binding]; other site 94122005486 Predicted proline hydroxylase [Posttranslational modification, protein turnover, chaperones]; Region: EGL-9; COG3751 94122005487 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; pfam13640 94122005488 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 94122005489 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 94122005490 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 94122005491 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122005492 Coenzyme A binding pocket [chemical binding]; other site 94122005493 Predicted membrane protein (DUF2157); Region: DUF2157; pfam09925 94122005494 Domain of unknown function (DUF4401); Region: DUF4401; pfam14351 94122005495 GDYXXLXY protein; Region: GDYXXLXY; pfam14345 94122005496 Predicted extracellular nuclease [General function prediction only]; Region: COG2374 94122005497 YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate...; Region: YhcR_OBF_like; cd04486 94122005498 generic binding surface II; other site 94122005499 generic binding surface I; other site 94122005500 Mycoplasma pulmonis MnuA nuclease-like; Region: MnuA_DNase1-like; cd10283 94122005501 putative active site [active] 94122005502 putative catalytic site [active] 94122005503 putative Mg binding site IVb [ion binding]; other site 94122005504 putative phosphate binding site [ion binding]; other site 94122005505 putative DNA binding site [nucleotide binding]; other site 94122005506 putative Mg binding site IVa [ion binding]; other site 94122005507 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cd00146 94122005508 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 94122005509 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 94122005510 DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]; Region: DnaJ; COG0484 94122005511 HSP70 interaction site [polypeptide binding]; other site 94122005512 23S rRNA m(2)G2445 methyltransferase; Provisional; Region: rlmL; PRK11783 94122005513 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 94122005514 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 94122005515 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 94122005516 S-adenosylmethionine binding site [chemical binding]; other site 94122005517 Glutaredoxin-like domain (DUF836); Region: DUF836; pfam05768 94122005518 ABC transporter ATPase component; Reviewed; Region: PRK11147 94122005519 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 94122005520 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122005521 Walker A/P-loop; other site 94122005522 ATP binding site [chemical binding]; other site 94122005523 Q-loop/lid; other site 94122005524 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 94122005525 ABC transporter signature motif; other site 94122005526 Walker B; other site 94122005527 D-loop; other site 94122005528 ABC transporter; Region: ABC_tran_2; pfam12848 94122005529 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 94122005530 Protein of unknown function (DUF3466); Region: DUF3466; pfam11949 94122005531 ribosome modulation factor; Provisional; Region: PRK14563 94122005532 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 94122005533 active site 1 [active] 94122005534 dimer interface [polypeptide binding]; other site 94122005535 active site 2 [active] 94122005536 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 94122005537 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 94122005538 response regulator; Provisional; Region: PRK09483 94122005539 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122005540 active site 94122005541 phosphorylation site [posttranslational modification] 94122005542 intermolecular recognition site; other site 94122005543 dimerization interface [polypeptide binding]; other site 94122005544 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 94122005545 DNA binding residues [nucleotide binding] 94122005546 dimerization interface [polypeptide binding]; other site 94122005547 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 94122005548 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 94122005549 GIY-YIG motif/motif A; other site 94122005550 active site 94122005551 catalytic site [active] 94122005552 putative DNA binding site [nucleotide binding]; other site 94122005553 metal binding site [ion binding]; metal-binding site 94122005554 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 94122005555 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 94122005556 Peptidase S8 family domain in Lantiobiotic (lanthionine-containing antibiotics) specific proteases; Region: Peptidases_S8_Lantibiotic_specific_protease; cd07482 94122005557 active site 94122005558 catalytic triad [active] 94122005559 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 94122005560 IHF dimer interface [polypeptide binding]; other site 94122005561 IHF - DNA interface [nucleotide binding]; other site 94122005562 RNA polymerase sigma factor, TIGR02999 family; Region: Sig-70_X6 94122005563 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cl17257 94122005564 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 94122005565 Catalytic domain of Protein Kinases; Region: PKc; cd00180 94122005566 active site 94122005567 ATP binding site [chemical binding]; other site 94122005568 substrate binding site [chemical binding]; other site 94122005569 activation loop (A-loop); other site 94122005570 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 94122005571 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122005572 Walker A/P-loop; other site 94122005573 ATP binding site [chemical binding]; other site 94122005574 Q-loop/lid; other site 94122005575 ABC transporter signature motif; other site 94122005576 Walker B; other site 94122005577 D-loop; other site 94122005578 H-loop/switch region; other site 94122005579 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 94122005580 hypothetical protein; Provisional; Region: PRK11239 94122005581 Protein of unknown function, DUF480; Region: DUF480; pfam04337 94122005582 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 94122005583 S1 domain; Region: S1_2; pfam13509 94122005584 S1 domain; Region: S1_2; pfam13509 94122005585 arginine decarboxylase; Provisional; Region: PRK05354 94122005586 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 94122005587 dimer interface [polypeptide binding]; other site 94122005588 active site 94122005589 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 94122005590 catalytic residues [active] 94122005591 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 94122005592 Adenosylmethionine decarboxylase; Region: SAM_decarbox; cl03253 94122005593 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 94122005594 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 94122005595 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 94122005596 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; pfam02639 94122005597 YceI-like domain; Region: YceI; pfam04264 94122005598 Protein of unknown function (DUF3802); Region: DUF3802; pfam12290 94122005599 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 94122005600 Putative ATP-dependant zinc protease; Region: Zn_protease; cl01682 94122005601 Putative ATP-dependant zinc protease; Region: Zn_protease; cl01682 94122005602 Cache domain; Region: Cache_1; pfam02743 94122005603 PAS fold; Region: PAS_4; pfam08448 94122005604 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 94122005605 putative active site [active] 94122005606 heme pocket [chemical binding]; other site 94122005607 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 94122005608 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 94122005609 ATP binding site [chemical binding]; other site 94122005610 Mg2+ binding site [ion binding]; other site 94122005611 G-X-G motif; other site 94122005612 disulfide bond formation protein B; Provisional; Region: PRK01749 94122005613 sodium/proton antiporter; Reviewed; Region: nhaB; PRK09547 94122005614 fatty acid metabolism regulator; Provisional; Region: PRK04984 94122005615 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 94122005616 DNA-binding site [nucleotide binding]; DNA binding site 94122005617 FadR C-terminal domain; Region: FadR_C; pfam07840 94122005618 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 94122005619 SpoVR family protein; Provisional; Region: PRK11767 94122005620 hypothetical protein; Provisional; Region: PRK05325 94122005621 PrkA family serine protein kinase; Provisional; Region: PRK15455 94122005622 AAA ATPase domain; Region: AAA_16; pfam13191 94122005623 Walker A motif; other site 94122005624 ATP binding site [chemical binding]; other site 94122005625 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 94122005626 superoxide dismutase; Provisional; Region: PRK10543 94122005627 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 94122005628 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 94122005629 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 94122005630 putative GSH binding site [chemical binding]; other site 94122005631 catalytic residues [active] 94122005632 Xanthine/uracil permeases [Nucleotide transport and metabolism]; Region: UraA; COG2233 94122005633 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3249 94122005634 Uncharacterized protein conserved in bacteria (DUF2066); Region: DUF2066; pfam09839 94122005635 DNA replication initiation factor; Provisional; Region: PRK08084 94122005636 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 94122005637 Walker A motif; other site 94122005638 ATP binding site [chemical binding]; other site 94122005639 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 94122005640 putative transposase OrfB; Reviewed; Region: PHA02517 94122005641 Integrase core domain; Region: rve; pfam00665 94122005642 Integrase core domain; Region: rve_3; pfam13683 94122005643 Predicted membrane protein (DUF2069); Region: DUF2069; pfam09842 94122005644 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 94122005645 ArsC family; Region: ArsC; pfam03960 94122005646 catalytic residues [active] 94122005647 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 94122005648 Peptidase family M48; Region: Peptidase_M48; cl12018 94122005649 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 94122005650 binding surface 94122005651 TPR motif; other site 94122005652 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cd00291 94122005653 CPxP motif; other site 94122005654 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 94122005655 Domain of unknown function DUF20; Region: UPF0118; pfam01594 94122005656 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 94122005657 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122005658 The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), for arginine exporter (ArgO); contains the type 2 periplasmic binding fold; Region: PBP2_IciA_ArgP; cd08428 94122005659 putative dimerization interface [polypeptide binding]; other site 94122005660 Lysine efflux permease [General function prediction only]; Region: COG1279 94122005661 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 94122005662 catalytic triad [active] 94122005663 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 94122005664 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 94122005665 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 94122005666 dihydrodipicolinate synthase; Region: dapA; TIGR00674 94122005667 dimer interface [polypeptide binding]; other site 94122005668 active site 94122005669 catalytic residue [active] 94122005670 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 94122005671 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 94122005672 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 94122005673 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 94122005674 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122005675 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 94122005676 Protein export membrane protein; Region: SecD_SecF; cl14618 94122005677 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 94122005678 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122005679 Coenzyme A binding pocket [chemical binding]; other site 94122005680 Putative FMN-binding domain; Region: FMN_bind_2; pfam04299 94122005681 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 94122005682 Putative amidotransferase; Region: DUF4066; pfam13278 94122005683 conserved cys residue [active] 94122005684 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 94122005685 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 94122005686 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 94122005687 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 94122005688 active site 94122005689 catalytic residues [active] 94122005690 metal binding site [ion binding]; metal-binding site 94122005691 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 94122005692 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 94122005693 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 94122005694 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 94122005695 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 94122005696 carboxyltransferase (CT) interaction site; other site 94122005697 biotinylation site [posttranslational modification]; other site 94122005698 enoyl-CoA hydratase; Provisional; Region: PRK05995 94122005699 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 94122005700 substrate binding site [chemical binding]; other site 94122005701 oxyanion hole (OAH) forming residues; other site 94122005702 trimer interface [polypeptide binding]; other site 94122005703 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 94122005704 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 94122005705 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 94122005706 isovaleryl-CoA dehydrogenase; Region: PLN02519 94122005707 substrate binding site [chemical binding]; other site 94122005708 FAD binding site [chemical binding]; other site 94122005709 catalytic base [active] 94122005710 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 94122005711 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 94122005712 DNA binding residues [nucleotide binding] 94122005713 putative dimer interface [polypeptide binding]; other site 94122005714 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 94122005715 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 94122005716 Predicted Peptidoglycan domain; Region: PG_binding_3; pfam09374 94122005717 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 94122005718 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 94122005719 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 94122005720 acyl-activating enzyme (AAE) consensus motif; other site 94122005721 AMP binding site [chemical binding]; other site 94122005722 active site 94122005723 CoA binding site [chemical binding]; other site 94122005724 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 94122005725 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 94122005726 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 94122005727 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 94122005728 Peptidase S8 family domain in Protein convertases; Region: Peptidases_S8_Protein_convertases_Kexins_Furin-lik; cd04059 94122005729 calcium binding site 1 [ion binding]; other site 94122005730 active site 94122005731 catalytic triad [active] 94122005732 calcium binding site 2 [ion binding]; other site 94122005733 calcium binding site 3 [ion binding]; other site 94122005734 Proprotein convertase P-domain; Region: P_proprotein; pfam01483 94122005735 Domain of unknown function (DUF4303); Region: DUF4303; pfam14136 94122005736 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122005737 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122005738 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 94122005739 dimerization interface [polypeptide binding]; other site 94122005740 DoxX-like family; Region: DoxX_2; pfam13564 94122005741 The Class III extradiol dioxygenase, 4,5-DOPA Dioxygenase, catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine; Region: 45_DOPA_Dioxygenase; cd07363 94122005742 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 94122005743 putative active site [active] 94122005744 metal binding site [ion binding]; metal-binding site 94122005745 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Validated; Region: PRK06080 94122005746 UbiA prenyltransferase family; Region: UbiA; pfam01040 94122005747 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 94122005748 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 94122005749 NAD(P) binding site [chemical binding]; other site 94122005750 active site 94122005751 acyl-CoA thioesterase II; Provisional; Region: PRK10526 94122005752 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat2; cd03445 94122005753 active site 94122005754 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat1; cd03444 94122005755 catalytic triad [active] 94122005756 dimer interface [polypeptide binding]; other site 94122005757 Type III secretion system lipoprotein chaperone (YscW); Region: YscW; cl15825 94122005758 Peptidase inhibitor I9; Region: Inhibitor_I9; pfam05922 94122005759 Peptidase S8 family domain, uncharacterized subfamily 3; Region: Peptidases_S8_3; cd04852 94122005760 Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones]; Region: AprE; COG1404 94122005761 active site 94122005762 catalytic triad [active] 94122005763 PA_subtilisin_1: Protease-associated domain containing subtilisin-like proteases, subgroup 1. A subgroup of PA domain-containing subtilisin-like proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined; Region: PA_subtilisin_1; cd04818 94122005764 PA/protease or protease-like domain interface [polypeptide binding]; other site 94122005765 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 94122005766 catalytic residues [active] 94122005767 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 94122005768 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122005769 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122005770 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 94122005771 dimerization interface [polypeptide binding]; other site 94122005772 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 94122005773 Major Facilitator Superfamily; Region: MFS_1; pfam07690 94122005774 putative substrate translocation pore; other site 94122005775 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 94122005776 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 94122005777 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 94122005778 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 94122005779 putative NAD(P) binding site [chemical binding]; other site 94122005780 putative substrate binding site [chemical binding]; other site 94122005781 catalytic Zn binding site [ion binding]; other site 94122005782 structural Zn binding site [ion binding]; other site 94122005783 dimer interface [polypeptide binding]; other site 94122005784 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 94122005785 Uncharacterized conserved protein [Function unknown]; Region: COG4925 94122005786 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 94122005787 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 94122005788 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 94122005789 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 94122005790 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 94122005791 multidrug efflux protein NorA; Provisional; Region: PRK00187 94122005792 Protein of unknown function (DUF2986); Region: DUF2986; pfam11661 94122005793 ASC-1 homology domain, subfamily similar to Escherichia coli Yqfb. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as...; Region: ASCH_yqfb_like; cd06552 94122005794 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 94122005795 Protein export membrane protein; Region: SecD_SecF; cl14618 94122005796 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 94122005797 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 94122005798 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 94122005799 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122005800 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 94122005801 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 94122005802 dimer interface [polypeptide binding]; other site 94122005803 active site 94122005804 citrylCoA binding site [chemical binding]; other site 94122005805 NADH binding [chemical binding]; other site 94122005806 cationic pore residues; other site 94122005807 oxalacetate/citrate binding site [chemical binding]; other site 94122005808 coenzyme A binding site [chemical binding]; other site 94122005809 catalytic triad [active] 94122005810 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 94122005811 Iron-sulfur protein interface; other site 94122005812 proximal quinone binding site [chemical binding]; other site 94122005813 SdhD (CybS) interface [polypeptide binding]; other site 94122005814 proximal heme binding site [chemical binding]; other site 94122005815 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 94122005816 SdhC subunit interface [polypeptide binding]; other site 94122005817 proximal heme binding site [chemical binding]; other site 94122005818 cardiolipin binding site; other site 94122005819 Iron-sulfur protein interface; other site 94122005820 proximal quinone binding site [chemical binding]; other site 94122005821 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK08958 94122005822 L-aspartate oxidase; Provisional; Region: PRK06175 94122005823 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 94122005824 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 94122005825 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 94122005826 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 94122005827 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 94122005828 TPP-binding site [chemical binding]; other site 94122005829 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 94122005830 PYR/PP interface [polypeptide binding]; other site 94122005831 dimer interface [polypeptide binding]; other site 94122005832 TPP binding site [chemical binding]; other site 94122005833 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 94122005834 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 94122005835 E3 interaction surface; other site 94122005836 lipoyl attachment site [posttranslational modification]; other site 94122005837 e3 binding domain; Region: E3_binding; pfam02817 94122005838 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 94122005839 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 94122005840 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 94122005841 CoA-ligase; Region: Ligase_CoA; pfam00549 94122005842 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 94122005843 CoA binding domain; Region: CoA_binding; pfam02629 94122005844 CoA-ligase; Region: Ligase_CoA; pfam00549 94122005845 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 94122005846 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 94122005847 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 94122005848 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 94122005849 Coenzyme A binding pocket [chemical binding]; other site 94122005850 ferric uptake regulator; Provisional; Region: fur; PRK09462 94122005851 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 94122005852 metal binding site 2 [ion binding]; metal-binding site 94122005853 putative DNA binding helix; other site 94122005854 metal binding site 1 [ion binding]; metal-binding site 94122005855 dimer interface [polypeptide binding]; other site 94122005856 structural Zn2+ binding site [ion binding]; other site 94122005857 NAD-dependent deacetylase; Provisional; Region: PRK00481 94122005858 SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which...; Region: SIRT5_Af1_CobB; cd01412 94122005859 NAD+ binding site [chemical binding]; other site 94122005860 substrate binding site [chemical binding]; other site 94122005861 Zn binding site [ion binding]; other site 94122005862 AAA domain; Region: AAA_33; pfam13671 94122005863 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 94122005864 Escherichia coli Mg2+ transporter CorA_like subgroup; Region: EcCorA-like_1; cd12835 94122005865 Cl binding site [ion binding]; other site 94122005866 oligomer interface [polypeptide binding]; other site 94122005867 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 94122005868 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 94122005869 Zn2+ binding site [ion binding]; other site 94122005870 Mg2+ binding site [ion binding]; other site 94122005871 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; cl17304 94122005872 sensor protein PhoQ; Provisional; Region: PRK10815 94122005873 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 94122005874 ATP binding site [chemical binding]; other site 94122005875 Mg2+ binding site [ion binding]; other site 94122005876 G-X-G motif; other site 94122005877 DNA-binding transcriptional regulator PhoP; Provisional; Region: PRK10816 94122005878 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122005879 active site 94122005880 phosphorylation site [posttranslational modification] 94122005881 intermolecular recognition site; other site 94122005882 dimerization interface [polypeptide binding]; other site 94122005883 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 94122005884 DNA binding site [nucleotide binding] 94122005885 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 94122005886 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 94122005887 Bacterial Ig-like domain (group 1); Region: Big_1; cl17740 94122005888 Bacterial Ig-like domain (group 1); Region: Big_1; cl17740 94122005889 succinylarginine dihydrolase; Provisional; Region: PRK13281 94122005890 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 94122005891 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the...; Region: TOPRIM_TopoIA_TopoI; cd03363 94122005892 active site 94122005893 interdomain interaction site; other site 94122005894 putative metal-binding site [ion binding]; other site 94122005895 nucleotide binding site [chemical binding]; other site 94122005896 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 94122005897 domain I; other site 94122005898 DNA binding groove [nucleotide binding] 94122005899 phosphate binding site [ion binding]; other site 94122005900 domain II; other site 94122005901 domain III; other site 94122005902 nucleotide binding site [chemical binding]; other site 94122005903 catalytic site [active] 94122005904 domain IV; other site 94122005905 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 94122005906 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 94122005907 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 94122005908 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 94122005909 transcriptional regulator CysB; Reviewed; Region: cysB; PRK12681 94122005910 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122005911 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 94122005912 substrate binding site [chemical binding]; other site 94122005913 dimerization interface [polypeptide binding]; other site 94122005914 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 94122005915 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122005916 active site 94122005917 phosphorylation site [posttranslational modification] 94122005918 intermolecular recognition site; other site 94122005919 dimerization interface [polypeptide binding]; other site 94122005920 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 94122005921 DNA binding residues [nucleotide binding] 94122005922 dimerization interface [polypeptide binding]; other site 94122005923 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 94122005924 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional; Region: PRK12756 94122005925 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 94122005926 PEP synthetase regulatory protein; Provisional; Region: PRK05339 94122005927 phosphoenolpyruvate synthase; Validated; Region: PRK06464 94122005928 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 94122005929 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 94122005930 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 94122005931 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 94122005932 FAD binding domain; Region: FAD_binding_4; pfam01565 94122005933 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 94122005934 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 94122005935 Protein of unknown function (DUF1285); Region: DUF1285; pfam06938 94122005936 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 94122005937 MarR family; Region: MarR; pfam01047 94122005938 Peptidase S8 family domain, uncharacterized subfamily 6; Region: Peptidases_S8_6; cd07490 94122005939 active site 94122005940 catalytic triad [active] 94122005941 PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain; Region: PA; cl08238 94122005942 PA/protease or protease-like domain interface [polypeptide binding]; other site 94122005943 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 94122005944 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; pfam00208 94122005945 NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase; Region: NAD_bind_Leu_Phe_Val_DH; cd01075 94122005946 NAD binding site [chemical binding]; other site 94122005947 Phe binding site; other site 94122005948 Cupin superfamily protein; Region: Cupin_4; pfam08007 94122005949 Cupin-like domain; Region: Cupin_8; pfam13621 94122005950 adenylosuccinate lyase; Provisional; Region: PRK09285 94122005951 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 94122005952 tetramer interface [polypeptide binding]; other site 94122005953 active site 94122005954 putative lysogenization regulator; Reviewed; Region: PRK00218 94122005955 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 94122005956 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 94122005957 Contains a crystal structure of the Nudix hydrolase from Nitrosomonas europaea, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes...; Region: Nudix_Hydrolase_2; cd03675 94122005958 nudix motif; other site 94122005959 23S rRNA pseudouridine synthase E; Provisional; Region: PRK11394 94122005960 Pseudouridine synthase, Escherichia coli RluE; Region: PseudoU_synth_RluE; cd02566 94122005961 probable active site [active] 94122005962 Monomeric isocitrate dehydrogenase [Energy production and conversion]; Region: Icd; COG2838 94122005963 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 94122005964 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 94122005965 DNA-binding site [nucleotide binding]; DNA binding site 94122005966 RNA-binding motif; other site 94122005967 Uncharacterized conserved protein [Function unknown]; Region: COG2127 94122005968 ATP-dependent Clp protease ATP-binding subunit; Provisional; Region: clpA; PRK11034 94122005969 Clp amino terminal domain; Region: Clp_N; pfam02861 94122005970 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 94122005971 Walker A motif; other site 94122005972 ATP binding site [chemical binding]; other site 94122005973 Walker B motif; other site 94122005974 arginine finger; other site 94122005975 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 94122005976 Walker A motif; other site 94122005977 ATP binding site [chemical binding]; other site 94122005978 Walker B motif; other site 94122005979 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 94122005980 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 94122005981 rRNA binding site [nucleotide binding]; other site 94122005982 predicted 30S ribosome binding site; other site 94122005983 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 94122005984 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 94122005985 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 94122005986 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 94122005987 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 94122005988 Uncharacterized conserved protein [Function unknown]; Region: COG0327 94122005989 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 94122005990 Predicted permeases [General function prediction only]; Region: COG0679 94122005991 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 94122005992 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 94122005993 active site 94122005994 HIGH motif; other site 94122005995 KMSKS motif; other site 94122005996 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 94122005997 tRNA binding surface [nucleotide binding]; other site 94122005998 anticodon binding site; other site 94122005999 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 94122006000 dimer interface [polypeptide binding]; other site 94122006001 putative tRNA-binding site [nucleotide binding]; other site 94122006002 antiporter inner membrane protein; Provisional; Region: PRK11670 94122006003 Domain of unknown function DUF59; Region: DUF59; cl00941 94122006004 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 94122006005 Walker A motif; other site 94122006006 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 94122006007 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 94122006008 Sugar specificity; other site 94122006009 Pyrimidine base specificity; other site 94122006010 ATP-binding site [chemical binding]; other site 94122006011 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 94122006012 trimer interface [polypeptide binding]; other site 94122006013 active site 94122006014 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 94122006015 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 94122006016 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122006017 catalytic residue [active] 94122006018 YceG-like family; Region: YceG; pfam02618 94122006019 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 94122006020 dimerization interface [polypeptide binding]; other site 94122006021 thymidylate kinase; Validated; Region: tmk; PRK00698 94122006022 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 94122006023 TMP-binding site; other site 94122006024 ATP-binding site [chemical binding]; other site 94122006025 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 94122006026 DNA polymerase III subunit delta'; Validated; Region: PRK08485 94122006027 PilZ domain; Region: PilZ; cl01260 94122006028 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 94122006029 active site 94122006030 rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed; Region: yebU; PRK11933 94122006031 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 94122006032 S-adenosylmethionine binding site [chemical binding]; other site 94122006033 pre-rRNA processing and ribosome biogenesis; Region: Nol1_Nop2_Fmu_2; pfam13636 94122006034 Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]; Region: SpmA; COG2715 94122006035 Uncharacterized membrane protein [Function unknown]; Region: SpmB; COG0700 94122006036 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 94122006037 mce related protein; Region: MCE; pfam02470 94122006038 mce related protein; Region: MCE; pfam02470 94122006039 mce related protein; Region: MCE; pfam02470 94122006040 mce related protein; Region: MCE; pfam02470 94122006041 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 94122006042 mce related protein; Region: MCE; pfam02470 94122006043 Paraquat-inducible protein A; Region: PqiA; pfam04403 94122006044 Paraquat-inducible protein A; Region: PqiA; pfam04403 94122006045 YebG protein; Region: YebG; pfam07130 94122006046 GAF domain-containing protein [Signal transduction mechanisms]; Region: COG1956 94122006047 GAF domain; Region: GAF_2; pfam13185 94122006048 ProP expression regulator; Provisional; Region: PRK04950 94122006049 ProQ/FINO family; Region: ProQ; smart00945 94122006050 carboxy-terminal protease; Provisional; Region: PRK11186 94122006051 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 94122006052 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 94122006053 protein binding site [polypeptide binding]; other site 94122006054 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 94122006055 Catalytic dyad [active] 94122006056 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 94122006057 aminopeptidase N; Provisional; Region: pepN; PRK14015 94122006058 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 94122006059 active site 94122006060 Zn binding site [ion binding]; other site 94122006061 Protein of unknown function (DUF2835); Region: DUF2835; pfam11197 94122006062 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 94122006063 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 94122006064 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 94122006065 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 94122006066 Sterol-sensing domain of SREBP cleavage-activation; Region: Sterol-sensing; pfam12349 94122006067 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 94122006068 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 94122006069 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 94122006070 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 94122006071 quinone interaction residues [chemical binding]; other site 94122006072 active site 94122006073 catalytic residues [active] 94122006074 FMN binding site [chemical binding]; other site 94122006075 substrate binding site [chemical binding]; other site 94122006076 Protein of unknown function (DUF1379); Region: DUF1379; pfam07126 94122006077 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional; Region: PRK13805 94122006078 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 94122006079 putative catalytic cysteine [active] 94122006080 C-terminal alcohol dehydrogenase domain of the acetaldehyde dehydrogenase-alcohol dehydrogenase bifunctional two-domain protein (AAD); Region: AAD_C; cd08178 94122006081 putative active site [active] 94122006082 metal binding site [ion binding]; metal-binding site 94122006083 hypothetical protein; Provisional; Region: PRK11111 94122006084 Nitrate and nitrite sensing; Region: NIT; pfam08376 94122006085 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 94122006086 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 94122006087 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122006088 dimer interface [polypeptide binding]; other site 94122006089 putative CheW interface [polypeptide binding]; other site 94122006090 integrase; Provisional; Region: PRK09692 94122006091 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 94122006092 active site 94122006093 Int/Topo IB signature motif; other site 94122006094 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 94122006095 active site 94122006096 NTP binding site [chemical binding]; other site 94122006097 metal binding triad [ion binding]; metal-binding site 94122006098 antibiotic binding site [chemical binding]; other site 94122006099 Protein of unknown function DUF86; Region: DUF86; pfam01934 94122006100 Protein of unknown function (DUF3987); Region: DUF3987; pfam13148 94122006101 Protein of unknown function (DUF3296); Region: DUF3296; pfam11726 94122006102 Plasmid stabilisation system protein; Region: Plasmid_stabil; pfam05016 94122006103 Predicted transcriptional regulator [Transcription]; Region: COG3905 94122006104 Lecithin retinol acyltransferase; Region: LRAT; pfam04970 94122006105 INT_SG3, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 3, catalytic domain. The CD contains various predicted bacterial and phage integrase/recombinase sequences for which not much experimental characterization is available; Region: INT_SG3_C; cd01186 94122006106 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 94122006107 Int/Topo IB signature motif; other site 94122006108 Protein of unknown function (DUF2787); Region: DUF2787; pfam10980 94122006109 Protein of unknown function (DUF2787); Region: DUF2787; pfam10980 94122006110 YagB/YeeU/YfjZ family; Region: YagB_YeeU_YfjZ; pfam06154 94122006111 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 94122006112 MPN+ (JAMM) motif; other site 94122006113 Zinc-binding site [ion binding]; other site 94122006114 Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Region: HTH_MerR-like; cd00592 94122006115 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 94122006116 DNA binding residues [nucleotide binding] 94122006117 Vault protein inter-alpha-trypsin domain; Region: VIT; cl02699 94122006118 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 94122006119 metal ion-dependent adhesion site (MIDAS); other site 94122006120 hypothetical protein; Provisional; Region: PRK10236 94122006121 Domain of unknown function (DUF3944); Region: DUF3944; pfam13099 94122006122 Mpr1p, Pad1p N-terminal (MPN) domains; Region: MPN; cl13996 94122006123 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 94122006124 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 94122006125 Walker A motif; other site 94122006126 ATP binding site [chemical binding]; other site 94122006127 Walker B motif; other site 94122006128 arginine finger; other site 94122006129 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 94122006130 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 94122006131 Walker A motif; other site 94122006132 ATP binding site [chemical binding]; other site 94122006133 Walker B motif; other site 94122006134 arginine finger; other site 94122006135 hypothetical protein; Provisional; Region: yieM; PRK10997 94122006136 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 94122006137 metal ion-dependent adhesion site (MIDAS); other site 94122006138 Methyltransferase domain; Region: Methyltransf_26; pfam13659 94122006139 Protein of unknown function DUF262; Region: DUF262; pfam03235 94122006140 Uncharacterized conserved protein [Function unknown]; Region: COG1479 94122006141 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 94122006142 PglZ domain; Region: PglZ; pfam08665 94122006143 Zeta toxin; Region: Zeta_toxin; pfam06414 94122006144 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4185 94122006145 DEAD-like helicases superfamily; Region: DEXDc; smart00487 94122006146 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 94122006147 ATP binding site [chemical binding]; other site 94122006148 putative Mg++ binding site [ion binding]; other site 94122006149 DEAD-like helicases superfamily; Region: DEXDc; smart00487 94122006150 AAA-like domain; Region: AAA_10; pfam12846 94122006151 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 94122006152 nucleotide binding site [chemical binding]; other site 94122006153 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 94122006154 active site 94122006155 metal binding site [ion binding]; metal-binding site 94122006156 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 94122006157 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 94122006158 active site 94122006159 DNA binding site [nucleotide binding] 94122006160 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 94122006161 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 94122006162 Catalytic site [active] 94122006163 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 94122006164 Catalytic site [active] 94122006165 Protein of unknown function (DUF938); Region: DUF938; pfam06080 94122006166 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 94122006167 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 94122006168 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122006169 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122006170 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like_1; cd08470 94122006171 putative effector binding pocket; other site 94122006172 putative dimerization interface [polypeptide binding]; other site 94122006173 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 94122006174 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 94122006175 substrate binding site [chemical binding]; other site 94122006176 catalytic Zn binding site [ion binding]; other site 94122006177 NAD binding site [chemical binding]; other site 94122006178 structural Zn binding site [ion binding]; other site 94122006179 dimer interface [polypeptide binding]; other site 94122006180 S-formylglutathione hydrolase; Region: PLN02442 94122006181 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 94122006182 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 94122006183 active site 94122006184 substrate binding sites [chemical binding]; other site 94122006185 Protein of unknown function (DUF1318); Region: DUF1318; pfam07027 94122006186 YnbE-like lipoprotein; Region: Lipoprotein_19; pfam13617 94122006187 Dicarboxylate transport; Region: DctA-YdbH; pfam11739 94122006188 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 94122006189 aromatic amino acid transport protein; Region: araaP; TIGR00837 94122006190 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 94122006191 Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]; Region: HisI; COG0139 94122006192 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 94122006193 metal binding site [ion binding]; metal-binding site 94122006194 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 94122006195 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 94122006196 substrate binding site [chemical binding]; other site 94122006197 glutamase interaction surface [polypeptide binding]; other site 94122006198 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 94122006199 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 94122006200 catalytic residues [active] 94122006201 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13170 94122006202 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 94122006203 putative active site [active] 94122006204 oxyanion strand; other site 94122006205 catalytic triad [active] 94122006206 imidazole glycerol-phosphate dehydratase/histidinol phosphatase; Provisional; Region: PRK05446 94122006207 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 94122006208 active site 94122006209 motif I; other site 94122006210 motif II; other site 94122006211 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 94122006212 putative active site pocket [active] 94122006213 4-fold oligomerization interface [polypeptide binding]; other site 94122006214 metal binding residues [ion binding]; metal-binding site 94122006215 3-fold/trimer interface [polypeptide binding]; other site 94122006216 histidinol-phosphate aminotransferase; Provisional; Region: PRK04635 94122006217 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 94122006218 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122006219 homodimer interface [polypeptide binding]; other site 94122006220 catalytic residue [active] 94122006221 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 94122006222 histidinol dehydrogenase; Region: hisD; TIGR00069 94122006223 NAD binding site [chemical binding]; other site 94122006224 dimerization interface [polypeptide binding]; other site 94122006225 product binding site; other site 94122006226 substrate binding site [chemical binding]; other site 94122006227 zinc binding site [ion binding]; other site 94122006228 catalytic residues [active] 94122006229 ATP phosphoribosyltransferase; Reviewed; Region: hisG; PRK00489 94122006230 ATP phosphoribosyltransferase; Region: hisG; TIGR00070 94122006231 ATP phosphoribosyltransferase, C-terminal domain; Region: HisG_C-term; TIGR03455 94122006232 Membrane bound O-acyl transferase family; Region: MBOAT_2; pfam13813 94122006233 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 94122006234 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 94122006235 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 94122006236 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 94122006237 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 94122006238 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122006239 N-terminal plug; other site 94122006240 ligand-binding site [chemical binding]; other site 94122006241 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 94122006242 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122006243 dimer interface [polypeptide binding]; other site 94122006244 putative CheW interface [polypeptide binding]; other site 94122006245 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 94122006246 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 94122006247 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 94122006248 dimer interface [polypeptide binding]; other site 94122006249 motif 1; other site 94122006250 active site 94122006251 motif 2; other site 94122006252 motif 3; other site 94122006253 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 94122006254 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 94122006255 putative tRNA-binding site [nucleotide binding]; other site 94122006256 B3/4 domain; Region: B3_4; pfam03483 94122006257 tRNA synthetase B5 domain; Region: B5; smart00874 94122006258 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 94122006259 dimer interface [polypeptide binding]; other site 94122006260 motif 1; other site 94122006261 motif 3; other site 94122006262 motif 2; other site 94122006263 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 94122006264 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 94122006265 IHF dimer interface [polypeptide binding]; other site 94122006266 IHF - DNA interface [nucleotide binding]; other site 94122006267 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 94122006268 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 94122006269 putative acyl-acceptor binding pocket; other site 94122006270 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 94122006271 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 94122006272 dimerization interface [polypeptide binding]; other site 94122006273 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 94122006274 ATP binding site [chemical binding]; other site 94122006275 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 94122006276 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 94122006277 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypC; COG0298 94122006278 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 94122006279 oxidoreductase alpha (molybdopterin) subunit; Region: Fdhalpha-like; TIGR01701 94122006280 The MopB_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins; Region: MopB_ydeP; cd02767 94122006281 putative molybdopterin cofactor binding site [chemical binding]; other site 94122006282 The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region...; Region: MopB_CT_ydeP; cd02787 94122006283 putative molybdopterin cofactor binding site; other site 94122006284 FdhD/NarQ family; Region: FdhD-NarQ; pfam02634 94122006285 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122006286 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122006287 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 94122006288 dimerization interface [polypeptide binding]; other site 94122006289 Acylphosphatase; Region: Acylphosphatase; pfam00708 94122006290 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 94122006291 HypF finger; Region: zf-HYPF; pfam07503 94122006292 HypF finger; Region: zf-HYPF; pfam07503 94122006293 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 94122006294 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 94122006295 Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD...; Region: H2MP_MemB-H2up; cd06062 94122006296 putative substrate-binding site; other site 94122006297 nickel binding site [ion binding]; other site 94122006298 Ni/Fe-hydrogenase, b-type cytochrome subunit; Region: CytB-hydogenase; TIGR02125 94122006299 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 94122006300 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 94122006301 Ni,Fe-hydrogenase I small subunit [Energy production and conversion]; Region: HyaA; COG1740 94122006302 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 94122006303 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 94122006304 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 94122006305 catalytic residues [active] 94122006306 Domain of unknown function (DUF4266); Region: DUF4266; pfam14086 94122006307 Protein of unknown function (DUF3570); Region: DUF3570; pfam12094 94122006308 ApbE family; Region: ApbE; pfam02424 94122006309 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 94122006310 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 94122006311 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122006312 active site 94122006313 phosphorylation site [posttranslational modification] 94122006314 intermolecular recognition site; other site 94122006315 dimerization interface [polypeptide binding]; other site 94122006316 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 94122006317 DNA binding site [nucleotide binding] 94122006318 sensor protein QseC; Provisional; Region: PRK10337 94122006319 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 94122006320 dimer interface [polypeptide binding]; other site 94122006321 phosphorylation site [posttranslational modification] 94122006322 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 94122006323 ATP binding site [chemical binding]; other site 94122006324 Mg2+ binding site [ion binding]; other site 94122006325 G-X-G motif; other site 94122006326 Periplasmic glucan biosynthesis protein, MdoG; Region: MdoG; cl15433 94122006327 glucan biosynthesis protein G; Provisional; Region: mdoG; PRK13274 94122006328 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 94122006329 Glucan_BSP_ModH catalyzes the elongation of beta-1,2 polyglucose chains of glucan; Region: Glucan_BSP_ModH; cd04191 94122006330 Ligand binding site; other site 94122006331 DXD motif; other site 94122006332 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 94122006333 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 94122006334 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 94122006335 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 94122006336 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 94122006337 Bacterial protein of unknown function (DUF882); Region: Peptidase_M15_2; pfam05951 94122006338 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 94122006339 5S rRNA interface [nucleotide binding]; other site 94122006340 CTC domain interface [polypeptide binding]; other site 94122006341 L16 interface [polypeptide binding]; other site 94122006342 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 94122006343 Family of unknown function (DUF490); Region: DUF490; pfam04357 94122006344 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 94122006345 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 94122006346 Surface antigen; Region: Bac_surface_Ag; pfam01103 94122006347 L-Asparaginase type 2. L-Asparaginase hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzyme undergoes an autoproteolytic cleavage into alpha and beta subunits to expose a threonine residue which becomes the N-terminal residue of the beta...; Region: Asparaginase_2; cd04701 94122006348 catalytic nucleophile [active] 94122006349 FOG: CBS domain [General function prediction only]; Region: COG0517 94122006350 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_16; cd04629 94122006351 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 94122006352 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 94122006353 ATP binding site [chemical binding]; other site 94122006354 putative Mg++ binding site [ion binding]; other site 94122006355 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 94122006356 nucleotide binding region [chemical binding]; other site 94122006357 ATP-binding site [chemical binding]; other site 94122006358 Helicase associated domain (HA2); Region: HA2; pfam04408 94122006359 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 94122006360 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 94122006361 Periplasmic nitrate reductase protein NapE; Region: NapE; pfam06796 94122006362 NapD protein; Region: NapD; pfam03927 94122006363 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 94122006364 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_Nitrate-R-NapA-like; cd02754 94122006365 [4Fe-4S] binding site [ion binding]; other site 94122006366 molybdopterin cofactor binding site; other site 94122006367 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 94122006368 molybdopterin cofactor binding site; other site 94122006369 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; pfam03892 94122006370 periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; Region: napC_nirT; TIGR02161 94122006371 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 94122006372 Restriction endonuclease; Region: Mrr_cat; pfam04471 94122006373 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122006374 Coenzyme A binding pocket [chemical binding]; other site 94122006375 Protein of unknown function (DUF2897); Region: DUF2897; pfam11446 94122006376 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 94122006377 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 94122006378 Ligand binding site; other site 94122006379 oligomer interface; other site 94122006380 Iron-containing alcohol dehydrogenases-like; Region: Fe-ADH3; cd08184 94122006381 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 94122006382 putative active site [active] 94122006383 metal binding site [ion binding]; metal-binding site 94122006384 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 94122006385 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 94122006386 inhibitor-cofactor binding pocket; inhibition site 94122006387 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122006388 catalytic residue [active] 94122006389 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeA; cd00883 94122006390 active site clefts [active] 94122006391 zinc binding site [ion binding]; other site 94122006392 dimer interface [polypeptide binding]; other site 94122006393 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 94122006394 D-alanyl-D-alanine carboxypeptidase; Region: VanY; pfam02557 94122006395 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 94122006396 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 94122006397 metal binding site [ion binding]; metal-binding site 94122006398 dimer interface [polypeptide binding]; other site 94122006399 Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine...; Region: ArsC_Yffb; cd03035 94122006400 ArsC family; Region: ArsC; pfam03960 94122006401 putative catalytic residues [active] 94122006402 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 94122006403 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122006404 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122006405 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122006406 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 94122006407 dimerization interface [polypeptide binding]; other site 94122006408 putative effector binding pocket; other site 94122006409 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 94122006410 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122006411 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 94122006412 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 94122006413 Uncharacterized paraquat-inducible protein A [Function unknown]; Region: PqiA; COG2995 94122006414 Paraquat-inducible protein A; Region: PqiA; pfam04403 94122006415 Paraquat-inducible protein A; Region: PqiA; pfam04403 94122006416 paraquat-inducible protein B; Provisional; Region: PRK10807 94122006417 mce related protein; Region: MCE; pfam02470 94122006418 mce related protein; Region: MCE; pfam02470 94122006419 mce related protein; Region: MCE; pfam02470 94122006420 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3009 94122006421 Protein of unknown function (DUF330); Region: DUF330; pfam03886 94122006422 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 94122006423 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 94122006424 transmembrane helices; other site 94122006425 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 94122006426 Helix-turn-helix domain; Region: HTH_18; pfam12833 94122006427 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 94122006428 Glycoside hydrolase family 15, N-terminal domain; Region: GH15_N; cd07430 94122006429 Domain interface; other site 94122006430 glucan 1,4-alpha-glucosidase; Region: glucan_glucosid; TIGR01535 94122006431 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 94122006432 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 94122006433 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 94122006434 YCII-related domain; Region: YCII; cl00999 94122006435 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122006436 Coenzyme A binding pocket [chemical binding]; other site 94122006437 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 94122006438 Uncharacterized conserved protein [Function unknown]; Region: COG2128 94122006439 Helix-turn-helix domain; Region: HTH_18; pfam12833 94122006440 Glycoside hydrolase 97; Region: Glyco_hydro_97; pfam10566 94122006441 Predicted SAM-dependent methyltransferase [General function prediction only]; Region: COG2384 94122006442 Family of unknown function (DUF633); Region: DUF633; pfam04816 94122006443 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_27; cd04686 94122006444 nudix motif; other site 94122006445 Haemolysin-III related; Region: HlyIII; cl03831 94122006446 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 94122006447 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 94122006448 ThiC-associated domain; Region: ThiC-associated; pfam13667 94122006449 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 94122006450 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 94122006451 dimer interface [polypeptide binding]; other site 94122006452 HMP-P kinase/thiamin-monophosphate pyrophosphorylase; Region: PLN02898 94122006453 substrate binding site [chemical binding]; other site 94122006454 ATP binding site [chemical binding]; other site 94122006455 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 94122006456 active site 94122006457 thiamine phosphate binding site [chemical binding]; other site 94122006458 pyrophosphate binding site [ion binding]; other site 94122006459 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism]; Region: ThiF; COG0476 94122006460 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 94122006461 ATP binding site [chemical binding]; other site 94122006462 substrate interface [chemical binding]; other site 94122006463 MoeZ/MoeB domain; Region: MoeZ_MoeB; pfam05237 94122006464 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 94122006465 thiS-thiF/thiG interaction site; other site 94122006466 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 94122006467 ThiS interaction site; other site 94122006468 putative active site [active] 94122006469 tetramer interface [polypeptide binding]; other site 94122006470 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09240 94122006471 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 94122006472 FeS/SAM binding site; other site 94122006473 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 94122006474 SprA-related family; Region: SprA-related; pfam12118 94122006475 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122006476 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122006477 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 94122006478 dimerization interface [polypeptide binding]; other site 94122006479 Domain of unknown function (DUF3541); Region: DUF3541; pfam12060 94122006480 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 94122006481 alpha-L-glutamate ligase-related protein; Region: rimK_rel_E_lig; TIGR02291 94122006482 Inactive transglutaminase fused to 7 transmembrane helices; Region: Transglut_i_TM; pfam14400 94122006483 7 transmembrane helices usually fused to an inactive transglutaminase; Region: 7TM_transglut; pfam14402 94122006484 Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones]; Region: COG4067 94122006485 Methyltransferase domain; Region: Methyltransf_23; pfam13489 94122006486 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 94122006487 S-adenosylmethionine binding site [chemical binding]; other site 94122006488 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 94122006489 S-adenosylmethionine binding site [chemical binding]; other site 94122006490 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 94122006491 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 94122006492 substrate binding pocket [chemical binding]; other site 94122006493 membrane-bound complex binding site; other site 94122006494 hinge residues; other site 94122006495 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 94122006496 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 94122006497 substrate binding pocket [chemical binding]; other site 94122006498 membrane-bound complex binding site; other site 94122006499 hinge residues; other site 94122006500 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 94122006501 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 94122006502 substrate binding pocket [chemical binding]; other site 94122006503 membrane-bound complex binding site; other site 94122006504 hinge residues; other site 94122006505 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122006506 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122006507 metal binding site [ion binding]; metal-binding site 94122006508 active site 94122006509 I-site; other site 94122006510 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 94122006511 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 94122006512 dimer interface [polypeptide binding]; other site 94122006513 anticodon binding site; other site 94122006514 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 94122006515 homodimer interface [polypeptide binding]; other site 94122006516 motif 1; other site 94122006517 active site 94122006518 motif 2; other site 94122006519 GAD domain; Region: GAD; pfam02938 94122006520 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 94122006521 active site 94122006522 motif 3; other site 94122006523 hypothetical protein; Validated; Region: PRK00110 94122006524 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 94122006525 active site 94122006526 putative DNA-binding cleft [nucleotide binding]; other site 94122006527 dimer interface [polypeptide binding]; other site 94122006528 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 94122006529 RuvA N terminal domain; Region: RuvA_N; pfam01330 94122006530 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 94122006531 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 94122006532 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 94122006533 Walker A motif; other site 94122006534 ATP binding site [chemical binding]; other site 94122006535 Walker B motif; other site 94122006536 arginine finger; other site 94122006537 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 94122006538 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 94122006539 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122006540 N-terminal plug; other site 94122006541 ligand-binding site [chemical binding]; other site 94122006542 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 94122006543 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122006544 active site 94122006545 phosphorylation site [posttranslational modification] 94122006546 intermolecular recognition site; other site 94122006547 dimerization interface [polypeptide binding]; other site 94122006548 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 94122006549 DNA binding site [nucleotide binding] 94122006550 Predicted carboxypeptidase [Amino acid transport and metabolism]; Region: COG2866 94122006551 Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases; uncharacterized bacterial subgroup; Region: M14_Nna1_like_1; cd06234 94122006552 putative active site [active] 94122006553 Zn binding site [ion binding]; other site 94122006554 bifunctional preprotein translocase subunit SecD/SecF; Provisional; Region: PRK14726 94122006555 Protein of unknown function (DUF1315); Region: DUF1315; cl01215 94122006556 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 94122006557 active site 94122006558 homodimer interface [polypeptide binding]; other site 94122006559 protease 4; Provisional; Region: PRK10949 94122006560 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 94122006561 tandem repeat interface [polypeptide binding]; other site 94122006562 oligomer interface [polypeptide binding]; other site 94122006563 active site residues [active] 94122006564 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 94122006565 tandem repeat interface [polypeptide binding]; other site 94122006566 oligomer interface [polypeptide binding]; other site 94122006567 active site residues [active] 94122006568 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 94122006569 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 94122006570 active site 94122006571 FMN binding site [chemical binding]; other site 94122006572 2,4-decadienoyl-CoA binding site; other site 94122006573 catalytic residue [active] 94122006574 4Fe-4S cluster binding site [ion binding]; other site 94122006575 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 94122006576 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 94122006577 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 94122006578 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 94122006579 catalytic loop [active] 94122006580 iron binding site [ion binding]; other site 94122006581 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 94122006582 dimer interface [polypeptide binding]; other site 94122006583 putative radical transfer pathway; other site 94122006584 diiron center [ion binding]; other site 94122006585 tyrosyl radical; other site 94122006586 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09103 94122006587 ATP cone domain; Region: ATP-cone; pfam03477 94122006588 Class I ribonucleotide reductase; Region: RNR_I; cd01679 94122006589 active site 94122006590 dimer interface [polypeptide binding]; other site 94122006591 catalytic residues [active] 94122006592 effector binding site; other site 94122006593 R2 peptide binding site; other site 94122006594 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 94122006595 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 94122006596 active site 94122006597 motif I; other site 94122006598 motif II; other site 94122006599 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 94122006600 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 94122006601 S-adenosylmethionine binding site [chemical binding]; other site 94122006602 DNA gyrase subunit A; Validated; Region: PRK05560 94122006603 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 94122006604 CAP-like domain; other site 94122006605 active site 94122006606 primary dimer interface [polypeptide binding]; other site 94122006607 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 94122006608 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 94122006609 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 94122006610 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 94122006611 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 94122006612 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 94122006613 3-phosphoserine/phosphohydroxythreonine aminotransferase; Provisional; Region: PRK05355 94122006614 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 94122006615 catalytic residue [active] 94122006616 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 94122006617 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 94122006618 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122006619 homodimer interface [polypeptide binding]; other site 94122006620 catalytic residue [active] 94122006621 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 94122006622 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 94122006623 hinge; other site 94122006624 active site 94122006625 cytidylate kinase; Provisional; Region: cmk; PRK00023 94122006626 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 94122006627 CMP-binding site; other site 94122006628 The sites determining sugar specificity; other site 94122006629 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 94122006630 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 94122006631 RNA binding site [nucleotide binding]; other site 94122006632 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 94122006633 RNA binding site [nucleotide binding]; other site 94122006634 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 94122006635 RNA binding site [nucleotide binding]; other site 94122006636 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 94122006637 RNA binding site [nucleotide binding]; other site 94122006638 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 94122006639 RNA binding site [nucleotide binding]; other site 94122006640 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 94122006641 RNA binding site [nucleotide binding]; other site 94122006642 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 94122006643 IHF dimer interface [polypeptide binding]; other site 94122006644 IHF - DNA interface [nucleotide binding]; other site 94122006645 Protein of unknown function (DUF1049); Region: DUF1049; pfam06305 94122006646 tetratricopeptide repeat protein; Provisional; Region: PRK11788 94122006647 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 94122006648 binding surface 94122006649 TPR motif; other site 94122006650 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 94122006651 active site 94122006652 dimer interface [polypeptide binding]; other site 94122006653 short chain dehydrogenase; Provisional; Region: PRK07576 94122006654 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 94122006655 NAD(P) binding site [chemical binding]; other site 94122006656 active site 94122006657 Uncharacterized protein conserved in bacteria (DUF2058); Region: DUF2058; pfam09831 94122006658 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 94122006659 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 94122006660 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 94122006661 active site 94122006662 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 94122006663 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; cl17429 94122006664 Domain of unknown function (DUF1904); Region: DUF1904; pfam08921 94122006665 phosphatidylserine synthase; Provisional; Region: pssA; PRK09428 94122006666 Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_1; cd09134 94122006667 domain interface [polypeptide binding]; other site 94122006668 putative active site [active] 94122006669 catalytic site [active] 94122006670 Catalytic domain, repeat 2, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_2; cd09136 94122006671 domain interface [polypeptide binding]; other site 94122006672 putative active site [active] 94122006673 catalytic site [active] 94122006674 multidrug resistance protein D; Provisional; Region: emrD; PRK11652 94122006675 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 94122006676 putative substrate translocation pore; other site 94122006677 beta-lactamase/D-alanine carboxypeptidase; Provisional; Region: ampC; PRK11289 94122006678 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 94122006679 Uncharacterized conserved protein [Function unknown]; Region: COG3148 94122006680 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 94122006681 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 94122006682 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122006683 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 94122006684 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 94122006685 Predicted phosphatase [General function prediction only]; Region: PhoX; COG3211 94122006686 TAT (twin-arginine translocation) pathway signal sequence; Region: TAT_signal; pfam10518 94122006687 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 94122006688 active site 94122006689 DNA binding site [nucleotide binding] 94122006690 Int/Topo IB signature motif; other site 94122006691 DEAD-like helicases superfamily; Region: DEXDc; smart00487 94122006692 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 94122006693 ATP binding site [chemical binding]; other site 94122006694 putative Mg++ binding site [ion binding]; other site 94122006695 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 94122006696 nucleotide binding region [chemical binding]; other site 94122006697 ATP-binding site [chemical binding]; other site 94122006698 ecotin; Provisional; Region: PRK03719 94122006699 secondary substrate binding site; other site 94122006700 primary substrate binding site; other site 94122006701 inhibition loop; other site 94122006702 dimerization interface [polypeptide binding]; other site 94122006703 Putative glycosyl/glycerophosphate transferases involved in teichoic acid biosynthesis TagF/TagB/EpsJ/RodC [Cell envelope biogenesis, outer membrane]; Region: TagB; COG1887 94122006704 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 94122006705 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 94122006706 active site 94122006707 nucleotide binding site [chemical binding]; other site 94122006708 HIGH motif; other site 94122006709 KMSKS motif; other site 94122006710 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 94122006711 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 94122006712 active site 94122006713 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 94122006714 putative trimer interface [polypeptide binding]; other site 94122006715 putative CoA binding site [chemical binding]; other site 94122006716 Bacterial sugar transferase; Region: Bac_transf; cl00939 94122006717 Teichoic acid biosynthesis proteins [Cell envelope biogenesis, outer membrane]; Region: WecG; COG1922 94122006718 The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common...; Region: Glyco_transf_WecG_TagA; cd06533 94122006719 Bacterial sugar transferase; Region: Bac_transf; pfam02397 94122006720 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 94122006721 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 94122006722 active site 94122006723 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_tuaB_like; cd13127 94122006724 O-antigen ligase like membrane protein; Region: O-antigen_lig; pfam13425 94122006725 Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane]; Region: GumC; COG3206 94122006726 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 94122006727 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 94122006728 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 94122006729 anti sigma factor interaction site; other site 94122006730 regulatory phosphorylation site [posttranslational modification]; other site 94122006731 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 94122006732 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 94122006733 Response regulator receiver domain; Region: Response_reg; pfam00072 94122006734 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122006735 active site 94122006736 phosphorylation site [posttranslational modification] 94122006737 intermolecular recognition site; other site 94122006738 dimerization interface [polypeptide binding]; other site 94122006739 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 94122006740 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 94122006741 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 94122006742 substrate binding pocket [chemical binding]; other site 94122006743 membrane-bound complex binding site; other site 94122006744 hinge residues; other site 94122006745 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 94122006746 dimerization interface [polypeptide binding]; other site 94122006747 PAS domain S-box; Region: sensory_box; TIGR00229 94122006748 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 94122006749 putative active site [active] 94122006750 heme pocket [chemical binding]; other site 94122006751 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 94122006752 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 94122006753 putative active site [active] 94122006754 heme pocket [chemical binding]; other site 94122006755 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 94122006756 dimer interface [polypeptide binding]; other site 94122006757 phosphorylation site [posttranslational modification] 94122006758 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 94122006759 ATP binding site [chemical binding]; other site 94122006760 Mg2+ binding site [ion binding]; other site 94122006761 G-X-G motif; other site 94122006762 Response regulator receiver domain; Region: Response_reg; pfam00072 94122006763 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122006764 active site 94122006765 phosphorylation site [posttranslational modification] 94122006766 intermolecular recognition site; other site 94122006767 dimerization interface [polypeptide binding]; other site 94122006768 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 94122006769 putative binding surface; other site 94122006770 active site 94122006771 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 94122006772 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122006773 active site 94122006774 phosphorylation site [posttranslational modification] 94122006775 intermolecular recognition site; other site 94122006776 dimerization interface [polypeptide binding]; other site 94122006777 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 94122006778 Walker A motif; other site 94122006779 ATP binding site [chemical binding]; other site 94122006780 Walker B motif; other site 94122006781 arginine finger; other site 94122006782 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 94122006783 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 94122006784 HAMP domain; Region: HAMP; pfam00672 94122006785 dimerization interface [polypeptide binding]; other site 94122006786 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 94122006787 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122006788 dimer interface [polypeptide binding]; other site 94122006789 putative CheW interface [polypeptide binding]; other site 94122006790 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 94122006791 active site 94122006792 DNA binding site [nucleotide binding] 94122006793 Int/Topo IB signature motif; other site 94122006794 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 94122006795 Zn2+ binding site [ion binding]; other site 94122006796 Mg2+ binding site [ion binding]; other site 94122006797 Domain of unknown function (DUF3596); Region: DUF3596; pfam12167 94122006798 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 94122006799 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 94122006800 active site 94122006801 DNA binding site [nucleotide binding] 94122006802 Int/Topo IB signature motif; other site 94122006803 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 94122006804 non-specific DNA binding site [nucleotide binding]; other site 94122006805 salt bridge; other site 94122006806 sequence-specific DNA binding site [nucleotide binding]; other site 94122006807 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 94122006808 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 94122006809 Walker A motif; other site 94122006810 ATP binding site [chemical binding]; other site 94122006811 Walker B motif; other site 94122006812 arginine finger; other site 94122006813 Domain of unknown function (DUF4145); Region: DUF4145; pfam13643 94122006814 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 94122006815 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 94122006816 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 94122006817 ATP binding site [chemical binding]; other site 94122006818 putative Mg++ binding site [ion binding]; other site 94122006819 HsdM N-terminal domain; Region: HsdM_N; pfam12161 94122006820 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 94122006821 Methyltransferase domain; Region: Methyltransf_26; pfam13659 94122006822 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 94122006823 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 94122006824 Domain of unknown function DUF87; Region: DUF87; pfam01935 94122006825 HerA helicase [Replication, recombination, and repair]; Region: COG0433 94122006826 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 94122006827 G1 box; other site 94122006828 GTP/Mg2+ binding site [chemical binding]; other site 94122006829 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 94122006830 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 94122006831 G3 box; other site 94122006832 Switch II region; other site 94122006833 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 94122006834 G1 box; other site 94122006835 GTP/Mg2+ binding site [chemical binding]; other site 94122006836 G2 box; other site 94122006837 Switch I region; other site 94122006838 G3 box; other site 94122006839 Switch II region; other site 94122006840 G4 box; other site 94122006841 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 94122006842 DEAD-like helicases superfamily; Region: DEXDc; smart00487 94122006843 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 94122006844 putative Mg++ binding site [ion binding]; other site 94122006845 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 94122006846 ATP-binding site [chemical binding]; other site 94122006847 Domain of unknown function (DUF1998); Region: DUF1998; pfam09369 94122006848 multidrug efflux protein; Reviewed; Region: PRK01766 94122006849 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 94122006850 cation binding site [ion binding]; other site 94122006851 riboflavin synthase subunit alpha; Provisional; Region: PRK13020 94122006852 Lumazine binding domain; Region: Lum_binding; pfam00677 94122006853 Lumazine binding domain; Region: Lum_binding; pfam00677 94122006854 Cysteine-rich CPXCG; Region: Cys_rich_CPXG; pfam14255 94122006855 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 94122006856 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 94122006857 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 94122006858 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 94122006859 active site 94122006860 dimer interface [polypeptide binding]; other site 94122006861 motif 1; other site 94122006862 motif 2; other site 94122006863 motif 3; other site 94122006864 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 94122006865 anticodon binding site; other site 94122006866 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 94122006867 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 94122006868 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 94122006869 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 94122006870 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 94122006871 23S rRNA binding site [nucleotide binding]; other site 94122006872 L21 binding site [polypeptide binding]; other site 94122006873 L13 binding site [polypeptide binding]; other site 94122006874 thioredoxin reductase; Provisional; Region: PRK10262 94122006875 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 94122006876 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 94122006877 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 94122006878 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 94122006879 hexamer interface [polypeptide binding]; other site 94122006880 ligand binding site [chemical binding]; other site 94122006881 putative active site [active] 94122006882 NAD(P) binding site [chemical binding]; other site 94122006883 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 94122006884 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 94122006885 putative DNA binding site [nucleotide binding]; other site 94122006886 putative Zn2+ binding site [ion binding]; other site 94122006887 AsnC family; Region: AsnC_trans_reg; pfam01037 94122006888 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 94122006889 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 94122006890 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 94122006891 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 94122006892 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 94122006893 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 94122006894 recombination factor protein RarA; Reviewed; Region: PRK13342 94122006895 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 94122006896 Walker A motif; other site 94122006897 ATP binding site [chemical binding]; other site 94122006898 Walker B motif; other site 94122006899 arginine finger; other site 94122006900 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 94122006901 camphor resistance protein CrcB; Provisional; Region: PRK14197 94122006902 seryl-tRNA synthetase; Provisional; Region: PRK05431 94122006903 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 94122006904 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 94122006905 dimer interface [polypeptide binding]; other site 94122006906 active site 94122006907 motif 1; other site 94122006908 motif 2; other site 94122006909 motif 3; other site 94122006910 Dissimilatory sulfite reductase (desulfoviridin), gamma subunit [Inorganic ion transport and metabolism]; Region: DsrC; COG2920 94122006911 sulfur relay protein, TusE/DsrC/DsvC family; Region: dsrC_tusE_dsvC; TIGR03342 94122006912 sulfur relay protein TusB/DsrH; Region: sulf_tusB_dsrH; TIGR03011 94122006913 sulfur relay protein TusC/DsrF; Region: sulf_tusC_dsrF; TIGR03010 94122006914 sulfur relay protein TusD/DsrE; Region: sulf_tusD_dsrE; TIGR03012 94122006915 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 94122006916 YccA-like proteins; Region: YccA_like; cd10433 94122006917 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 94122006918 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122006919 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 94122006920 dimerization interface [polypeptide binding]; other site 94122006921 putative transporter; Provisional; Region: PRK11043 94122006922 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 94122006923 putative substrate translocation pore; other site 94122006924 ribulokinase; Provisional; Region: PRK04123 94122006925 Ribulokinases; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_RBK; cd07781 94122006926 N- and C-terminal domain interface [polypeptide binding]; other site 94122006927 active site 94122006928 MgATP binding site [chemical binding]; other site 94122006929 catalytic site [active] 94122006930 metal binding site [ion binding]; metal-binding site 94122006931 carbohydrate binding site [chemical binding]; other site 94122006932 homodimer interface [polypeptide binding]; other site 94122006933 L-ribulose-5-phosphate 4-epimerase; Reviewed; Region: araD; PRK08193 94122006934 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 94122006935 intersubunit interface [polypeptide binding]; other site 94122006936 active site 94122006937 Zn2+ binding site [ion binding]; other site 94122006938 L-arabinose isomerase; Provisional; Region: PRK02929 94122006939 L-fucose isomerase (FucIase) and L-arabinose isomerase (AI) family; composed of FucIase, AI and similar proteins. FucIase converts L-fucose, an aldohexose, to its ketose form, which prepares it for aldol cleavage (similar to the isomerization of glucose...; Region: L-fuc_L-ara-isomerases; cl00947 94122006940 hexamer (dimer of trimers) interface [polypeptide binding]; other site 94122006941 trimer interface [polypeptide binding]; other site 94122006942 substrate binding site [chemical binding]; other site 94122006943 Mn binding site [ion binding]; other site 94122006944 fructose-1-P/6-phosphogluconate phosphatase; Provisional; Region: PRK10725 94122006945 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 94122006946 active site 94122006947 motif I; other site 94122006948 motif II; other site 94122006949 Transcriptional regulators [Transcription]; Region: FadR; COG2186 94122006950 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 94122006951 DNA-binding site [nucleotide binding]; DNA binding site 94122006952 FCD domain; Region: FCD; pfam07729 94122006953 Glycosyl hydrolase family 43, includes arabinoxylan arabinofuranohydrolase, beta-xylosidase, endo-1,4-beta-xylanase, alpha-L-arabinofuranosidase; Region: GH43_AXH_like; cd08990 94122006954 substrate binding site [chemical binding]; other site 94122006955 active site 94122006956 dihydroxy-acid dehydratase; Validated; Region: PRK06131 94122006957 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 94122006958 classical (c) SDRs; Region: SDR_c; cd05233 94122006959 NAD(P) binding site [chemical binding]; other site 94122006960 active site 94122006961 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 94122006962 active site 94122006963 catalytic residues [active] 94122006964 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 94122006965 Periplasmic binding domain of ABC-type YtfQ-like transport systems; Region: PBP1_YtfQ_like; cd06309 94122006966 putative ligand binding site [chemical binding]; other site 94122006967 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 94122006968 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 94122006969 Walker A/P-loop; other site 94122006970 ATP binding site [chemical binding]; other site 94122006971 Q-loop/lid; other site 94122006972 ABC transporter signature motif; other site 94122006973 Walker B; other site 94122006974 D-loop; other site 94122006975 H-loop/switch region; other site 94122006976 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 94122006977 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 94122006978 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 94122006979 TM-ABC transporter signature motif; other site 94122006980 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 94122006981 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 94122006982 TM-ABC transporter signature motif; other site 94122006983 Glycosyl hydrolase family 43; Region: GH43_1; cd08980 94122006984 active site 94122006985 Glycosyl hydrolase family 43; Region: GH43_1; cd08980 94122006986 active site 94122006987 Domain of unknown function (DUF4303); Region: DUF4303; pfam14136 94122006988 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3533 94122006989 Putative glycosyl hydrolase of unknown function (DUF1680); Region: DUF1680; pfam07944 94122006990 Na+/melibiose symporter and related transporters [Carbohydrate transport and metabolism]; Region: MelB; COG2211 94122006991 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 94122006992 Glycosyl hydrolase family 43; Region: GH43_ABN_1; cd08998 94122006993 substrate binding site [chemical binding]; other site 94122006994 active site 94122006995 Glycosyl hydrolase family 43; Region: GH43_1; cd08980 94122006996 active site 94122006997 Ricin-type beta-trefoil lectin domain-like; Region: RicinB_lectin_2; pfam14200 94122006998 Ricin-type beta-trefoil lectin domain-like; Region: RicinB_lectin_2; pfam14200 94122006999 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 94122007000 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 94122007001 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122007002 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122007003 Beta-xylosidase [Carbohydrate transport and metabolism]; Region: XynB; COG3507 94122007004 Glycosyl hydrolase family 43; Region: GH43_ABN_1; cd08998 94122007005 substrate binding site [chemical binding]; other site 94122007006 active site 94122007007 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 94122007008 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 94122007009 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 94122007010 formate dehydrogenase, alpha subunit, proteobacterial-type; Region: formate-DH-alph; TIGR01553 94122007011 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_Formate-Dh-Na-like; cd02752 94122007012 [4Fe-4S] binding site [ion binding]; other site 94122007013 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 94122007014 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 94122007015 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_CT_Formate-Dh-Na-like; cd02792 94122007016 molybdopterin cofactor binding site; other site 94122007017 formate dehydrogenase, beta subunit, Fe-S containing; Region: FDH-beta; TIGR01582 94122007018 4Fe-4S binding domain; Region: Fer4; pfam00037 94122007019 Formate dehydrogenase N, transmembrane; Region: Form-deh_trans; pfam09163 94122007020 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 94122007021 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 94122007022 formate dehydrogenase accessory protein FdhE; Region: FdhE; TIGR01562 94122007023 Protein involved in formate dehydrogenase formation; Region: FdhE; pfam04216 94122007024 Transposase; Region: HTH_Tnp_1; cl17663 94122007025 Predicted transcriptional regulator [Transcription]; Region: COG2378 94122007026 WYL domain; Region: WYL; pfam13280 94122007027 KicB killing factor; Region: KicB; cl11468 94122007028 MukE-like family; Region: MukE; cl11471 94122007029 cell division protein MukB; Provisional; Region: mukB; PRK04863 94122007030 P-loop containing region of AAA domain; Region: AAA_29; cl17516 94122007031 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 94122007032 Transposase; Region: HTH_Tnp_1; cl17663 94122007033 HD domain; Region: HD_3; pfam13023 94122007034 Restriction endonuclease; Region: Mrr_cat; pfam04471 94122007035 Restriction endonuclease; Region: Mrr_cat; pfam04471 94122007036 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 94122007037 Int/Topo IB signature motif; other site 94122007038 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 94122007039 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 94122007040 active site 94122007041 phosphorylation site [posttranslational modification] 94122007042 intermolecular recognition site; other site 94122007043 Domain of unknown function (DUF3369); Region: DUF3369; pfam11849 94122007044 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 94122007045 Zn2+ binding site [ion binding]; other site 94122007046 Mg2+ binding site [ion binding]; other site 94122007047 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction...; Region: cbb3_Oxidase_I; cd01661 94122007048 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 94122007049 Low-spin heme binding site [chemical binding]; other site 94122007050 Putative water exit pathway; other site 94122007051 Binuclear center (active site) [active] 94122007052 Putative proton exit pathway; other site 94122007053 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 94122007054 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 94122007055 Cbb3-type cytochrome oxidase component FixQ; Region: FixQ; pfam05545 94122007056 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 94122007057 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 94122007058 Cytochrome c; Region: Cytochrom_C; pfam00034 94122007059 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3198 94122007060 FixH; Region: FixH; pfam05751 94122007061 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 94122007062 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 94122007063 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 94122007064 metal-binding site [ion binding] 94122007065 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 94122007066 Soluble P-type ATPase [General function prediction only]; Region: COG4087 94122007067 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; pfam03597 94122007068 Family description; Region: DsbD_2; pfam13386 94122007069 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 94122007070 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 94122007071 ligand binding site [chemical binding]; other site 94122007072 flexible hinge region; other site 94122007073 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 94122007074 putative switch regulator; other site 94122007075 non-specific DNA interactions [nucleotide binding]; other site 94122007076 DNA binding site [nucleotide binding] 94122007077 sequence specific DNA binding site [nucleotide binding]; other site 94122007078 putative cAMP binding site [chemical binding]; other site 94122007079 universal stress protein UspE; Provisional; Region: PRK11175 94122007080 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 94122007081 Ligand Binding Site [chemical binding]; other site 94122007082 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 94122007083 Ligand Binding Site [chemical binding]; other site 94122007084 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 94122007085 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 94122007086 Ligand Binding Site [chemical binding]; other site 94122007087 Protein of unknown function (DUF2987); Region: DUF2987; pfam11205 94122007088 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; cl17361 94122007089 conserved hypothetical protein, cofD-related; Region: CofD_related; TIGR01826 94122007090 family of mostly uncharacterized proteins similar to B.subtilis YvcK; Region: YvcK_like; cd07187 94122007091 phosphate binding site [ion binding]; other site 94122007092 putative substrate binding pocket [chemical binding]; other site 94122007093 dimer interface [polypeptide binding]; other site 94122007094 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 94122007095 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 94122007096 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122007097 homodimer interface [polypeptide binding]; other site 94122007098 catalytic residue [active] 94122007099 glyceraldehyde-3-phosphate dehydrogenase; Reviewed; Region: PRK08289 94122007100 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 94122007101 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 94122007102 Protein of unknown function (DUF2989); Region: DUF2989; pfam11207 94122007103 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 94122007104 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 94122007105 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 94122007106 Cu/Zn superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodC; COG2032 94122007107 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 94122007108 E-class dimer interface [polypeptide binding]; other site 94122007109 P-class dimer interface [polypeptide binding]; other site 94122007110 active site 94122007111 Cu2+ binding site [ion binding]; other site 94122007112 Zn2+ binding site [ion binding]; other site 94122007113 HTH-like domain; Region: HTH_21; pfam13276 94122007114 Integrase core domain; Region: rve; pfam00665 94122007115 Integrase core domain; Region: rve_3; pfam13683 94122007116 quinolinate synthetase; Provisional; Region: PRK09375 94122007117 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 94122007118 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 94122007119 E3 interaction surface; other site 94122007120 lipoyl attachment site [posttranslational modification]; other site 94122007121 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 94122007122 E3 interaction surface; other site 94122007123 lipoyl attachment site [posttranslational modification]; other site 94122007124 e3 binding domain; Region: E3_binding; pfam02817 94122007125 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 94122007126 3-methyl-2-oxobutanate dehydrogenase; Provisional; Region: PTZ00182 94122007127 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 94122007128 alpha subunit interface [polypeptide binding]; other site 94122007129 TPP binding site [chemical binding]; other site 94122007130 heterodimer interface [polypeptide binding]; other site 94122007131 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 94122007132 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]; Region: AcoA; COG1071 94122007133 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 94122007134 tetramer interface [polypeptide binding]; other site 94122007135 TPP-binding site [chemical binding]; other site 94122007136 heterodimer interface [polypeptide binding]; other site 94122007137 phosphorylation loop region [posttranslational modification] 94122007138 Peptidase M14 Succinylglutamate desuccinylase (ASTE) subfamily; Region: M14_ASTE; cd03855 94122007139 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 94122007140 putative active site [active] 94122007141 Zn binding site [ion binding]; other site 94122007142 methionine sulfoxide reductase A; Provisional; Region: PRK14054 94122007143 phosphoglucomutase; Validated; Region: PRK07564 94122007144 This bacterial PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl...; Region: PGM_like3; cd05801 94122007145 active site 94122007146 substrate binding site [chemical binding]; other site 94122007147 metal binding site [ion binding]; metal-binding site 94122007148 SeqA protein; Region: SeqA; pfam03925 94122007149 PGAP1-like protein; Region: PGAP1; pfam07819 94122007150 acyl-CoA esterase; Provisional; Region: PRK10673 94122007151 Protein of unknown function (DUF2788); Region: DUF2788; pfam10981 94122007152 LexA regulated protein; Provisional; Region: PRK11675 94122007153 flavodoxin FldA; Validated; Region: PRK09267 94122007154 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4394 94122007155 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; pfam10093 94122007156 elongation factor P; Validated; Region: PRK00529 94122007157 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 94122007158 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 94122007159 RNA binding site [nucleotide binding]; other site 94122007160 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 94122007161 RNA binding site [nucleotide binding]; other site 94122007162 HTH-like domain; Region: HTH_21; pfam13276 94122007163 Integrase core domain; Region: rve; pfam00665 94122007164 Integrase core domain; Region: rve_3; pfam13683 94122007165 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 94122007166 Short chain fatty acid transporter; Region: SCFA_trans; cl17380 94122007167 aminotransferase AlaT; Validated; Region: PRK09265 94122007168 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 94122007169 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122007170 homodimer interface [polypeptide binding]; other site 94122007171 catalytic residue [active] 94122007172 5'-nucleotidase; Provisional; Region: PRK03826 94122007173 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK05318 94122007174 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 94122007175 Zn2+ binding site [ion binding]; other site 94122007176 Mg2+ binding site [ion binding]; other site 94122007177 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 94122007178 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 94122007179 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 94122007180 active site 94122007181 intersubunit interface [polypeptide binding]; other site 94122007182 catalytic residue [active] 94122007183 phosphogluconate dehydratase; Validated; Region: PRK09054 94122007184 6-phosphogluconate dehydratase; Region: edd; TIGR01196 94122007185 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 94122007186 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 94122007187 putative active site [active] 94122007188 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 94122007189 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 94122007190 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 94122007191 DNA-binding transcriptional regulator HexR; Provisional; Region: PRK11302 94122007192 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 94122007193 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 94122007194 putative active site [active] 94122007195 pyruvate kinase; Provisional; Region: PRK05826 94122007196 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 94122007197 domain interfaces; other site 94122007198 active site 94122007199 acyl-CoA dehydrogenase; Reviewed; Region: PRK13026 94122007200 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 94122007201 active site 94122007202 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 94122007203 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 94122007204 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 94122007205 Peptidase family M2 Angiotensin converting enzyme (ACE); Region: M2_ACE; cd06461 94122007206 active site 94122007207 Zn binding site [ion binding]; other site 94122007208 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 94122007209 Smr domain; Region: Smr; pfam01713 94122007210 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3012 94122007211 SEC-C motif; Region: SEC-C; pfam02810 94122007212 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 94122007213 GAF domain; Region: GAF; pfam01590 94122007214 PAS domain S-box; Region: sensory_box; TIGR00229 94122007215 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 94122007216 putative active site [active] 94122007217 heme pocket [chemical binding]; other site 94122007218 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122007219 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122007220 metal binding site [ion binding]; metal-binding site 94122007221 active site 94122007222 I-site; other site 94122007223 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 94122007224 Protein of unknown function (DUF406); Region: DUF406; pfam04175 94122007225 Ribosomal S4P (gammaproteobacterial); Region: Ribosomal_S4Pg; pfam11993 94122007226 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 94122007227 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Region: rSAM_QueE_Ecoli; TIGR04322 94122007228 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 94122007229 Ligand Binding Site [chemical binding]; other site 94122007230 rhomboid family GlyGly-CTERM serine protease; Region: rhom_GG_sort; TIGR03902 94122007231 excinuclease ABC subunit B; Provisional; Region: PRK05298 94122007232 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 94122007233 ATP binding site [chemical binding]; other site 94122007234 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 94122007235 nucleotide binding region [chemical binding]; other site 94122007236 ATP-binding site [chemical binding]; other site 94122007237 Ultra-violet resistance protein B; Region: UvrB; pfam12344 94122007238 UvrB/uvrC motif; Region: UVR; pfam02151 94122007239 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122007240 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122007241 active site 94122007242 I-site; other site 94122007243 metal binding site [ion binding]; metal-binding site 94122007244 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 94122007245 electron transport complex protein RsxA; Provisional; Region: PRK05151 94122007246 ferredoxin; Provisional; Region: PRK08764 94122007247 Putative Fe-S cluster; Region: FeS; pfam04060 94122007248 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 94122007249 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 94122007250 SLBB domain; Region: SLBB; pfam10531 94122007251 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 94122007252 electron transport complex protein RnfD; Reviewed; Region: rnfD; PRK00816 94122007253 electron transport complex protein RnfG; Validated; Region: PRK01908 94122007254 electron transport complex RsxE subunit; Provisional; Region: PRK12405 94122007255 endonuclease III; Provisional; Region: PRK10702 94122007256 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 94122007257 minor groove reading motif; other site 94122007258 helix-hairpin-helix signature motif; other site 94122007259 substrate binding pocket [chemical binding]; other site 94122007260 active site 94122007261 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 94122007262 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 94122007263 active site 94122007264 catalytic residues [active] 94122007265 DNA binding site [nucleotide binding] 94122007266 Int/Topo IB signature motif; other site 94122007267 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 94122007268 DNA binding site [nucleotide binding] 94122007269 active site 94122007270 Int/Topo IB signature motif; other site 94122007271 HNH endonuclease; Region: HNH_2; pfam13391 94122007272 hypothetical protein; Provisional; Region: PRK06921 94122007273 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 94122007274 Uncharacterized protein conserved in bacteria C-term(DUF2220); Region: DUF2220; pfam09983 94122007275 WYL domain; Region: WYL; pfam13280 94122007276 Domain of unknown function (DUF4277); Region: DUF4277; pfam14104 94122007277 Transposase [DNA replication, recombination, and repair]; Region: COG5421 94122007278 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 94122007279 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 94122007280 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 94122007281 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 94122007282 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 94122007283 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 94122007284 dimer interface [polypeptide binding]; other site 94122007285 phosphorylation site [posttranslational modification] 94122007286 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 94122007287 ATP binding site [chemical binding]; other site 94122007288 Mg2+ binding site [ion binding]; other site 94122007289 G-X-G motif; other site 94122007290 Response regulator receiver domain; Region: Response_reg; pfam00072 94122007291 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122007292 active site 94122007293 phosphorylation site [posttranslational modification] 94122007294 intermolecular recognition site; other site 94122007295 dimerization interface [polypeptide binding]; other site 94122007296 Response regulator receiver domain; Region: Response_reg; pfam00072 94122007297 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122007298 active site 94122007299 phosphorylation site [posttranslational modification] 94122007300 intermolecular recognition site; other site 94122007301 dimerization interface [polypeptide binding]; other site 94122007302 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 94122007303 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 94122007304 putative substrate translocation pore; other site 94122007305 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 94122007306 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 94122007307 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122007308 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122007309 metal binding site [ion binding]; metal-binding site 94122007310 active site 94122007311 I-site; other site 94122007312 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 94122007313 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 94122007314 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122007315 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122007316 Phytase; Region: Phytase; cl17685 94122007317 Phytase; Region: Phytase; cl17685 94122007318 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 94122007319 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 94122007320 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122007321 Walker A/P-loop; other site 94122007322 ATP binding site [chemical binding]; other site 94122007323 ABC transporter signature motif; other site 94122007324 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 94122007325 Walker B; other site 94122007326 ABC transporter; Region: ABC_tran_2; pfam12848 94122007327 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 94122007328 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_2; cd08895 94122007329 putative hydrophobic ligand binding site [chemical binding]; other site 94122007330 Nuclease-related domain; Region: NERD; pfam08378 94122007331 Hpt domain; Region: Hpt; pfam01627 94122007332 putative binding surface; other site 94122007333 active site 94122007334 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 94122007335 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122007336 active site 94122007337 phosphorylation site [posttranslational modification] 94122007338 intermolecular recognition site; other site 94122007339 dimerization interface [polypeptide binding]; other site 94122007340 Response regulator receiver domain; Region: Response_reg; pfam00072 94122007341 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122007342 active site 94122007343 phosphorylation site [posttranslational modification] 94122007344 intermolecular recognition site; other site 94122007345 dimerization interface [polypeptide binding]; other site 94122007346 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122007347 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122007348 metal binding site [ion binding]; metal-binding site 94122007349 active site 94122007350 I-site; other site 94122007351 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 94122007352 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122007353 active site 94122007354 phosphorylation site [posttranslational modification] 94122007355 intermolecular recognition site; other site 94122007356 dimerization interface [polypeptide binding]; other site 94122007357 CheB methylesterase; Region: CheB_methylest; pfam01339 94122007358 chemoreceptor glutamine deamidase CheD; Provisional; Region: PRK13487 94122007359 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 94122007360 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 94122007361 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 94122007362 PAS fold; Region: PAS; pfam00989 94122007363 PAS domain; Region: PAS; smart00091 94122007364 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122007365 dimer interface [polypeptide binding]; other site 94122007366 putative CheW interface [polypeptide binding]; other site 94122007367 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 94122007368 putative CheA interaction surface; other site 94122007369 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 94122007370 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 94122007371 putative binding surface; other site 94122007372 active site 94122007373 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 94122007374 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 94122007375 ATP binding site [chemical binding]; other site 94122007376 Mg2+ binding site [ion binding]; other site 94122007377 G-X-G motif; other site 94122007378 CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling...; Region: CheA_reg; cd00731 94122007379 Response regulator receiver domain; Region: Response_reg; pfam00072 94122007380 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122007381 active site 94122007382 phosphorylation site [posttranslational modification] 94122007383 intermolecular recognition site; other site 94122007384 dimerization interface [polypeptide binding]; other site 94122007385 Response regulator receiver domain; Region: Response_reg; pfam00072 94122007386 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122007387 active site 94122007388 phosphorylation site [posttranslational modification] 94122007389 intermolecular recognition site; other site 94122007390 dimerization interface [polypeptide binding]; other site 94122007391 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 94122007392 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 94122007393 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 94122007394 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 94122007395 anti sigma factor interaction site; other site 94122007396 regulatory phosphorylation site [posttranslational modification]; other site 94122007397 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 94122007398 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122007399 dimer interface [polypeptide binding]; other site 94122007400 putative CheW interface [polypeptide binding]; other site 94122007401 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 94122007402 CoA binding domain; Region: CoA_binding_2; pfam13380 94122007403 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 94122007404 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 94122007405 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 94122007406 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 94122007407 putative substrate translocation pore; other site 94122007408 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 94122007409 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 94122007410 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 94122007411 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122007412 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 94122007413 MarR family; Region: MarR_2; pfam12802 94122007414 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122007415 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122007416 metal binding site [ion binding]; metal-binding site 94122007417 active site 94122007418 I-site; other site 94122007419 putative metal dependent hydrolase; Provisional; Region: PRK11598 94122007420 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 94122007421 Sulfatase; Region: Sulfatase; pfam00884 94122007422 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 94122007423 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 94122007424 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 94122007425 MarR family; Region: MarR; pfam01047 94122007426 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 94122007427 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 94122007428 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 94122007429 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 94122007430 dimer interface [polypeptide binding]; other site 94122007431 active site 94122007432 metal binding site [ion binding]; metal-binding site 94122007433 glutathione binding site [chemical binding]; other site 94122007434 putative sulfite oxidase subunit YedZ; Reviewed; Region: PRK05419 94122007435 TMAO/DMSO reductase; Reviewed; Region: PRK05363 94122007436 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 94122007437 Moco binding site; other site 94122007438 metal coordination site [ion binding]; other site 94122007439 DNA recombination protein RmuC; Provisional; Region: PRK10361 94122007440 RmuC family; Region: RmuC; pfam02646 94122007441 lytic murein transglycosylase; Provisional; Region: PRK11619 94122007442 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 94122007443 N-acetyl-D-glucosamine binding site [chemical binding]; other site 94122007444 catalytic residue [active] 94122007445 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 94122007446 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 94122007447 Acetyltransferase (GNAT) domain; Region: Acetyltransf_8; pfam13523 94122007448 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122007449 Coenzyme A binding pocket [chemical binding]; other site 94122007450 MoxR-like ATPases [General function prediction only]; Region: COG0714 94122007451 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 94122007452 Walker A motif; other site 94122007453 ATP binding site [chemical binding]; other site 94122007454 Walker B motif; other site 94122007455 arginine finger; other site 94122007456 Protein of unknown function DUF58; Region: DUF58; pfam01882 94122007457 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 94122007458 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 94122007459 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 94122007460 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 94122007461 Exodeoxyribonuclease V, gamma subunit; Region: Exonuc_V_gamma; pfam04257 94122007462 exonuclease V subunit beta; Provisional; Region: recB; PRK10876 94122007463 Family description; Region: UvrD_C_2; pfam13538 94122007464 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 94122007465 exonuclease V subunit alpha; Provisional; Region: recD; PRK10875 94122007466 AAA domain; Region: AAA_30; pfam13604 94122007467 Family description; Region: UvrD_C_2; pfam13538 94122007468 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 94122007469 S-adenosylmethionine binding site [chemical binding]; other site 94122007470 PAS domain; Region: PAS_9; pfam13426 94122007471 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 94122007472 putative active site [active] 94122007473 heme pocket [chemical binding]; other site 94122007474 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 94122007475 PAS domain; Region: PAS_9; pfam13426 94122007476 putative active site [active] 94122007477 heme pocket [chemical binding]; other site 94122007478 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122007479 dimer interface [polypeptide binding]; other site 94122007480 putative CheW interface [polypeptide binding]; other site 94122007481 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 94122007482 active site 94122007483 catalytic site [active] 94122007484 substrate binding site [chemical binding]; other site 94122007485 Transcriptional regulators [Transcription]; Region: PurR; COG1609 94122007486 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 94122007487 DNA binding site [nucleotide binding] 94122007488 domain linker motif; other site 94122007489 Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators; Region: PBP1_CelR; cd06295 94122007490 putative dimerization interface [polypeptide binding]; other site 94122007491 putative ligand binding site [chemical binding]; other site 94122007492 Protein of unknown function (DUF3334); Region: DUF3334; pfam11813 94122007493 Cache domain; Region: Cache_2; pfam08269 94122007494 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 94122007495 dimerization interface [polypeptide binding]; other site 94122007496 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 94122007497 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122007498 dimer interface [polypeptide binding]; other site 94122007499 putative CheW interface [polypeptide binding]; other site 94122007500 Uncharacterized conserved protein [Function unknown]; Region: COG3603 94122007501 Family description; Region: ACT_7; pfam13840 94122007502 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 94122007503 dimerization domain swap beta strand [polypeptide binding]; other site 94122007504 regulatory protein interface [polypeptide binding]; other site 94122007505 active site 94122007506 regulatory phosphorylation site [posttranslational modification]; other site 94122007507 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 94122007508 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 94122007509 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 94122007510 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 94122007511 PTS system glucose-specific transporter subunit; Provisional; Region: PRK09439 94122007512 HPr interaction site; other site 94122007513 glycerol kinase (GK) interaction site [polypeptide binding]; other site 94122007514 active site 94122007515 phosphorylation site [posttranslational modification] 94122007516 Predicted sulfurtransferase [General function prediction only]; Region: COG1054 94122007517 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 94122007518 active site residue [active] 94122007519 GST_N family, Omega-like subfamily; composed of uncharacterized proteins with similarity to class Omega GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_Omega_like; cd03060 94122007520 Glutaredoxin 2 [Posttranslational modification, protein turnover, chaperones]; Region: GrxB; COG2999 94122007521 putative GSH binding site (G-site) [chemical binding]; other site 94122007522 active site cysteine [active] 94122007523 putative C-terminal domain interface [polypeptide binding]; other site 94122007524 putative dimer interface [polypeptide binding]; other site 94122007525 C-terminal, alpha helical domain of an unknown subfamily 5 of Glutathione S-transferases; Region: GST_C_5; cd03196 94122007526 putative N-terminal domain interface [polypeptide binding]; other site 94122007527 putative dimer interface [polypeptide binding]; other site 94122007528 putative substrate binding pocket (H-site) [chemical binding]; other site 94122007529 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 94122007530 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 94122007531 Sulfate transporter family; Region: Sulfate_transp; pfam00916 94122007532 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 94122007533 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 94122007534 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 94122007535 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 94122007536 DNA-binding site [nucleotide binding]; DNA binding site 94122007537 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 94122007538 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122007539 homodimer interface [polypeptide binding]; other site 94122007540 catalytic residue [active] 94122007541 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 94122007542 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 94122007543 putative substrate translocation pore; other site 94122007544 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK08979 94122007545 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 94122007546 PYR/PP interface [polypeptide binding]; other site 94122007547 dimer interface [polypeptide binding]; other site 94122007548 TPP binding site [chemical binding]; other site 94122007549 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 94122007550 Thiamine pyrophosphate (TPP) family, Acetohydroxyacid synthase (AHAS) subfamily, TPP-binding module; composed of proteins similar to the large catalytic subunit of AHAS. AHAS catalyzes the condensation of two molecules of pyruvate to give the...; Region: TPP_AHAS; cd02015 94122007551 TPP-binding site [chemical binding]; other site 94122007552 dimer interface [polypeptide binding]; other site 94122007553 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 94122007554 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 94122007555 putative valine binding site [chemical binding]; other site 94122007556 dimer interface [polypeptide binding]; other site 94122007557 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 94122007558 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 94122007559 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 94122007560 putative dimer interface [polypeptide binding]; other site 94122007561 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 94122007562 active site 94122007563 multimer interface [polypeptide binding]; other site 94122007564 FeS assembly protein IscX; Region: iscX_yfhJ; TIGR03412 94122007565 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 94122007566 ATP-grasp domain; Region: ATP-grasp_4; cl17255 94122007567 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 94122007568 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 94122007569 catalytic loop [active] 94122007570 iron binding site [ion binding]; other site 94122007571 chaperone protein HscA; Provisional; Region: hscA; PRK05183 94122007572 Nucleotide-binding domain of HscA and similar proteins; Region: HscA_like_NBD; cd10236 94122007573 nucleotide binding site [chemical binding]; other site 94122007574 putative NEF/HSP70 interaction site [polypeptide binding]; other site 94122007575 SBD interface [polypeptide binding]; other site 94122007576 co-chaperone HscB; Provisional; Region: hscB; PRK05014 94122007577 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 94122007578 HSP70 interaction site [polypeptide binding]; other site 94122007579 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 94122007580 iron-sulfur cluster assembly protein IscA; Region: IscA; TIGR02011 94122007581 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 94122007582 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 94122007583 trimerization site [polypeptide binding]; other site 94122007584 active site 94122007585 cysteine desulfurase; Provisional; Region: PRK14012 94122007586 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 94122007587 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 94122007588 catalytic residue [active] 94122007589 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 94122007590 Rrf2 family protein; Region: rrf2_super; TIGR00738 94122007591 serine O-acetyltransferase; Region: cysE; TIGR01172 94122007592 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 94122007593 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 94122007594 trimer interface [polypeptide binding]; other site 94122007595 active site 94122007596 substrate binding site [chemical binding]; other site 94122007597 CoA binding site [chemical binding]; other site 94122007598 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional; Region: PRK15114 94122007599 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 94122007600 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 94122007601 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 94122007602 active site 94122007603 dimerization interface [polypeptide binding]; other site 94122007604 outer membrane-specific lipoprotein transporter subunit LolE; Provisional; Region: PRK11146 94122007605 FtsX-like permease family; Region: FtsX; pfam02687 94122007606 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 94122007607 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 94122007608 Walker A/P-loop; other site 94122007609 ATP binding site [chemical binding]; other site 94122007610 Q-loop/lid; other site 94122007611 ABC transporter signature motif; other site 94122007612 Walker B; other site 94122007613 D-loop; other site 94122007614 H-loop/switch region; other site 94122007615 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 94122007616 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 94122007617 transcription-repair coupling factor; Provisional; Region: PRK10689 94122007618 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 94122007619 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 94122007620 ATP binding site [chemical binding]; other site 94122007621 putative Mg++ binding site [ion binding]; other site 94122007622 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 94122007623 nucleotide binding region [chemical binding]; other site 94122007624 ATP-binding site [chemical binding]; other site 94122007625 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 94122007626 Protein of unknown function (DUF2803); Region: DUF2803; pfam10972 94122007627 Protein of unknown function (DUF2803); Region: DUF2803; pfam10972 94122007628 acylphosphatase; Provisional; Region: PRK14429 94122007629 hypothetical protein; Provisional; Region: PRK04940 94122007630 beta-hexosaminidase; Provisional; Region: PRK05337 94122007631 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 94122007632 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 94122007633 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 94122007634 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 94122007635 HTH-like domain; Region: HTH_21; pfam13276 94122007636 Integrase core domain; Region: rve; pfam00665 94122007637 Integrase core domain; Region: rve_3; pfam13683 94122007638 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_4; cd06231 94122007639 putative active site [active] 94122007640 Zn binding site [ion binding]; other site 94122007641 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 94122007642 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 94122007643 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 94122007644 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 94122007645 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 94122007646 Fumarase C-terminus; Region: Fumerase_C; pfam05683 94122007647 aminodeoxychorismate synthase subunit I; Provisional; Region: pabB; PRK15465 94122007648 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 94122007649 chorismate binding enzyme; Region: Chorismate_bind; cl10555 94122007650 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 94122007651 putative active site [active] 94122007652 putative CoA binding site [chemical binding]; other site 94122007653 nudix motif; other site 94122007654 metal binding site [ion binding]; metal-binding site 94122007655 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 94122007656 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 94122007657 putative anticodon binding site; other site 94122007658 putative dimer interface [polypeptide binding]; other site 94122007659 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 94122007660 homodimer interface [polypeptide binding]; other site 94122007661 motif 1; other site 94122007662 motif 2; other site 94122007663 active site 94122007664 motif 3; other site 94122007665 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 94122007666 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 94122007667 ATP-grasp domain; Region: ATP-grasp_4; cl17255 94122007668 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 94122007669 GAF domain; Region: GAF; pfam01590 94122007670 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 94122007671 PAS domain; Region: PAS_9; pfam13426 94122007672 putative active site [active] 94122007673 heme pocket [chemical binding]; other site 94122007674 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122007675 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122007676 metal binding site [ion binding]; metal-binding site 94122007677 active site 94122007678 I-site; other site 94122007679 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 94122007680 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 94122007681 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 94122007682 S-adenosylmethionine binding site [chemical binding]; other site 94122007683 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 94122007684 Major Facilitator Superfamily; Region: MFS_1; pfam07690 94122007685 putative substrate translocation pore; other site 94122007686 glucose/galactose transporter; Region: gluP; TIGR01272 94122007687 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 94122007688 Alpha amylase catalytic domain found in oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase) and related proteins; Region: AmyAc_OligoGlu; cd11330 94122007689 active site 94122007690 catalytic site [active] 94122007691 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 94122007692 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122007693 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122007694 Cyclomaltodextrinase, N-terminal; Region: Cyc-maltodext_N; pfam09087 94122007695 Alpha amylase catalytic domain found in bacterial cyclomaltodextrinases and related proteins; Region: AmyAc_bac_CMD_like_3; cd11340 94122007696 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 94122007697 Ca binding site [ion binding]; other site 94122007698 active site 94122007699 homodimer interface [polypeptide binding]; other site 94122007700 catalytic site [active] 94122007701 Cyclo-malto-dextrinase C-terminal domain; Region: Cyc-maltodext_C; pfam10438 94122007702 Alpha amylase catalytic domain found in an uncharacterized protein family; Region: AmyAc_3; cd11349 94122007703 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 94122007704 active site 94122007705 catalytic site [active] 94122007706 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_1; cd08352 94122007707 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 94122007708 Protein of unknown function (DUF1878); Region: DUF1878; pfam08963 94122007709 rhombotail lipoprotein; Region: rhombo_lipo; TIGR04179 94122007710 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 94122007711 active site 94122007712 catalytic residues [active] 94122007713 metal binding site [ion binding]; metal-binding site 94122007714 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 94122007715 active site 94122007716 DNA binding site [nucleotide binding] 94122007717 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 94122007718 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 94122007719 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 94122007720 putative active site [active] 94122007721 putative dimer interface [polypeptide binding]; other site 94122007722 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 94122007723 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 94122007724 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 94122007725 active site 94122007726 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 94122007727 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 94122007728 TrkA-N domain; Region: TrkA_N; pfam02254 94122007729 Domain of unknown function (DUF4277); Region: DUF4277; pfam14104 94122007730 Transposase [DNA replication, recombination, and repair]; Region: COG5421 94122007731 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 94122007732 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 94122007733 transcriptional activator FtrA; Provisional; Region: ftrA; PRK09393 94122007734 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 94122007735 conserved cys residue [active] 94122007736 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 94122007737 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 94122007738 Major Facilitator Superfamily; Region: MFS_1; pfam07690 94122007739 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 94122007740 glyceraldehyde-3-phosphate dehydrogenase; Validated; Region: PRK08955 94122007741 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 94122007742 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 94122007743 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 94122007744 Thioredoxin domain; Region: Thioredoxin_3; pfam13192 94122007745 Predicted permeases [General function prediction only]; Region: COG0701 94122007746 Low molecular weight phosphatase family; Region: LMWPc; cd00115 94122007747 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 94122007748 active site 94122007749 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 94122007750 dimerization interface [polypeptide binding]; other site 94122007751 putative DNA binding site [nucleotide binding]; other site 94122007752 putative Zn2+ binding site [ion binding]; other site 94122007753 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 94122007754 Low molecular weight phosphatase family; Region: LMWPc; cd00115 94122007755 active site 94122007756 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 94122007757 dimerization interface [polypeptide binding]; other site 94122007758 putative DNA binding site [nucleotide binding]; other site 94122007759 putative Zn2+ binding site [ion binding]; other site 94122007760 Predicted permease; Region: DUF318; cl17795 94122007761 Eukaryotic Glutathione Synthetase (eu-GS); catalyses the production of glutathione from gamma-glutamylcysteine and glycine in an ATP-dependent manner. Belongs to the ATP-grasp superfamily; Region: eu-GS; cl00170 94122007762 glutathione (GSH) binding pocket [chemical binding]; other site 94122007763 active site residues [active] 94122007764 ATP binding pocket [chemical binding]; other site 94122007765 magnesium binding site [ion binding]; other site 94122007766 glycine rich loop; other site 94122007767 alanine rich loop; other site 94122007768 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 94122007769 4Fe-4S binding domain; Region: Fer4; pfam00037 94122007770 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 94122007771 This CD includes the respiratory arsenate reductase, As(V), catalytic subunit (ArrA) and other related proteins. These members belong to the molybdopterin_binding (MopB) superfamily of proteins; Region: MopB_Arsenate-R; cd02757 94122007772 putative [Fe4-S4] binding site [ion binding]; other site 94122007773 putative molybdopterin cofactor binding site [chemical binding]; other site 94122007774 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 94122007775 This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins; Region: MopB_CT_Tetrathionate_Arsenate-R; cd02780 94122007776 putative molybdopterin cofactor binding site; other site 94122007777 Arsenical resistance operon trans-acting repressor ArsD; Region: ArsD; pfam06953 94122007778 arsenical pump-driving ATPase; Region: arsen_driv_ArsA; TIGR04291 94122007779 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 94122007780 P loop; other site 94122007781 Nucleotide binding site [chemical binding]; other site 94122007782 DTAP/Switch II; other site 94122007783 Switch I; other site 94122007784 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 94122007785 P loop; other site 94122007786 Nucleotide binding site [chemical binding]; other site 94122007787 DTAP/Switch II; other site 94122007788 Switch I; other site 94122007789 arsenical pump membrane protein; Provisional; Region: PRK15445 94122007790 Anion permease ArsB. These permeases have been shown to export arsenate and antimonite in eubacteria and archaea. A typical ArsB permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a...; Region: ArsB_permease; cd01118 94122007791 transmembrane helices; other site 94122007792 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 94122007793 ArsC family; Region: ArsC; pfam03960 94122007794 catalytic residues [active] 94122007795 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 94122007796 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 94122007797 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122007798 Thioredoxin domain; Region: Thioredoxin_3; pfam13192 94122007799 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 94122007800 dimerization interface [polypeptide binding]; other site 94122007801 putative DNA binding site [nucleotide binding]; other site 94122007802 putative Zn2+ binding site [ion binding]; other site 94122007803 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 94122007804 active site 94122007805 Int/Topo IB signature motif; other site 94122007806 catalytic residues [active] 94122007807 DNA binding site [nucleotide binding] 94122007808 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 94122007809 Zn2+ binding site [ion binding]; other site 94122007810 Mg2+ binding site [ion binding]; other site 94122007811 Domain of unknown function (DUF3596); Region: DUF3596; pfam12167 94122007812 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 94122007813 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 94122007814 active site 94122007815 DNA binding site [nucleotide binding] 94122007816 Int/Topo IB signature motif; other site 94122007817 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 94122007818 non-specific DNA binding site [nucleotide binding]; other site 94122007819 salt bridge; other site 94122007820 sequence-specific DNA binding site [nucleotide binding]; other site 94122007821 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 94122007822 Transposase; Region: HTH_Tnp_1; pfam01527 94122007823 HTH-like domain; Region: HTH_21; pfam13276 94122007824 Integrase core domain; Region: rve; pfam00665 94122007825 Integrase core domain; Region: rve_2; pfam13333 94122007826 NnrS protein; Region: NnrS; pfam05940 94122007827 Cytochrome c552; Region: Cytochrom_C552; pfam02335 94122007828 TIGR03503 family protein; Region: TIGR03503 94122007829 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 94122007830 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 94122007831 active site 94122007832 catalytic site [active] 94122007833 substrate binding site [chemical binding]; other site 94122007834 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 94122007835 RNA/DNA hybrid binding site [nucleotide binding]; other site 94122007836 active site 94122007837 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 94122007838 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122007839 C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; Region: PBP2_CysL_like; cd08420 94122007840 putative dimerization interface [polypeptide binding]; other site 94122007841 Methyltransferase domain; Region: Methyltransf_11; pfam08241 94122007842 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 94122007843 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 94122007844 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 94122007845 N-acetyl-D-glucosamine binding site [chemical binding]; other site 94122007846 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 94122007847 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 94122007848 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 94122007849 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 94122007850 Intracellular proteinase inhibitor; Region: BsuPI; pfam12690 94122007851 AsmA family; Region: AsmA; pfam05170 94122007852 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 94122007853 ribonuclease activity regulator protein RraA; Reviewed; Region: PRK12487 94122007854 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 94122007855 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 94122007856 DEAD-like helicases superfamily; Region: DEXDc; smart00487 94122007857 ATP binding site [chemical binding]; other site 94122007858 Mg++ binding site [ion binding]; other site 94122007859 motif III; other site 94122007860 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 94122007861 nucleotide binding region [chemical binding]; other site 94122007862 ATP-binding site [chemical binding]; other site 94122007863 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 94122007864 substrate binding site [chemical binding]; other site 94122007865 Domain of unknown function (DUF4277); Region: DUF4277; pfam14104 94122007866 Transposase [DNA replication, recombination, and repair]; Region: COG5421 94122007867 hypothetical protein; Provisional; Region: PRK05170 94122007868 Transglycosylase SLT domain; Region: SLT_2; pfam13406 94122007869 murein hydrolase B; Provisional; Region: PRK10760; cl17906 94122007870 YcgL domain; Region: YcgL; pfam05166 94122007871 septum formation inhibitor; Reviewed; Region: minC; PRK04804 94122007872 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 94122007873 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 94122007874 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 94122007875 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 94122007876 Switch I; other site 94122007877 Switch II; other site 94122007878 cell division topological specificity factor MinE; Reviewed; Region: minE; PRK00296 94122007879 ribonuclease D; Region: rnd; TIGR01388 94122007880 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 94122007881 catalytic site [active] 94122007882 putative active site [active] 94122007883 putative substrate binding site [chemical binding]; other site 94122007884 HRDC domain; Region: HRDC; pfam00570 94122007885 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08974 94122007886 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 94122007887 acyl-activating enzyme (AAE) consensus motif; other site 94122007888 putative AMP binding site [chemical binding]; other site 94122007889 putative active site [active] 94122007890 putative CoA binding site [chemical binding]; other site 94122007891 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 94122007892 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 94122007893 Predicted methyltransferase [General function prediction only]; Region: COG4798 94122007894 Methyltransferase domain; Region: Methyltransf_23; pfam13489 94122007895 Peptidase M50B-like; Region: Peptidase_M50B; pfam13398 94122007896 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 94122007897 Glycoprotease family; Region: Peptidase_M22; pfam00814 94122007898 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 94122007899 dimer interface [polypeptide binding]; other site 94122007900 active site 94122007901 Schiff base residues; other site 94122007902 bifunctional methionine sulfoxide reductase B/A protein; Provisional; Region: PRK05550 94122007903 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229; cl15841 94122007904 methionine sulfoxide reductase A; Provisional; Region: PRK14054 94122007905 aminocyclopropanecarboxylate oxidase; Region: PLN02403 94122007906 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; pfam14226 94122007907 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 94122007908 GTPase YlqF; Reviewed; Region: rbgA; PRK09563 94122007909 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 94122007910 GTP/Mg2+ binding site [chemical binding]; other site 94122007911 G4 box; other site 94122007912 G5 box; other site 94122007913 G1 box; other site 94122007914 Switch I region; other site 94122007915 G2 box; other site 94122007916 G3 box; other site 94122007917 Switch II region; other site 94122007918 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 94122007919 Low molecular weight phosphatase family; Region: LMWPc; cd00115 94122007920 active site 94122007921 DNA ligase; Provisional; Region: PRK09125 94122007922 Adenylation domain of kDNA ligases and similar proteins; Region: Adenylation_kDNA_ligase_like; cd07896 94122007923 DNA binding site [nucleotide binding] 94122007924 active site 94122007925 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; Region: OBF_kDNA_ligase_like; cd08041 94122007926 DNA binding site [nucleotide binding] 94122007927 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 94122007928 transcriptional regulator HdfR; Provisional; Region: PRK03601 94122007929 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122007930 LysR substrate binding domain; Region: LysR_substrate; pfam03466 94122007931 hypothetical protein; Provisional; Region: PRK11027 94122007932 alpha-L-glutamate ligases, RimK family; Region: rimK_fam; TIGR00768 94122007933 ATP-grasp domain; Region: ATP-grasp_4; cl17255 94122007934 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 94122007935 PA_M28_1_2: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 2. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic...; Region: PA_M28_1_2; cd04821 94122007936 PA/protease or protease-like domain interface [polypeptide binding]; other site 94122007937 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA_1; cd05660 94122007938 Peptidase family M28; Region: Peptidase_M28; pfam04389 94122007939 metal binding site [ion binding]; metal-binding site 94122007940 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122007941 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122007942 metal binding site [ion binding]; metal-binding site 94122007943 active site 94122007944 I-site; other site 94122007945 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved...; Region: Sortase_D_4; cd05828 94122007946 active site 94122007947 catalytic site [active] 94122007948 Vault protein inter-alpha-trypsin domain; Region: VIT; cl02699 94122007949 marine proteobacterial sortase target protein; Region: marine_srt_targ; TIGR03788 94122007950 vWA_interalpha trypsin inhibitor (ITI): ITI is a glycoprotein composed of three polypeptides- two heavy chains and one light chain (bikunin). Bikunin confers the protease-inhibitor function while the heavy chains are involved in rendering stability to...; Region: vWA_interalpha_trypsin_inhibitor; cd01461 94122007951 metal ion-dependent adhesion site (MIDAS); other site 94122007952 proteobacterial sortase system OmpA family protein; Region: pdsO; TIGR03789 94122007953 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 94122007954 ligand binding site [chemical binding]; other site 94122007955 proteobacterial dedicated sortase system response regulator; Region: marine_sort_RR; TIGR03787 94122007956 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122007957 active site 94122007958 phosphorylation site [posttranslational modification] 94122007959 intermolecular recognition site; other site 94122007960 dimerization interface [polypeptide binding]; other site 94122007961 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 94122007962 DNA binding site [nucleotide binding] 94122007963 proteobacterial dedicated sortase system histidine kinase; Region: marine_sort_HK; TIGR03785 94122007964 DOMON-like type 9 carbohydrate binding module at the N-terminus of bacterial sensor histidine kinases; Region: CBM9_like_HisKa; cd09622 94122007965 putative ligand binding site [chemical binding]; other site 94122007966 HAMP domain; Region: HAMP; pfam00672 94122007967 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 94122007968 dimer interface [polypeptide binding]; other site 94122007969 phosphorylation site [posttranslational modification] 94122007970 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 94122007971 ATP binding site [chemical binding]; other site 94122007972 Mg2+ binding site [ion binding]; other site 94122007973 G-X-G motif; other site 94122007974 cystathionine beta-lyase; Provisional; Region: PRK09028 94122007975 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 94122007976 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 94122007977 catalytic residue [active] 94122007978 Uncharacterized protein conserved in bacteria [Function unknown]; Region: CreA; COG3045 94122007979 CreA protein; Region: CreA; pfam05981 94122007980 putative chaperone; Provisional; Region: PRK11678 94122007981 Escherichia coli YegD, a putative chaperone protein, and related proteins; Region: YegD_like; cd10231 94122007982 nucleotide binding site [chemical binding]; other site 94122007983 putative NEF/HSP70 interaction site [polypeptide binding]; other site 94122007984 SBD interface [polypeptide binding]; other site 94122007985 polyphosphate kinase 1; Region: poly_P_kin; TIGR03705 94122007986 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 94122007987 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 94122007988 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 94122007989 putative active site [active] 94122007990 catalytic site [active] 94122007991 Catalytic C-terminal domain, second repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C2_like; cd09167 94122007992 domain interface [polypeptide binding]; other site 94122007993 active site 94122007994 catalytic site [active] 94122007995 exopolyphosphatase; Region: exo_poly_only; TIGR03706 94122007996 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 94122007997 Ion transport protein; Region: Ion_trans; pfam00520 94122007998 Ion channel; Region: Ion_trans_2; pfam07885 94122007999 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 94122008000 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_4; cd07268 94122008001 putative metal binding site [ion binding]; other site 94122008002 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 94122008003 Peptidase family M23; Region: Peptidase_M23; pfam01551 94122008004 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 94122008005 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 94122008006 Nucleoid-associated protein [General function prediction only]; Region: COG3081 94122008007 nucleoid-associated protein NdpA; Validated; Region: PRK00378 94122008008 hypothetical protein; Provisional; Region: PRK13689 94122008009 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 94122008010 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 94122008011 Sulfatase; Region: Sulfatase; cl17466 94122008012 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 94122008013 Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing...; Region: OYE_YqiM_FMN; cd02932 94122008014 active site 94122008015 FMN binding site [chemical binding]; other site 94122008016 substrate binding site [chemical binding]; other site 94122008017 homotetramer interface [polypeptide binding]; other site 94122008018 catalytic residue [active] 94122008019 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122008020 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122008021 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 94122008022 dimerization interface [polypeptide binding]; other site 94122008023 PAS domain; Region: PAS_9; pfam13426 94122008024 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122008025 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122008026 metal binding site [ion binding]; metal-binding site 94122008027 active site 94122008028 I-site; other site 94122008029 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122008030 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122008031 metal binding site [ion binding]; metal-binding site 94122008032 active site 94122008033 I-site; other site 94122008034 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 94122008035 NAD synthase [Coenzyme metabolism]; Region: NadE; COG0171 94122008036 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 94122008037 homodimer interface [polypeptide binding]; other site 94122008038 NAD binding pocket [chemical binding]; other site 94122008039 ATP binding pocket [chemical binding]; other site 94122008040 Mg binding site [ion binding]; other site 94122008041 active-site loop [active] 94122008042 inosine/guanosine kinase; Provisional; Region: PRK15074 94122008043 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 94122008044 substrate binding site [chemical binding]; other site 94122008045 ATP binding site [chemical binding]; other site 94122008046 ferrochelatase; Reviewed; Region: hemH; PRK00035 94122008047 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 94122008048 C-terminal domain interface [polypeptide binding]; other site 94122008049 active site 94122008050 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 94122008051 active site 94122008052 N-terminal domain interface [polypeptide binding]; other site 94122008053 adenylate kinase; Reviewed; Region: adk; PRK00279 94122008054 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 94122008055 AMP-binding site [chemical binding]; other site 94122008056 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 94122008057 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 94122008058 ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria; Region: ybbN; cd02956 94122008059 heat shock protein 90; Provisional; Region: PRK05218 94122008060 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 94122008061 ATP binding site [chemical binding]; other site 94122008062 Mg2+ binding site [ion binding]; other site 94122008063 G-X-G motif; other site 94122008064 recombination protein RecR; Reviewed; Region: recR; PRK00076 94122008065 RecR protein; Region: RecR; pfam02132 94122008066 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 94122008067 putative active site [active] 94122008068 putative metal-binding site [ion binding]; other site 94122008069 tetramer interface [polypeptide binding]; other site 94122008070 hypothetical protein; Validated; Region: PRK00153 94122008071 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14949 94122008072 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 94122008073 Walker A motif; other site 94122008074 ATP binding site [chemical binding]; other site 94122008075 Walker B motif; other site 94122008076 DNA polymerase III subunit delta'; Validated; Region: PRK08485 94122008077 arginine finger; other site 94122008078 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 94122008079 DNA polymerase III tau subunit V interacting with alpha; Region: DNA_pol3_tau_5; pfam12170 94122008080 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 94122008081 active site 94122008082 hypothetical protein; Provisional; Region: PRK10527 94122008083 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 94122008084 hypothetical protein; Provisional; Region: PRK05409 94122008085 tRNA-dihydrouridine synthase C; Provisional; Region: PRK10550 94122008086 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 94122008087 FMN binding site [chemical binding]; other site 94122008088 active site 94122008089 catalytic residues [active] 94122008090 substrate binding site [chemical binding]; other site 94122008091 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; pfam01258 94122008092 bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor; Reviewed; Region: ushA; PRK09558 94122008093 Escherichia coli UshA and related proteins, N-terminal metallophosphatase domain; Region: MPP_UshA_N; cd07405 94122008094 active site 94122008095 metal binding site [ion binding]; metal-binding site 94122008096 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 94122008097 putative hydrolase; Provisional; Region: PRK11460 94122008098 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 94122008099 Protein of unknown function (DUF3389); Region: DUF3389; pfam11869 94122008100 leukotriene A-4 hydrolase/aminopeptidase; Region: leuko_A4_hydro; TIGR02411 94122008101 Peptidase M1 family contains leukotriene A4 hydrolase; Region: M1_LTA4H; cd09599 94122008102 active site 94122008103 Zn binding site [ion binding]; other site 94122008104 Leukotriene A4 hydrolase, C-terminal; Region: Leuk-A4-hydro_C; pfam09127 94122008105 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 94122008106 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 94122008107 Transglycosylase SLT domain; Region: SLT_2; pfam13406 94122008108 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 94122008109 N-acetyl-D-glucosamine binding site [chemical binding]; other site 94122008110 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 94122008111 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 94122008112 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 94122008113 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 94122008114 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122008115 active site 94122008116 phosphorylation site [posttranslational modification] 94122008117 intermolecular recognition site; other site 94122008118 dimerization interface [polypeptide binding]; other site 94122008119 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 94122008120 S-adenosylmethionine binding site [chemical binding]; other site 94122008121 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]; Region: COG2802 94122008122 RNA polymerase sigma factor; Provisional; Region: PRK11924 94122008123 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 94122008124 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 94122008125 DNA binding residues [nucleotide binding] 94122008126 anti-sigma factor, putative, ChrR family; Region: anti_sig_ChrR; TIGR02451 94122008127 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 94122008128 Protein involved in propanediol utilization, and related proteins (includes coumermycin biosynthetic protein), possible kinase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PduX; COG4542 94122008129 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism]; Region: Acd; COG2515 94122008130 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 94122008131 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 94122008132 catalytic residue [active] 94122008133 hypothetical protein; Provisional; Region: PRK11770 94122008134 Domain of unknown function (DUF307); Region: DUF307; pfam03733 94122008135 Domain of unknown function (DUF307); Region: DUF307; pfam03733 94122008136 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 94122008137 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 94122008138 active site 94122008139 Zn binding site [ion binding]; other site 94122008140 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 94122008141 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 94122008142 membrane-bound complex binding site; other site 94122008143 hinge residues; other site 94122008144 Putative transmembrane protein (PGPGW); Region: PGPGW; pfam09656 94122008145 AMP-binding domain protein; Validated; Region: PRK08315 94122008146 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 94122008147 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_2; cd05917 94122008148 acyl-activating enzyme (AAE) consensus motif; other site 94122008149 putative AMP binding site [chemical binding]; other site 94122008150 putative active site [active] 94122008151 putative CoA binding site [chemical binding]; other site 94122008152 Uncharacterized conserved protein [Function unknown]; Region: COG2947 94122008153 Mitochondrial biogenesis AIM24; Region: AIM24; pfam01987 94122008154 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122008155 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122008156 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 94122008157 dimerization interface [polypeptide binding]; other site 94122008158 homogentisate 1,2-dioxygenase; Region: HgmA; cl17306 94122008159 4-hydroxyphenylpyruvate dioxygenase; Region: 4HPPD; TIGR01263 94122008160 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 94122008161 dimer interface [polypeptide binding]; other site 94122008162 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 94122008163 active site 94122008164 Fe binding site [ion binding]; other site 94122008165 MASE1; Region: MASE1; cl17823 94122008166 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122008167 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122008168 metal binding site [ion binding]; metal-binding site 94122008169 active site 94122008170 I-site; other site 94122008171 maltose O-acetyltransferase; Provisional; Region: PRK10092 94122008172 Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively at the C6...; Region: LbH_MAT_GAT; cd03357 94122008173 active site 94122008174 substrate binding site [chemical binding]; other site 94122008175 trimer interface [polypeptide binding]; other site 94122008176 CoA binding site [chemical binding]; other site 94122008177 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 94122008178 Protein of unknown function, DUF482; Region: DUF482; pfam04339 94122008179 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 94122008180 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 94122008181 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 94122008182 Predicted integral membrane protein (DUF2189); Region: DUF2189; cl02291 94122008183 hypothetical protein; Provisional; Region: PRK06156 94122008184 M20 Peptidase Xaa-His dipeptidase (PepV) degrades hydrophobic dipeptides; Region: M20_PepV; cd03888 94122008185 active site 94122008186 metal binding site [ion binding]; metal-binding site 94122008187 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 94122008188 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 94122008189 active site 94122008190 Zn binding site [ion binding]; other site 94122008191 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 94122008192 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 94122008193 Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a...; Region: Arsenite_oxidase; cd02135 94122008194 putative FMN binding site [chemical binding]; other site 94122008195 DoxX; Region: DoxX; cl17842 94122008196 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 94122008197 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 94122008198 active site 94122008199 ATP binding site [chemical binding]; other site 94122008200 Phosphotransferase enzyme family; Region: APH; pfam01636 94122008201 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 94122008202 substrate binding site [chemical binding]; other site 94122008203 Nicotinamide mononucleotide transporter; Region: NMN_transporter; pfam04973 94122008204 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 94122008205 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122008206 N-terminal plug; other site 94122008207 ligand-binding site [chemical binding]; other site 94122008208 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 94122008209 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 94122008210 ligand binding site [chemical binding]; other site 94122008211 flexible hinge region; other site 94122008212 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cl17320 94122008213 putative transporter; Provisional; Region: PRK03699 94122008214 purine nucleoside phosphorylase; Provisional; Region: PRK13374 94122008215 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 94122008216 Putative periplasmic lipoprotein; Region: DUF1425; cd09030 94122008217 putative dimer interface [polypeptide binding]; other site 94122008218 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 94122008219 CoenzymeA binding site [chemical binding]; other site 94122008220 subunit interaction site [polypeptide binding]; other site 94122008221 PHB binding site; other site 94122008222 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 94122008223 CoenzymeA binding site [chemical binding]; other site 94122008224 subunit interaction site [polypeptide binding]; other site 94122008225 PHB binding site; other site 94122008226 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 94122008227 nucleotide binding site/active site [active] 94122008228 HIT family signature motif; other site 94122008229 catalytic residue [active] 94122008230 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 94122008231 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 94122008232 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 94122008233 DNA-binding transcriptional regulator CsgD; Provisional; Region: PRK10100 94122008234 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 94122008235 DNA binding residues [nucleotide binding] 94122008236 dimerization interface [polypeptide binding]; other site 94122008237 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 94122008238 heat shock protein HtpX; Provisional; Region: PRK05457 94122008239 Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E; Region: GAT1_Peptidase_E; cd03146 94122008240 active site pocket [active] 94122008241 oxyanion hole [active] 94122008242 catalytic triad [active] 94122008243 active site nucleophile [active] 94122008244 glucan biosynthesis protein G; Provisional; Region: mdoG; PRK13274 94122008245 glucan biosynthesis protein D; Provisional; Region: mdoD; PRK13273 94122008246 Protein of unknown function (DUF3187); Region: DUF3187; pfam11383 94122008247 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 94122008248 AAA domain; Region: AAA_26; pfam13500 94122008249 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 94122008250 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 94122008251 S-adenosylmethionine binding site [chemical binding]; other site 94122008252 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 94122008253 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 94122008254 substrate-cofactor binding pocket; other site 94122008255 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122008256 catalytic residue [active] 94122008257 biotin synthase; Provisional; Region: PRK15108 94122008258 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 94122008259 FeS/SAM binding site; other site 94122008260 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 94122008261 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 94122008262 adenosylmethionine-8-amino-7-oxononanoate transaminase; Region: bioA; TIGR00508 94122008263 inhibitor-cofactor binding pocket; inhibition site 94122008264 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122008265 catalytic residue [active] 94122008266 Cache domain; Region: Cache_2; pfam08269 94122008267 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 94122008268 dimerization interface [polypeptide binding]; other site 94122008269 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 94122008270 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122008271 dimer interface [polypeptide binding]; other site 94122008272 putative CheW interface [polypeptide binding]; other site 94122008273 Na+/proline symporter [Amino acid transport and metabolism / General function prediction only]; Region: PutP; COG0591 94122008274 Na binding site [ion binding]; other site 94122008275 PAS domain; Region: PAS; smart00091 94122008276 PAS fold; Region: PAS_7; pfam12860 94122008277 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 94122008278 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 94122008279 dimer interface [polypeptide binding]; other site 94122008280 phosphorylation site [posttranslational modification] 94122008281 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 94122008282 ATP binding site [chemical binding]; other site 94122008283 Mg2+ binding site [ion binding]; other site 94122008284 G-X-G motif; other site 94122008285 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 94122008286 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122008287 active site 94122008288 phosphorylation site [posttranslational modification] 94122008289 intermolecular recognition site; other site 94122008290 dimerization interface [polypeptide binding]; other site 94122008291 acetyl-CoA synthetase; Provisional; Region: PRK00174 94122008292 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 94122008293 active site 94122008294 CoA binding site [chemical binding]; other site 94122008295 acyl-activating enzyme (AAE) consensus motif; other site 94122008296 AMP binding site [chemical binding]; other site 94122008297 acetate binding site [chemical binding]; other site 94122008298 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 94122008299 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 94122008300 ATP binding site [chemical binding]; other site 94122008301 putative Mg++ binding site [ion binding]; other site 94122008302 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 94122008303 nucleotide binding region [chemical binding]; other site 94122008304 ATP-binding site [chemical binding]; other site 94122008305 Double zinc ribbon; Region: DZR; pfam12773 94122008306 Glutaredoxin (GRX) family; composed of GRX, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide...; Region: GRX_family; cd02066 94122008307 GSH binding site [chemical binding]; other site 94122008308 catalytic residues [active] 94122008309 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 94122008310 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 94122008311 binding surface 94122008312 TPR motif; other site 94122008313 peptidoglycan-associated outer membrane lipoprotein; Provisional; Region: PRK10802 94122008314 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 94122008315 ligand binding site [chemical binding]; other site 94122008316 translocation protein TolB; Provisional; Region: tolB; PRK04792 94122008317 TolB amino-terminal domain; Region: TolB_N; pfam04052 94122008318 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 94122008319 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 94122008320 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 94122008321 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 94122008322 TolA protein; Region: tolA_full; TIGR02794 94122008323 TolA C-terminal; Region: TolA; pfam06519 94122008324 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 94122008325 TolR protein; Region: tolR; TIGR02801 94122008326 TolQ protein; Region: tolQ; TIGR02796 94122008327 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 94122008328 active site 94122008329 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 94122008330 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 94122008331 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 94122008332 Predicted transcriptional regulator [Transcription]; Region: COG1959 94122008333 Transcriptional regulator; Region: Rrf2; pfam02082 94122008334 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 94122008335 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 94122008336 ligand binding site [chemical binding]; other site 94122008337 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 94122008338 DEDDh 3'-5' exonuclease domain of RNase T; Region: RNaseT; cd06134 94122008339 dimer interface [polypeptide binding]; other site 94122008340 catalytic site [active] 94122008341 putative active site [active] 94122008342 putative substrate binding site [chemical binding]; other site 94122008343 peroxidase; Provisional; Region: PRK15000 94122008344 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 94122008345 dimer interface [polypeptide binding]; other site 94122008346 decamer (pentamer of dimers) interface [polypeptide binding]; other site 94122008347 catalytic triad [active] 94122008348 peroxidatic and resolving cysteines [active] 94122008349 Predicted permease [General function prediction only]; Region: COG2056 94122008350 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 94122008351 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122008352 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122008353 metal binding site [ion binding]; metal-binding site 94122008354 active site 94122008355 I-site; other site 94122008356 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 94122008357 active site 94122008358 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 94122008359 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 94122008360 dimerization interface [polypeptide binding]; other site 94122008361 putative ATP binding site [chemical binding]; other site 94122008362 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 94122008363 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 94122008364 active site 94122008365 substrate binding site [chemical binding]; other site 94122008366 cosubstrate binding site; other site 94122008367 catalytic site [active] 94122008368 UMP phosphatase; Provisional; Region: PRK10444 94122008369 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 94122008370 active site 94122008371 motif I; other site 94122008372 motif II; other site 94122008373 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 94122008374 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 94122008375 PA_M28_1_2: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 2. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic...; Region: PA_M28_1_2; cd04821 94122008376 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 94122008377 PA/protease or protease-like domain interface [polypeptide binding]; other site 94122008378 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA_1; cd05660 94122008379 metal binding site [ion binding]; metal-binding site 94122008380 asparagine synthetase B; Provisional; Region: asnB; PRK09431 94122008381 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 94122008382 active site 94122008383 dimer interface [polypeptide binding]; other site 94122008384 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 94122008385 Ligand Binding Site [chemical binding]; other site 94122008386 Molecular Tunnel; other site 94122008387 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 94122008388 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 94122008389 active site 94122008390 nucleophile elbow; other site 94122008391 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 94122008392 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122008393 N-terminal plug; other site 94122008394 ligand-binding site [chemical binding]; other site 94122008395 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 94122008396 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 94122008397 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 94122008398 active site 94122008399 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 94122008400 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 94122008401 active site 94122008402 phosphate binding residues; other site 94122008403 catalytic residues [active] 94122008404 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 94122008405 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 94122008406 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 94122008407 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 94122008408 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 94122008409 dimer interface [polypeptide binding]; other site 94122008410 active site 94122008411 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 94122008412 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 94122008413 NAD(P) binding site [chemical binding]; other site 94122008414 homotetramer interface [polypeptide binding]; other site 94122008415 homodimer interface [polypeptide binding]; other site 94122008416 active site 94122008417 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 94122008418 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 94122008419 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 94122008420 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 94122008421 dimer interface [polypeptide binding]; other site 94122008422 active site 94122008423 CoA binding pocket [chemical binding]; other site 94122008424 putative phosphate acyltransferase; Provisional; Region: PRK05331 94122008425 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 94122008426 hypothetical protein; Provisional; Region: PRK11193 94122008427 Maf-like protein; Region: Maf; pfam02545 94122008428 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 94122008429 active site 94122008430 dimer interface [polypeptide binding]; other site 94122008431 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 94122008432 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 94122008433 motif II; other site 94122008434 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 94122008435 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 94122008436 RNA binding surface [nucleotide binding]; other site 94122008437 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 94122008438 active site 94122008439 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 94122008440 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 94122008441 homodimer interface [polypeptide binding]; other site 94122008442 oligonucleotide binding site [chemical binding]; other site 94122008443 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 94122008444 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 94122008445 Sulfate transporter family; Region: Sulfate_transp; pfam00916 94122008446 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 94122008447 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 94122008448 DNA-binding site [nucleotide binding]; DNA binding site 94122008449 RNA-binding motif; other site 94122008450 23S rRNA methyltransferase A; Provisional; Region: rrmA; PRK11088 94122008451 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 94122008452 S-adenosylmethionine binding site [chemical binding]; other site 94122008453 exonuclease I; Provisional; Region: sbcB; PRK11779 94122008454 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 94122008455 active site 94122008456 catalytic site [active] 94122008457 substrate binding site [chemical binding]; other site 94122008458 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 94122008459 cytidine deaminase; Provisional; Region: PRK09027 94122008460 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 94122008461 active site 94122008462 catalytic motif [active] 94122008463 Zn binding site [ion binding]; other site 94122008464 Cytidine and deoxycytidylate deaminase zinc-binding region; Region: dCMP_cyt_deam_2; pfam08211 94122008465 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 94122008466 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 94122008467 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 94122008468 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 94122008469 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 94122008470 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 94122008471 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 94122008472 Glutathione S-transferase, N-terminal domain; Region: GST_N_3; pfam13417 94122008473 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 94122008474 Predicted membrane protein [Function unknown]; Region: COG3235 94122008475 Uncharacterized conserved protein [Function unknown]; Region: COG2835 94122008476 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 94122008477 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 94122008478 lipid transporter ATP-binding/permease protein; Provisional; Region: PRK11176 94122008479 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 94122008480 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 94122008481 Walker A/P-loop; other site 94122008482 ATP binding site [chemical binding]; other site 94122008483 Q-loop/lid; other site 94122008484 ABC transporter signature motif; other site 94122008485 Walker B; other site 94122008486 D-loop; other site 94122008487 H-loop/switch region; other site 94122008488 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 94122008489 ComEC family competence protein; Provisional; Region: PRK11539 94122008490 Competence protein; Region: Competence; pfam03772 94122008491 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 94122008492 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; pfam09835 94122008493 NnrS protein; Region: NnrS; pfam05940 94122008494 Phosphate-starvation-inducible E; Region: PsiE; pfam06146 94122008495 PilZ domain; Region: PilZ; pfam07238 94122008496 ParA-like protein; Provisional; Region: PHA02518 94122008497 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 94122008498 P-loop; other site 94122008499 Magnesium ion binding site [ion binding]; other site 94122008500 Protein of unknown function (DUF2492); Region: DUF2492; cl11278 94122008501 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 94122008502 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 94122008503 GAF domain; Region: GAF; pfam01590 94122008504 Histidine kinase; Region: His_kinase; pfam06580 94122008505 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 94122008506 ATP binding site [chemical binding]; other site 94122008507 Mg2+ binding site [ion binding]; other site 94122008508 G-X-G motif; other site 94122008509 putative two-component response-regulatory protein YehT; Provisional; Region: PRK11697 94122008510 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122008511 active site 94122008512 phosphorylation site [posttranslational modification] 94122008513 intermolecular recognition site; other site 94122008514 dimerization interface [polypeptide binding]; other site 94122008515 LytTr DNA-binding domain; Region: LytTR; pfam04397 94122008516 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 94122008517 Carbon starvation protein CstA; Region: CstA; pfam02554 94122008518 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 94122008519 Uncharacterized conserved protein (DUF2132); Region: DUF2132; pfam09905 94122008520 putative membrane-bound dehydrogenase domain; Region: Piru_Ver_Nterm; TIGR02604 94122008521 RNA pol II promoter Fmp27 protein domain; Region: Fmp27_WPPW; pfam10359 94122008522 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 94122008523 dimerization interface [polypeptide binding]; other site 94122008524 active site 94122008525 hypothetical protein; Provisional; Region: PRK11020 94122008526 anaerobic ribonucleotide reductase-activating protein; Provisional; Region: nrdG; PRK11121 94122008527 4Fe-4S single cluster domain; Region: Fer4_12; pfam13353 94122008528 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK09263 94122008529 ATP cone domain; Region: ATP-cone; pfam03477 94122008530 Class III ribonucleotide reductase; Region: RNR_III; cd01675 94122008531 effector binding site; other site 94122008532 active site 94122008533 Zn binding site [ion binding]; other site 94122008534 glycine loop; other site 94122008535 hypothetical protein; Provisional; Region: PRK10279 94122008536 Bacterial patatin-like phospholipase domain containing protein 6; Region: Pat_NTE_like_bacteria; cd07228 94122008537 active site 94122008538 nucleophile elbow; other site 94122008539 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 94122008540 DEAD-like helicases superfamily; Region: DEXDc; smart00487 94122008541 ATP binding site [chemical binding]; other site 94122008542 Mg++ binding site [ion binding]; other site 94122008543 motif III; other site 94122008544 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 94122008545 nucleotide binding region [chemical binding]; other site 94122008546 ATP-binding site [chemical binding]; other site 94122008547 Protein of unknown function (DUF3010); Region: DUF3010; pfam11215 94122008548 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 94122008549 putative peptidase; Provisional; Region: PRK11649 94122008550 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 94122008551 Peptidase family M23; Region: Peptidase_M23; pfam01551 94122008552 ATP-binding cassette domain of sbcCD; Region: ABC_sbcCD; cd03279 94122008553 AAA domain; Region: AAA_23; pfam13476 94122008554 Walker A/P-loop; other site 94122008555 ATP binding site [chemical binding]; other site 94122008556 Q-loop/lid; other site 94122008557 ATP-binding cassette domain of sbcCD; Region: ABC_sbcCD; cd03279 94122008558 ABC transporter signature motif; other site 94122008559 Walker B; other site 94122008560 D-loop; other site 94122008561 H-loop/switch region; other site 94122008562 DNA repair exonuclease [DNA replication, recombination, and repair]; Region: SbcD; COG0420 94122008563 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 94122008564 active site 94122008565 metal binding site [ion binding]; metal-binding site 94122008566 DNA binding site [nucleotide binding] 94122008567 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 94122008568 hypothetical protein; Provisional; Region: PRK10621 94122008569 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 94122008570 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 94122008571 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122008572 The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_like; cd08481 94122008573 dimerization interface [polypeptide binding]; other site 94122008574 substrate binding pocket [chemical binding]; other site 94122008575 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 94122008576 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 94122008577 RNA binding surface [nucleotide binding]; other site 94122008578 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 94122008579 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 94122008580 PPIC-type PPIASE domain; Region: Rotamase_2; cl08278 94122008581 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 94122008582 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122008583 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122008584 metal binding site [ion binding]; metal-binding site 94122008585 active site 94122008586 I-site; other site 94122008587 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 94122008588 TPR motif; other site 94122008589 binding surface 94122008590 TPR repeat; Region: TPR_11; pfam13414 94122008591 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 94122008592 TPR motif; other site 94122008593 binding surface 94122008594 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 94122008595 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 94122008596 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 94122008597 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 94122008598 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 94122008599 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 94122008600 Protein of unknown function (DUF3450); Region: DUF3450; pfam11932 94122008601 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122008602 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 94122008603 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122008604 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 94122008605 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 94122008606 trimer interface [polypeptide binding]; other site 94122008607 eyelet of channel; other site 94122008608 DNA polymerase II; Reviewed; Region: PRK05762 94122008609 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases; Region: DNA_polB_II_exo; cd05784 94122008610 active site 94122008611 catalytic site [active] 94122008612 substrate binding site [chemical binding]; other site 94122008613 DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as...; Region: POLBc_Pol_II; cd05537 94122008614 active site 94122008615 metal-binding site 94122008616 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 94122008617 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 94122008618 hypothetical protein; Provisional; Region: PRK10621 94122008619 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 94122008620 Primosomal replication protein priB and priC; Region: priB_priC; cl11483 94122008621 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; pfam09829 94122008622 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 94122008623 Histone deacetylase class IV also known as histone deacetylase 11; Region: HDAC_classIV; cd09993 94122008624 putative active site [active] 94122008625 Zn binding site [ion binding]; other site 94122008626 Late competence development protein ComFB; Region: ComFB; pfam10719 94122008627 Part of AAA domain; Region: AAA_19; pfam13245 94122008628 multiple promoter invertase; Provisional; Region: mpi; PRK13413 94122008629 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 94122008630 catalytic residues [active] 94122008631 catalytic nucleophile [active] 94122008632 Presynaptic Site I dimer interface [polypeptide binding]; other site 94122008633 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 94122008634 Synaptic Flat tetramer interface [polypeptide binding]; other site 94122008635 Synaptic Site I dimer interface [polypeptide binding]; other site 94122008636 DNA binding site [nucleotide binding] 94122008637 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 94122008638 DNA-binding interface [nucleotide binding]; DNA binding site 94122008639 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 94122008640 Predicted P-loop ATPase [General function prediction only]; Region: COG4928 94122008641 Domain of unknown function (DUF4277); Region: DUF4277; pfam14104 94122008642 Transposase [DNA replication, recombination, and repair]; Region: COG5421 94122008643 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 94122008644 INT_SG2, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 2, C-terminal catalytic domain. The CD contains mainly predicted integrase/recombinases and phage-related integrases. Some have N-terminal domains, which show little sequence...; Region: INT_SG2_C; cd01184 94122008645 Int/Topo IB signature motif; other site 94122008646 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 94122008647 methionine gamma-lyase; Provisional; Region: PRK06234 94122008648 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 94122008649 homodimer interface [polypeptide binding]; other site 94122008650 substrate-cofactor binding pocket; other site 94122008651 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122008652 catalytic residue [active] 94122008653 hypothetical protein; Provisional; Region: PRK05415 94122008654 Domain of unknown function (DUF697); Region: DUF697; pfam05128 94122008655 YcjX-like family, DUF463; Region: DUF463; pfam04317 94122008656 PspC domain; Region: PspC; cl00864 94122008657 phage shock protein C; Region: phageshock_pspC; TIGR02978 94122008658 phage shock protein B; Provisional; Region: pspB; PRK09458 94122008659 phage shock protein A; Region: phageshock_pspA; TIGR02977 94122008660 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 94122008661 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 94122008662 Walker A motif; other site 94122008663 ATP binding site [chemical binding]; other site 94122008664 Walker B motif; other site 94122008665 arginine finger; other site 94122008666 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 94122008667 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 94122008668 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 94122008669 peptide binding site [polypeptide binding]; other site 94122008670 nickel ABC transporter, permease subunit NikB; Region: nickel_nikB; TIGR02789 94122008671 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 94122008672 dimer interface [polypeptide binding]; other site 94122008673 conserved gate region; other site 94122008674 putative PBP binding loops; other site 94122008675 ABC-ATPase subunit interface; other site 94122008676 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SapC; COG4171 94122008677 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 94122008678 dimer interface [polypeptide binding]; other site 94122008679 conserved gate region; other site 94122008680 putative PBP binding loops; other site 94122008681 ABC-ATPase subunit interface; other site 94122008682 antimicrobial peptide ABC transporter ATP-binding protein; Provisional; Region: PRK15093 94122008683 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 94122008684 Walker A/P-loop; other site 94122008685 ATP binding site [chemical binding]; other site 94122008686 Q-loop/lid; other site 94122008687 ABC transporter signature motif; other site 94122008688 Walker B; other site 94122008689 D-loop; other site 94122008690 H-loop/switch region; other site 94122008691 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 94122008692 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SapF; COG4167 94122008693 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 94122008694 Walker A/P-loop; other site 94122008695 ATP binding site [chemical binding]; other site 94122008696 Q-loop/lid; other site 94122008697 ABC transporter signature motif; other site 94122008698 Walker B; other site 94122008699 D-loop; other site 94122008700 H-loop/switch region; other site 94122008701 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 94122008702 trans-2-enoyl-CoA reductase; Provisional; Region: PRK13656 94122008703 NAD(P)H binding domain of trans-2-enoyl-CoA reductase; Region: Eno-Rase_NADH_b; pfam12242 94122008704 Trans-2-enoyl-CoA reductase catalytic region; Region: Enoyl_reductase; pfam12241 94122008705 Enoyl reductase FAD binding domain; Region: Eno-Rase_FAD_bd; pfam07055 94122008706 Molybdopterin-binding protein [Coenzyme metabolism]; Region: MopI; COG3585 94122008707 periplasmic folding chaperone; Provisional; Region: PRK10788 94122008708 SurA N-terminal domain; Region: SurA_N_3; cl07813 94122008709 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 94122008710 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 94122008711 IHF dimer interface [polypeptide binding]; other site 94122008712 IHF - DNA interface [nucleotide binding]; other site 94122008713 DNA-binding ATP-dependent protease La; Provisional; Region: PRK10787 94122008714 Found in ATP-dependent protease La (LON); Region: LON; smart00464 94122008715 Found in ATP-dependent protease La (LON); Region: LON; smart00464 94122008716 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 94122008717 Walker A motif; other site 94122008718 ATP binding site [chemical binding]; other site 94122008719 Walker B motif; other site 94122008720 arginine finger; other site 94122008721 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 94122008722 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 94122008723 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 94122008724 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 94122008725 Walker A motif; other site 94122008726 ATP binding site [chemical binding]; other site 94122008727 Walker B motif; other site 94122008728 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 94122008729 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 94122008730 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 94122008731 oligomer interface [polypeptide binding]; other site 94122008732 active site residues [active] 94122008733 trigger factor; Provisional; Region: tig; PRK01490 94122008734 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 94122008735 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 94122008736 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 94122008737 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 94122008738 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 94122008739 homodimer interface [polypeptide binding]; other site 94122008740 NADP binding site [chemical binding]; other site 94122008741 substrate binding site [chemical binding]; other site 94122008742 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 94122008743 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 94122008744 active site 94122008745 HIGH motif; other site 94122008746 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 94122008747 KMSKS motif; other site 94122008748 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 94122008749 tRNA binding surface [nucleotide binding]; other site 94122008750 anticodon binding site; other site 94122008751 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 94122008752 substrate binding site [chemical binding]; other site 94122008753 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 94122008754 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 94122008755 putative active site [active] 94122008756 putative metal binding site [ion binding]; other site 94122008757 MiaE tRNA-modifying nonheme diiron monooxygenase, ferritin-like diiron-binding domain; Region: MiaE; cd07910 94122008758 active site 94122008759 dinuclear metal binding site [ion binding]; other site 94122008760 dimerization interface [polypeptide binding]; other site 94122008761 Protein of unknown function (DUF1282); Region: DUF1282; pfam06930 94122008762 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 94122008763 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 94122008764 active site 94122008765 HIGH motif; other site 94122008766 nucleotide binding site [chemical binding]; other site 94122008767 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 94122008768 KMSKS motif; other site 94122008769 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 94122008770 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 94122008771 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 94122008772 G1 box; other site 94122008773 GTP/Mg2+ binding site [chemical binding]; other site 94122008774 Switch I region; other site 94122008775 G2 box; other site 94122008776 G3 box; other site 94122008777 Switch II region; other site 94122008778 G4 box; other site 94122008779 G5 box; other site 94122008780 Nucleoside recognition; Region: Gate; pfam07670 94122008781 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 94122008782 Nucleoside recognition; Region: Gate; pfam07670 94122008783 FeoA domain; Region: FeoA; pfam04023 94122008784 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 94122008785 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 94122008786 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 94122008787 Protein of unknown function (DUF3374); Region: DUF3374; pfam11854 94122008788 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 94122008789 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cd08168 94122008790 heme-binding residues [chemical binding]; other site 94122008791 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 94122008792 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 94122008793 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cd08168 94122008794 heme-binding residues [chemical binding]; other site 94122008795 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 94122008796 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 94122008797 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 94122008798 Protein of unknown function (DUF3374); Region: DUF3374; pfam11854 94122008799 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_1; cd10033 94122008800 putative uracil binding site [chemical binding]; other site 94122008801 putative active site [active] 94122008802 Fungalysin/Thermolysin Propeptide Motif; Region: FTP; pfam07504 94122008803 Zinc metalloprotease (elastase) [Amino acid transport and metabolism]; Region: LasB; COG3227 94122008804 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 94122008805 Peptidase M4 family includes thermolysin, protealysin, aureolysin and neutral protease; Region: M4_neutral_protease; cd09597 94122008806 active site 94122008807 Zn binding site [ion binding]; other site 94122008808 carbohydrate diacid transcriptional activator CdaR; Provisional; Region: PRK11477 94122008809 Putative sugar diacid recognition; Region: Diacid_rec; pfam05651 94122008810 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 94122008811 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 94122008812 putative heme binding pocket [chemical binding]; other site 94122008813 H+/gluconate symporter and related permeases [Carbohydrate transport and metabolism / Amino acid transport and metabolism]; Region: GntT; COG2610 94122008814 fructuronate transporter; Provisional; Region: PRK10034; cl15264 94122008815 Glycerate kinase [Carbohydrate transport and metabolism]; Region: COG1929 94122008816 putative pyridoxal-dependent aspartate 1-decarboxylase; Region: NOD_PanD_pyr; TIGR03799 94122008817 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 94122008818 catalytic residue [active] 94122008819 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 94122008820 Dimer interface [polypeptide binding]; other site 94122008821 SnoaL-like domain; Region: SnoaL_2; pfam12680 94122008822 short chain dehydrogenase; Provisional; Region: PRK07478 94122008823 classical (c) SDRs; Region: SDR_c; cd05233 94122008824 NAD(P) binding site [chemical binding]; other site 94122008825 active site 94122008826 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 94122008827 Helix-turn-helix domain; Region: HTH_18; pfam12833 94122008828 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 94122008829 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 94122008830 DNA binding site [nucleotide binding] 94122008831 active site 94122008832 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 94122008833 trimer interface [polypeptide binding]; other site 94122008834 active site 94122008835 substrate binding site [chemical binding]; other site 94122008836 CoA binding site [chemical binding]; other site 94122008837 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 94122008838 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 94122008839 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 94122008840 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 94122008841 Predicted branched-chain amino acid permease (azaleucine resistance) [Amino acid transport and metabolism]; Region: AzlC; COG1296 94122008842 Branched-chain amino acid transport protein (AzlD); Region: AzlD; cl00735 94122008843 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 94122008844 L-fucose transporter; Provisional; Region: PRK10133; cl17665 94122008845 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate. This is the first committed step in the biosynthetic pathway to...; Region: NagA; cd00854 94122008846 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 94122008847 active site 94122008848 dimer interface [polypeptide binding]; other site 94122008849 fructokinase; Reviewed; Region: PRK09557 94122008850 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 94122008851 nucleotide binding site [chemical binding]; other site 94122008852 putative sugar isomerase, AgaS family; Region: agaS_fam; TIGR02815 94122008853 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 94122008854 dimer interface [polypeptide binding]; other site 94122008855 active site 94122008856 AgaS-like protein. AgaS contains a SIS (Sugar ISomerase) domain which is found in many phosphosugar isomerases and phosphosugar binding proteins. AgaS is a putative isomerase in Escherichia coli. It is similar to the glucosamine-6-phosphate synthases; Region: SIS_AgaS_like; cd05010 94122008857 putative active site [active] 94122008858 Tagatose 6 phosphate kinase; Region: Tagatose_6_P_K; pfam08013 94122008859 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 94122008860 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 94122008861 DNA-binding transcriptional regulator AgaR; Provisional; Region: PRK09802 94122008862 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 94122008863 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 94122008864 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 94122008865 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122008866 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122008867 ligand-binding site [chemical binding]; other site 94122008868 Predicted transcriptional regulator [Transcription]; Region: COG2378 94122008869 HTH domain; Region: HTH_11; pfam08279 94122008870 WYL domain; Region: WYL; pfam13280 94122008871 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 94122008872 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 94122008873 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 94122008874 phosphoglucomutase-2-like protein; Provisional; Region: PTZ00150 94122008875 This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and...; Region: PGM2; cd05799 94122008876 active site 94122008877 substrate binding site [chemical binding]; other site 94122008878 metal binding site [ion binding]; metal-binding site 94122008879 integral membrane protein, TerC family; Region: R_switched_Alx; TIGR03718 94122008880 Protein of unknown function (DUF3624); Region: DUF3624; pfam12292 94122008881 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 94122008882 3-beta hydroxysteroid dehydrogenase/isomerase family; Region: 3Beta_HSD; pfam01073 94122008883 NAD(P) binding site [chemical binding]; other site 94122008884 active site 94122008885 peptide synthase; Provisional; Region: PRK09274 94122008886 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 94122008887 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_1; cd05910 94122008888 acyl-activating enzyme (AAE) consensus motif; other site 94122008889 putative AMP binding site [chemical binding]; other site 94122008890 putative active site [active] 94122008891 putative CoA binding site [chemical binding]; other site 94122008892 haloalkane dehalogenase; Provisional; Region: PRK03592 94122008893 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09258 94122008894 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 94122008895 dimer interface [polypeptide binding]; other site 94122008896 active site 94122008897 CoA binding pocket [chemical binding]; other site 94122008898 Methyltransferase domain; Region: Methyltransf_32; pfam13679 94122008899 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 94122008900 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 94122008901 active site 94122008902 BCCT family transporter; Region: BCCT; pfam02028 94122008903 Protein of unknown function (DUF502); Region: DUF502; pfam04367 94122008904 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_2; cd07253 94122008905 dimer interface [polypeptide binding]; other site 94122008906 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 94122008907 metal binding site [ion binding]; metal-binding site 94122008908 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122008909 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122008910 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 94122008911 putative effector binding pocket; other site 94122008912 dimerization interface [polypeptide binding]; other site 94122008913 EamA-like transporter family; Region: EamA; pfam00892 94122008914 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 94122008915 EamA-like transporter family; Region: EamA; pfam00892 94122008916 putative acetyltransferase; Provisional; Region: PRK03624 94122008917 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122008918 Coenzyme A binding pocket [chemical binding]; other site 94122008919 transcriptional regulator PhoU; Provisional; Region: PRK11115 94122008920 PhoU domain; Region: PhoU; pfam01895 94122008921 PhoU domain; Region: PhoU; pfam01895 94122008922 phosphate transporter ATP-binding protein; Provisional; Region: PRK14236 94122008923 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 94122008924 Walker A/P-loop; other site 94122008925 ATP binding site [chemical binding]; other site 94122008926 Q-loop/lid; other site 94122008927 ABC transporter signature motif; other site 94122008928 Walker B; other site 94122008929 D-loop; other site 94122008930 H-loop/switch region; other site 94122008931 ABC-type phosphate transport system, auxiliary component [Inorganic ion transport and metabolism]; Region: COG4985 94122008932 phosphate ABC transporter, permease protein PstA; Region: 3a0107s02c; TIGR00974 94122008933 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 94122008934 dimer interface [polypeptide binding]; other site 94122008935 conserved gate region; other site 94122008936 putative PBP binding loops; other site 94122008937 ABC-ATPase subunit interface; other site 94122008938 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4590 94122008939 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 94122008940 conserved gate region; other site 94122008941 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 94122008942 ABC-ATPase subunit interface; other site 94122008943 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 94122008944 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cd02116 94122008945 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 94122008946 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 94122008947 EamA-like transporter family; Region: EamA; pfam00892 94122008948 EamA-like transporter family; Region: EamA; pfam00892 94122008949 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819 94122008950 Protein of unknown function (DUF2797); Region: DUF2797; pfam10977 94122008951 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_24; cd09012 94122008952 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 94122008953 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 94122008954 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 94122008955 Protein of unknown function (DUF1415); Region: DUF1415; pfam07209 94122008956 NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family; Region: LDH_MDH_like; cl17195 94122008957 Peptidase S8 family domain in Subtilisin proteins; Region: Peptidases_S8_Subtilisin_subset; cd07477 94122008958 active site 94122008959 catalytic residues [active] 94122008960 PA_VapT_like: Protease-associated domain containing proteins like VapT from Vibrio metschnikovii strain RH530. This group contains various PA domain-containing proteins similar to V. metschnikovii VapT, including the serine alkaline protease SapSh from...; Region: PA_VapT_like; cd04817 94122008961 PA/subtilisin-like domain interface [polypeptide binding]; other site 94122008962 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 94122008963 catalytic residues [active] 94122008964 SseB protein; Region: SseB; cl06279 94122008965 butyryl-CoA:acetate CoA-transferase; Region: butyr_acet_CoA; TIGR03948 94122008966 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 94122008967 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 94122008968 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 94122008969 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 94122008970 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 94122008971 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 94122008972 Walker A/P-loop; other site 94122008973 ATP binding site [chemical binding]; other site 94122008974 Q-loop/lid; other site 94122008975 ABC transporter signature motif; other site 94122008976 Walker B; other site 94122008977 D-loop; other site 94122008978 H-loop/switch region; other site 94122008979 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 94122008980 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122008981 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 94122008982 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 94122008983 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 94122008984 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 94122008985 DNA binding site [nucleotide binding] 94122008986 AAA ATPase domain; Region: AAA_16; pfam13191 94122008987 Domain of unknown function (DUF1888); Region: DUF1888; pfam08985 94122008988 PAS domain S-box; Region: sensory_box; TIGR00229 94122008989 PAS domain; Region: PAS; smart00091 94122008990 putative active site [active] 94122008991 heme pocket [chemical binding]; other site 94122008992 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122008993 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122008994 metal binding site [ion binding]; metal-binding site 94122008995 active site 94122008996 I-site; other site 94122008997 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 94122008998 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 94122008999 FAD binding domain; Region: FAD_binding_4; pfam01565 94122009000 Berberine and berberine like; Region: BBE; pfam08031 94122009001 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 94122009002 EamA-like transporter family; Region: EamA; pfam00892 94122009003 EamA-like transporter family; Region: EamA; pfam00892 94122009004 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 94122009005 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 94122009006 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122009007 Walker A/P-loop; other site 94122009008 ATP binding site [chemical binding]; other site 94122009009 Q-loop/lid; other site 94122009010 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 94122009011 Walker B; other site 94122009012 ABC transporter; Region: ABC_tran_2; pfam12848 94122009013 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 94122009014 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 94122009015 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 94122009016 metal-binding site [ion binding] 94122009017 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 94122009018 Soluble P-type ATPase [General function prediction only]; Region: COG4087 94122009019 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 94122009020 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 94122009021 DNA binding residues [nucleotide binding] 94122009022 dimer interface [polypeptide binding]; other site 94122009023 copper binding site [ion binding]; other site 94122009024 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 94122009025 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 94122009026 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08217 94122009027 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 94122009028 NAD(P) binding site [chemical binding]; other site 94122009029 active site 94122009030 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 94122009031 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 94122009032 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 94122009033 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 94122009034 substrate binding site [chemical binding]; other site 94122009035 oxyanion hole (OAH) forming residues; other site 94122009036 trimer interface [polypeptide binding]; other site 94122009037 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 94122009038 enoyl-CoA hydratase; Provisional; Region: PRK09076 94122009039 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 94122009040 substrate binding site [chemical binding]; other site 94122009041 oxyanion hole (OAH) forming residues; other site 94122009042 trimer interface [polypeptide binding]; other site 94122009043 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 94122009044 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 94122009045 active site 94122009046 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 94122009047 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 94122009048 tetrameric interface [polypeptide binding]; other site 94122009049 NAD binding site [chemical binding]; other site 94122009050 catalytic residues [active] 94122009051 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 94122009052 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 94122009053 dimer interface [polypeptide binding]; other site 94122009054 active site 94122009055 homoserine O-succinyltransferase; Provisional; Region: PRK05368 94122009056 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 94122009057 proposed active site lysine [active] 94122009058 conserved cys residue [active] 94122009059 Type III secretion system lipoprotein chaperone (YscW); Region: YscW; cl15825 94122009060 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 94122009061 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 94122009062 NAD(P) binding site [chemical binding]; other site 94122009063 active site 94122009064 outer membrane protein W; Provisional; Region: PRK10959 94122009065 Bacterial protein of unknown function (DUF925); Region: DUF925; pfam06042 94122009066 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 94122009067 maleylacetoacetate isomerase; Region: maiA; TIGR01262 94122009068 C-terminal domain interface [polypeptide binding]; other site 94122009069 GSH binding site (G-site) [chemical binding]; other site 94122009070 putative dimer interface [polypeptide binding]; other site 94122009071 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 94122009072 dimer interface [polypeptide binding]; other site 94122009073 N-terminal domain interface [polypeptide binding]; other site 94122009074 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 94122009075 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 94122009076 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 94122009077 DNA-binding transcriptional regulator TyrR; Provisional; Region: PRK10820 94122009078 N-terminal ACT domain of the TyrR protein; Region: ACT_TyrR; cd04877 94122009079 putative aromatic amino acid binding site; other site 94122009080 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 94122009081 Walker A motif; other site 94122009082 ATP binding site [chemical binding]; other site 94122009083 Walker B motif; other site 94122009084 arginine finger; other site 94122009085 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 94122009086 aromatic arch; other site 94122009087 DCoH dimer interaction site [polypeptide binding]; other site 94122009088 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 94122009089 DCoH tetramer interaction site [polypeptide binding]; other site 94122009090 substrate binding site [chemical binding]; other site 94122009091 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 94122009092 cofactor binding site; other site 94122009093 metal binding site [ion binding]; metal-binding site 94122009094 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 94122009095 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 94122009096 active site 94122009097 tetramer interface; other site 94122009098 UDP-glucose 4-epimerase; Region: PLN02240 94122009099 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 94122009100 NAD binding site [chemical binding]; other site 94122009101 homodimer interface [polypeptide binding]; other site 94122009102 active site 94122009103 substrate binding site [chemical binding]; other site 94122009104 ferredoxin-type protein; Provisional; Region: PRK10194 94122009105 4Fe-4S binding domain; Region: Fer4; pfam00037 94122009106 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 94122009107 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122009108 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 94122009109 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 94122009110 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 94122009111 Protein of unknown function (DUF2982); Region: DUF2982; pfam11201 94122009112 Uncharacterized conserved protein [Function unknown]; Region: COG1434 94122009113 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 94122009114 putative active site [active] 94122009115 fructokinase; Reviewed; Region: PRK09557 94122009116 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 94122009117 nucleotide binding site [chemical binding]; other site 94122009118 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 94122009119 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 94122009120 active site 94122009121 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 94122009122 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 94122009123 NADP binding site [chemical binding]; other site 94122009124 active site 94122009125 putative substrate binding site [chemical binding]; other site 94122009126 putative hydrolase; Validated; Region: PRK09248 94122009127 Polymerase and Histidinol Phosphatase domain of Ycdx like; Region: PHP_HisPPase_Ycdx_like; cd07437 94122009128 active site 94122009129 SWIM zinc finger; Region: SWIM; pfam04434 94122009130 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 94122009131 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 94122009132 ATP binding site [chemical binding]; other site 94122009133 putative Mg++ binding site [ion binding]; other site 94122009134 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 94122009135 nucleotide binding region [chemical binding]; other site 94122009136 ATP-binding site [chemical binding]; other site 94122009137 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 94122009138 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 94122009139 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 94122009140 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 94122009141 TrkA-N domain; Region: TrkA_N; pfam02254 94122009142 TrkA-C domain; Region: TrkA_C; pfam02080 94122009143 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122009144 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122009145 metal binding site [ion binding]; metal-binding site 94122009146 active site 94122009147 I-site; other site 94122009148 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 94122009149 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 94122009150 Ligand Binding Site [chemical binding]; other site 94122009151 TilS substrate binding domain; Region: TilS; pfam09179 94122009152 TilS substrate C-terminal domain; Region: TilS_C; pfam11734 94122009153 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 94122009154 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 94122009155 putative active site [active] 94122009156 putative PHP Thumb interface [polypeptide binding]; other site 94122009157 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 94122009158 generic binding surface II; other site 94122009159 generic binding surface I; other site 94122009160 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 94122009161 RNA/DNA hybrid binding site [nucleotide binding]; other site 94122009162 active site 94122009163 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 94122009164 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 94122009165 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 94122009166 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 94122009167 active site 94122009168 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 94122009169 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 94122009170 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 94122009171 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 94122009172 trimer interface [polypeptide binding]; other site 94122009173 active site 94122009174 UDP-GlcNAc binding site [chemical binding]; other site 94122009175 lipid binding site [chemical binding]; lipid-binding site 94122009176 periplasmic chaperone; Provisional; Region: PRK10780 94122009177 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 94122009178 outer membrane protein assembly factor YaeT; Provisional; Region: PRK11067 94122009179 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 94122009180 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 94122009181 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 94122009182 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 94122009183 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 94122009184 Surface antigen; Region: Bac_surface_Ag; pfam01103 94122009185 zinc metallopeptidase RseP; Provisional; Region: PRK10779 94122009186 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 94122009187 active site 94122009188 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 94122009189 protein binding site [polypeptide binding]; other site 94122009190 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 94122009191 protein binding site [polypeptide binding]; other site 94122009192 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 94122009193 putative substrate binding region [chemical binding]; other site 94122009194 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 94122009195 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 94122009196 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 94122009197 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 94122009198 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 94122009199 CDP-diglyceride synthase; Provisional; Region: cdsA; PRK11624 94122009200 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 94122009201 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cl00230 94122009202 catalytic residue [active] 94122009203 putative FPP diphosphate binding site; other site 94122009204 putative FPP binding hydrophobic cleft; other site 94122009205 dimer interface [polypeptide binding]; other site 94122009206 putative IPP diphosphate binding site; other site 94122009207 ribosome recycling factor; Reviewed; Region: frr; PRK00083 94122009208 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 94122009209 hinge region; other site 94122009210 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 94122009211 putative nucleotide binding site [chemical binding]; other site 94122009212 uridine monophosphate binding site [chemical binding]; other site 94122009213 homohexameric interface [polypeptide binding]; other site 94122009214 elongation factor Ts; Provisional; Region: tsf; PRK09377 94122009215 UBA/TS-N domain; Region: UBA; pfam00627 94122009216 Elongation factor TS; Region: EF_TS; pfam00889 94122009217 Elongation factor TS; Region: EF_TS; pfam00889 94122009218 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 94122009219 rRNA interaction site [nucleotide binding]; other site 94122009220 S8 interaction site; other site 94122009221 putative laminin-1 binding site; other site 94122009222 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 94122009223 active site 94122009224 PII uridylyl-transferase; Provisional; Region: PRK05007 94122009225 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 94122009226 metal binding triad; other site 94122009227 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 94122009228 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 94122009229 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 94122009230 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 94122009231 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 94122009232 trimer interface [polypeptide binding]; other site 94122009233 active site 94122009234 substrate binding site [chemical binding]; other site 94122009235 CoA binding site [chemical binding]; other site 94122009236 Protein of unknown function (DUF3718); Region: DUF3718; pfam12514 94122009237 GAF domain; Region: GAF; cl17456 94122009238 GAF domain; Region: GAF_2; pfam13185 94122009239 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 94122009240 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 94122009241 Zn2+ binding site [ion binding]; other site 94122009242 Mg2+ binding site [ion binding]; other site 94122009243 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 94122009244 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 94122009245 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 94122009246 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 94122009247 putative active site [active] 94122009248 putative substrate binding site [chemical binding]; other site 94122009249 putative cosubstrate binding site; other site 94122009250 catalytic site [active] 94122009251 PTS system glucose-specific transporter subunits IIBC; Provisional; Region: PRK11089 94122009252 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; COG1263 94122009253 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_glc; cd00212 94122009254 active site turn [active] 94122009255 phosphorylation site [posttranslational modification] 94122009256 flavodoxin; Provisional; Region: PRK08105 94122009257 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 94122009258 tRNA pseudouridine isomerase C; Region: PseudoU_synth_TruC; cd02563 94122009259 probable active site [active] 94122009260 tRNA pseudouridine synthase C; Region: DUF446; pfam04287 94122009261 Protein of unknown function (DUF3549); Region: DUF3549; pfam12069 94122009262 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 94122009263 Protein of unknown function (DUF962); Region: DUF962; pfam06127 94122009264 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122009265 Coenzyme A binding pocket [chemical binding]; other site 94122009266 Protein of unknown function (DUF2789); Region: DUF2789; pfam10982 94122009267 Protein of unknown function (DUF3192); Region: DUF3192; pfam11399 94122009268 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); Region: DUF2310; pfam10071 94122009269 SecY interacting protein Syd; Provisional; Region: PRK04968 94122009270 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 94122009271 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 94122009272 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 94122009273 Sporulation control protein [General function prediction only]; Region: Spo0M; COG4326 94122009274 SpoOM protein; Region: Spo0M; pfam07070 94122009275 Phosphopantetheinyl transferase [Coenzyme metabolism]; Region: Sfp; COG2091 94122009276 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; pfam01648 94122009277 Winged helix-turn helix; Region: HTH_29; pfam13551 94122009278 Homeodomain-like domain; Region: HTH_23; pfam13384 94122009279 polyketide-type polyunsaturated fatty acid synthase PfaA; Region: omega_3_PfaA; TIGR02813 94122009280 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 94122009281 active site 94122009282 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 94122009283 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 94122009284 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 94122009285 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 94122009286 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 94122009287 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 94122009288 ketoreductase (KR), subgroup 2, complex (x) SDRs; Region: KR_2_SDR_x; cd08953 94122009289 putative NADP binding site [chemical binding]; other site 94122009290 active site 94122009291 Acyl transferase domain; Region: Acyl_transf_1; cl08282 94122009292 3-oxoacyl-(acyl-carrier-protein) synthase [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: FabB; COG0304 94122009293 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 94122009294 active site 94122009295 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 94122009296 active site 94122009297 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 94122009298 active site 2 [active] 94122009299 dimer interface [polypeptide binding]; other site 94122009300 active site 1 [active] 94122009301 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 94122009302 active site 1 [active] 94122009303 dimer interface [polypeptide binding]; other site 94122009304 active site 2 [active] 94122009305 2-Nitropropane dioxygenase (NPD)-like domain, associated with the (acyl-carrier-protein) S-malonyltransferase FabD. NPD is part of the nitroalkaneoxidizing enzyme family, that catalyzes oxidative denitrification of nitroalkanes to their corresponding...; Region: NPD_FabD; cd04742 94122009306 FMN binding site [chemical binding]; other site 94122009307 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 94122009308 substrate binding site [chemical binding]; other site 94122009309 putative catalytic residue [active] 94122009310 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 94122009311 non-specific DNA binding site [nucleotide binding]; other site 94122009312 salt bridge; other site 94122009313 sequence-specific DNA binding site [nucleotide binding]; other site 94122009314 Domain of unknown function (DUF4277); Region: DUF4277; pfam14104 94122009315 Transposase [DNA replication, recombination, and repair]; Region: COG5421 94122009316 hypothetical protein; Provisional; Region: PRK12361 94122009317 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 94122009318 active site 94122009319 catalytic residues [active] 94122009320 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 94122009321 PEP-CTERM-box response regulator transcription factor; Region: PEP_resp_reg; TIGR02915 94122009322 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 94122009323 Walker A motif; other site 94122009324 ATP binding site [chemical binding]; other site 94122009325 Walker B motif; other site 94122009326 arginine finger; other site 94122009327 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 94122009328 Domain of unknown function (DUF2383); Region: DUF2383; cl17556 94122009329 BON domain; Region: BON; pfam04972 94122009330 BON domain; Region: BON; pfam04972 94122009331 Protein of unknown function (DUF3224); Region: DUF3224; pfam11528 94122009332 Bacterial inner membrane protein; Region: Imp-YgjV; pfam10688 94122009333 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 94122009334 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 94122009335 ligand binding site [chemical binding]; other site 94122009336 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 94122009337 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 94122009338 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup; Region: M14_ASTE_ASPA_like_1; cd06251 94122009339 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 94122009340 putative active site [active] 94122009341 Zn binding site [ion binding]; other site 94122009342 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 94122009343 MarR family; Region: MarR; pfam01047 94122009344 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 94122009345 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 94122009346 putative substrate translocation pore; other site 94122009347 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; smart00782 94122009348 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 94122009349 PhnA protein; Region: PhnA; pfam03831 94122009350 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 94122009351 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122009352 N-terminal plug; other site 94122009353 ligand-binding site [chemical binding]; other site 94122009354 TIGR02453 family protein; Region: TIGR02453 94122009355 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 94122009356 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 94122009357 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 94122009358 GST_N family, Saccharomyces cerevisiae GTT2-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT2. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing...; Region: GST_N_GTT2_like; cd03051 94122009359 putative C-terminal domain interface [polypeptide binding]; other site 94122009360 putative GSH binding site (G-site) [chemical binding]; other site 94122009361 putative dimer interface [polypeptide binding]; other site 94122009362 C-terminal, alpha helical domain of GTT2-like Glutathione S-transferases; Region: GST_C_GTT2_like; cd03182 94122009363 putative N-terminal domain interface [polypeptide binding]; other site 94122009364 putative dimer interface [polypeptide binding]; other site 94122009365 putative substrate binding pocket (H-site) [chemical binding]; other site 94122009366 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 94122009367 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 94122009368 C-terminal domain interface [polypeptide binding]; other site 94122009369 GSH binding site (G-site) [chemical binding]; other site 94122009370 dimer interface [polypeptide binding]; other site 94122009371 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 94122009372 N-terminal domain interface [polypeptide binding]; other site 94122009373 putative dimer interface [polypeptide binding]; other site 94122009374 active site 94122009375 NOL1/NOP2/sun family; Region: Nol1_Nop2_Fmu; pfam01189 94122009376 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 94122009377 S-adenosylmethionine binding site [chemical binding]; other site 94122009378 Acetoacetate decarboxylase (ADC); Region: ADC; cl01919 94122009379 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 94122009380 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 94122009381 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 94122009382 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122009383 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122009384 metal binding site [ion binding]; metal-binding site 94122009385 active site 94122009386 I-site; other site 94122009387 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 94122009388 EamA-like transporter family; Region: EamA; pfam00892 94122009389 EamA-like transporter family; Region: EamA; cl17759 94122009390 YfaZ precursor; Region: YfaZ; pfam07437 94122009391 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122009392 Coenzyme A binding pocket [chemical binding]; other site 94122009393 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 94122009394 MgtE intracellular N domain; Region: MgtE_N; smart00924 94122009395 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 94122009396 Divalent cation transporter; Region: MgtE; cl00786 94122009397 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 94122009398 catalytic residues [active] 94122009399 dimer interface [polypeptide binding]; other site 94122009400 leukotriene A-4 hydrolase/aminopeptidase; Region: leuko_A4_hydro; TIGR02411 94122009401 Peptidase M1 family contains leukotriene A4 hydrolase; Region: M1_LTA4H; cd09599 94122009402 active site 94122009403 Zn binding site [ion binding]; other site 94122009404 Leukotriene A4 hydrolase, C-terminal; Region: Leuk-A4-hydro_C; pfam09127 94122009405 PBP superfamily domain; Region: PBP_like_2; cl17296 94122009406 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 94122009407 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 94122009408 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 94122009409 putative active site [active] 94122009410 heme pocket [chemical binding]; other site 94122009411 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 94122009412 dimer interface [polypeptide binding]; other site 94122009413 phosphorylation site [posttranslational modification] 94122009414 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 94122009415 ATP binding site [chemical binding]; other site 94122009416 Mg2+ binding site [ion binding]; other site 94122009417 G-X-G motif; other site 94122009418 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 94122009419 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122009420 active site 94122009421 phosphorylation site [posttranslational modification] 94122009422 intermolecular recognition site; other site 94122009423 dimerization interface [polypeptide binding]; other site 94122009424 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 94122009425 DNA binding site [nucleotide binding] 94122009426 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 94122009427 trimer interface [polypeptide binding]; other site 94122009428 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 94122009429 eyelet of channel; other site 94122009430 recombination associated protein; Reviewed; Region: rdgC; PRK00321 94122009431 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 94122009432 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 94122009433 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 94122009434 protein binding site [polypeptide binding]; other site 94122009435 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 94122009436 binding surface 94122009437 TPR motif; other site 94122009438 Tetratricopeptide repeat; Region: TPR_12; pfam13424 94122009439 Tetratricopeptide repeat; Region: TPR_12; pfam13424 94122009440 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 94122009441 TPR motif; other site 94122009442 binding surface 94122009443 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122009444 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122009445 metal binding site [ion binding]; metal-binding site 94122009446 active site 94122009447 I-site; other site 94122009448 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 94122009449 Domain of unknown function (DUF3412); Region: DUF3412; pfam11892 94122009450 flap endonuclease-like protein; Provisional; Region: PRK09482 94122009451 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 94122009452 active site 94122009453 metal binding site 1 [ion binding]; metal-binding site 94122009454 putative 5' ssDNA interaction site; other site 94122009455 metal binding site 3; metal-binding site 94122009456 metal binding site 2 [ion binding]; metal-binding site 94122009457 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 94122009458 putative DNA binding site [nucleotide binding]; other site 94122009459 putative metal binding site [ion binding]; other site 94122009460 Protein of unknown function (DUF3192); Region: DUF3192; pfam11399 94122009461 Domain of unknown function (DUF1963); Region: DUF1963; cl01600 94122009462 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 94122009463 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 94122009464 isocitrate dehydrogenase; Provisional; Region: PRK08997 94122009465 tartrate dehydrogenase; Region: TTC; TIGR02089 94122009466 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional; Region: PRK11760 94122009467 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 94122009468 Protein of unknown function (DUF423); Region: DUF423; pfam04241 94122009469 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG3571 94122009470 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 94122009471 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122009472 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 94122009473 dimerization interface [polypeptide binding]; other site 94122009474 substrate binding pocket [chemical binding]; other site 94122009475 tRNA s(4)U8 sulfurtransferase; Provisional; Region: PRK01269 94122009476 THUMP domain of thiamine biosynthesis protein ThiI; Region: THUMP_ThiI; cd11716 94122009477 ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide; Region: ThiI; cd01712 94122009478 Ligand Binding Site [chemical binding]; other site 94122009479 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 94122009480 active site residue [active] 94122009481 flagellar motor protein MotB; Reviewed; Region: motB; PRK08944 94122009482 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 94122009483 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 94122009484 ligand binding site [chemical binding]; other site 94122009485 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 94122009486 flagellar motor protein PomA; Reviewed; Region: PRK08990 94122009487 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 94122009488 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 94122009489 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 94122009490 substrate binding pocket [chemical binding]; other site 94122009491 chain length determination region; other site 94122009492 substrate-Mg2+ binding site; other site 94122009493 catalytic residues [active] 94122009494 aspartate-rich region 1; other site 94122009495 active site lid residues [active] 94122009496 aspartate-rich region 2; other site 94122009497 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 94122009498 Thiamine pyrophosphate (TPP) family, DXS subfamily, TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products...; Region: TPP_DXS; cd02007 94122009499 TPP-binding site; other site 94122009500 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 94122009501 PYR/PP interface [polypeptide binding]; other site 94122009502 dimer interface [polypeptide binding]; other site 94122009503 TPP binding site [chemical binding]; other site 94122009504 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 94122009505 GrpE; Region: GrpE; pfam01025 94122009506 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 94122009507 dimer interface [polypeptide binding]; other site 94122009508 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 94122009509 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK03378 94122009510 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 94122009511 L-lactate permease; Region: Lactate_perm; cl00701 94122009512 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 94122009513 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 94122009514 FAD binding domain; Region: FAD_binding_4; pfam01565 94122009515 4Fe-4S binding domain; Region: Fer4; pfam00037 94122009516 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 94122009517 Heterodisulfide reductase, subunit B [Energy production and conversion]; Region: HdrB; COG2048 94122009518 Cysteine-rich domain; Region: CCG; pfam02754 94122009519 Cysteine-rich domain; Region: CCG; pfam02754 94122009520 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 94122009521 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 94122009522 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 94122009523 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 94122009524 Domain of unknown function DUF20; Region: UPF0118; pfam01594 94122009525 HlyD family secretion protein; Region: HlyD; pfam00529 94122009526 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 94122009527 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122009528 Ion channel; Region: Ion_trans_2; pfam07885 94122009529 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 94122009530 active site 94122009531 Int/Topo IB signature motif; other site 94122009532 catalytic residues [active] 94122009533 DNA binding site [nucleotide binding] 94122009534 Putative phage integrase; Region: Phage_Integr_2; pfam13009 94122009535 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 94122009536 dinuclear metal binding motif [ion binding]; other site 94122009537 helicase, putative, RecD/TraA family; Region: recD_rel; TIGR01448 94122009538 AAA domain; Region: AAA_30; pfam13604 94122009539 Family description; Region: UvrD_C_2; pfam13538 94122009540 multidrug efflux pump VmrA; Reviewed; Region: vmrA; PRK09575 94122009541 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 94122009542 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 94122009543 Major Facilitator Superfamily; Region: MFS_1; pfam07690 94122009544 putative substrate translocation pore; other site 94122009545 Protein of unknown function (DUF3087); Region: DUF3087; pfam11286 94122009546 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 94122009547 substrate binding pocket [chemical binding]; other site 94122009548 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 94122009549 membrane-bound complex binding site; other site 94122009550 hinge residues; other site 94122009551 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 94122009552 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 94122009553 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 94122009554 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 94122009555 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 94122009556 ATP binding site [chemical binding]; other site 94122009557 Mg++ binding site [ion binding]; other site 94122009558 motif III; other site 94122009559 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 94122009560 nucleotide binding region [chemical binding]; other site 94122009561 ATP-binding site [chemical binding]; other site 94122009562 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 94122009563 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 94122009564 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 94122009565 putative active site [active] 94122009566 heme pocket [chemical binding]; other site 94122009567 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 94122009568 PAS domain; Region: PAS_9; pfam13426 94122009569 putative active site [active] 94122009570 heme pocket [chemical binding]; other site 94122009571 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122009572 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122009573 metal binding site [ion binding]; metal-binding site 94122009574 active site 94122009575 I-site; other site 94122009576 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 94122009577 This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family...; Region: GT1_Glycogen_synthase_DULL1_like; cd03791 94122009578 glycogen/starch synthase, ADP-glucose type; Region: glgA; TIGR02095 94122009579 ADP-binding pocket [chemical binding]; other site 94122009580 homodimer interface [polypeptide binding]; other site 94122009581 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 94122009582 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 94122009583 ligand binding site; other site 94122009584 oligomer interface; other site 94122009585 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and...; Region: LbH_G1P_AT_C; cd04651 94122009586 dimer interface [polypeptide binding]; other site 94122009587 N-terminal domain interface [polypeptide binding]; other site 94122009588 sulfate 1 binding site; other site 94122009589 This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of...; Region: GT1_Glycogen_Phosphorylase; cd04300 94122009590 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 94122009591 homodimer interface [polypeptide binding]; other site 94122009592 active site pocket [active] 94122009593 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 94122009594 N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme and bacterial isoamylase (also called glycogen 6-glucanohydrolase); Region: E_set_GDE_Isoamylase_N; cd02856 94122009595 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 94122009596 active site 94122009597 catalytic site [active] 94122009598 glycogen branching enzyme; Provisional; Region: PRK05402 94122009599 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 94122009600 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 94122009601 active site 94122009602 catalytic site [active] 94122009603 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 94122009604 4-alpha-glucanotransferase [Carbohydrate transport and metabolism]; Region: MalQ; COG1640 94122009605 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; cl00197 94122009606 active site 94122009607 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 94122009608 MarR family; Region: MarR; pfam01047 94122009609 MarR family; Region: MarR_2; cl17246 94122009610 putative alcohol dehydrogenase; Provisional; Region: PRK09860 94122009611 Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria; Region: LPO; cd08176 94122009612 dimer interface [polypeptide binding]; other site 94122009613 active site 94122009614 metal binding site [ion binding]; metal-binding site 94122009615 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 94122009616 isocitrate lyase; Provisional; Region: PRK15063 94122009617 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 94122009618 tetramer interface [polypeptide binding]; other site 94122009619 active site 94122009620 Mg2+/Mn2+ binding site [ion binding]; other site 94122009621 malate synthase A; Region: malate_syn_A; TIGR01344 94122009622 Malate synthase A (MSA), present in some bacteria, plants and fungi. Prokaryotic MSAs tend to be monomeric, whereas eukaryotic enzymes are homomultimers. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to...; Region: malate_synt_A; cd00727 94122009623 active site 94122009624 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 94122009625 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122009626 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122009627 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 94122009628 transporter, monovalent cation:proton antiporter-2 (CPA2) family; Region: 2a37; TIGR00932 94122009629 TrkA-N domain; Region: TrkA_N; pfam02254 94122009630 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122009631 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122009632 metal binding site [ion binding]; metal-binding site 94122009633 active site 94122009634 I-site; other site 94122009635 Subunit A of Class III extradiol dioxygenases; Region: Extradiol_Dioxygenase_3A_like; cl06673 94122009636 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 94122009637 active site 94122009638 SAM binding site [chemical binding]; other site 94122009639 homodimer interface [polypeptide binding]; other site 94122009640 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 94122009641 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 94122009642 RnfH family Ubiquitin; Region: Ub-RnfH; cl17382 94122009643 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 94122009644 putative coenzyme Q binding site [chemical binding]; other site 94122009645 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 94122009646 SmpB-tmRNA interface; other site 94122009647 integrase; Provisional; Region: PRK09692 94122009648 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 94122009649 active site 94122009650 Int/Topo IB signature motif; other site 94122009651 Helix-turn-helix domain; Region: HTH_36; pfam13730 94122009652 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 94122009653 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 94122009654 active site 94122009655 TIGR02646 family protein; Region: TIGR02646 94122009656 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM)-like family; contains proteins similar to MCM, and the large subunit of Streptomyces coenzyme B12-dependent isobutyryl-CoA mutase (ICM). MCM catalyzes the isomerization of...; Region: MM_CoA_mutase; cl00817 94122009657 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122009658 AAA domain; Region: AAA_21; pfam13304 94122009659 Walker A/P-loop; other site 94122009660 ATP binding site [chemical binding]; other site 94122009661 AAA domain; Region: AAA_21; pfam13304 94122009662 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cd00267 94122009663 ATP binding site [chemical binding]; other site 94122009664 ABC transporter signature motif; other site 94122009665 Walker B; other site 94122009666 D-loop; other site 94122009667 H-loop/switch region; other site 94122009668 EcoKI restriction-modification system protein HsdS; Provisional; Region: PRK09737 94122009669 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 94122009670 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 94122009671 HsdM N-terminal domain; Region: HsdM_N; pfam12161 94122009672 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 94122009673 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 94122009674 S-adenosylmethionine binding site [chemical binding]; other site 94122009675 Fic family protein [Function unknown]; Region: COG3177 94122009676 Fic/DOC family N-terminal; Region: Fic_N; pfam13784 94122009677 Fic/DOC family; Region: Fic; pfam02661 94122009678 type I restriction enzyme EcoKI subunit R; Provisional; Region: hsdR; PRK11448 94122009679 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 94122009680 ATP binding site [chemical binding]; other site 94122009681 putative Mg++ binding site [ion binding]; other site 94122009682 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 94122009683 nucleotide binding region [chemical binding]; other site 94122009684 ATP-binding site [chemical binding]; other site 94122009685 Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized proteins with a DEAD domain; Region: PLDc_Bfil_DEXD_like; cd09117 94122009686 PLD-like domain; Region: PLDc_2; pfam13091 94122009687 homodimer interface [polypeptide binding]; other site 94122009688 putative active site [active] 94122009689 catalytic site [active] 94122009690 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 94122009691 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 94122009692 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 94122009693 metal-binding site [ion binding] 94122009694 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 94122009695 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 94122009696 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 94122009697 threonine/serine transporter TdcC; Provisional; Region: PRK13629; cl17672 94122009698 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 94122009699 homotrimer interaction site [polypeptide binding]; other site 94122009700 putative active site [active] 94122009701 L-cysteine desulfidase [Amino acid transport and metabolism]; Region: COG3681 94122009702 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 94122009703 YheO-like PAS domain; Region: PAS_6; pfam08348 94122009704 HTH domain; Region: HTH_22; pfam13309 94122009705 Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton]; Region: ATS1; COG5184 94122009706 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 94122009707 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 94122009708 Domain of unknown function (DUF368); Region: DUF368; pfam04018 94122009709 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 94122009710 CoenzymeA binding site [chemical binding]; other site 94122009711 subunit interaction site [polypeptide binding]; other site 94122009712 PHB binding site; other site 94122009713 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 94122009714 nucleoside/Zn binding site; other site 94122009715 dimer interface [polypeptide binding]; other site 94122009716 catalytic motif [active] 94122009717 Predicted membrane protein [Function unknown]; Region: COG2311 94122009718 Protein of unknown function (DUF418); Region: DUF418; cl12135 94122009719 2-hydroxycarboxylate transporter family; Region: 2HCT; cl01386 94122009720 Protein of unknown function (DUF1294); Region: DUF1294; pfam06961 94122009721 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 94122009722 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 94122009723 HPP family; Region: HPP; pfam04982 94122009724 Short chain fatty acids transporter [Lipid metabolism]; Region: AtoE; COG2031 94122009725 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 94122009726 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 94122009727 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 94122009728 N-terminal Early set domain associated with the catalytic domain of chitinase; Region: E_set_Chitinase_N; cd02848 94122009729 Chitinase [Carbohydrate transport and metabolism]; Region: ChiA; COG3325 94122009730 The GH18 (glycosyl hydrolases, family 18) type II chitinases hydrolyze chitin, an abundant polymer of N-acetylglucosamine and have been identified in bacteria, fungi, insects, plants, viruses, and protozoan parasites. The structure of this domain is an...; Region: GH18_chitinase; cd06548 94122009731 active site 94122009732 Chitin-binding domain of chitinase C; Region: ChiC_BD; cd12215 94122009733 aromatic chitin/cellulose binding site residues [chemical binding]; other site 94122009734 Chitin-binding domain of chitinase C; Region: ChiC_BD; cd12215 94122009735 aromatic chitin/cellulose binding site residues [chemical binding]; other site 94122009736 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 94122009737 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 94122009738 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 94122009739 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 94122009740 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP; cd01085 94122009741 active site 94122009742 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 94122009743 PAS domain; Region: PAS_9; pfam13426 94122009744 putative active site [active] 94122009745 heme pocket [chemical binding]; other site 94122009746 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 94122009747 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122009748 dimer interface [polypeptide binding]; other site 94122009749 putative CheW interface [polypeptide binding]; other site 94122009750 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 94122009751 DEAD-like helicases superfamily; Region: DEXDc; smart00487 94122009752 ATP binding site [chemical binding]; other site 94122009753 Mg++ binding site [ion binding]; other site 94122009754 motif III; other site 94122009755 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 94122009756 nucleotide binding region [chemical binding]; other site 94122009757 ATP-binding site [chemical binding]; other site 94122009758 Uncharacterized conserved protein [Function unknown]; Region: COG5361 94122009759 Protein of unknown function (DUF1254); Region: DUF1254; pfam06863 94122009760 Protein of unknown function (DUF1214); Region: DUF1214; pfam06742 94122009761 Peroxiredoxin (PRX)-like 2 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a CXXC motif, similar to TRX. The second cysteine in the motif corresponds to the peroxidatic cysteine of PRX, however, these...; Region: PRX_like2; cd02970 94122009762 putative catalytic residues [active] 94122009763 Protein of unknown function (DUF2913); Region: DUF2913; pfam11140 94122009764 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 94122009765 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 94122009766 membrane-bound complex binding site; other site 94122009767 hinge residues; other site 94122009768 Uncharacterized protein related to arylsulfate sulfotransferase involved in siderophore biosynthesis [General function prediction only]; Region: COG4321 94122009769 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_1; cd03169 94122009770 intracellular protease, PfpI family; Region: PfpI; TIGR01382 94122009771 conserved cys residue [active] 94122009772 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2268 94122009773 Band_7_flotillin: a subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. These two proteins are lipid raft-associated. Individual proteins of...; Region: Band_7_flotillin; cd03399 94122009774 Protein of unknown function (DUF1449); Region: DUF1449; pfam07290 94122009775 DsrE/DsrF-like family; Region: DrsE; pfam02635 94122009776 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 94122009777 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 94122009778 active site 94122009779 Zn binding site [ion binding]; other site 94122009780 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 94122009781 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122009782 Coenzyme A binding pocket [chemical binding]; other site 94122009783 Protein of unknown function, DUF486; Region: DUF486; pfam04342 94122009784 Protein of unknown function (DUF2960); Region: DUF2960; pfam11173 94122009785 RDD family; Region: RDD; pfam06271 94122009786 lipopolysaccharide ABC transporter permease; Provisional; Region: PRK15071 94122009787 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 94122009788 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 94122009789 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 94122009790 multifunctional aminopeptidase A; Provisional; Region: PRK00913 94122009791 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 94122009792 interface (dimer of trimers) [polypeptide binding]; other site 94122009793 Substrate-binding/catalytic site; other site 94122009794 Zn-binding sites [ion binding]; other site 94122009795 bifunctional chorismate mutase/prephenate dehydratase; Provisional; Region: pheA; PRK10622 94122009796 chorismate mutase domain of proteobacterial P-protein, clade 1; Region: CM_P_1; TIGR01797 94122009797 Prephenate dehydratase; Region: PDT; pfam00800 94122009798 C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme; Region: ACT_CM-PDT; cd04905 94122009799 putative L-Phe binding site [chemical binding]; other site 94122009800 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; cl17225 94122009801 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 94122009802 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_1; cd06215 94122009803 HCP oxidoreductase, NADH-dependent; Provisional; Region: PRK10684 94122009804 FAD binding pocket [chemical binding]; other site 94122009805 FAD binding motif [chemical binding]; other site 94122009806 phosphate binding motif [ion binding]; other site 94122009807 beta-alpha-beta structure motif; other site 94122009808 NAD binding pocket [chemical binding]; other site 94122009809 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 94122009810 catalytic loop [active] 94122009811 iron binding site [ion binding]; other site 94122009812 hybrid cluster protein; Provisional; Region: PRK05290 94122009813 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 94122009814 ACS interaction site; other site 94122009815 CODH interaction site; other site 94122009816 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 94122009817 ACS interaction site; other site 94122009818 CODH interaction site; other site 94122009819 metal cluster binding site [ion binding]; other site 94122009820 bifunctional chorismate mutase/prephenate dehydrogenase; Provisional; Region: tyrA; PRK11199 94122009821 chorismate mutase domain of T-protein; Region: CM_T; TIGR01799 94122009822 prephenate dehydrogenase; Validated; Region: PRK08507 94122009823 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional; Region: PRK12755 94122009824 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 94122009825 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 94122009826 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 94122009827 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 94122009828 RimM N-terminal domain; Region: RimM; pfam01782 94122009829 PRC-barrel domain; Region: PRC; pfam05239 94122009830 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 94122009831 signal recognition particle protein; Provisional; Region: PRK10867 94122009832 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 94122009833 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 94122009834 P loop; other site 94122009835 GTP binding site [chemical binding]; other site 94122009836 Signal peptide binding domain; Region: SRP_SPB; pfam02978 94122009837 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 94122009838 Domain of unknown function DUF21; Region: DUF21; pfam01595 94122009839 hypothetical protein; Provisional; Region: PRK11573 94122009840 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 94122009841 Transporter associated domain; Region: CorC_HlyC; smart01091 94122009842 Protein of unknown function (DUF962); Region: DUF962; cl01879 94122009843 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 94122009844 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 94122009845 active site 94122009846 hydrophilic channel; other site 94122009847 dimerization interface [polypeptide binding]; other site 94122009848 catalytic residues [active] 94122009849 active site lid [active] 94122009850 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 94122009851 Recombination protein O N terminal; Region: RecO_N; pfam11967 94122009852 Recombination protein O C terminal; Region: RecO_C; pfam02565 94122009853 GTPase Era; Reviewed; Region: era; PRK00089 94122009854 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 94122009855 G1 box; other site 94122009856 GTP/Mg2+ binding site [chemical binding]; other site 94122009857 Switch I region; other site 94122009858 G2 box; other site 94122009859 Switch II region; other site 94122009860 G3 box; other site 94122009861 G4 box; other site 94122009862 G5 box; other site 94122009863 KH domain; Region: KH_2; pfam07650 94122009864 ribonuclease III; Reviewed; Region: rnc; PRK00102 94122009865 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 94122009866 dimerization interface [polypeptide binding]; other site 94122009867 active site 94122009868 metal binding site [ion binding]; metal-binding site 94122009869 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 94122009870 dsRNA binding site [nucleotide binding]; other site 94122009871 signal peptidase I; Provisional; Region: PRK10861 94122009872 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 94122009873 Catalytic site [active] 94122009874 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 94122009875 GTP-binding protein LepA; Provisional; Region: PRK05433 94122009876 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 94122009877 G1 box; other site 94122009878 putative GEF interaction site [polypeptide binding]; other site 94122009879 GTP/Mg2+ binding site [chemical binding]; other site 94122009880 Switch I region; other site 94122009881 G2 box; other site 94122009882 G3 box; other site 94122009883 Switch II region; other site 94122009884 G4 box; other site 94122009885 G5 box; other site 94122009886 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 94122009887 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 94122009888 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 94122009889 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 94122009890 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseB; COG3026 94122009891 anti-sigma E factor; Provisional; Region: rseB; PRK09455 94122009892 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 94122009893 anti-RNA polymerase sigma factor SigE; Provisional; Region: PRK10863 94122009894 Anti sigma-E protein RseA, C-terminal domain; Region: RseA_C; pfam03873 94122009895 RNA polymerase sigma factor AlgU; Provisional; Region: algU; PRK11923 94122009896 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 94122009897 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 94122009898 DNA binding residues [nucleotide binding] 94122009899 L-aspartate oxidase; Provisional; Region: PRK09077 94122009900 L-aspartate oxidase; Provisional; Region: PRK06175 94122009901 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 94122009902 Uncharacterized conserved protein [Function unknown]; Region: COG2938 94122009903 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 94122009904 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122009905 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 94122009906 dimerization interface [polypeptide binding]; other site 94122009907 pH-dependent sodium/proton antiporter; Reviewed; Region: nhaA; PRK09561 94122009908 thymidylate synthase; Reviewed; Region: thyA; PRK01827 94122009909 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 94122009910 dimerization interface [polypeptide binding]; other site 94122009911 active site 94122009912 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 94122009913 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 94122009914 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional; Region: PRK11061 94122009915 GAF domain; Region: GAF; pfam01590 94122009916 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 94122009917 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 94122009918 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 94122009919 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 94122009920 putative active site [active] 94122009921 Ap4A binding site [chemical binding]; other site 94122009922 nudix motif; other site 94122009923 putative metal binding site [ion binding]; other site 94122009924 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 94122009925 putative DNA-binding cleft [nucleotide binding]; other site 94122009926 putative DNA clevage site; other site 94122009927 molecular lever; other site 94122009928 cyclase homology domain; Region: CHD; cd07302 94122009929 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 94122009930 nucleotidyl binding site; other site 94122009931 metal binding site [ion binding]; metal-binding site 94122009932 dimer interface [polypeptide binding]; other site 94122009933 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122009934 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122009935 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 94122009936 dimerization interface [polypeptide binding]; other site 94122009937 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 94122009938 putative binding surface; other site 94122009939 active site 94122009940 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 94122009941 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 94122009942 FeS/SAM binding site; other site 94122009943 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 94122009944 Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The...; Region: GltS; cd00713 94122009945 active site 94122009946 dimer interface [polypeptide binding]; other site 94122009947 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 94122009948 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 94122009949 active site 94122009950 FMN binding site [chemical binding]; other site 94122009951 substrate binding site [chemical binding]; other site 94122009952 3Fe-4S cluster binding site [ion binding]; other site 94122009953 gltb_C. This domain is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS). GltS encodes a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the...; Region: gltB_C; cd00982 94122009954 domain interface; other site 94122009955 glutamate synthase small subunit family protein, proteobacterial; Region: gltD_gamma_fam; TIGR01318 94122009956 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 94122009957 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 94122009958 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 94122009959 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 94122009960 Cobalamin biosynthesis protein CobD/CbiB [Coenzyme metabolism]; Region: CbiB; COG1270 94122009961 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 94122009962 hypothetical protein; Provisional; Region: PRK10578 94122009963 UPF0126 domain; Region: UPF0126; pfam03458 94122009964 UPF0126 domain; Region: UPF0126; pfam03458 94122009965 SnoaL-like domain; Region: SnoaL_2; pfam12680 94122009966 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 94122009967 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 94122009968 active site 94122009969 HIGH motif; other site 94122009970 dimer interface [polypeptide binding]; other site 94122009971 KMSKS motif; other site 94122009972 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 94122009973 RNA binding surface [nucleotide binding]; other site 94122009974 putative peptidase; Provisional; Region: PRK11649 94122009975 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 94122009976 Peptidase family M23; Region: Peptidase_M23; pfam01551 94122009977 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 94122009978 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 94122009979 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 94122009980 DNA binding site [nucleotide binding] 94122009981 Periplasmic component of the Tol biopolymer transport system [Intracellular trafficking and secretion]; Region: TolB; COG0823 94122009982 tol-pal system beta propeller repeat protein TolB; Region: propeller_TolB; TIGR02800 94122009983 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 94122009984 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 94122009985 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 94122009986 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122009987 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal...; Region: MIP; cd00333 94122009988 amphipathic channel; other site 94122009989 Asn-Pro-Ala signature motifs; other site 94122009990 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 94122009991 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 94122009992 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cd00400 94122009993 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 94122009994 Cl- selectivity filter; other site 94122009995 Cl- binding residues [ion binding]; other site 94122009996 pore gating glutamate residue; other site 94122009997 dimer interface [polypeptide binding]; other site 94122009998 aspartate carbamoyltransferase; Provisional; Region: PRK08192 94122009999 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 94122010000 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 94122010001 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 94122010002 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 94122010003 inhibitor-cofactor binding pocket; inhibition site 94122010004 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122010005 catalytic residue [active] 94122010006 NHAD transporter family protein; Provisional; Region: PLN00137; cl17324 94122010007 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 94122010008 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 94122010009 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 94122010010 Walker A motif; other site 94122010011 ATP binding site [chemical binding]; other site 94122010012 Walker B motif; other site 94122010013 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 94122010014 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 94122010015 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 94122010016 active site 94122010017 NTP binding site [chemical binding]; other site 94122010018 metal binding triad [ion binding]; metal-binding site 94122010019 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 94122010020 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 94122010021 Zn2+ binding site [ion binding]; other site 94122010022 Mg2+ binding site [ion binding]; other site 94122010023 Murein lipoprotein [Cell envelope biogenesis, outer membrane]; Region: COG4238; cl11539 94122010024 23S rRNA methyltransferase A; Provisional; Region: rrmA; PRK11088 94122010025 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 94122010026 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 94122010027 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 94122010028 catalytic center binding site [active] 94122010029 ATP binding site [chemical binding]; other site 94122010030 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 94122010031 homooctamer interface [polypeptide binding]; other site 94122010032 active site 94122010033 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 94122010034 UGMP family protein; Validated; Region: PRK09604 94122010035 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 94122010036 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 94122010037 Yqey-like protein; Region: YqeY; pfam09424 94122010038 DNA primase; Validated; Region: dnaG; PRK05667 94122010039 CHC2 zinc finger; Region: zf-CHC2; pfam01807 94122010040 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 94122010041 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 94122010042 active site 94122010043 metal binding site [ion binding]; metal-binding site 94122010044 interdomain interaction site; other site 94122010045 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 94122010046 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; pfam08278 94122010047 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 94122010048 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 94122010049 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 94122010050 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 94122010051 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 94122010052 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 94122010053 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 94122010054 DNA binding residues [nucleotide binding] 94122010055 Cache domain; Region: Cache_1; pfam02743 94122010056 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 94122010057 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 94122010058 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122010059 dimer interface [polypeptide binding]; other site 94122010060 putative CheW interface [polypeptide binding]; other site 94122010061 dipeptide/tripeptide permease B; Provisional; Region: PRK10207 94122010062 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 94122010063 putative substrate translocation pore; other site 94122010064 POT family; Region: PTR2; cl17359 94122010065 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cd00347 94122010066 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 94122010067 probable oxidoreductase, LLM family; Region: LLM_2I7G; TIGR03858 94122010068 4-aminobutyrate aminotransferase; Validated; Region: PRK08088 94122010069 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 94122010070 inhibitor-cofactor binding pocket; inhibition site 94122010071 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122010072 catalytic residue [active] 94122010073 succinate-semialdehyde dehydrogenase I; Provisional; Region: gabD; PRK11241 94122010074 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 94122010075 tetramerization interface [polypeptide binding]; other site 94122010076 NAD(P) binding site [chemical binding]; other site 94122010077 catalytic residues [active] 94122010078 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 94122010079 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 94122010080 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 94122010081 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 94122010082 dimer interface [polypeptide binding]; other site 94122010083 conserved gate region; other site 94122010084 putative PBP binding loops; other site 94122010085 ABC-ATPase subunit interface; other site 94122010086 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 94122010087 dimer interface [polypeptide binding]; other site 94122010088 conserved gate region; other site 94122010089 putative PBP binding loops; other site 94122010090 ABC-ATPase subunit interface; other site 94122010091 putrescine transporter ATP-binding subunit; Provisional; Region: potG; PRK11607 94122010092 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122010093 Walker A/P-loop; other site 94122010094 ATP binding site [chemical binding]; other site 94122010095 Q-loop/lid; other site 94122010096 ABC transporter signature motif; other site 94122010097 Walker B; other site 94122010098 D-loop; other site 94122010099 H-loop/switch region; other site 94122010100 TOBE domain; Region: TOBE_2; pfam08402 94122010101 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 94122010102 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 94122010103 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 94122010104 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 94122010105 Peptidase C26; Region: Peptidase_C26; pfam07722 94122010106 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 94122010107 catalytic triad [active] 94122010108 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 94122010109 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 94122010110 non-specific DNA binding site [nucleotide binding]; other site 94122010111 salt bridge; other site 94122010112 sequence-specific DNA binding site [nucleotide binding]; other site 94122010113 Cupin domain; Region: Cupin_2; pfam07883 94122010114 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 94122010115 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 94122010116 Protein of unknown function (DUF2937); Region: DUF2937; pfam11157 94122010117 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 94122010118 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it...; Region: TST_Repeat_1; cd01448 94122010119 active site residue [active] 94122010120 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue; Region: TST_Repeat_2; cd01449 94122010121 active site residue [active] 94122010122 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 94122010123 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 94122010124 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; Provisional; Region: PRK09847 94122010125 Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like; Region: ALDH_GABALDH-PuuC; cd07112 94122010126 NAD(P) binding site [chemical binding]; other site 94122010127 catalytic residues [active] 94122010128 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 94122010129 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 94122010130 inhibitor-cofactor binding pocket; inhibition site 94122010131 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122010132 catalytic residue [active] 94122010133 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 94122010134 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 94122010135 tetrameric interface [polypeptide binding]; other site 94122010136 NAD binding site [chemical binding]; other site 94122010137 catalytic residues [active] 94122010138 Predicted enzyme of the cupin superfamily [General function prediction only]; Region: COG3450 94122010139 conserved hypothetical protein, proteobacterial; Region: gcw_chp; TIGR02001 94122010140 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 94122010141 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 94122010142 putative substrate translocation pore; other site 94122010143 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4299 94122010144 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 94122010145 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate. This is the first committed step in the biosynthetic pathway to...; Region: NagA; cd00854 94122010146 active site 94122010147 dimer interface [polypeptide binding]; other site 94122010148 Predicted phosphosugar isomerases [Cell envelope biogenesis, outer membrane]; Region: AgaS; COG2222 94122010149 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 94122010150 dimer interface [polypeptide binding]; other site 94122010151 active site 94122010152 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 94122010153 dimer interface [polypeptide binding]; other site 94122010154 active site 94122010155 Predicted N-acetylglucosamine kinase [Carbohydrate transport and metabolism]; Region: COG2971 94122010156 Putative carbohydrate binding domain; Region: CHB_HEX; smart01081 94122010157 The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a...; Region: GH20_Sm-chitobiase-like; cd06569 94122010158 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 94122010159 active site 94122010160 C-terminal Early set domain associated with the catalytic domain of chitobiase (also called N-acetylglucosaminidase); Region: E_set_Chitobiase_C; cd02847 94122010161 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 94122010162 dimerization interface [polypeptide binding]; other site 94122010163 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 94122010164 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122010165 dimer interface [polypeptide binding]; other site 94122010166 putative CheW interface [polypeptide binding]; other site 94122010167 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 94122010168 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 94122010169 Tryptophan halogenase; Region: Trp_halogenase; pfam04820 94122010170 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 94122010171 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122010172 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122010173 Transcriptional regulators [Transcription]; Region: PurR; COG1609 94122010174 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 94122010175 DNA binding site [nucleotide binding] 94122010176 domain linker motif; other site 94122010177 Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_SalR; cd01545 94122010178 putative ligand binding site [chemical binding]; other site 94122010179 putative dimerization interface [polypeptide binding]; other site 94122010180 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 94122010181 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 94122010182 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 94122010183 Nitrogen regulatory protein P-II; Region: P-II; smart00938 94122010184 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 94122010185 Type II transport protein GspH; Region: GspH; pfam12019 94122010186 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 94122010187 Type II transport protein GspH; Region: GspH; pfam12019 94122010188 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 94122010189 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 94122010190 Type IV pilin PilA; Region: Pilin_PilA; pfam14245 94122010191 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 94122010192 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 94122010193 PilX N-terminal; Region: PilX_N; pfam14341 94122010194 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 94122010195 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 94122010196 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 94122010197 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 94122010198 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 94122010199 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 94122010200 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 94122010201 lipoprotein signal peptidase; Provisional; Region: PRK14787 94122010202 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 94122010203 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 94122010204 active site 94122010205 HIGH motif; other site 94122010206 nucleotide binding site [chemical binding]; other site 94122010207 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 94122010208 active site 94122010209 KMSKS motif; other site 94122010210 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 94122010211 tRNA binding surface [nucleotide binding]; other site 94122010212 anticodon binding site; other site 94122010213 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 94122010214 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 94122010215 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 94122010216 active site 94122010217 Riboflavin kinase; Region: Flavokinase; smart00904 94122010218 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 94122010219 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 94122010220 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 94122010221 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 94122010222 dimerization interface [polypeptide binding]; other site 94122010223 putative DNA binding site [nucleotide binding]; other site 94122010224 putative Zn2+ binding site [ion binding]; other site 94122010225 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 94122010226 PA_M28_2: Protease-associated (PA) domain, peptidase family M28, subfamily-2. A subfamily of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions; Region: PA_M28_2; cd04815 94122010227 PA/protease or protease-like domain interface [polypeptide binding]; other site 94122010228 M28 Zn-Peptidase Plasma glutamate carboxypeptidase; Region: M28_Pgcp_like; cd03883 94122010229 Peptidase family M28; Region: Peptidase_M28; pfam04389 94122010230 metal binding site [ion binding]; metal-binding site 94122010231 hypothetical protein; Validated; Region: PRK02101 94122010232 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 94122010233 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 94122010234 putative phosphoketolase; Provisional; Region: PRK05261 94122010235 Thiamine pyrophosphate (TPP) family, Phosphoketolase (PK) subfamily, TPP-binding module; PK catalyzes the conversion of D-xylulose 5-phosphate and phosphate to acetyl phosphate, D-glyceraldehyde-3-phosphate and H2O. This enzyme requires divalent...; Region: TPP_PK; cd02011 94122010236 TPP-binding site; other site 94122010237 XFP C-terminal domain; Region: XFP_C; pfam09363 94122010238 outer membrane protein A; Reviewed; Region: PRK10808 94122010239 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 94122010240 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 94122010241 ligand binding site [chemical binding]; other site 94122010242 transaldolase-like protein; Provisional; Region: PTZ00411 94122010243 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 94122010244 active site 94122010245 dimer interface [polypeptide binding]; other site 94122010246 catalytic residue [active] 94122010247 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 94122010248 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 94122010249 active site 94122010250 dimer interface [polypeptide binding]; other site 94122010251 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 94122010252 dimer interface [polypeptide binding]; other site 94122010253 active site 94122010254 Protein of unknown function (DUF3545); Region: DUF3545; pfam12065 94122010255 Hemerythrin-like domain; Region: Hr-like; cd12108 94122010256 Fe binding site [ion binding]; other site 94122010257 RNA polymerase sigma factor; Provisional; Region: PRK12513 94122010258 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 94122010259 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cl17257 94122010260 DNA binding residues [nucleotide binding] 94122010261 von Willebrand factor; Region: vWF_A; pfam12450 94122010262 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG2304 94122010263 VWA subgroup: 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_subgroup; cd01465 94122010264 metal ion-dependent adhesion site (MIDAS); other site 94122010265 Domain of unknown function (DUF3520); Region: DUF3520; pfam12034 94122010266 putative transporter; Provisional; Region: PRK11660 94122010267 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 94122010268 Sulfate transporter family; Region: Sulfate_transp; pfam00916 94122010269 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 94122010270 Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]; Region: PurE; COG0041 94122010271 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 94122010272 ATP-grasp domain; Region: ATP-grasp; pfam02222 94122010273 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 94122010274 GAF domain; Region: GAF; pfam01590 94122010275 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122010276 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122010277 metal binding site [ion binding]; metal-binding site 94122010278 active site 94122010279 I-site; other site 94122010280 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 94122010281 N-acetyl-D-glucosamine binding site [chemical binding]; other site 94122010282 catalytic residue [active] 94122010283 glutamate--cysteine ligase; Provisional; Region: PRK02107 94122010284 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 94122010285 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 94122010286 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 94122010287 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 94122010288 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 94122010289 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 94122010290 Predicted membrane protein [Function unknown]; Region: COG1238 94122010291 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 94122010292 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 94122010293 Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, beta subunit [Energy production and conversion]; Region: OadB; COG1883 94122010294 oxaloacetate decarboxylase; Provisional; Region: PRK14040 94122010295 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 94122010296 active site 94122010297 catalytic residues [active] 94122010298 metal binding site [ion binding]; metal-binding site 94122010299 homodimer binding site [polypeptide binding]; other site 94122010300 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 94122010301 carboxyltransferase (CT) interaction site; other site 94122010302 biotinylation site [posttranslational modification]; other site 94122010303 Oxaloacetate decarboxylase, gamma chain; Region: OAD_gamma; pfam04277 94122010304 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 94122010305 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 94122010306 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 94122010307 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 94122010308 Clp amino terminal domain; Region: Clp_N; pfam02861 94122010309 Clp amino terminal domain; Region: Clp_N; pfam02861 94122010310 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 94122010311 Walker A motif; other site 94122010312 ATP binding site [chemical binding]; other site 94122010313 Walker B motif; other site 94122010314 arginine finger; other site 94122010315 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 94122010316 Walker A motif; other site 94122010317 ATP binding site [chemical binding]; other site 94122010318 Walker B motif; other site 94122010319 arginine finger; other site 94122010320 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 94122010321 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 94122010322 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 94122010323 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 94122010324 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 94122010325 RNA binding surface [nucleotide binding]; other site 94122010326 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 94122010327 active site 94122010328 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 94122010329 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 94122010330 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 94122010331 HAMP domain; Region: HAMP; pfam00672 94122010332 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122010333 dimer interface [polypeptide binding]; other site 94122010334 putative CheW interface [polypeptide binding]; other site 94122010335 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 94122010336 Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen...; Region: globin; cd01040 94122010337 heme-binding site [chemical binding]; other site 94122010338 FAD_NAD(P)H binding domain of flavohemoglobin. Flavohemoglobins have a globin domain containing a B-type heme fused with a ferredoxin reductase-like FAD/NAD-binding domain. Flavohemoglobins detoxify nitric oxide (NO) via an NO dioxygenase reaction. The...; Region: flavohem_like_fad_nad_binding; cd06184 94122010339 FAD binding pocket [chemical binding]; other site 94122010340 FAD binding motif [chemical binding]; other site 94122010341 phosphate binding motif [ion binding]; other site 94122010342 beta-alpha-beta structure motif; other site 94122010343 NAD binding pocket [chemical binding]; other site 94122010344 Heme binding pocket [chemical binding]; other site 94122010345 16S rRNA pseudouridylate synthase A; Provisional; Region: PRK10839 94122010346 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 94122010347 active site 94122010348 uracil binding [chemical binding]; other site 94122010349 Predicted transcriptional regulator [Transcription]; Region: COG2345 94122010350 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 94122010351 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 94122010352 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 94122010353 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 94122010354 active site 94122010355 metal binding site [ion binding]; metal-binding site 94122010356 YcxB-like protein; Region: YcxB; pfam14317 94122010357 GPR1/FUN34/yaaH family; Region: Grp1_Fun34_YaaH; cl00685 94122010358 MltA-interacting protein MipA; Region: MipA; pfam06629 94122010359 Protein of unknown function (DUF3019); Region: DUF3019; pfam11456 94122010360 DNA-binding transcriptional regulator RstA; Provisional; Region: PRK10701 94122010361 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122010362 active site 94122010363 phosphorylation site [posttranslational modification] 94122010364 intermolecular recognition site; other site 94122010365 dimerization interface [polypeptide binding]; other site 94122010366 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 94122010367 DNA binding site [nucleotide binding] 94122010368 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 94122010369 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 94122010370 dimer interface [polypeptide binding]; other site 94122010371 phosphorylation site [posttranslational modification] 94122010372 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 94122010373 ATP binding site [chemical binding]; other site 94122010374 Mg2+ binding site [ion binding]; other site 94122010375 G-X-G motif; other site 94122010376 Predicted Fe-S protein [General function prediction only]; Region: COG3313 94122010377 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 94122010378 cysteine synthase B; Region: cysM; TIGR01138 94122010379 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 94122010380 dimer interface [polypeptide binding]; other site 94122010381 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122010382 catalytic residue [active] 94122010383 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: CysP; COG4150 94122010384 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 94122010385 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 94122010386 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 94122010387 dimer interface [polypeptide binding]; other site 94122010388 conserved gate region; other site 94122010389 putative PBP binding loops; other site 94122010390 ABC-ATPase subunit interface; other site 94122010391 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 94122010392 dimer interface [polypeptide binding]; other site 94122010393 conserved gate region; other site 94122010394 putative PBP binding loops; other site 94122010395 ABC-ATPase subunit interface; other site 94122010396 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 94122010397 ATP-binding cassette domain of the sulfate transporter; Region: ABC_CysA_sulfate_importer; cd03296 94122010398 Walker A/P-loop; other site 94122010399 ATP binding site [chemical binding]; other site 94122010400 Q-loop/lid; other site 94122010401 ABC transporter signature motif; other site 94122010402 Walker B; other site 94122010403 D-loop; other site 94122010404 H-loop/switch region; other site 94122010405 TOBE-like domain; Region: TOBE_3; pfam12857 94122010406 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 94122010407 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 94122010408 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122010409 Protein of unknown function (DUF3302); Region: DUF3302; pfam11742 94122010410 Ycf46; Provisional; Region: ycf46; CHL00195 94122010411 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 94122010412 Walker A motif; other site 94122010413 ATP binding site [chemical binding]; other site 94122010414 Walker B motif; other site 94122010415 arginine finger; other site 94122010416 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 94122010417 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain; Region: 2-Hacid_dh_C; pfam02826 94122010418 ATP-grasp domain; Region: ATP-grasp; pfam02222 94122010419 Protein of unknown function (DUF3142); Region: DUF3142; pfam11340 94122010420 Tetratricopeptide repeat; Region: TPR_1; pfam00515 94122010421 glycerate dehydrogenase; Provisional; Region: PRK06487 94122010422 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_4; cd12162 94122010423 putative ligand binding site [chemical binding]; other site 94122010424 putative NAD binding site [chemical binding]; other site 94122010425 catalytic site [active] 94122010426 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 94122010427 Dna-J like membrane chaperone protein; Provisional; Region: djlA; PRK09430 94122010428 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 94122010429 putative metal binding site [ion binding]; other site 94122010430 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 94122010431 HSP70 interaction site [polypeptide binding]; other site 94122010432 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 94122010433 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 94122010434 Substrate binding site; other site 94122010435 metal-binding site 94122010436 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 94122010437 Phosphotransferase enzyme family; Region: APH; pfam01636 94122010438 LPS assembly outer membrane complex protein LptD; Provisional; Region: PRK03761 94122010439 OstA-like protein; Region: OstA; cl00844 94122010440 Organic solvent tolerance protein; Region: OstA_C; pfam04453 94122010441 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 94122010442 SurA N-terminal domain; Region: SurA_N; pfam09312 94122010443 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 94122010444 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 94122010445 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed; Region: pdxA; PRK00232 94122010446 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 94122010447 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 94122010448 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 94122010449 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 94122010450 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 94122010451 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 94122010452 active site 94122010453 metal binding site [ion binding]; metal-binding site 94122010454 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 94122010455 dimerization interface [polypeptide binding]; other site 94122010456 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 94122010457 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122010458 dimer interface [polypeptide binding]; other site 94122010459 putative CheW interface [polypeptide binding]; other site 94122010460 Protein of unknown function (DUF3718); Region: DUF3718; pfam12514 94122010461 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 94122010462 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 94122010463 NADP+ binding site [chemical binding]; other site 94122010464 folate binding site [chemical binding]; other site 94122010465 Protein of unknown function (DUF3815); Region: DUF3815; cl01118 94122010466 Uncharacterized conserved protein [Function unknown]; Region: COG2966 94122010467 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 94122010468 GTPase CgtA; Reviewed; Region: obgE; PRK12298 94122010469 GTP1/OBG; Region: GTP1_OBG; pfam01018 94122010470 Obg GTPase; Region: Obg; cd01898 94122010471 G1 box; other site 94122010472 GTP/Mg2+ binding site [chemical binding]; other site 94122010473 Switch I region; other site 94122010474 G2 box; other site 94122010475 G3 box; other site 94122010476 Switch II region; other site 94122010477 G4 box; other site 94122010478 G5 box; other site 94122010479 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 94122010480 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 94122010481 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 94122010482 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 94122010483 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 94122010484 substrate binding pocket [chemical binding]; other site 94122010485 chain length determination region; other site 94122010486 substrate-Mg2+ binding site; other site 94122010487 catalytic residues [active] 94122010488 aspartate-rich region 1; other site 94122010489 active site lid residues [active] 94122010490 aspartate-rich region 2; other site 94122010491 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 94122010492 ligand binding site [chemical binding]; other site 94122010493 active site 94122010494 UGI interface [polypeptide binding]; other site 94122010495 catalytic site [active] 94122010496 Protein of unknown function (DUF3144); Region: DUF3144; pfam11342 94122010497 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 94122010498 Carboxypeptidase C (cathepsin A) [Amino acid transport and metabolism]; Region: COG2939 94122010499 Serine carboxypeptidase; Region: Peptidase_S10; cl08270 94122010500 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 94122010501 DsbD alpha interface [polypeptide binding]; other site 94122010502 catalytic residues [active] 94122010503 PAS domain S-box; Region: sensory_box; TIGR00229 94122010504 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 94122010505 putative active site [active] 94122010506 heme pocket [chemical binding]; other site 94122010507 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 94122010508 phage shock protein operon transcriptional activator; Provisional; Region: pspF; PRK11608 94122010509 Walker A motif; other site 94122010510 ATP binding site [chemical binding]; other site 94122010511 Walker B motif; other site 94122010512 arginine finger; other site 94122010513 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 94122010514 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 94122010515 4Fe-4S binding domain; Region: Fer4_5; pfam12801 94122010516 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 94122010517 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 94122010518 Protein of unknown function (DUF3423); Region: DUF3423; pfam11903 94122010519 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 94122010520 active site 94122010521 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK05677 94122010522 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 94122010523 acyl-activating enzyme (AAE) consensus motif; other site 94122010524 putative AMP binding site [chemical binding]; other site 94122010525 putative active site [active] 94122010526 putative CoA binding site [chemical binding]; other site 94122010527 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 94122010528 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 94122010529 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122010530 Walker A/P-loop; other site 94122010531 ATP binding site [chemical binding]; other site 94122010532 Q-loop/lid; other site 94122010533 ABC transporter signature motif; other site 94122010534 Walker B; other site 94122010535 D-loop; other site 94122010536 H-loop/switch region; other site 94122010537 Putative heme iron utilization protein [Inorganic ion transport and metabolism]; Region: HugZ; COG0748 94122010538 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 94122010539 Haem utilisation ChuX/HutX; Region: ChuX_HutX; pfam06228 94122010540 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 94122010541 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122010542 N-terminal plug; other site 94122010543 ligand-binding site [chemical binding]; other site 94122010544 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 94122010545 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 94122010546 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 94122010547 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 94122010548 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 94122010549 intersubunit interface [polypeptide binding]; other site 94122010550 Class I aldolases; Region: Aldolase_Class_I; cl17187 94122010551 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 94122010552 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 94122010553 ABC-ATPase subunit interface; other site 94122010554 dimer interface [polypeptide binding]; other site 94122010555 putative PBP binding regions; other site 94122010556 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 94122010557 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 94122010558 Walker A/P-loop; other site 94122010559 ATP binding site [chemical binding]; other site 94122010560 Q-loop/lid; other site 94122010561 ABC transporter signature motif; other site 94122010562 Walker B; other site 94122010563 D-loop; other site 94122010564 H-loop/switch region; other site 94122010565 Protein of unknown function (DUF2956); Region: DUF2956; pfam11169 94122010566 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 94122010567 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 94122010568 Uncharacterized protein conserved in bacteria (DUF2131); Region: DUF2131; pfam09904 94122010569 Bacterial protein of unknown function (DUF924); Region: DUF924; pfam06041 94122010570 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 94122010571 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 94122010572 substrate binding pocket [chemical binding]; other site 94122010573 membrane-bound complex binding site; other site 94122010574 hinge residues; other site 94122010575 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 94122010576 Ligand Binding Site [chemical binding]; other site 94122010577 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 94122010578 Ligand Binding Site [chemical binding]; other site 94122010579 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 94122010580 aldehyde dehydrogenase family protein; Provisional; Region: PTZ00381 94122010581 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 94122010582 NAD(P) binding site [chemical binding]; other site 94122010583 catalytic residues [active] 94122010584 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 94122010585 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 94122010586 Curli production assembly/transport component CsgG; Region: CsgG; pfam03783 94122010587 Type VIII secretion system (T8SS), CsgF protein; Region: CsgF; cl08082 94122010588 Curli assembly protein CsgE; Region: CsgE; pfam10627 94122010589 HAMP domain; Region: HAMP; pfam00672 94122010590 nitrogen regulation protein NR(II); Provisional; Region: glnL; PRK11073 94122010591 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 94122010592 ATP binding site [chemical binding]; other site 94122010593 Mg2+ binding site [ion binding]; other site 94122010594 G-X-G motif; other site 94122010595 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 94122010596 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122010597 active site 94122010598 phosphorylation site [posttranslational modification] 94122010599 intermolecular recognition site; other site 94122010600 dimerization interface [polypeptide binding]; other site 94122010601 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 94122010602 Walker A motif; other site 94122010603 ATP binding site [chemical binding]; other site 94122010604 Walker B motif; other site 94122010605 arginine finger; other site 94122010606 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 94122010607 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 94122010608 FtsX-like permease family; Region: FtsX; pfam02687 94122010609 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 94122010610 FtsX-like permease family; Region: FtsX; pfam02687 94122010611 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 94122010612 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 94122010613 Walker A/P-loop; other site 94122010614 ATP binding site [chemical binding]; other site 94122010615 Q-loop/lid; other site 94122010616 ABC transporter signature motif; other site 94122010617 Walker B; other site 94122010618 D-loop; other site 94122010619 H-loop/switch region; other site 94122010620 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 94122010621 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 94122010622 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122010623 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 94122010624 active site 94122010625 substrate binding pocket [chemical binding]; other site 94122010626 dimer interface [polypeptide binding]; other site 94122010627 DMSO reductase family type II enzyme, molybdopterin subunit; Region: DMSO_red_II_alp; TIGR03479 94122010628 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 94122010629 Protein of unknown function (DUF3144); Region: DUF3144; pfam11342 94122010630 MAPEG family; Region: MAPEG; cl09190 94122010631 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122010632 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 94122010633 Coenzyme A binding pocket [chemical binding]; other site 94122010634 AAA domain; Region: AAA_33; pfam13671 94122010635 AAA domain; Region: AAA_17; pfam13207 94122010636 vitamin B12-transporter protein BtuF; Provisional; Region: PRK03379 94122010637 Cobalamin binding protein BtuF. These proteins have been shown to function as initial receptors in ABC transport of vitamin B12 (cobalamin) in eubacterial and some archaeal species. They belong to the TroA superfamily of helical backbone metal receptor...; Region: BtuF; cd01144 94122010638 cobalamin binding residues [chemical binding]; other site 94122010639 putative BtuC binding residues; other site 94122010640 dimer interface [polypeptide binding]; other site 94122010641 Uncharacterized conserved protein (DUF2235); Region: DUF2235; pfam09994 94122010642 Cob(I)alamin adenosyltransferase N terminal; Region: Co_AT_N; pfam12557 94122010643 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 94122010644 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer; Region: CobA_CobO_BtuR; cd00561 94122010645 homodimer interface [polypeptide binding]; other site 94122010646 Walker A motif; other site 94122010647 ATP binding site [chemical binding]; other site 94122010648 hydroxycobalamin binding site [chemical binding]; other site 94122010649 Walker B motif; other site 94122010650 cobyric acid synthase; Provisional; Region: PRK00784 94122010651 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 94122010652 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 94122010653 catalytic triad [active] 94122010654 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a...; Region: CobU; cd00544 94122010655 homotrimer interface [polypeptide binding]; other site 94122010656 Walker A motif; other site 94122010657 GTP binding site [chemical binding]; other site 94122010658 Walker B motif; other site 94122010659 cobalamin synthase; Reviewed; Region: cobS; PRK00235 94122010660 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 94122010661 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 94122010662 putative dimer interface [polypeptide binding]; other site 94122010663 active site pocket [active] 94122010664 putative cataytic base [active] 94122010665 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 94122010666 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 94122010667 ABC-ATPase subunit interface; other site 94122010668 dimer interface [polypeptide binding]; other site 94122010669 putative PBP binding regions; other site 94122010670 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 94122010671 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 94122010672 Walker A/P-loop; other site 94122010673 ATP binding site [chemical binding]; other site 94122010674 Q-loop/lid; other site 94122010675 ABC transporter signature motif; other site 94122010676 Walker B; other site 94122010677 D-loop; other site 94122010678 H-loop/switch region; other site 94122010679 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 94122010680 catalytic core [active] 94122010681 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 94122010682 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 94122010683 MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent...; Region: MeTr; cd00740 94122010684 substrate binding pocket [chemical binding]; other site 94122010685 B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy); Region: methionine_synthase_B12_BD; cd02069 94122010686 B12 binding site [chemical binding]; other site 94122010687 cobalt ligand [ion binding]; other site 94122010688 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 94122010689 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 94122010690 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 94122010691 putative major pilin subunit; Provisional; Region: PRK10574 94122010692 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 94122010693 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 94122010694 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 94122010695 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 94122010696 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 94122010697 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 94122010698 calcium/sodium:proton antiporter; Provisional; Region: PRK10599 94122010699 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 94122010700 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 94122010701 D-alanyl-D-alanine endopeptidase; Provisional; Region: pbpG; PRK11669 94122010702 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 94122010703 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122010704 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122010705 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 94122010706 dimerization interface [polypeptide binding]; other site 94122010707 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 94122010708 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 94122010709 active site 94122010710 metal binding site [ion binding]; metal-binding site 94122010711 Protein of unknown function (DUF2846); Region: DUF2846; pfam11008 94122010712 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 94122010713 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 94122010714 dimer interface [polypeptide binding]; other site 94122010715 putative anticodon binding site; other site 94122010716 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 94122010717 motif 1; other site 94122010718 active site 94122010719 motif 2; other site 94122010720 motif 3; other site 94122010721 peptide chain release factor 2; Validated; Region: prfB; PRK00578 94122010722 This domain is found in peptide chain release factors; Region: PCRF; smart00937 94122010723 RF-1 domain; Region: RF-1; pfam00472 94122010724 putative NADPH-dependent glutamate synthase small subunit; Provisional; Region: PRK12814 94122010725 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 94122010726 catalytic loop [active] 94122010727 iron binding site [ion binding]; other site 94122010728 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 94122010729 4Fe-4S binding domain; Region: Fer4_6; pfam12837 94122010730 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 94122010731 4Fe-4S binding domain; Region: Fer4; pfam00037 94122010732 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 94122010733 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_Formate-Dh-H; cd02753 94122010734 [4Fe-4S] binding site [ion binding]; other site 94122010735 molybdopterin cofactor binding site; other site 94122010736 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_CT_Formate-Dh_H; cd02790 94122010737 molybdopterin cofactor binding site; other site 94122010738 Cache domain; Region: Cache_2; pfam08269 94122010739 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 94122010740 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 94122010741 dimerization interface [polypeptide binding]; other site 94122010742 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122010743 dimer interface [polypeptide binding]; other site 94122010744 putative CheW interface [polypeptide binding]; other site 94122010745 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 94122010746 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 94122010747 Chromate transporter; Region: Chromate_transp; pfam02417 94122010748 Peptidase inhibitor I9; Region: Inhibitor_I9; pfam05922 94122010749 Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones]; Region: AprE; COG1404 94122010750 Peptidase S8 family domain, uncharacterized subfamily 3; Region: Peptidases_S8_3; cd04852 94122010751 active site 94122010752 catalytic triad [active] 94122010753 PA_subtilisin_like: Protease-associated domain containing subtilisin-like proteases. This group contains various PA domain-containing subtilisin-like proteases including melon cucumisin, Arabidopsis thaliana Ara12, a nodule specific serine protease from...; Region: PA_subtilisin_like; cd02120 94122010754 PA/protease or protease-like domain interface [polypeptide binding]; other site 94122010755 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 94122010756 catalytic residues [active] 94122010757 HTH-like domain; Region: HTH_21; pfam13276 94122010758 Integrase core domain; Region: rve; pfam00665 94122010759 Integrase core domain; Region: rve_3; pfam13683 94122010760 Peptidase inhibitor I9; Region: Inhibitor_I9; pfam05922 94122010761 Peptidase S8 family domain, uncharacterized subfamily 3; Region: Peptidases_S8_3; cd04852 94122010762 Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones]; Region: AprE; COG1404 94122010763 active site 94122010764 catalytic triad [active] 94122010765 PA_subtilisin_like: Protease-associated domain containing subtilisin-like proteases. This group contains various PA domain-containing subtilisin-like proteases including melon cucumisin, Arabidopsis thaliana Ara12, a nodule specific serine protease from...; Region: PA_subtilisin_like; cd02120 94122010766 PA/protease or protease-like domain interface [polypeptide binding]; other site 94122010767 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 94122010768 catalytic residues [active] 94122010769 MltA-interacting protein MipA; Region: MipA; cl01504 94122010770 Protein of unknown function (DUF3019); Region: DUF3019; pfam11456 94122010771 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 94122010772 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122010773 active site 94122010774 phosphorylation site [posttranslational modification] 94122010775 intermolecular recognition site; other site 94122010776 dimerization interface [polypeptide binding]; other site 94122010777 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 94122010778 DNA binding site [nucleotide binding] 94122010779 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 94122010780 dimer interface [polypeptide binding]; other site 94122010781 phosphorylation site [posttranslational modification] 94122010782 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 94122010783 ATP binding site [chemical binding]; other site 94122010784 Mg2+ binding site [ion binding]; other site 94122010785 G-X-G motif; other site 94122010786 23S rRNA methyluridine methyltransferase; Reviewed; Region: rumB; PRK03522 94122010787 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 94122010788 FAD dependent oxidoreductase; Region: DAO; pfam01266 94122010789 Transcriptional regulators [Transcription]; Region: MarR; COG1846 94122010790 MarR family; Region: MarR; pfam01047 94122010791 peroxiredoxin, Ohr subfamily; Region: organ_hyd_perox; TIGR03561 94122010792 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 94122010793 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 94122010794 Methyltransferase domain; Region: Methyltransf_31; pfam13847 94122010795 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 94122010796 S-adenosylmethionine binding site [chemical binding]; other site 94122010797 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cd08168 94122010798 heme-binding residues [chemical binding]; other site 94122010799 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 94122010800 L-aspartate oxidase; Provisional; Region: PRK06175 94122010801 D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains; Region: LDH_like_2; cd12183 94122010802 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 94122010803 putative ligand binding site [chemical binding]; other site 94122010804 putative NAD binding site [chemical binding]; other site 94122010805 catalytic site [active] 94122010806 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 94122010807 Domain of unknown function (DUF3332); Region: DUF3332; pfam11810 94122010808 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 94122010809 Mechanosensitive ion channel; Region: MS_channel; pfam00924 94122010810 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 94122010811 multifunctional aminopeptidase A; Provisional; Region: PRK00913 94122010812 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 94122010813 interface (dimer of trimers) [polypeptide binding]; other site 94122010814 Substrate-binding/catalytic site; other site 94122010815 Zn-binding sites [ion binding]; other site 94122010816 peroxiredoxin; Region: AhpC; TIGR03137 94122010817 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 94122010818 dimer interface [polypeptide binding]; other site 94122010819 decamer (pentamer of dimers) interface [polypeptide binding]; other site 94122010820 catalytic triad [active] 94122010821 peroxidatic and resolving cysteines [active] 94122010822 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 94122010823 Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the reduction...; Region: AhpF_NTD_N; cd02974 94122010824 catalytic residue [active] 94122010825 TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then...; Region: AhpF_NTD_C; cd03026 94122010826 catalytic residues [active] 94122010827 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 94122010828 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 94122010829 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 94122010830 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122010831 Coenzyme A binding pocket [chemical binding]; other site 94122010832 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 94122010833 DHH family; Region: DHH; pfam01368 94122010834 DHHA1 domain; Region: DHHA1; pfam02272 94122010835 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 94122010836 dimerization domain [polypeptide binding]; other site 94122010837 dimer interface [polypeptide binding]; other site 94122010838 catalytic residues [active] 94122010839 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 94122010840 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 94122010841 active site 94122010842 Int/Topo IB signature motif; other site 94122010843 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 94122010844 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 94122010845 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 94122010846 S-adenosylmethionine binding site [chemical binding]; other site 94122010847 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 94122010848 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122010849 active site 94122010850 phosphorylation site [posttranslational modification] 94122010851 intermolecular recognition site; other site 94122010852 dimerization interface [polypeptide binding]; other site 94122010853 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 94122010854 Zn2+ binding site [ion binding]; other site 94122010855 Mg2+ binding site [ion binding]; other site 94122010856 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 94122010857 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 94122010858 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 94122010859 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 94122010860 PAS domain S-box; Region: sensory_box; TIGR00229 94122010861 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 94122010862 putative active site [active] 94122010863 heme pocket [chemical binding]; other site 94122010864 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 94122010865 PAS fold; Region: PAS_3; pfam08447 94122010866 putative active site [active] 94122010867 heme pocket [chemical binding]; other site 94122010868 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 94122010869 dimer interface [polypeptide binding]; other site 94122010870 phosphorylation site [posttranslational modification] 94122010871 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 94122010872 ATP binding site [chemical binding]; other site 94122010873 Mg2+ binding site [ion binding]; other site 94122010874 G-X-G motif; other site 94122010875 Response regulator receiver domain; Region: Response_reg; pfam00072 94122010876 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122010877 active site 94122010878 phosphorylation site [posttranslational modification] 94122010879 intermolecular recognition site; other site 94122010880 dimerization interface [polypeptide binding]; other site 94122010881 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 94122010882 putative binding surface; other site 94122010883 active site 94122010884 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 94122010885 DEAD-like helicases superfamily; Region: DEXDc; smart00487 94122010886 ATP binding site [chemical binding]; other site 94122010887 Mg++ binding site [ion binding]; other site 94122010888 motif III; other site 94122010889 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 94122010890 nucleotide binding region [chemical binding]; other site 94122010891 ATP-binding site [chemical binding]; other site 94122010892 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 94122010893 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122010894 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 94122010895 Protein export membrane protein; Region: SecD_SecF; cl14618 94122010896 radical SAM protein, TatD family-associated; Region: tatD_link_rSAM; TIGR04038 94122010897 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 94122010898 FeS/SAM binding site; other site 94122010899 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 94122010900 PAS domain; Region: PAS_9; pfam13426 94122010901 putative active site [active] 94122010902 heme pocket [chemical binding]; other site 94122010903 PAS domain; Region: PAS_9; pfam13426 94122010904 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122010905 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 94122010906 DNA binding site [nucleotide binding] 94122010907 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 94122010908 DNA binding site [nucleotide binding] 94122010909 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 94122010910 NHAD transporter family protein; Provisional; Region: PLN00137; cl17324 94122010911 Protein of unknown function, DUF481; Region: DUF481; pfam04338 94122010912 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 94122010913 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 94122010914 intersubunit interface [polypeptide binding]; other site 94122010915 active site 94122010916 zinc binding site [ion binding]; other site 94122010917 Na+ binding site [ion binding]; other site 94122010918 Phosphoglycerate kinase; Region: PGK; pfam00162 94122010919 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 94122010920 substrate binding site [chemical binding]; other site 94122010921 hinge regions; other site 94122010922 ADP binding site [chemical binding]; other site 94122010923 catalytic site [active] 94122010924 erythrose 4-phosphate dehydrogenase; Provisional; Region: PRK13535 94122010925 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 94122010926 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 94122010927 transketolase; Reviewed; Region: PRK12753 94122010928 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 94122010929 TPP-binding site [chemical binding]; other site 94122010930 dimer interface [polypeptide binding]; other site 94122010931 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 94122010932 PYR/PP interface [polypeptide binding]; other site 94122010933 dimer interface [polypeptide binding]; other site 94122010934 TPP binding site [chemical binding]; other site 94122010935 S-adenosylmethionine synthetase; Validated; Region: PRK05250 94122010936 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 94122010937 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 94122010938 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 94122010939 Phosphotransferase system cellobiose-specific component IIC [Carbohydrate transport and metabolism]; Region: CelB; COG1455 94122010940 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 94122010941 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122010942 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122010943 metal binding site [ion binding]; metal-binding site 94122010944 active site 94122010945 I-site; other site 94122010946 META domain; Region: META; pfam03724 94122010947 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 94122010948 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 94122010949 Domain of unknown function (DUF4234); Region: DUF4234; pfam14018 94122010950 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 94122010951 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122010952 Coenzyme A binding pocket [chemical binding]; other site 94122010953 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 94122010954 serine transporter; Region: stp; TIGR00814 94122010955 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 94122010956 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 94122010957 Cephalosporin acylase (CA) belongs to a family of beta-lactam acylases that includes penicillin G acylase (PGA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and...; Region: Ntn_CA; cd01936 94122010958 active site 94122010959 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 94122010960 inosine/xanthosine triphosphatase; Reviewed; Region: PRK05074 94122010961 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 94122010962 MarR family; Region: MarR; pfam01047 94122010963 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122010964 Coenzyme A binding pocket [chemical binding]; other site 94122010965 Beta-lactamase; Region: Beta-lactamase; pfam00144 94122010966 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 94122010967 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 94122010968 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 94122010969 catalytic loop [active] 94122010970 iron binding site [ion binding]; other site 94122010971 Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+ oxidoreductase; Region: NADH_quinone_reductase; cd06188 94122010972 FAD binding pocket [chemical binding]; other site 94122010973 FAD binding motif [chemical binding]; other site 94122010974 phosphate binding motif [ion binding]; other site 94122010975 beta-alpha-beta structure motif; other site 94122010976 NAD binding pocket [chemical binding]; other site 94122010977 Na(+)-translocating NADH-quinone reductase subunit E; Provisional; Region: PRK02830 94122010978 Na(+)-translocating NADH-quinone reductase subunit D; Validated; Region: PRK09292 94122010979 Na(+)-translocating NADH-quinone reductase subunit C; Provisional; Region: PRK05346 94122010980 NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit; Region: nqrC; TIGR01938 94122010981 Na(+)-translocating NADH-quinone reductase subunit B; Provisional; Region: PRK05349 94122010982 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 94122010983 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 94122010984 E3 interaction surface; other site 94122010985 lipoyl attachment site [posttranslational modification]; other site 94122010986 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 94122010987 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 94122010988 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 94122010989 active site 94122010990 catalytic tetrad [active] 94122010991 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 94122010992 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_16; cd07263 94122010993 Uncharacterized protein family (UPF0167); Region: UPF0167; pfam03691 94122010994 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 94122010995 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 94122010996 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122010997 N-terminal plug; other site 94122010998 ligand-binding site [chemical binding]; other site 94122010999 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 94122011000 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 94122011001 ATP binding site [chemical binding]; other site 94122011002 Mg++ binding site [ion binding]; other site 94122011003 motif III; other site 94122011004 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 94122011005 nucleotide binding region [chemical binding]; other site 94122011006 ATP-binding site [chemical binding]; other site 94122011007 RNA recognition motif in Escherichia coli RNA helicase dbpA and similar proteins; Region: RRM_EcDbpA_like; cd12501 94122011008 putative RNA binding site [nucleotide binding]; other site 94122011009 Pirin-related protein [General function prediction only]; Region: COG1741 94122011010 Pirin; Region: Pirin; pfam02678 94122011011 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 94122011012 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 94122011013 conserved hypothetical metal-binding protein; Region: TIGR02443 94122011014 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 94122011015 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 94122011016 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 94122011017 ABC transporter; Region: ABC_tran_2; pfam12848 94122011018 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 94122011019 Protein of unknown function (DUF2390); Region: DUF2390; pfam09523 94122011020 Uncharacterized conserved protein [Function unknown]; Region: COG3791 94122011021 GMC oxidoreductase; Region: GMC_oxred_N; pfam00732 94122011022 dehydrogenase, Rv0697 family; Region: Rv0697; TIGR03970 94122011023 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 94122011024 putative hydrolase; Provisional; Region: PRK10985 94122011025 Uncharacterized protein family (UPF0270); Region: UPF0270; pfam06794 94122011026 phosphoribulokinase; Provisional; Region: PRK15453 94122011027 active site 94122011028 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 94122011029 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122011030 Coenzyme A binding pocket [chemical binding]; other site 94122011031 aminopeptidase B; Provisional; Region: PRK05015 94122011032 Peptidase; Region: DUF3663; pfam12404 94122011033 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 94122011034 interface (dimer of trimers) [polypeptide binding]; other site 94122011035 Substrate-binding/catalytic site; other site 94122011036 Zn-binding sites [ion binding]; other site 94122011037 putative DNA-binding transcriptional regulator; Reviewed; Region: PRK00347 94122011038 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 94122011039 glutamyl-Q tRNA(Asp) synthetase; Reviewed; Region: PRK05710 94122011040 active site 94122011041 HIGH motif; other site 94122011042 nucleotide binding site [chemical binding]; other site 94122011043 active site 94122011044 KMSKS motif; other site 94122011045 poly(A) polymerase; Region: pcnB; TIGR01942 94122011046 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 94122011047 active site 94122011048 NTP binding site [chemical binding]; other site 94122011049 metal binding triad [ion binding]; metal-binding site 94122011050 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 94122011051 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 94122011052 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 94122011053 catalytic center binding site [active] 94122011054 ATP binding site [chemical binding]; other site 94122011055 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 94122011056 oligomerization interface [polypeptide binding]; other site 94122011057 active site 94122011058 metal binding site [ion binding]; metal-binding site 94122011059 Pantoate-beta-alanine ligase; Region: PanC; cd00560 94122011060 pantoate--beta-alanine ligase; Region: panC; TIGR00018 94122011061 active site 94122011062 ATP-binding site [chemical binding]; other site 94122011063 pantoate-binding site; other site 94122011064 HXXH motif; other site 94122011065 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 94122011066 Peptidase inhibitor I9; Region: Inhibitor_I9; pfam05922 94122011067 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like; cd07473 94122011068 catalytic triad [active] 94122011069 putative active site [active] 94122011070 Proprotein convertase P-domain; Region: P_proprotein; pfam01483 94122011071 FOG: PKD repeat [General function prediction only]; Region: COG3291 94122011072 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cd00146 94122011073 Curlin associated repeat; Region: Curlin_rpt; pfam07012 94122011074 Curlin associated repeat; Region: Curlin_rpt; pfam07012 94122011075 curlin minor subunit CsgB; Provisional; Region: csgB; PRK10101 94122011076 curlin minor subunit CsgB; Provisional; Region: csgB; PRK10101 94122011077 Curlin associated repeat; Region: Curlin_rpt; pfam07012 94122011078 major curlin subunit; Provisional; Region: csgA; PRK10051 94122011079 Curlin associated repeat; Region: Curlin_rpt; pfam07012 94122011080 Curlin associated repeat; Region: Curlin_rpt; pfam07012 94122011081 Curlin associated repeat; Region: Curlin_rpt; pfam07012 94122011082 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 94122011083 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 94122011084 DNA binding residues [nucleotide binding] 94122011085 dimerization interface [polypeptide binding]; other site 94122011086 Predicted membrane protein (DUF2238); Region: DUF2238; pfam09997 94122011087 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 94122011088 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_3; cd12176 94122011089 ligand binding site [chemical binding]; other site 94122011090 NAD binding site [chemical binding]; other site 94122011091 tetramer interface [polypeptide binding]; other site 94122011092 catalytic site [active] 94122011093 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 94122011094 L-serine binding site [chemical binding]; other site 94122011095 ACT domain interface; other site 94122011096 putative global regulator; Reviewed; Region: PRK09559 94122011097 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 94122011098 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 94122011099 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122011100 active site 94122011101 phosphorylation site [posttranslational modification] 94122011102 intermolecular recognition site; other site 94122011103 dimerization interface [polypeptide binding]; other site 94122011104 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 94122011105 Zn2+ binding site [ion binding]; other site 94122011106 Mg2+ binding site [ion binding]; other site 94122011107 Cache domain; Region: Cache_1; pfam02743 94122011108 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 94122011109 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 94122011110 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 94122011111 putative active site [active] 94122011112 heme pocket [chemical binding]; other site 94122011113 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 94122011114 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 94122011115 putative active site [active] 94122011116 heme pocket [chemical binding]; other site 94122011117 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 94122011118 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 94122011119 putative active site [active] 94122011120 heme pocket [chemical binding]; other site 94122011121 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 94122011122 putative active site [active] 94122011123 heme pocket [chemical binding]; other site 94122011124 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 94122011125 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 94122011126 dimer interface [polypeptide binding]; other site 94122011127 phosphorylation site [posttranslational modification] 94122011128 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 94122011129 ATP binding site [chemical binding]; other site 94122011130 Mg2+ binding site [ion binding]; other site 94122011131 G-X-G motif; other site 94122011132 Response regulator receiver domain; Region: Response_reg; pfam00072 94122011133 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122011134 active site 94122011135 phosphorylation site [posttranslational modification] 94122011136 intermolecular recognition site; other site 94122011137 dimerization interface [polypeptide binding]; other site 94122011138 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122011139 Response regulator receiver domain; Region: Response_reg; pfam00072 94122011140 active site 94122011141 phosphorylation site [posttranslational modification] 94122011142 intermolecular recognition site; other site 94122011143 dimerization interface [polypeptide binding]; other site 94122011144 FOG: HPt domain [Signal transduction mechanisms]; Region: ArcB; COG2198 94122011145 putative binding surface; other site 94122011146 active site 94122011147 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 94122011148 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 94122011149 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 94122011150 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 94122011151 Walker A/P-loop; other site 94122011152 ATP binding site [chemical binding]; other site 94122011153 Q-loop/lid; other site 94122011154 ABC transporter signature motif; other site 94122011155 Walker B; other site 94122011156 D-loop; other site 94122011157 H-loop/switch region; other site 94122011158 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 94122011159 FtsX-like permease family; Region: FtsX; pfam02687 94122011160 Hydroxyneurosporene synthase (CrtC); Region: CrtC; pfam07143 94122011161 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 94122011162 Type II transport protein GspH; Region: GspH; pfam12019 94122011163 Tfp pilus assembly protein PilV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilV; COG4967 94122011164 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 94122011165 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 94122011166 NapD protein; Region: NapD; pfam03927 94122011167 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 94122011168 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_Nitrate-R-NapA-like; cd02754 94122011169 [4Fe-4S] binding site [ion binding]; other site 94122011170 molybdopterin cofactor binding site; other site 94122011171 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 94122011172 molybdopterin cofactor binding site; other site 94122011173 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 94122011174 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 94122011175 4Fe-4S binding domain; Region: Fer4_5; pfam12801 94122011176 4Fe-4S binding domain; Region: Fer4_5; pfam12801 94122011177 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; pfam03892 94122011178 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122011179 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122011180 The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; Region: PBP2_CidR; cd08438 94122011181 putative dimerization interface [polypeptide binding]; other site 94122011182 elongation factor G; Reviewed; Region: PRK00007 94122011183 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 94122011184 G1 box; other site 94122011185 putative GEF interaction site [polypeptide binding]; other site 94122011186 GTP/Mg2+ binding site [chemical binding]; other site 94122011187 Switch I region; other site 94122011188 G2 box; other site 94122011189 G3 box; other site 94122011190 Switch II region; other site 94122011191 G4 box; other site 94122011192 G5 box; other site 94122011193 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 94122011194 Elongation Factor G-like domain IV. This family includes the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria), ribosomal protection proteins that mediate tetracycline resistance and, an evolutionarily...; Region: EFG_like_IV; cl02789 94122011195 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 94122011196 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 94122011197 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 94122011198 substrate binding pocket [chemical binding]; other site 94122011199 membrane-bound complex binding site; other site 94122011200 hinge residues; other site 94122011201 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122011202 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122011203 metal binding site [ion binding]; metal-binding site 94122011204 active site 94122011205 I-site; other site 94122011206 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 94122011207 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 94122011208 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 94122011209 ATP-grasp domain; Region: ATP-grasp_4; cl17255 94122011210 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 94122011211 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 94122011212 carboxyltransferase (CT) interaction site; other site 94122011213 biotinylation site [posttranslational modification]; other site 94122011214 LysR family transcriptional regulator; Provisional; Region: PRK14997 94122011215 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122011216 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 94122011217 putative effector binding pocket; other site 94122011218 dimerization interface [polypeptide binding]; other site 94122011219 Beta-lactamase class D [Defense mechanisms]; Region: COG2602 94122011220 Pyroglutamyl peptidase (PGP) type I, also known as pyrrolidone carboxyl peptidase (pcp) type I: Enzymes responsible for cleaving pyroglutamate (pGlu) from the N-terminal end of specialized proteins. The N-terminal pGlu protects these proteins from...; Region: Peptidase_C15; cl00237 94122011221 putative substrate binding pocket [chemical binding]; other site 94122011222 AC domain interface; other site 94122011223 catalytic triad [active] 94122011224 AB domain interface; other site 94122011225 hypothetical protein; Provisional; Region: PRK04860 94122011226 Zn-dependent metalloprotease, SprT family [General function prediction only]; Region: SprT; COG3091 94122011227 Endonuclease I [DNA replication, recombination, and repair]; Region: EndA; COG2356 94122011228 RNA methyltransferase, RsmE family; Region: TIGR00046 94122011229 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 94122011230 glutathione synthetase; Provisional; Region: PRK05246 94122011231 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 94122011232 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 94122011233 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cd00016 94122011234 dimer interface [polypeptide binding]; other site 94122011235 Alkaline phosphatase homologues; Region: alkPPc; smart00098 94122011236 active site 94122011237 16S ribosomal RNA m2G1207 methyltransferase; Provisional; Region: rsmC; PRK09489 94122011238 Methyltransferase small domain N-terminal; Region: MTS_N; pfam08468 94122011239 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 94122011240 S-adenosylmethionine binding site [chemical binding]; other site 94122011241 Protein of unknown function (DUF342); Region: DUF342; pfam03961 94122011242 protein structure with unknown function; Region: DUF4144; pfam13642 94122011243 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_2; cd06160 94122011244 Peptidase family M50; Region: Peptidase_M50; pfam02163 94122011245 active site 94122011246 putative substrate binding region [chemical binding]; other site 94122011247 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 94122011248 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 94122011249 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 94122011250 Walker A/P-loop; other site 94122011251 ATP binding site [chemical binding]; other site 94122011252 Q-loop/lid; other site 94122011253 ABC transporter signature motif; other site 94122011254 Walker B; other site 94122011255 D-loop; other site 94122011256 H-loop/switch region; other site 94122011257 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 94122011258 FtsX-like permease family; Region: FtsX; pfam02687 94122011259 macrolide transporter subunit MacA; Provisional; Region: PRK11578 94122011260 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 94122011261 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122011262 Poly(3-hydroxybutyrate) depolymerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: LpqC; COG3509 94122011263 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 94122011264 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122011265 N-terminal plug; other site 94122011266 ligand-binding site [chemical binding]; other site 94122011267 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 94122011268 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122011269 active site 94122011270 phosphorylation site [posttranslational modification] 94122011271 intermolecular recognition site; other site 94122011272 dimerization interface [polypeptide binding]; other site 94122011273 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 94122011274 DNA binding residues [nucleotide binding] 94122011275 dimerization interface [polypeptide binding]; other site 94122011276 Na+/proline symporter [Amino acid transport and metabolism / General function prediction only]; Region: PutP; COG0591 94122011277 Na binding site [ion binding]; other site 94122011278 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 94122011279 PAS fold; Region: PAS_7; pfam12860 94122011280 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 94122011281 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 94122011282 dimer interface [polypeptide binding]; other site 94122011283 phosphorylation site [posttranslational modification] 94122011284 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 94122011285 ATP binding site [chemical binding]; other site 94122011286 Mg2+ binding site [ion binding]; other site 94122011287 G-X-G motif; other site 94122011288 Response regulator receiver domain; Region: Response_reg; pfam00072 94122011289 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122011290 active site 94122011291 phosphorylation site [posttranslational modification] 94122011292 intermolecular recognition site; other site 94122011293 dimerization interface [polypeptide binding]; other site 94122011294 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 94122011295 Major Facilitator Superfamily; Region: MFS_1; pfam07690 94122011296 putative substrate translocation pore; other site 94122011297 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 94122011298 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 94122011299 substrate binding pocket [chemical binding]; other site 94122011300 amidase; Validated; Region: PRK06565 94122011301 Amidase; Region: Amidase; cl11426 94122011302 Amidase; Region: Amidase; cl11426 94122011303 agmatine deiminase; Provisional; Region: PRK13551 94122011304 agmatine deiminase; Region: agmatine_aguA; TIGR03380 94122011305 3-hydroxybutyrate dehydrogenase; Provisional; Region: PRK12429 94122011306 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 94122011307 NAD(P) binding site [chemical binding]; other site 94122011308 active site 94122011309 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 94122011310 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 94122011311 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 94122011312 CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_N_terminal_like; cd03312 94122011313 THF binding site; other site 94122011314 CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_C_terminal_like; cd03311 94122011315 substrate binding site [chemical binding]; other site 94122011316 THF binding site; other site 94122011317 zinc-binding site [ion binding]; other site 94122011318 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122011319 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122011320 The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; Region: PBP2_MetR; cd08441 94122011321 putative dimerization interface [polypeptide binding]; other site 94122011322 HDOD domain; Region: HDOD; pfam08668 94122011323 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 94122011324 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122011325 N-terminal plug; other site 94122011326 ligand-binding site [chemical binding]; other site 94122011327 Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton]; Region: ATS1; COG5184 94122011328 nuc_hydro_IU_UC_XIUA: inosine-uridine preferring, xanthosine-inosine-uridine-adenosine-preferring and, uridine-cytidine preferring nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the...; Region: nuc_hydro_IU_UC_XIUA; cd02651 94122011329 active site 94122011330 tetramer interface [polypeptide binding]; other site 94122011331 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 94122011332 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides...; Region: ribokinase; cd01174 94122011333 substrate binding site [chemical binding]; other site 94122011334 dimer interface [polypeptide binding]; other site 94122011335 ATP binding site [chemical binding]; other site 94122011336 azurin; Region: azurin; TIGR02695 94122011337 Protein of unknown function (DUF3622); Region: DUF3622; pfam12286 94122011338 Glycerophosphodiester phosphodiesterase domain similar to Escherichia coli periplasmic phosphodiesterase (GlpQ) include uncharacterized proteins; Region: GDPD_EcGlpQ_like_1; cd08560 94122011339 putative active site [active] 94122011340 catalytic site [active] 94122011341 putative metal binding site [ion binding]; other site 94122011342 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 94122011343 active site 94122011344 PhoD-like phosphatase; Region: PhoD; pfam09423 94122011345 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 94122011346 putative active site [active] 94122011347 putative metal binding site [ion binding]; other site 94122011348 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 94122011349 FOG: CBS domain [General function prediction only]; Region: COG0517 94122011350 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_15; cd04803 94122011351 Domain of unknown function (DUF4274); Region: DUF4274; pfam14096 94122011352 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_8; cd13134 94122011353 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 94122011354 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 94122011355 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 94122011356 substrate binding pocket [chemical binding]; other site 94122011357 Cupin superfamily (DUF985); Region: Cupin_5; pfam06172 94122011358 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122011359 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122011360 metal binding site [ion binding]; metal-binding site 94122011361 active site 94122011362 I-site; other site 94122011363 YcaO domain protein; Region: TIGR03549 94122011364 OsmC-like protein; Region: OsmC; pfam02566 94122011365 YcaO-like family; Region: YcaO; pfam02624 94122011366 Cache domain; Region: Cache_2; pfam08269 94122011367 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 94122011368 dimerization interface [polypeptide binding]; other site 94122011369 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 94122011370 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122011371 dimer interface [polypeptide binding]; other site 94122011372 putative CheW interface [polypeptide binding]; other site 94122011373 Ribosome recycling factor; Region: RRF_GI; pfam12614 94122011374 Protein of unknown function (DUF3297); Region: DUF3297; pfam11730 94122011375 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 94122011376 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 94122011377 glycine dehydrogenase; Provisional; Region: PRK05367 94122011378 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 94122011379 tetramer interface [polypeptide binding]; other site 94122011380 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122011381 catalytic residue [active] 94122011382 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 94122011383 tetramer interface [polypeptide binding]; other site 94122011384 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122011385 catalytic residue [active] 94122011386 glycine cleavage system protein H; Provisional; Region: PRK13380 94122011387 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 94122011388 lipoyl attachment site [posttranslational modification]; other site 94122011389 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 94122011390 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 94122011391 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 94122011392 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 94122011393 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 94122011394 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 94122011395 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 94122011396 Cell division protein ZapA; Region: ZapA; pfam05164 94122011397 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 94122011398 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212; cl00360 94122011399 dihydromonapterin reductase; Provisional; Region: PRK06483 94122011400 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 94122011401 NAD(P) binding site [chemical binding]; other site 94122011402 active site 94122011403 Protein of unknown function, DUF393; Region: DUF393; pfam04134 94122011404 malate dehydrogenase; Provisional; Region: PRK05086 94122011405 Glyoxysomal and mitochondrial malate dehydrogenases; Region: MDH_glyoxysomal_mitochondrial; cd01337 94122011406 NAD binding site [chemical binding]; other site 94122011407 dimerization interface [polypeptide binding]; other site 94122011408 Substrate binding site [chemical binding]; other site 94122011409 arginine repressor; Provisional; Region: PRK05066 94122011410 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 94122011411 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 94122011412 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 94122011413 NADH(P)-binding; Region: NAD_binding_10; pfam13460 94122011414 NAD binding site [chemical binding]; other site 94122011415 substrate binding site [chemical binding]; other site 94122011416 putative active site [active] 94122011417 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122011418 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122011419 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 94122011420 putative effector binding pocket; other site 94122011421 dimerization interface [polypeptide binding]; other site 94122011422 Dyp-type peroxidase family; Region: Dyp_perox; cl01067 94122011423 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 94122011424 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 94122011425 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 94122011426 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 94122011427 Walker A/P-loop; other site 94122011428 ATP binding site [chemical binding]; other site 94122011429 Q-loop/lid; other site 94122011430 ABC transporter signature motif; other site 94122011431 Walker B; other site 94122011432 D-loop; other site 94122011433 H-loop/switch region; other site 94122011434 TOBE domain; Region: TOBE_2; pfam08402 94122011435 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 94122011436 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 94122011437 dimer interface [polypeptide binding]; other site 94122011438 conserved gate region; other site 94122011439 putative PBP binding loops; other site 94122011440 ABC-ATPase subunit interface; other site 94122011441 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 94122011442 dimer interface [polypeptide binding]; other site 94122011443 conserved gate region; other site 94122011444 putative PBP binding loops; other site 94122011445 ABC-ATPase subunit interface; other site 94122011446 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 94122011447 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 94122011448 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 94122011449 GST_N family, unknown subfamily 3; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_3; cd03049 94122011450 putative C-terminal domain interface [polypeptide binding]; other site 94122011451 putative GSH binding site (G-site) [chemical binding]; other site 94122011452 putative dimer interface [polypeptide binding]; other site 94122011453 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 94122011454 substrate binding pocket (H-site) [chemical binding]; other site 94122011455 N-terminal domain interface [polypeptide binding]; other site 94122011456 ferredoxin-NADP reductase; Provisional; Region: PRK10926 94122011457 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 94122011458 FAD binding pocket [chemical binding]; other site 94122011459 FAD binding motif [chemical binding]; other site 94122011460 phosphate binding motif [ion binding]; other site 94122011461 beta-alpha-beta structure motif; other site 94122011462 NAD binding pocket [chemical binding]; other site 94122011463 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 94122011464 catalytic core [active] 94122011465 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 94122011466 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 94122011467 active site 94122011468 FMN binding site [chemical binding]; other site 94122011469 substrate binding site [chemical binding]; other site 94122011470 3Fe-4S cluster binding site [ion binding]; other site 94122011471 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 94122011472 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 94122011473 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122011474 Walker A/P-loop; other site 94122011475 ATP binding site [chemical binding]; other site 94122011476 Q-loop/lid; other site 94122011477 ABC transporter signature motif; other site 94122011478 Walker B; other site 94122011479 D-loop; other site 94122011480 H-loop/switch region; other site 94122011481 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 94122011482 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 94122011483 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 94122011484 binding surface 94122011485 TPR motif; other site 94122011486 TPR repeat; Region: TPR_11; pfam13414 94122011487 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 94122011488 binding surface 94122011489 TPR motif; other site 94122011490 probable ammonium transporter, marine subtype; Region: marine_trans_1; TIGR03644 94122011491 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 94122011492 Nitrogen regulatory protein P-II; Region: P-II; smart00938 94122011493 Isochorismatase family; Region: Isochorismatase; pfam00857 94122011494 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 94122011495 catalytic triad [active] 94122011496 dimer interface [polypeptide binding]; other site 94122011497 conserved cis-peptide bond; other site 94122011498 LysE type translocator; Region: LysE; cl00565 94122011499 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 94122011500 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 94122011501 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 94122011502 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 94122011503 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cd00016 94122011504 Alkaline phosphatase homologues; Region: alkPPc; smart00098 94122011505 active site 94122011506 dimer interface [polypeptide binding]; other site 94122011507 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cd00016 94122011508 dimer interface [polypeptide binding]; other site 94122011509 Alkaline phosphatase homologues; Region: alkPPc; smart00098 94122011510 active site 94122011511 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 94122011512 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122011513 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 94122011514 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 94122011515 putative active site [active] 94122011516 heme pocket [chemical binding]; other site 94122011517 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122011518 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122011519 metal binding site [ion binding]; metal-binding site 94122011520 active site 94122011521 I-site; other site 94122011522 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 94122011523 DNA-binding site [nucleotide binding]; DNA binding site 94122011524 RNA-binding motif; other site 94122011525 Excalibur calcium-binding domain; Region: Excalibur; pfam05901 94122011526 Peptidase inhibitor I9; Region: Inhibitor_I9; pfam05922 94122011527 Peptidase S8 family domain, uncharacterized subfamily 3; Region: Peptidases_S8_3; cd04852 94122011528 active site 94122011529 catalytic triad [active] 94122011530 PA_subtilisin_like: Protease-associated domain containing subtilisin-like proteases. This group contains various PA domain-containing subtilisin-like proteases including melon cucumisin, Arabidopsis thaliana Ara12, a nodule specific serine protease from...; Region: PA_subtilisin_like; cd02120 94122011531 PA/protease or protease-like domain interface [polypeptide binding]; other site 94122011532 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 94122011533 catalytic residues [active] 94122011534 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 94122011535 catalytic residues [active] 94122011536 putative molybdenum transport ATP-binding protein ModF; Provisional; Region: PRK10938 94122011537 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122011538 ABC transporter signature motif; other site 94122011539 Walker B; other site 94122011540 D-loop; other site 94122011541 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122011542 Walker A/P-loop; other site 94122011543 ATP binding site [chemical binding]; other site 94122011544 Q-loop/lid; other site 94122011545 ABC transporter signature motif; other site 94122011546 Walker B; other site 94122011547 D-loop; other site 94122011548 H-loop/switch region; other site 94122011549 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 94122011550 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 94122011551 dimer interface [polypeptide binding]; other site 94122011552 active site 94122011553 heme binding site [chemical binding]; other site 94122011554 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 94122011555 Protein of unknown function (DUF2999); Region: DUF2999; pfam11212 94122011556 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 94122011557 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 94122011558 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 94122011559 motif II; other site 94122011560 Oxygen tolerance; Region: BatD; pfam13584 94122011561 hypothetical protein; Provisional; Region: PRK13685 94122011562 von Willebrand factor type A domain; Region: VWA_2; pfam13519 94122011563 metal ion-dependent adhesion site (MIDAS); other site 94122011564 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 94122011565 metal ion-dependent adhesion site (MIDAS); other site 94122011566 Domain of unknown function (DUF4381); Region: DUF4381; pfam14316 94122011567 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 94122011568 Protein of unknown function DUF58; Region: DUF58; pfam01882 94122011569 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 94122011570 metal ion-dependent adhesion site (MIDAS); other site 94122011571 MoxR-like ATPases [General function prediction only]; Region: COG0714 94122011572 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 94122011573 Walker A motif; other site 94122011574 ATP binding site [chemical binding]; other site 94122011575 Walker B motif; other site 94122011576 arginine finger; other site 94122011577 anaerobic sulfatase-maturating enzyme; Region: sulfatase_rSAM; TIGR03942 94122011578 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 94122011579 FeS/SAM binding site; other site 94122011580 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 94122011581 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122011582 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122011583 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 94122011584 putative substrate binding pocket [chemical binding]; other site 94122011585 putative dimerization interface [polypeptide binding]; other site 94122011586 Uncharacterized subfamily of N-terminal LabA-like domains; Region: LabA_like_N_1; cd11297 94122011587 putative metal binding site [ion binding]; other site 94122011588 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cd10146 94122011589 Domain of unknown function (DUF4277); Region: DUF4277; pfam14104 94122011590 Transposase [DNA replication, recombination, and repair]; Region: COG5421 94122011591 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 94122011592 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 94122011593 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 94122011594 ring oligomerisation interface [polypeptide binding]; other site 94122011595 ATP/Mg binding site [chemical binding]; other site 94122011596 stacking interactions; other site 94122011597 hinge regions; other site 94122011598 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 94122011599 oligomerisation interface [polypeptide binding]; other site 94122011600 mobile loop; other site 94122011601 roof hairpin; other site 94122011602 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 94122011603 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 94122011604 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122011605 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122011606 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 94122011607 putative effector binding pocket; other site 94122011608 dimerization interface [polypeptide binding]; other site 94122011609 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 94122011610 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122011611 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 94122011612 FxsA cytoplasmic membrane protein; Region: FxsA; pfam04186 94122011613 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 94122011614 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 94122011615 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 94122011616 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 94122011617 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 94122011618 DsbD alpha interface [polypeptide binding]; other site 94122011619 catalytic residues [active] 94122011620 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 94122011621 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 94122011622 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 94122011623 TrkA-N domain; Region: TrkA_N; pfam02254 94122011624 galactokinase; Provisional; Region: PRK05101 94122011625 Galactokinase galactose-binding signature; Region: GalKase_gal_bdg; pfam10509 94122011626 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 94122011627 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 94122011628 active site 94122011629 catalytic residues [active] 94122011630 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 94122011631 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 94122011632 NAD(P) binding site [chemical binding]; other site 94122011633 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 94122011634 Leucine rich repeat; Region: LRR_8; pfam13855 94122011635 Leucine rich repeat; Region: LRR_8; pfam13855 94122011636 Protein kinase domain; Region: Pkinase; pfam00069 94122011637 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 94122011638 active site 94122011639 ATP binding site [chemical binding]; other site 94122011640 substrate binding site [chemical binding]; other site 94122011641 activation loop (A-loop); other site 94122011642 MltD lipid attachment motif; Region: MLTD_N; pfam06474 94122011643 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 94122011644 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 94122011645 N-acetyl-D-glucosamine binding site [chemical binding]; other site 94122011646 catalytic residue [active] 94122011647 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 94122011648 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 94122011649 DNA-binding transcriptional regulator YidZ; Provisional; Region: PRK10216 94122011650 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122011651 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 94122011652 substrate binding pocket [chemical binding]; other site 94122011653 dimerization interface [polypeptide binding]; other site 94122011654 multidrug efflux system protein MdtL; Provisional; Region: PRK10473 94122011655 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 94122011656 putative substrate translocation pore; other site 94122011657 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 94122011658 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 94122011659 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 94122011660 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 94122011661 Domain of unknown function (DUF4234); Region: DUF4234; pfam14018 94122011662 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 94122011663 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 94122011664 dimer interface [polypeptide binding]; other site 94122011665 ssDNA binding site [nucleotide binding]; other site 94122011666 tetramer (dimer of dimers) interface [polypeptide binding]; other site 94122011667 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 94122011668 Major Facilitator Superfamily; Region: MFS_1; pfam07690 94122011669 putative substrate translocation pore; other site 94122011670 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 94122011671 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 94122011672 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 94122011673 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 94122011674 M28 Zn-Peptidases; Region: M28_like_2; cd05662 94122011675 Peptidase family M28; Region: Peptidase_M28; pfam04389 94122011676 metal binding site [ion binding]; metal-binding site 94122011677 ATP-dependent RNA helicase DeaD; Provisional; Region: PRK11634 94122011678 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 94122011679 ATP binding site [chemical binding]; other site 94122011680 Mg++ binding site [ion binding]; other site 94122011681 motif III; other site 94122011682 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 94122011683 nucleotide binding region [chemical binding]; other site 94122011684 ATP-binding site [chemical binding]; other site 94122011685 RNA recognition motif in Escherichia coli cold-shock DEAD box protein A (CsdA) and similar proteins; Region: RRM_EcCsdA_like; cd12499 94122011686 putative RNA binding site [nucleotide binding]; other site 94122011687 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 94122011688 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 94122011689 putative substrate translocation pore; other site 94122011690 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122011691 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122011692 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 94122011693 dimerization interface [polypeptide binding]; other site 94122011694 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 94122011695 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 94122011696 active site 94122011697 catalytic tetrad [active] 94122011698 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 94122011699 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 94122011700 active site 94122011701 motif I; other site 94122011702 motif II; other site 94122011703 rarD protein; Region: rarD; TIGR00688 94122011704 EamA-like transporter family; Region: EamA; pfam00892 94122011705 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 94122011706 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 94122011707 Cysteine-rich CWC; Region: Cys_rich_CWC; pfam14375 94122011708 Cytochrome c [Energy production and conversion]; Region: COG3258 94122011709 Cytochrome c; Region: Cytochrom_C; pfam00034 94122011710 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 94122011711 Cytochrome c; Region: Cytochrom_C; cl11414 94122011712 Cytochrome c; Region: Cytochrom_C; pfam00034 94122011713 Protein of unknown function (DUF2955); Region: DUF2955; pfam11168 94122011714 multidrug resistance protein MdtN; Provisional; Region: PRK10476 94122011715 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 94122011716 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122011717 transcriptional regulator SlyA; Provisional; Region: PRK03573 94122011718 Winged helix DNA-binding domain; Region: HTH_27; pfam13463 94122011719 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 94122011720 dimerization interface [polypeptide binding]; other site 94122011721 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 94122011722 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122011723 dimer interface [polypeptide binding]; other site 94122011724 putative CheW interface [polypeptide binding]; other site 94122011725 Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase...; Region: MTHFR; cd00537 94122011726 FAD binding site [chemical binding]; other site 94122011727 bifunctional aspartate kinase II/homoserine dehydrogenase II; Provisional; Region: metL; PRK09466 94122011728 AAK_AK-HSDH: Amino Acid Kinase Superfamily (AAK), AK-HSDH; this CD includes the N-terminal catalytic domain of aspartokinase (AK) of the bifunctional enzyme AK - homoserine dehydrogenase (HSDH). These aspartokinases are found in bacteria (E. coli...; Region: AAK_AK-HSDH; cd04257 94122011729 putative catalytic residues [active] 94122011730 putative nucleotide binding site [chemical binding]; other site 94122011731 putative aspartate binding site [chemical binding]; other site 94122011732 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 94122011733 O-succinylhomoserine (thiol)-lyase; Region: O_succ_thio_ly; TIGR02080 94122011734 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 94122011735 homodimer interface [polypeptide binding]; other site 94122011736 substrate-cofactor binding pocket; other site 94122011737 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122011738 catalytic residue [active] 94122011739 Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox'...; Region: Met_repressor_MetJ; cd00490 94122011740 dimerization interface [polypeptide binding]; other site 94122011741 DNA binding site [nucleotide binding] 94122011742 corepressor binding sites; other site 94122011743 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 94122011744 Polysulphide reductase, NrfD; Region: NrfD; pfam03916 94122011745 cytochrome c nitrite reductase, NrfD subunit; Region: cyt_nit_nrfD; TIGR03148 94122011746 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 94122011747 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 94122011748 thiosulfate reductase PhsA; Provisional; Region: PRK15488 94122011749 The MopB_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme...; Region: MopB_Thiosulfate-R-like; cd02755 94122011750 putative [Fe4-S4] binding site [ion binding]; other site 94122011751 putative molybdopterin cofactor binding site [chemical binding]; other site 94122011752 The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme...; Region: MopB_CT_Thiosulfate-R-like; cd02778 94122011753 putative molybdopterin cofactor binding site; other site 94122011754 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 94122011755 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 94122011756 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 94122011757 ATP binding site [chemical binding]; other site 94122011758 active site 94122011759 substrate binding site [chemical binding]; other site 94122011760 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 94122011761 Uncharacterized conserved protein [Function unknown]; Region: COG2968 94122011762 oxidative stress defense protein; Provisional; Region: PRK11087 94122011763 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 94122011764 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 94122011765 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 94122011766 FeS/SAM binding site; other site 94122011767 Domain of unknown function; Region: DUF331; pfam03889 94122011768 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 94122011769 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 94122011770 substrate binding pocket [chemical binding]; other site 94122011771 membrane-bound complex binding site; other site 94122011772 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 94122011773 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 94122011774 peptidase PmbA; Provisional; Region: PRK11040 94122011775 hypothetical protein; Provisional; Region: PRK05255 94122011776 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 94122011777 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 94122011778 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 94122011779 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 94122011780 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 94122011781 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 94122011782 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 94122011783 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 94122011784 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 94122011785 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122011786 Outer membrane efflux protein; Region: OEP; pfam02321 94122011787 Outer membrane efflux protein; Region: OEP; pfam02321 94122011788 protease TldD; Provisional; Region: tldD; PRK10735 94122011789 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 94122011790 putative active site [active] 94122011791 catalytic triad [active] 94122011792 dimer interface [polypeptide binding]; other site 94122011793 TIGR02099 family protein; Region: TIGR02099 94122011794 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 94122011795 ribonuclease G; Provisional; Region: PRK11712 94122011796 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 94122011797 homodimer interface [polypeptide binding]; other site 94122011798 oligonucleotide binding site [chemical binding]; other site 94122011799 Maf-like protein; Region: Maf; pfam02545 94122011800 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 94122011801 active site 94122011802 dimer interface [polypeptide binding]; other site 94122011803 rod shape-determining protein MreD; Region: MreD; cl01087 94122011804 rod shape-determining protein MreC; Region: mreC; TIGR00219 94122011805 rod shape-determining protein MreC; Region: MreC; pfam04085 94122011806 rod shape-determining protein MreB; Provisional; Region: PRK13927 94122011807 MreB and similar proteins; Region: MreB_like; cd10225 94122011808 nucleotide binding site [chemical binding]; other site 94122011809 Mg binding site [ion binding]; other site 94122011810 putative protofilament interaction site [polypeptide binding]; other site 94122011811 RodZ interaction site [polypeptide binding]; other site 94122011812 legume lectins; Region: lectin_L-type; cl14058 94122011813 homotetramer interaction site [polypeptide binding]; other site 94122011814 homodimer interaction site [polypeptide binding]; other site 94122011815 carbohydrate binding site [chemical binding]; other site 94122011816 metal binding site [ion binding]; metal-binding site 94122011817 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 94122011818 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 94122011819 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 94122011820 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 94122011821 Domain of unknown function (DUF4277); Region: DUF4277; pfam14104 94122011822 Transposase [DNA replication, recombination, and repair]; Region: COG5421 94122011823 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 94122011824 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 94122011825 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 94122011826 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 94122011827 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 94122011828 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 94122011829 Walker A motif; other site 94122011830 ATP binding site [chemical binding]; other site 94122011831 Walker B motif; other site 94122011832 Tetratricopeptide repeat; Region: TPR_16; pfam13432 94122011833 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 94122011834 TPR motif; other site 94122011835 binding surface 94122011836 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 94122011837 binding surface 94122011838 TPR motif; other site 94122011839 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 94122011840 AAA ATPase domain; Region: AAA_16; pfam13191 94122011841 Secretin N-terminal domain; Region: Secretin_N_2; pfam07655 94122011842 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 94122011843 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 94122011844 Type IV pilus biogenesis; Region: Pilus_PilP; pfam11356 94122011845 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 94122011846 type II secretion system protein L; Region: typeII_sec_gspL; TIGR01709 94122011847 regulatory protein CsrD; Provisional; Region: PRK11059 94122011848 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122011849 metal binding site [ion binding]; metal-binding site 94122011850 active site 94122011851 I-site; other site 94122011852 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 94122011853 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 94122011854 Malic enzyme, N-terminal domain; Region: malic; pfam00390 94122011855 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 94122011856 putative NAD(P) binding site [chemical binding]; other site 94122011857 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 94122011858 FimV N-terminal domain; Region: FimV_core; TIGR03505 94122011859 primosome assembly protein PriA; Validated; Region: PRK05580 94122011860 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 94122011861 ATP binding site [chemical binding]; other site 94122011862 putative Mg++ binding site [ion binding]; other site 94122011863 helicase superfamily c-terminal domain; Region: HELICc; smart00490 94122011864 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 94122011865 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 94122011866 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 94122011867 active site 94122011868 HIGH motif; other site 94122011869 KMSK motif region; other site 94122011870 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 94122011871 tRNA binding surface [nucleotide binding]; other site 94122011872 anticodon binding site; other site 94122011873 Cell division protein [Cell division and chromosome partitioning]; Region: FtsN; COG3087 94122011874 Sporulation related domain; Region: SPOR; pfam05036 94122011875 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 94122011876 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 94122011877 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 94122011878 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 94122011879 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 94122011880 Nucleoside-specific channel-forming protein, Tsx; Region: Channel_Tsx; cl04114 94122011881 uridine phosphorylase; Provisional; Region: PRK11178 94122011882 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 94122011883 Protein of unknown function (DUF465); Region: DUF465; cl01070 94122011884 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 94122011885 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 94122011886 dimer interface [polypeptide binding]; other site 94122011887 active site 94122011888 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 94122011889 catalytic residues [active] 94122011890 substrate binding site [chemical binding]; other site 94122011891 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 94122011892 Mechanosensitive ion channel; Region: MS_channel; pfam00924 94122011893 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 94122011894 Sel1-like repeats; Region: SEL1; smart00671 94122011895 Sel1-like repeats; Region: SEL1; smart00671 94122011896 Sel1-like repeats; Region: SEL1; smart00671 94122011897 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122011898 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122011899 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 94122011900 dimerization interface [polypeptide binding]; other site 94122011901 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 94122011902 classical (c) SDRs; Region: SDR_c; cd05233 94122011903 NAD(P) binding site [chemical binding]; other site 94122011904 active site 94122011905 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 94122011906 Protein of unknown function (DUF3373); Region: DUF3373; pfam11853 94122011907 Mite allergen Blo t 5; Region: Blo-t-5; pfam11642 94122011908 octaheme c-type cytochrome, tetrathionate reductase family; Region: octaheme_Shew; TIGR04315 94122011909 Cytochrome c bacterial; Region: Cytochrome_cB; pfam11783 94122011910 Putative catalytic domain of Synechocystis sp. Sll1306 protein and other bacterial homologs; Region: CE4_Sll1306_like; cd10978 94122011911 putative urate catabolism protein; Region: uraD_N-term-dom; TIGR03212 94122011912 putative active site [active] 94122011913 putative catalytic site [active] 94122011914 SnoaL-like polyketide cyclase; Region: SnoaL; pfam07366 94122011915 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122011916 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122011917 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 94122011918 putative effector binding pocket; other site 94122011919 dimerization interface [polypeptide binding]; other site 94122011920 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 94122011921 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 94122011922 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 94122011923 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 94122011924 ATP binding site [chemical binding]; other site 94122011925 Mg2+ binding site [ion binding]; other site 94122011926 G-X-G motif; other site 94122011927 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 94122011928 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122011929 active site 94122011930 phosphorylation site [posttranslational modification] 94122011931 intermolecular recognition site; other site 94122011932 dimerization interface [polypeptide binding]; other site 94122011933 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 94122011934 DNA binding residues [nucleotide binding] 94122011935 dimerization interface [polypeptide binding]; other site 94122011936 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 94122011937 active site 94122011938 HslU subunit interaction site [polypeptide binding]; other site 94122011939 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 94122011940 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 94122011941 Walker A motif; other site 94122011942 ATP binding site [chemical binding]; other site 94122011943 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 94122011944 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 94122011945 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3536 94122011946 Domain of unknown function (DUF4375); Region: DUF4375; pfam14300 94122011947 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 94122011948 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 94122011949 C factor cell-cell signaling protein; Provisional; Region: PRK09009 94122011950 carbonyl reductase sniffer-like, classical (c) SDRs; Region: carb_red_sniffer_like_SDR_c; cd05325 94122011951 NADP binding site [chemical binding]; other site 94122011952 homodimer interface [polypeptide binding]; other site 94122011953 active site 94122011954 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 94122011955 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122011956 active site 94122011957 phosphorylation site [posttranslational modification] 94122011958 intermolecular recognition site; other site 94122011959 dimerization interface [polypeptide binding]; other site 94122011960 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 94122011961 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 94122011962 ATP binding site [chemical binding]; other site 94122011963 Mg2+ binding site [ion binding]; other site 94122011964 G-X-G motif; other site 94122011965 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 94122011966 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 94122011967 NADP binding site [chemical binding]; other site 94122011968 active site 94122011969 putative substrate binding site [chemical binding]; other site 94122011970 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 94122011971 metal binding site [ion binding]; metal-binding site 94122011972 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 94122011973 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 94122011974 pseudouridine synthase, RluA family; Region: rluA_subfam; TIGR00005 94122011975 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 94122011976 active site 94122011977 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 94122011978 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 94122011979 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122011980 N-terminal plug; other site 94122011981 ligand-binding site [chemical binding]; other site 94122011982 Domain of unknown function (DUF386); Region: DUF386; cl01047 94122011983 putative manganese-dependent inorganic pyrophosphatase; Provisional; Region: PRK05427 94122011984 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 94122011985 DHHA2 domain; Region: DHHA2; pfam02833 94122011986 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 94122011987 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 94122011988 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 94122011989 Glycosyl transferase family 1; Region: Glyco_trans_1_3; pfam13528 94122011990 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 94122011991 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 94122011992 active site 94122011993 ribonuclease activity regulator protein RraA; Provisional; Region: PRK09372 94122011994 Formimidoylglutamase or HutE; Region: Formimidoylglutamase; cd09988 94122011995 putative active site [active] 94122011996 putative metal binding site [ion binding]; other site 94122011997 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 94122011998 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 94122011999 S-adenosylmethionine binding site [chemical binding]; other site 94122012000 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 94122012001 SCP-2 sterol transfer family; Region: SCP2; pfam02036 94122012002 putative ubiquinone biosynthesis protein UbiB; Reviewed; Region: ubiB; PRK04750 94122012003 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 94122012004 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 94122012005 sec-independent translocase; Provisional; Region: PRK01770 94122012006 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 94122012007 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 94122012008 active site 94122012009 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 94122012010 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 94122012011 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122012012 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122012013 metal binding site [ion binding]; metal-binding site 94122012014 active site 94122012015 I-site; other site 94122012016 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS_aspartate_rich; cd04823 94122012017 dimer interface [polypeptide binding]; other site 94122012018 allosteric magnesium binding site [ion binding]; other site 94122012019 active site 94122012020 aspartate-rich active site metal binding site; other site 94122012021 Schiff base residues; other site 94122012022 preprotein translocase subunit SecA; Reviewed; Region: PRK13107 94122012023 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 94122012024 SEC-C motif; Region: SEC-C; pfam02810 94122012025 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 94122012026 Peptidase family M23; Region: Peptidase_M23; pfam01551 94122012027 Protein of unknown function (DUF721); Region: DUF721; cl02324 94122012028 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 94122012029 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 94122012030 cell division protein FtsZ; Validated; Region: PRK09330 94122012031 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 94122012032 nucleotide binding site [chemical binding]; other site 94122012033 SulA interaction site; other site 94122012034 cell division protein FtsA; Reviewed; Region: ftsA; PRK09472 94122012035 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 94122012036 nucleotide binding site [chemical binding]; other site 94122012037 Cell division protein FtsA; Region: FtsA; pfam14450 94122012038 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 94122012039 Cell division protein FtsQ; Region: FtsQ; pfam03799 94122012040 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 94122012041 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 94122012042 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 94122012043 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 94122012044 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 94122012045 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 94122012046 active site 94122012047 homodimer interface [polypeptide binding]; other site 94122012048 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 94122012049 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03803 94122012050 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 94122012051 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 94122012052 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 94122012053 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 94122012054 Mg++ binding site [ion binding]; other site 94122012055 putative catalytic motif [active] 94122012056 putative substrate binding site [chemical binding]; other site 94122012057 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed; Region: murF; PRK10773 94122012058 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 94122012059 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 94122012060 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 94122012061 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 94122012062 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 94122012063 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 94122012064 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 94122012065 peptidoglycan synthase FtsI; Provisional; Region: PRK15105 94122012066 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 94122012067 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 94122012068 Cell division protein FtsL; Region: FtsL; pfam04999 94122012069 MraW methylase family; Region: Methyltransf_5; pfam01795 94122012070 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 94122012071 cell division protein MraZ; Reviewed; Region: PRK00326 94122012072 MraZ protein; Region: MraZ; pfam02381 94122012073 MraZ protein; Region: MraZ; pfam02381 94122012074 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 94122012075 glycerol kinase; Provisional; Region: glpK; PRK00047 94122012076 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 94122012077 N- and C-terminal domain interface [polypeptide binding]; other site 94122012078 active site 94122012079 MgATP binding site [chemical binding]; other site 94122012080 catalytic site [active] 94122012081 metal binding site [ion binding]; metal-binding site 94122012082 glycerol binding site [chemical binding]; other site 94122012083 homotetramer interface [polypeptide binding]; other site 94122012084 homodimer interface [polypeptide binding]; other site 94122012085 FBP binding site [chemical binding]; other site 94122012086 protein IIAGlc interface [polypeptide binding]; other site 94122012087 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; pfam03349 94122012088 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 94122012089 Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate...; Region: IPMI_Swivel; cd01577 94122012090 substrate binding site [chemical binding]; other site 94122012091 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 94122012092 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 94122012093 substrate binding site [chemical binding]; other site 94122012094 ligand binding site [chemical binding]; other site 94122012095 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 94122012096 tartrate dehydrogenase; Region: TTC; TIGR02089 94122012097 2-isopropylmalate synthase; Validated; Region: PRK00915 94122012098 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 94122012099 active site 94122012100 catalytic residues [active] 94122012101 metal binding site [ion binding]; metal-binding site 94122012102 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 94122012103 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122012104 metal binding site [ion binding]; metal-binding site 94122012105 active site 94122012106 I-site; other site 94122012107 ATP-dependent DNA helicase RecQ; Provisional; Region: PRK11057 94122012108 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 94122012109 ATP binding site [chemical binding]; other site 94122012110 putative Mg++ binding site [ion binding]; other site 94122012111 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 94122012112 nucleotide binding region [chemical binding]; other site 94122012113 ATP-binding site [chemical binding]; other site 94122012114 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 94122012115 HRDC domain; Region: HRDC; pfam00570 94122012116 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 94122012117 CoenzymeA binding site [chemical binding]; other site 94122012118 subunit interaction site [polypeptide binding]; other site 94122012119 PHB binding site; other site 94122012120 putative chloramphenical resistance permease RarD; Provisional; Region: PRK15430 94122012121 N-acetylglutamate synthase; Validated; Region: PRK05279 94122012122 AAK_NAGS-ABP: N-acetylglutamate (NAG) kinase-like domain of the NAG Synthase (NAGS) of the arginine-biosynthesis pathway (ABP) found in gamma- and beta-proteobacteria and higher plant chloroplasts. Domain architecture of these NAGS consisted of an...; Region: AAK_NAGS-ABP; cd04237 94122012123 putative feedback inhibition sensing region; other site 94122012124 putative nucleotide binding site [chemical binding]; other site 94122012125 putative substrate binding site [chemical binding]; other site 94122012126 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122012127 Coenzyme A binding pocket [chemical binding]; other site 94122012128 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 94122012129 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 94122012130 hypothetical protein; Reviewed; Region: PRK00024 94122012131 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 94122012132 MPN+ (JAMM) motif; other site 94122012133 Zinc-binding site [ion binding]; other site 94122012134 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 94122012135 Flavoprotein; Region: Flavoprotein; pfam02441 94122012136 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 94122012137 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 94122012138 trimer interface [polypeptide binding]; other site 94122012139 active site 94122012140 division inhibitor protein; Provisional; Region: slmA; PRK09480 94122012141 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 94122012142 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 94122012143 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 94122012144 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 94122012145 GTP cyclohydrolase I; Provisional; Region: PLN03044 94122012146 active site 94122012147 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 94122012148 active site 94122012149 ribonuclease PH; Reviewed; Region: rph; PRK00173 94122012150 Ribonuclease PH; Region: RNase_PH_bact; cd11362 94122012151 hexamer interface [polypeptide binding]; other site 94122012152 active site 94122012153 hypothetical protein; Provisional; Region: PRK11820 94122012154 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 94122012155 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 94122012156 integrase; Provisional; Region: PRK09692 94122012157 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 94122012158 active site 94122012159 Int/Topo IB signature motif; other site 94122012160 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 94122012161 Protein of unknown function (DUF3296); Region: DUF3296; pfam11726 94122012162 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 94122012163 ligand binding site [chemical binding]; other site 94122012164 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 94122012165 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 94122012166 ATP binding site [chemical binding]; other site 94122012167 putative Mg++ binding site [ion binding]; other site 94122012168 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cl17351 94122012169 nucleotide binding region [chemical binding]; other site 94122012170 ATP-binding site [chemical binding]; other site 94122012171 Restriction endonuclease; Region: Mrr_cat; pfam04471 94122012172 Protein of unknown function DUF45; Region: DUF45; pfam01863 94122012173 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 94122012174 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 94122012175 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 94122012176 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 94122012177 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 94122012178 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 94122012179 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 94122012180 HsdM N-terminal domain; Region: HsdM_N; pfam12161 94122012181 Methyltransferase domain; Region: Methyltransf_26; pfam13659 94122012182 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 94122012183 active site 94122012184 GIY-YIG domain of uncharacterized proteins from bacteria and their eukaryotic homologs; Region: GIY-YIG_COG3680; cd10440 94122012185 GIY-YIG motif/motif A; other site 94122012186 putative active site [active] 94122012187 putative metal binding site [ion binding]; other site 94122012188 dUMP phosphatase; Provisional; Region: PRK09449 94122012189 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 94122012190 motif II; other site 94122012191 Protein of unknown function, DUF606; Region: DUF606; pfam04657 94122012192 Protein of unknown function, DUF606; Region: DUF606; pfam04657 94122012193 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122012194 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122012195 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 94122012196 putative effector binding pocket; other site 94122012197 dimerization interface [polypeptide binding]; other site 94122012198 Uncharacterized conserved protein (DUF2075); Region: DUF2075; pfam09848 94122012199 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 94122012200 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 94122012201 non-specific DNA binding site [nucleotide binding]; other site 94122012202 salt bridge; other site 94122012203 sequence-specific DNA binding site [nucleotide binding]; other site 94122012204 Fic family protein [Function unknown]; Region: COG3177 94122012205 Domain of unknown function (DUF4172); Region: DUF4172; pfam13776 94122012206 Fic/DOC family; Region: Fic; pfam02661 94122012207 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cl17326 94122012208 putative DNA binding helix; other site 94122012209 Sulfotransferase family; Region: Sulfotransfer_3; pfam13469 94122012210 Major Facilitator Superfamily; Region: MFS_1; pfam07690 94122012211 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 94122012212 putative substrate translocation pore; other site 94122012213 Phosphotransferase enzyme family; Region: APH; pfam01636 94122012214 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 94122012215 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 94122012216 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 94122012217 active site 94122012218 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 94122012219 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 94122012220 catalytic site [active] 94122012221 G-X2-G-X-G-K; other site 94122012222 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 94122012223 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional; Region: PRK11092 94122012224 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 94122012225 Zn2+ binding site [ion binding]; other site 94122012226 Mg2+ binding site [ion binding]; other site 94122012227 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 94122012228 synthetase active site [active] 94122012229 NTP binding site [chemical binding]; other site 94122012230 metal binding site [ion binding]; metal-binding site 94122012231 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 94122012232 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 94122012233 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 94122012234 homotrimer interaction site [polypeptide binding]; other site 94122012235 putative active site [active] 94122012236 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 94122012237 Bacterial long-chain fatty acid CoA synthetase (LC-FACS), including Marinobacter hydrocarbonoclasticus isoprenoid Coenzyme A synthetase; Region: LC_FACS_bac; cd05932 94122012238 acyl-activating enzyme (AAE) consensus motif; other site 94122012239 putative AMP binding site [chemical binding]; other site 94122012240 putative active site [active] 94122012241 putative CoA binding site [chemical binding]; other site 94122012242 putative calcium/sodium:proton antiporter; Provisional; Region: PRK10734 94122012243 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 94122012244 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 94122012245 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 94122012246 Histidine kinase; Region: HisKA_3; pfam07730 94122012247 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 94122012248 ATP binding site [chemical binding]; other site 94122012249 Mg2+ binding site [ion binding]; other site 94122012250 G-X-G motif; other site 94122012251 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 94122012252 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122012253 active site 94122012254 phosphorylation site [posttranslational modification] 94122012255 intermolecular recognition site; other site 94122012256 dimerization interface [polypeptide binding]; other site 94122012257 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 94122012258 DNA binding residues [nucleotide binding] 94122012259 dimerization interface [polypeptide binding]; other site 94122012260 Domain of unknown function (DUF1963); Region: DUF1963; cl01600 94122012261 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 94122012262 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 94122012263 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 94122012264 Walker A motif; other site 94122012265 ATP binding site [chemical binding]; other site 94122012266 Walker B motif; other site 94122012267 arginine finger; other site 94122012268 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 94122012269 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 94122012270 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 94122012271 putative acyl-acceptor binding pocket; other site 94122012272 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 94122012273 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 94122012274 putative acyl-acceptor binding pocket; other site 94122012275 Uncharacterized conserved protein [Function unknown]; Region: COG1683 94122012276 Transcriptional regulators [Transcription]; Region: GntR; COG1802 94122012277 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 94122012278 DNA-binding site [nucleotide binding]; DNA binding site 94122012279 FCD domain; Region: FCD; pfam07729 94122012280 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 94122012281 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 94122012282 tetramer interface [polypeptide binding]; other site 94122012283 active site 94122012284 Mg2+/Mn2+ binding site [ion binding]; other site 94122012285 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 94122012286 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 94122012287 dimer interface [polypeptide binding]; other site 94122012288 active site 94122012289 citrylCoA binding site [chemical binding]; other site 94122012290 oxalacetate/citrate binding site [chemical binding]; other site 94122012291 coenzyme A binding site [chemical binding]; other site 94122012292 catalytic triad [active] 94122012293 2-methylisocitrate dehydratase, Fe/S-dependent; Region: 2met_isocit_dHY; TIGR02333 94122012294 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 94122012295 substrate binding site [chemical binding]; other site 94122012296 ligand binding site [chemical binding]; other site 94122012297 Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme...; Region: Aconitase_swivel; cl00215 94122012298 substrate binding site [chemical binding]; other site 94122012299 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 94122012300 carbohydrate-binding modules from Bacteroides thetaiotaomicron SusE, SusF and similar proteins; Region: CBM_SusE-F_like; cl17376 94122012301 starch binding site [chemical binding]; other site 94122012302 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 94122012303 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 94122012304 PAS domain S-box; Region: sensory_box; TIGR00229 94122012305 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 94122012306 putative active site [active] 94122012307 heme pocket [chemical binding]; other site 94122012308 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 94122012309 PAS domain; Region: PAS_9; pfam13426 94122012310 putative active site [active] 94122012311 heme pocket [chemical binding]; other site 94122012312 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122012313 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122012314 metal binding site [ion binding]; metal-binding site 94122012315 active site 94122012316 I-site; other site 94122012317 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 94122012318 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 94122012319 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and...; Region: BCAT_beta_family; cd01557 94122012320 homodimer interface [polypeptide binding]; other site 94122012321 substrate-cofactor binding pocket; other site 94122012322 catalytic residue [active] 94122012323 Protein of unknown function (DUF1223); Region: DUF1223; pfam06764 94122012324 Modulator of Rho-dependent transcription termination (ROF); Region: ROF; pfam07073 94122012325 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_2; cd06150 94122012326 homotrimer interaction site [polypeptide binding]; other site 94122012327 putative active site [active] 94122012328 Na+/H+ antiporter family; Region: Na_H_antiporter; pfam03553 94122012329 Protein of unknown function (DUF1107); Region: DUF1107; pfam06526 94122012330 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 94122012331 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 94122012332 catalytic residues [active] 94122012333 hinge region; other site 94122012334 alpha helical domain; other site 94122012335 serine/threonine protein kinase; Provisional; Region: PRK11768 94122012336 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 94122012337 Protein of unknown function (DUF3630); Region: DUF3630; pfam12305 94122012338 Uncharacterized conserved protein [Function unknown]; Region: COG0397 94122012339 hypothetical protein; Validated; Region: PRK00029 94122012340 DsrE/DsrF-like family; Region: DrsE; cl00672 94122012341 Nitrous oxide-stimulated promoter; Region: YgbA_NO; pfam11756 94122012342 The SYLF domain (also called DUF500), a novel lipid-binding module; Region: SYLF; cd11524 94122012343 putative amphipathic alpha helix; other site 94122012344 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 94122012345 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 94122012346 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122012347 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 94122012348 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 94122012349 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 94122012350 Bacterial transcriptional repressor; Region: TetR_C_6; pfam13977 94122012351 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122012352 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122012353 metal binding site [ion binding]; metal-binding site 94122012354 active site 94122012355 I-site; other site 94122012356 CRISPR/Cas system-associated RAMP superfamily protein Cas6f; Region: Cas6_I-F; cd09739 94122012357 CRISPR/Cas system-associated RAMP superfamily protein Csy3; Region: Csy3_I-F; cd09737 94122012358 CRISPR/Cas system-associated RAMP superfamily protein Csy2; Region: Csy2_I-F; cl12127 94122012359 TniQ; Region: TniQ; pfam06527 94122012360 Piwi_piwi-like_ProArk: PIWI domain, Piwi-like subfamily found in Archaea and Bacteria. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs; Region: Piwi_piwi-like_ProArk; cd04659 94122012361 5' RNA guide strand anchoring site; other site 94122012362 active site 94122012363 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 94122012364 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 94122012365 non-specific DNA binding site [nucleotide binding]; other site 94122012366 salt bridge; other site 94122012367 sequence-specific DNA binding site [nucleotide binding]; other site 94122012368 AAA domain; Region: AAA_22; pfam13401 94122012369 Bacterial TniB protein; Region: TniB; pfam05621 94122012370 Integrase core domain; Region: rve; pfam00665 94122012371 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 94122012372 TnsA endonuclease N terminal; Region: Tn7_Tnp_TnsA_N; pfam08722 94122012373 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 94122012374 Acyltransferase family; Region: Acyl_transf_3; pfam01757 94122012375 Predicted O-acyltransferase [General function prediction only]; Region: COG3274 94122012376 Uncharacterized conserved protein [Function unknown]; Region: COG3339 94122012377 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 94122012378 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 94122012379 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 94122012380 substrate binding site [chemical binding]; other site 94122012381 Protein of unknown function (DUF2618); Region: DUF2618; pfam10940 94122012382 ornithine decarboxylase; Provisional; Region: PRK13578 94122012383 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 94122012384 Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and lysine...; Region: Orn_deC_like; cd00615 94122012385 homodimer interface [polypeptide binding]; other site 94122012386 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122012387 catalytic residue [active] 94122012388 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 94122012389 putrescine transporter; Provisional; Region: potE; PRK10655 94122012390 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 94122012391 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 94122012392 trimer interface [polypeptide binding]; other site 94122012393 eyelet of channel; other site 94122012394 hypothetical protein; Provisional; Region: PRK01254 94122012395 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 94122012396 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 94122012397 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 94122012398 MAPEG family; Region: MAPEG; cl09190 94122012399 Uncharacterized conserved protein [Function unknown]; Region: COG2966 94122012400 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 94122012401 Uncharacterized conserved protein [Function unknown]; Region: COG3610 94122012402 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 94122012403 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 94122012404 SAM-dependent 16S ribosomal RNA C1402 ribose 2'-O-methyltransferase; Provisional; Region: PRK14994 94122012405 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 94122012406 putative SAM binding site [chemical binding]; other site 94122012407 putative homodimer interface [polypeptide binding]; other site 94122012408 Putative lipoprotein [General function prediction only]; Region: LppC; COG3107 94122012409 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 94122012410 putative ligand binding site [chemical binding]; other site 94122012411 hypothetical protein; Reviewed; Region: PRK12497 94122012412 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 94122012413 dimer interface [polypeptide binding]; other site 94122012414 active site 94122012415 outer membrane lipoprotein; Provisional; Region: PRK11023 94122012416 BON domain; Region: BON; pfam04972 94122012417 BON domain; Region: BON; pfam04972 94122012418 EamA-like transporter family; Region: EamA; pfam00892 94122012419 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 94122012420 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 94122012421 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122012422 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 94122012423 dimerization interface [polypeptide binding]; other site 94122012424 substrate binding pocket [chemical binding]; other site 94122012425 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 94122012426 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 94122012427 active site 94122012428 HIGH motif; other site 94122012429 dimer interface [polypeptide binding]; other site 94122012430 KMSKS motif; other site 94122012431 phosphoglycolate phosphatase; Provisional; Region: PRK13222 94122012432 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 94122012433 motif II; other site 94122012434 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 94122012435 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 94122012436 substrate binding site [chemical binding]; other site 94122012437 hexamer interface [polypeptide binding]; other site 94122012438 metal binding site [ion binding]; metal-binding site 94122012439 Protein of unknown function (DUF2970); Region: DUF2970; pfam11174 94122012440 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 94122012441 AAA domain; Region: AAA_22; pfam13401 94122012442 Sporulation related domain; Region: SPOR; pfam05036 94122012443 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 94122012444 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 94122012445 active site 94122012446 dimer interface [polypeptide binding]; other site 94122012447 metal binding site [ion binding]; metal-binding site 94122012448 shikimate kinase; Reviewed; Region: aroK; PRK00131 94122012449 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 94122012450 ADP binding site [chemical binding]; other site 94122012451 magnesium binding site [ion binding]; other site 94122012452 putative shikimate binding site; other site 94122012453 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 94122012454 Secretin and TonB N terminus short domain; Region: STN; smart00965 94122012455 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 94122012456 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 94122012457 Pilus assembly protein, PilP; Region: PilP; pfam04351 94122012458 Pilus assembly protein, PilO; Region: PilO; pfam04350 94122012459 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 94122012460 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 94122012461 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 94122012462 Competence protein A; Region: Competence_A; pfam11104 94122012463 nucleotide binding site [chemical binding]; other site 94122012464 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 94122012465 penicillin-binding protein 1a; Provisional; Region: mrcA; PRK11636 94122012466 Transglycosylase; Region: Transgly; pfam00912 94122012467 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 94122012468 argininosuccinate lyase; Provisional; Region: PRK04833 94122012469 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 94122012470 active sites [active] 94122012471 tetramer interface [polypeptide binding]; other site 94122012472 argininosuccinate synthase; Provisional; Region: PRK13820 94122012473 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 94122012474 ANP binding site [chemical binding]; other site 94122012475 Substrate Binding Site II [chemical binding]; other site 94122012476 Substrate Binding Site I [chemical binding]; other site 94122012477 ornithine carbamoyltransferase; Provisional; Region: PRK14805 94122012478 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 94122012479 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 94122012480 acetylglutamate kinase; Provisional; Region: PRK00942 94122012481 nucleotide binding site [chemical binding]; other site 94122012482 substrate binding site [chemical binding]; other site 94122012483 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 94122012484 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 94122012485 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 94122012486 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 94122012487 Protein of unknown function (DUF1439); Region: DUF1439; pfam07273 94122012488 competence damage-inducible protein A; Provisional; Region: PRK00549 94122012489 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 94122012490 putative MPT binding site; other site 94122012491 Competence-damaged protein; Region: CinA; pfam02464 94122012492 Helix-turn-helix domain; Region: HTH_17; pfam12728 94122012493 PBP superfamily domain; Region: PBP_like; pfam12727 94122012494 FdhD/NarQ family; Region: FdhD-NarQ; pfam02634 94122012495 Protein of unknown function (DUF3305); Region: DUF3305; pfam11749 94122012496 Protein of unknown function (DUF3306); Region: DUF3306; pfam11748 94122012497 Ferredoxin [Energy production and conversion]; Region: COG1146 94122012498 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 94122012499 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 94122012500 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 94122012501 formate dehydrogenase region TAT target; Region: formate_TAT; TIGR02811 94122012502 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_Formate-Dh-Na-like; cd02752 94122012503 [4Fe-4S] binding site [ion binding]; other site 94122012504 molybdopterin cofactor binding site; other site 94122012505 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 94122012506 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 94122012507 molybdopterin cofactor binding site; other site 94122012508 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 94122012509 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 94122012510 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 94122012511 formate dehydrogenase region TAT target; Region: formate_TAT; TIGR02811 94122012512 formate dehydrogenase, alpha subunit, proteobacterial-type; Region: formate-DH-alph; TIGR01553 94122012513 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_Formate-Dh-Na-like; cd02752 94122012514 [4Fe-4S] binding site [ion binding]; other site 94122012515 molybdopterin cofactor binding site; other site 94122012516 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 94122012517 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_CT_Formate-Dh-Na-like; cd02792 94122012518 molybdopterin cofactor binding site; other site 94122012519 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 94122012520 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 94122012521 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 94122012522 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 94122012523 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122012524 N-terminal plug; other site 94122012525 ligand-binding site [chemical binding]; other site 94122012526 HAMP domain; Region: HAMP; pfam00672 94122012527 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122012528 dimer interface [polypeptide binding]; other site 94122012529 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 94122012530 putative CheW interface [polypeptide binding]; other site 94122012531 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 94122012532 Sodium Bile acid symporter family; Region: SBF; pfam01758 94122012533 coproporphyrinogen III oxidase; Provisional; Region: PRK08629 94122012534 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 94122012535 FeS/SAM binding site; other site 94122012536 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 94122012537 Domain of unknown function (DUF4424); Region: DUF4424; pfam14415 94122012538 enterobactin receptor protein; Provisional; Region: PRK13483 94122012539 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122012540 N-terminal plug; other site 94122012541 ligand-binding site [chemical binding]; other site 94122012542 transcriptional regulator; Provisional; Region: PRK10632 94122012543 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122012544 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 94122012545 putative effector binding pocket; other site 94122012546 dimerization interface [polypeptide binding]; other site 94122012547 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 94122012548 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 94122012549 active site 94122012550 nucleophile elbow; other site 94122012551 DNA-binding transcriptional regulator YidZ; Provisional; Region: PRK10216 94122012552 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122012553 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 94122012554 substrate binding pocket [chemical binding]; other site 94122012555 dimerization interface [polypeptide binding]; other site 94122012556 EamA-like transporter family; Region: EamA; pfam00892 94122012557 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 94122012558 EamA-like transporter family; Region: EamA; pfam00892 94122012559 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 94122012560 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 94122012561 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 94122012562 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 94122012563 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 94122012564 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 94122012565 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 94122012566 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 94122012567 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 94122012568 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 94122012569 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 94122012570 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like2; cd05667 94122012571 metal binding site [ion binding]; metal-binding site 94122012572 putative dimer interface [polypeptide binding]; other site 94122012573 HTH domain; Region: HTH_11; cl17392 94122012574 WYL domain; Region: WYL; pfam13280 94122012575 cell division protein FtsZ; Validated; Region: PRK09330 94122012576 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 94122012577 nucleotide binding site [chemical binding]; other site 94122012578 SulA interaction site; other site 94122012579 Methyltransferase domain; Region: Methyltransf_23; pfam13489 94122012580 Methyltransferase domain; Region: Methyltransf_11; pfam08241 94122012581 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 94122012582 PAS domain; Region: PAS_9; pfam13426 94122012583 putative active site [active] 94122012584 heme pocket [chemical binding]; other site 94122012585 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122012586 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122012587 metal binding site [ion binding]; metal-binding site 94122012588 active site 94122012589 I-site; other site 94122012590 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 94122012591 DTW domain; Region: DTW; cl01221 94122012592 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 94122012593 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 94122012594 putative substrate translocation pore; other site 94122012595 DNA-binding transcriptional regulator YidZ; Provisional; Region: PRK10216 94122012596 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122012597 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 94122012598 substrate binding pocket [chemical binding]; other site 94122012599 dimerization interface [polypeptide binding]; other site 94122012600 Cache domain; Region: Cache_1; pfam02743 94122012601 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 94122012602 dimerization interface [polypeptide binding]; other site 94122012603 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122012604 dimer interface [polypeptide binding]; other site 94122012605 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 94122012606 putative CheW interface [polypeptide binding]; other site 94122012607 Domain of unknown function (DUF4145); Region: DUF4145; pfam13643 94122012608 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 94122012609 Sel1-like repeats; Region: SEL1; smart00671 94122012610 Protein of unknown function VcgC/VcgE (DUF2780); Region: DUF2780; pfam11075 94122012611 tellurium resistance terB-like protein, subgroup 2; Region: terB_like_2; cd07313 94122012612 putative metal binding site [ion binding]; other site 94122012613 HDOD domain; Region: HDOD; pfam08668 94122012614 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 94122012615 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 94122012616 putative transporter; Provisional; Region: PRK11021 94122012617 helix_turn_helix ASNC type; Region: HTH_ASNC; smart00344 94122012618 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 94122012619 dimerization interface [polypeptide binding]; other site 94122012620 putative Zn2+ binding site [ion binding]; other site 94122012621 putative DNA binding site [nucleotide binding]; other site 94122012622 AsnC family; Region: AsnC_trans_reg; pfam01037 94122012623 cytochrome c nitrite reductase, NrfD subunit; Region: cyt_nit_nrfD; TIGR03148 94122012624 Formate-dependent nitrite reductase, membrane component [Inorganic ion transport and metabolism]; Region: NrfD; COG3301 94122012625 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 94122012626 cytochrome c nitrite reductase, pentaheme subunit; Region: cyt_nit_nrfB; TIGR03146 94122012627 Protein of unknown function (DUF2726); Region: DUF2726; pfam10881 94122012628 Transcriptional regulator [Transcription]; Region: LysR; COG0583 94122012629 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 94122012630 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 94122012631 dimerization interface [polypeptide binding]; other site 94122012632 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase; Validated; Region: PRK07449 94122012633 Pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1- carboxylate synthase (MenD) and related proteins; Region: TPP_PYR_MenD; cd07037 94122012634 dimer interface [polypeptide binding]; other site 94122012635 tetramer interface [polypeptide binding]; other site 94122012636 PYR/PP interface [polypeptide binding]; other site 94122012637 TPP binding site [chemical binding]; other site 94122012638 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 94122012639 Thiamine pyrophosphate (TPP) family, SHCHC synthase subfamily, TPP-binding module; composed of proteins similar to Escherichia coli 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) synthase (also called MenD). SHCHC synthase plays a key...; Region: TPP_SHCHC_synthase; cd02009 94122012640 TPP-binding site; other site 94122012641 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase; Region: menH_SHCHC; TIGR03695 94122012642 O-succinylbenzoate synthase; Provisional; Region: PRK05105 94122012643 o-Succinylbenzoate synthase (OSBS) catalyzes the conversion of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 4-(2'-carboxyphenyl)-4-oxobutyrate (o-succinylbenzoate or OSB), a reaction in the menaquinone biosynthetic pathway; Region: OSBS; cd03320 94122012644 active site 94122012645 O-succinylbenzoic acid--CoA ligase; Provisional; Region: PRK09029 94122012646 O-succinylbenzoate-CoA ligase (also known as O-succinylbenzoate-CoA synthase, OSB-CoA synthetase, or MenE); Region: OSB_CoA_lg; cd05912 94122012647 acyl-activating enzyme (AAE) consensus motif; other site 94122012648 putative AMP binding site [chemical binding]; other site 94122012649 putative active site [active] 94122012650 putative CoA binding site [chemical binding]; other site 94122012651 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 94122012652 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 94122012653 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 94122012654 DNA binding residues [nucleotide binding] 94122012655 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 94122012656 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 94122012657 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 94122012658 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122012659 Walker A/P-loop; other site 94122012660 ATP binding site [chemical binding]; other site 94122012661 Q-loop/lid; other site 94122012662 ABC transporter signature motif; other site 94122012663 Walker B; other site 94122012664 D-loop; other site 94122012665 H-loop/switch region; other site 94122012666 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 94122012667 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 94122012668 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 94122012669 P loop; other site 94122012670 GTP binding site [chemical binding]; other site 94122012671 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 94122012672 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 94122012673 S-adenosylmethionine binding site [chemical binding]; other site 94122012674 Protein of unknown function (DUF1145); Region: DUF1145; cl11481 94122012675 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 94122012676 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_2; cd03138 94122012677 conserved cys residue [active] 94122012678 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 94122012679 Isochorismatase family; Region: Isochorismatase; pfam00857 94122012680 Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia; Region: nicotinamidase_related; cd01014 94122012681 catalytic triad [active] 94122012682 conserved cis-peptide bond; other site 94122012683 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 94122012684 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 94122012685 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; cl11437 94122012686 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 94122012687 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122012688 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 94122012689 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 94122012690 B1 nucleotide binding pocket [chemical binding]; other site 94122012691 B2 nucleotide binding pocket [chemical binding]; other site 94122012692 CAS motifs; other site 94122012693 active site 94122012694 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 94122012695 dimerization interface [polypeptide binding]; other site 94122012696 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 94122012697 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122012698 dimer interface [polypeptide binding]; other site 94122012699 putative CheW interface [polypeptide binding]; other site 94122012700 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 94122012701 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 94122012702 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 94122012703 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 94122012704 aromatic amino acid transport protein; Region: araaP; TIGR00837 94122012705 glycerol-3-phosphate O-acyltransferase; Region: plsB; TIGR03703 94122012706 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like; Region: LPLAT_DHAPAT-like; cd07993 94122012707 putative acyl-acceptor binding pocket; other site 94122012708 LexA repressor; Validated; Region: PRK00215 94122012709 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 94122012710 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 94122012711 Catalytic site [active] 94122012712 Cell division inhibitor SulA; Region: SulA; cl01880 94122012713 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 94122012714 cytochrome c oxidase, subunit II; Region: CoxB; TIGR02866 94122012715 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 94122012716 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 94122012717 Cytochrome c; Region: Cytochrom_C; pfam00034 94122012718 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 94122012719 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 94122012720 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 94122012721 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 94122012722 Subunit I/III interface [polypeptide binding]; other site 94122012723 D-pathway; other site 94122012724 Subunit I/VIIc interface [polypeptide binding]; other site 94122012725 Subunit I/IV interface [polypeptide binding]; other site 94122012726 Subunit I/II interface [polypeptide binding]; other site 94122012727 Low-spin heme (heme a) binding site [chemical binding]; other site 94122012728 Subunit I/VIIa interface [polypeptide binding]; other site 94122012729 Subunit I/VIa interface [polypeptide binding]; other site 94122012730 Dimer interface; other site 94122012731 Putative water exit pathway; other site 94122012732 Binuclear center (heme a3/CuB) [ion binding]; other site 94122012733 K-pathway; other site 94122012734 Subunit I/Vb interface [polypeptide binding]; other site 94122012735 Putative proton exit pathway; other site 94122012736 Subunit I/VIb interface; other site 94122012737 Subunit I/VIc interface [polypeptide binding]; other site 94122012738 Electron transfer pathway; other site 94122012739 Subunit I/VIIIb interface [polypeptide binding]; other site 94122012740 Subunit I/VIIb interface [polypeptide binding]; other site 94122012741 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 94122012742 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 94122012743 Subunit III/VIIa interface [polypeptide binding]; other site 94122012744 Phospholipid binding site [chemical binding]; other site 94122012745 Subunit I/III interface [polypeptide binding]; other site 94122012746 Subunit III/VIb interface [polypeptide binding]; other site 94122012747 Subunit III/VIa interface; other site 94122012748 Subunit III/Vb interface [polypeptide binding]; other site 94122012749 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 94122012750 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 94122012751 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 94122012752 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 94122012753 UbiA prenyltransferase family; Region: UbiA; pfam01040 94122012754 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 94122012755 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 94122012756 Cu(I) binding site [ion binding]; other site 94122012757 Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases which consist of a 5-stranded beta/alpha barrel; Region: CE4_DAC_u4_5s; cd10973 94122012758 putative active site [active] 94122012759 putative metal binding site [ion binding]; other site 94122012760 DinF and similar proteins, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_DinF_like; cd13136 94122012761 DNA-damage-inducible SOS response protein; Provisional; Region: PRK10367 94122012762 Fe/S biogenesis protein NfuA; Provisional; Region: PRK11190 94122012763 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 94122012764 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 94122012765 FMN-binding domain; Region: FMN_bind; pfam04205 94122012766 L-aspartate oxidase; Provisional; Region: PRK06175 94122012767 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 94122012768 Predicted oxidoreductase [General function prediction only]; Region: COG3573 94122012769 Nucleoside-specific channel-forming protein, Tsx; Region: Channel_Tsx; cl04114 94122012770 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 94122012771 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 94122012772 dimer interface [polypeptide binding]; other site 94122012773 phosphorylation site [posttranslational modification] 94122012774 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 94122012775 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122012776 active site 94122012777 phosphorylation site [posttranslational modification] 94122012778 intermolecular recognition site; other site 94122012779 dimerization interface [polypeptide binding]; other site 94122012780 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 94122012781 DNA binding site [nucleotide binding] 94122012782 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 94122012783 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 94122012784 dimerization interface [polypeptide binding]; other site 94122012785 DNA binding residues [nucleotide binding] 94122012786 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 94122012787 pimelyl-[acyl-carrier protein] methyl ester esterase; Region: bioH; TIGR01738 94122012788 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 94122012789 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 94122012790 Sulfatase; Region: Sulfatase; pfam00884 94122012791 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 94122012792 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 94122012793 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 94122012794 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 94122012795 RNA binding site [nucleotide binding]; other site 94122012796 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 94122012797 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 94122012798 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 94122012799 Response regulator receiver domain; Region: Response_reg; pfam00072 94122012800 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122012801 active site 94122012802 phosphorylation site [posttranslational modification] 94122012803 intermolecular recognition site; other site 94122012804 dimerization interface [polypeptide binding]; other site 94122012805 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122012806 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122012807 metal binding site [ion binding]; metal-binding site 94122012808 active site 94122012809 I-site; other site 94122012810 CHASE domain; Region: CHASE; pfam03924 94122012811 PAS domain S-box; Region: sensory_box; TIGR00229 94122012812 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 94122012813 putative active site [active] 94122012814 heme pocket [chemical binding]; other site 94122012815 PAS domain; Region: PAS_9; pfam13426 94122012816 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 94122012817 putative active site [active] 94122012818 heme pocket [chemical binding]; other site 94122012819 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 94122012820 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 94122012821 putative active site [active] 94122012822 heme pocket [chemical binding]; other site 94122012823 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 94122012824 putative active site [active] 94122012825 heme pocket [chemical binding]; other site 94122012826 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 94122012827 dimer interface [polypeptide binding]; other site 94122012828 phosphorylation site [posttranslational modification] 94122012829 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 94122012830 ATP binding site [chemical binding]; other site 94122012831 Mg2+ binding site [ion binding]; other site 94122012832 G-X-G motif; other site 94122012833 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 94122012834 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122012835 active site 94122012836 phosphorylation site [posttranslational modification] 94122012837 intermolecular recognition site; other site 94122012838 dimerization interface [polypeptide binding]; other site 94122012839 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 94122012840 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122012841 active site 94122012842 phosphorylation site [posttranslational modification] 94122012843 intermolecular recognition site; other site 94122012844 dimerization interface [polypeptide binding]; other site 94122012845 osmolarity response regulator; Provisional; Region: ompR; PRK09468 94122012846 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122012847 active site 94122012848 phosphorylation site [posttranslational modification] 94122012849 intermolecular recognition site; other site 94122012850 dimerization interface [polypeptide binding]; other site 94122012851 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 94122012852 DNA binding site [nucleotide binding] 94122012853 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 94122012854 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 94122012855 dimerization interface [polypeptide binding]; other site 94122012856 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 94122012857 dimer interface [polypeptide binding]; other site 94122012858 phosphorylation site [posttranslational modification] 94122012859 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 94122012860 ATP binding site [chemical binding]; other site 94122012861 Mg2+ binding site [ion binding]; other site 94122012862 G-X-G motif; other site 94122012863 Negative regulator of septation ring formation [Cell division and chromosome partitioning]; Region: EzrA; COG4477 94122012864 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 94122012865 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 94122012866 dimerization interface [polypeptide binding]; other site 94122012867 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 94122012868 dimer interface [polypeptide binding]; other site 94122012869 putative CheW interface [polypeptide binding]; other site 94122012870 Peroxiredoxin (PRX) family, PRX5-like subfamily; members are similar to the human protein, PRX5, a homodimeric TRX peroxidase, widely expressed in tissues and found cellularly in mitochondria, peroxisomes and the cytosol. The cellular location of PRX5...; Region: PRX5_like; cd03013 94122012871 catalytic triad [active] 94122012872 dimer interface [polypeptide binding]; other site 94122012873 Predicted membrane protein [Function unknown]; Region: COG3212 94122012874 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 94122012875 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 94122012876 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122012877 active site 94122012878 phosphorylation site [posttranslational modification] 94122012879 intermolecular recognition site; other site 94122012880 dimerization interface [polypeptide binding]; other site 94122012881 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 94122012882 DNA binding site [nucleotide binding] 94122012883 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 94122012884 dimer interface [polypeptide binding]; other site 94122012885 phosphorylation site [posttranslational modification] 94122012886 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 94122012887 ATP binding site [chemical binding]; other site 94122012888 Mg2+ binding site [ion binding]; other site 94122012889 G-X-G motif; other site 94122012890 Protein of unknown function (DUF3300); Region: DUF3300; pfam11737 94122012891 MASE1; Region: MASE1; cl17823 94122012892 CHASE domain; Region: CHASE; pfam03924 94122012893 PAS domain S-box; Region: sensory_box; TIGR00229 94122012894 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 94122012895 putative active site [active] 94122012896 heme pocket [chemical binding]; other site 94122012897 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 94122012898 PAS domain; Region: PAS_9; pfam13426 94122012899 putative active site [active] 94122012900 heme pocket [chemical binding]; other site 94122012901 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 94122012902 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122012903 metal binding site [ion binding]; metal-binding site 94122012904 active site 94122012905 I-site; other site 94122012906 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 94122012907 cytochrome o ubiquinol oxidase subunit II; Provisional; Region: PRK10525 94122012908 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 94122012909 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 94122012910 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 94122012911 Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons...; Region: Ubiquinol_Oxidase_I; cd01662 94122012912 D-pathway; other site 94122012913 Putative ubiquinol binding site [chemical binding]; other site 94122012914 Low-spin heme (heme b) binding site [chemical binding]; other site 94122012915 Putative water exit pathway; other site 94122012916 Binuclear center (heme o3/CuB) [ion binding]; other site 94122012917 K-pathway; other site 94122012918 Putative proton exit pathway; other site 94122012919 Ubiquinol oxidase subunit III subfamily. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously...; Region: Ubiquinol_oxidase_III; cd02863 94122012920 Subunit I/III interface [polypeptide binding]; other site 94122012921 Subunit III/IV interface [polypeptide binding]; other site 94122012922 cytochrome o ubiquinol oxidase subunit IV; Region: CyoD; TIGR02847 94122012923 protoheme IX farnesyltransferase; Provisional; Region: PRK13362 94122012924 UbiA prenyltransferase family; Region: UbiA; pfam01040 94122012925 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 94122012926 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 94122012927 active site 94122012928 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 94122012929 S-adenosylmethionine binding site [chemical binding]; other site 94122012930 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 94122012931 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 94122012932 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 94122012933 N-acetyl-D-glucosamine binding site [chemical binding]; other site 94122012934 catalytic residue [active] 94122012935 Protein of unknown function (DUF3137); Region: DUF3137; pfam11335 94122012936 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 94122012937 AbgT putative transporter family; Region: ABG_transport; pfam03806 94122012938 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 94122012939 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 94122012940 Protein export membrane protein; Region: SecD_SecF; cl14618 94122012941 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 94122012942 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 94122012943 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122012944 conserved hypothetical protein, proteobacterial; Region: gcw_chp; TIGR02001 94122012945 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 94122012946 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 94122012947 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 94122012948 C-terminal domain interface [polypeptide binding]; other site 94122012949 GSH binding site (G-site) [chemical binding]; other site 94122012950 dimer interface [polypeptide binding]; other site 94122012951 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 94122012952 N-terminal domain interface [polypeptide binding]; other site 94122012953 dimer interface [polypeptide binding]; other site 94122012954 substrate binding pocket (H-site) [chemical binding]; other site 94122012955 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 94122012956 active site 94122012957 oligopeptidase A; Provisional; Region: PRK10911 94122012958 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 94122012959 active site 94122012960 Zn binding site [ion binding]; other site 94122012961 glutathione reductase; Validated; Region: PRK06116 94122012962 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 94122012963 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 94122012964 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 94122012965 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 94122012966 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 94122012967 Na binding site [ion binding]; other site 94122012968 gamma-glutamyl kinase; Provisional; Region: PRK13402 94122012969 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 94122012970 nucleotide binding site [chemical binding]; other site 94122012971 homotetrameric interface [polypeptide binding]; other site 94122012972 putative phosphate binding site [ion binding]; other site 94122012973 putative allosteric binding site; other site 94122012974 PUA domain; Region: PUA; cl00607 94122012975 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 94122012976 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 94122012977 putative catalytic cysteine [active] 94122012978 Predicted P-loop ATPase [General function prediction only]; Region: COG4928 94122012979 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 94122012980 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 94122012981 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 94122012982 non-specific DNA binding site [nucleotide binding]; other site 94122012983 salt bridge; other site 94122012984 sequence-specific DNA binding site [nucleotide binding]; other site 94122012985 Protein of unknown function (DUF3612); Region: DUF3612; pfam12268 94122012986 malate synthase; Provisional; Region: PRK08951 94122012987 Predicted membrane protein [Function unknown]; Region: COG2855 94122012988 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 94122012989 helix_turn_helix, Lux Regulon; Region: HTH_LUXR; smart00421 94122012990 DNA binding residues [nucleotide binding] 94122012991 dimerization interface [polypeptide binding]; other site 94122012992 HlyD family secretion protein; Region: HlyD_3; pfam13437 94122012993 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 94122012994 Protein of unknown function (DUF3240); Region: DUF3240; pfam11582 94122012995 Paraquat-inducible protein A; Region: PqiA; pfam04403 94122012996 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 94122012997 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 94122012998 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 94122012999 Zn2+ binding site [ion binding]; other site 94122013000 Mg2+ binding site [ion binding]; other site 94122013001 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 94122013002 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 94122013003 Walker A/P-loop; other site 94122013004 ATP binding site [chemical binding]; other site 94122013005 Q-loop/lid; other site 94122013006 ABC transporter signature motif; other site 94122013007 Walker B; other site 94122013008 D-loop; other site 94122013009 H-loop/switch region; other site 94122013010 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 94122013011 cobalt transport protein ATP-binding subunit; Region: cbiO; TIGR01166 94122013012 Walker A/P-loop; other site 94122013013 ATP binding site [chemical binding]; other site 94122013014 Q-loop/lid; other site 94122013015 ABC transporter signature motif; other site 94122013016 Walker B; other site 94122013017 D-loop; other site 94122013018 H-loop/switch region; other site 94122013019 Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: MenF; COG1169 94122013020 chorismate binding enzyme; Region: Chorismate_bind; cl10555 94122013021 hypothetical protein; Provisional; Region: PRK11212 94122013022 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 94122013023 Coenzyme A binding pocket [chemical binding]; other site 94122013024 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 94122013025 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 94122013026 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 94122013027 dimer interface [polypeptide binding]; other site 94122013028 phosphorylation site [posttranslational modification] 94122013029 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 94122013030 ATP binding site [chemical binding]; other site 94122013031 G-X-G motif; other site 94122013032 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 94122013033 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 94122013034 active site 94122013035 phosphorylation site [posttranslational modification] 94122013036 intermolecular recognition site; other site 94122013037 dimerization interface [polypeptide binding]; other site 94122013038 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 94122013039 Walker A motif; other site 94122013040 ATP binding site [chemical binding]; other site 94122013041 Walker B motif; other site 94122013042 arginine finger; other site 94122013043 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 94122013044 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 94122013045 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 94122013046 dimerization interface [polypeptide binding]; other site 94122013047 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 94122013048 dimer interface [polypeptide binding]; other site 94122013049 conserved gate region; other site 94122013050 putative PBP binding loops; other site 94122013051 ABC-ATPase subunit interface; other site 94122013052 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 94122013053 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 94122013054 Walker A/P-loop; other site 94122013055 ATP binding site [chemical binding]; other site 94122013056 Q-loop/lid; other site 94122013057 ABC transporter signature motif; other site 94122013058 Walker B; other site 94122013059 D-loop; other site 94122013060 H-loop/switch region; other site 94122013061 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 94122013062 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 94122013063 GTP binding site; other site 94122013064 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoeA; Provisional; Region: PRK14491 94122013065 Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa; Region: MobB; cd03116 94122013066 Walker A motif; other site 94122013067 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 94122013068 dimer interface [polypeptide binding]; other site 94122013069 putative functional site; other site 94122013070 putative MPT binding site; other site 94122013071 molybdenum cofactor biosynthesis protein A; Provisional; Region: PRK13361 94122013072 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 94122013073 FeS/SAM binding site; other site 94122013074 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 94122013075 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 94122013076 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 94122013077 DNA binding site [nucleotide binding] 94122013078 catalytic residue [active] 94122013079 H2TH interface [polypeptide binding]; other site 94122013080 putative catalytic residues [active] 94122013081 turnover-facilitating residue; other site 94122013082 intercalation triad [nucleotide binding]; other site 94122013083 8OG recognition residue [nucleotide binding]; other site 94122013084 putative reading head residues; other site 94122013085 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 94122013086 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 94122013087 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 94122013088 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 94122013089 Uncharacterized conserved protein [Function unknown]; Region: COG0398 94122013090 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 94122013091 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 94122013092 Ligand binding site; other site 94122013093 Putative Catalytic site; other site 94122013094 DXD motif; other site 94122013095 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 94122013096 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 94122013097 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 94122013098 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 94122013099 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 94122013100 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 94122013101 putative NAD(P) binding site [chemical binding]; other site 94122013102 active site 94122013103 putative substrate binding site [chemical binding]; other site 94122013104 Capsule assembly protein Wzi; Region: Caps_assemb_Wzi; pfam14052 94122013105 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 94122013106 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 94122013107 active site 94122013108 (T/H)XGH motif; other site 94122013109 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 94122013110 This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core; Region: GT1_WabH_like; cd03811 94122013111 putative ADP-binding pocket [chemical binding]; other site 94122013112 capsule biosynthesis phosphatase; Region: EcbF-BcbF; TIGR01689 94122013113 GT2_BcbE_like is likely involved in the biosynthesis of the polysaccharide capsule; Region: GT2_BcE_like; cd04183 94122013114 Ligand binding site; other site 94122013115 WavE lipopolysaccharide synthesis; Region: WavE; pfam07507 94122013116 Putative glycosyl/glycerophosphate transferases involved in teichoic acid biosynthesis TagF/TagB/EpsJ/RodC [Cell envelope biogenesis, outer membrane]; Region: TagB; COG1887 94122013117 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 94122013118 This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core; Region: GT1_WabH_like; cd03811 94122013119 putative ADP-binding pocket [chemical binding]; other site 94122013120 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 94122013121 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 94122013122 putative active site [active] 94122013123 3-deoxy-D-manno-octulosonic-acid kinase; Reviewed; Region: PRK01723 94122013124 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; pfam06293 94122013125 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 94122013126 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 94122013127 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 94122013128 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 94122013129 Bacterial transcriptional repressor; Region: TetR; pfam13972 94122013130 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 94122013131 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 94122013132 substrate-cofactor binding pocket; other site 94122013133 pyridoxal 5'-phosphate binding site [chemical binding]; other site 94122013134 catalytic residue [active] 94122013135 L-threonine 3-dehydrogenase; Validated; Region: tdh; PRK05396 94122013136 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 94122013137 NAD(P) binding site [chemical binding]; other site 94122013138 GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily. Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a...; Region: GlpE_ST; cd01444 94122013139 active site residue [active] 94122013140 Protein of unknown function (DUF3582); Region: DUF3582; pfam12122 94122013141 rhomboid family protease GlpG; Region: rhombo_GlpG; TIGR04239 94122013142 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 94122013143 isoprenoid biosynthesis protein with amidotransferase-like domain; Provisional; Region: PRK11780 94122013144 Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1; Region: GATase1_ES1; cd03133 94122013145 conserved cys residue [active] 94122013146 DNA polymerase I; Provisional; Region: PRK05755 94122013147 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 94122013148 active site 94122013149 metal binding site 1 [ion binding]; metal-binding site 94122013150 putative 5' ssDNA interaction site; other site 94122013151 metal binding site 3; metal-binding site 94122013152 metal binding site 2 [ion binding]; metal-binding site 94122013153 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 94122013154 putative DNA binding site [nucleotide binding]; other site 94122013155 putative metal binding site [ion binding]; other site 94122013156 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 94122013157 active site 94122013158 catalytic site [active] 94122013159 substrate binding site [chemical binding]; other site 94122013160 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 94122013161 active site 94122013162 DNA binding site [nucleotide binding] 94122013163 catalytic site [active] 94122013164 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 94122013165 G1 box; other site 94122013166 GTP/Mg2+ binding site [chemical binding]; other site 94122013167 Switch I region; other site 94122013168 G2 box; other site 94122013169 G3 box; other site 94122013170 Switch II region; other site 94122013171 G4 box; other site 94122013172 G5 box; other site 94122013173 Cytochrome c553 [Energy production and conversion]; Region: COG2863 94122013174 Cytochrome c; Region: Cytochrom_C; cl11414 94122013175 Methyltransferase domain; Region: Methyltransf_23; pfam13489 94122013176 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 94122013177 Der GTPase activator (YihI); Region: YihI; pfam04220 94122013178 Protein of unknown function (DUF2489); Region: DUF2489; pfam10675 94122013179 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 94122013180 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 94122013181 FeS/SAM binding site; other site 94122013182 HemN C-terminal domain; Region: HemN_C; pfam06969 94122013183 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 94122013184 adenosine deaminase; Provisional; Region: PRK09358 94122013185 active site 94122013186 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 94122013187 lysophospholipase L2; Provisional; Region: PRK10749 94122013188 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 94122013189 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 94122013190 PAS fold; Region: PAS_3; pfam08447 94122013191 putative active site [active] 94122013192 heme pocket [chemical binding]; other site 94122013193 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 94122013194 metal binding site [ion binding]; metal-binding site 94122013195 active site 94122013196 I-site; other site 94122013197 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 94122013198 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 94122013199 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 94122013200 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 94122013201 Enoyl-CoA hydratase/isomerase family; Region: ECH; pfam00378 94122013202 substrate binding site [chemical binding]; other site 94122013203 oxyanion hole (OAH) forming residues; other site 94122013204 trimer interface [polypeptide binding]; other site 94122013205 Predicted membrane protein (DUF2061); Region: DUF2061; cl01257 94122013206 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 94122013207 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 94122013208 glutaminase active site [active] 94122013209 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 94122013210 dimer interface [polypeptide binding]; other site 94122013211 active site 94122013212 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 94122013213 dimer interface [polypeptide binding]; other site 94122013214 active site 94122013215 DNA-bindng transcriptional repressor SrlR; Provisional; Region: srlR; PRK10434 94122013216 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 94122013217 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 94122013218 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 94122013219 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 94122013220 N-terminal plug; other site 94122013221 ligand-binding site [chemical binding]; other site 94122013222 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK09451 94122013223 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 94122013224 Substrate binding site; other site 94122013225 Mg++ binding site; other site 94122013226 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 94122013227 active site 94122013228 substrate binding site [chemical binding]; other site 94122013229 CoA binding site [chemical binding]; other site 94122013230 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 94122013231 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 94122013232 gamma subunit interface [polypeptide binding]; other site 94122013233 epsilon subunit interface [polypeptide binding]; other site 94122013234 LBP interface [polypeptide binding]; other site 94122013235 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 94122013236 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 94122013237 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 94122013238 alpha subunit interaction interface [polypeptide binding]; other site 94122013239 Walker A motif; other site 94122013240 ATP binding site [chemical binding]; other site 94122013241 Walker B motif; other site 94122013242 inhibitor binding site; inhibition site 94122013243 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 94122013244 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 94122013245 core domain interface [polypeptide binding]; other site 94122013246 delta subunit interface [polypeptide binding]; other site 94122013247 epsilon subunit interface [polypeptide binding]; other site 94122013248 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 94122013249 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 94122013250 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 94122013251 beta subunit interaction interface [polypeptide binding]; other site 94122013252 Walker A motif; other site 94122013253 ATP binding site [chemical binding]; other site 94122013254 Walker B motif; other site 94122013255 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 94122013256 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 94122013257 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 94122013258 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 94122013259 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 94122013260 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 94122013261 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 94122013262 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 94122013263 F0F1 ATP synthase subunit I; Validated; Region: PRK05760 94122013264 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 94122013265 ParB-like nuclease domain; Region: ParBc; pfam02195 94122013266 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 94122013267 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 94122013268 P-loop; other site 94122013269 Magnesium ion binding site [ion binding]; other site 94122013270 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 94122013271 Magnesium ion binding site [ion binding]; other site