-- dump date 20111121_012033 -- class Genbank::misc_feature -- table misc_feature_note -- id note 316407000001 bifunctional aspartokinase I/homoserine dehydrogenase I; Provisional; Region: thrA; PRK09436 316407000002 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 AKI-...; Region: AAK_AK-HSDH; cd04257 316407000003 putative catalytic residues; other site 316407000004 putative nucleotide binding site; other site 316407000005 putative aspartate binding site; other site 316407000006 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA-like_1; cd04921 316407000007 dimer interface; other site 316407000008 putative threonine allosteric regulatory site; other site 316407000009 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA_2; cd04922 316407000010 putative threonine allosteric regulatory site; other site 316407000011 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407000012 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 316407000013 homoserine kinase; Region: thrB; TIGR00191 316407000014 Protein of unknown function; Region: YhfT; pfam10797 316407000015 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 316407000016 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 316407000017 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 316407000018 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants...; Region: Thr-synth_2; cd01560 316407000019 pyridoxal 5'-phosphate binding site; other site 316407000020 catalytic residue; other site 316407000021 Protein of unknown function (DUF2502); Region: DUF2502; pfam10697 316407000022 Protein of unknown function (DUF328); Region: DUF328; cl01143 316407000023 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 316407000024 transaldolase-like protein; Provisional; Region: PTZ00411 316407000025 Transaldolases including both TalA and TalB. The enzyme catalyses the reversible transfer of a dyhydroxyacetone moiety, derived from fructose-6-phosphate to erythrose-4-phosphate yielding sedoheptulose-7-phosphate and glyceraldehyde-3-phosphate. The...; Region: Transaldolase_TalAB; cd00957 316407000026 active site 316407000027 dimer interface; other site 316407000028 catalytic residue; other site 316407000029 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 316407000030 MPT binding site; other site 316407000031 trimer interface; other site 316407000032 GPR1/FUN34/yaaH family; Region: Grp1_Fun34_YaaH; cl00685 316407000033 Ubiquinol-cytochrome C chaperone; Region: Ubiq_cyt_C_chap; cl12045 316407000034 Protein of unknown function (DUF2541); Region: DUF2541; cl08090 316407000035 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 316407000036 chaperone protein DnaJ; Provisional; Region: PRK10767 316407000037 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...; Region: DnaJ; cd06257 316407000038 HSP70 interaction site; other site 316407000039 DnaJ C terminal region; Region: DnaJ_C; pfam01556 316407000040 Transposase DDE domain; Region: Transposase_11; pfam01609 316407000041 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 316407000042 Hok/gef family; Region: HOK_GEF; cl11494 316407000043 Hok/gef family; Region: HOK_GEF; cl11494 316407000044 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 316407000045 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 316407000046 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407000047 The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold; Region: PBP2_NhaR; cd08429 316407000048 putative dimerization interface; other site 316407000049 IS1 transposase; Region: Transposase_27; cl00721 316407000050 Insertion element protein; Region: Ins_element1; pfam03811 316407000051 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 316407000052 Protein of unknown function (DUF2575); Region: DUF2575; pfam10837 316407000053 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 316407000054 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 316407000055 active site 316407000056 Riboflavin kinase; Region: Flavokinase; pfam01687 316407000057 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 316407000058 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 316407000059 HIGH motif; other site 316407000060 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 316407000061 active site 316407000062 KMSKS motif; other site 316407000063 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 316407000064 tRNA binding surface; other site 316407000065 anticodon binding site; other site 316407000066 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 316407000067 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 316407000068 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 316407000069 LytB protein; Region: LYTB; cl00507 316407000070 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 316407000071 Inosine-uridine preferring nucleoside hydrolase; Region: IU_nuc_hydro; pfam01156 316407000072 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 316407000073 active site 316407000074 tetramer interface; other site 316407000075 dihydrodipicolinate reductase; Provisional; Region: PRK00048 316407000076 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407000077 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 316407000078 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 316407000079 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; pfam00988 316407000080 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 316407000081 catalytic site; other site 316407000082 subunit interface; other site 316407000083 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 316407000084 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 316407000085 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 316407000086 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 316407000087 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 316407000088 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 316407000089 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 316407000090 IMP binding site; other site 316407000091 dimer interface; other site 316407000092 interdomain contacts; other site 316407000093 partial ornithine binding site; other site 316407000094 DNA-binding transcriptional activator CaiF; Provisional; Region: PRK11476 316407000095 carnitine operon protein CaiE; Provisional; Region: PRK13627 316407000096 paaY-like: This group is composed by uncharacterized proteins with similarity to the protein product of the E. coli paaY gene, which is part of the paa gene cluster responsible for phenylacetic acid degradation. Proteins in this group are expected to...; Region: LbH_paaY_like; cd04745 316407000097 putative trimer interface; other site 316407000098 putative metal binding site; other site 316407000099 enoyl-CoA hydratase; Provisional; Region: PRK06688 316407000100 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 316407000101 substrate binding site; other site 316407000102 oxyanion hole (OAH) forming residues; other site 316407000103 trimer interface; other site 316407000104 putative crotonobetaine/carnitine-CoA ligase; Validated; Region: caiC; PRK08008 316407000105 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 316407000106 CoA-transferase family III; Region: CoA_transf_3; cl00778 316407000107 crotonobetainyl-CoA dehydrogenase; Validated; Region: PRK03354 316407000108 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 316407000109 active site 316407000110 BCCT family transporter; Region: BCCT; cl00569 316407000111 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 316407000112 Ligand binding site; other site 316407000113 putative electron transfer flavoprotein FixB; Provisional; Region: fixB; PRK03363 316407000114 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; cd01985 316407000115 Ligand binding site; other site 316407000116 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 316407000117 putative oxidoreductase FixC; Provisional; Region: PRK10157 316407000118 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407000119 ferredoxin-like protein FixX; Provisional; Region: PRK15449 316407000120 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 316407000121 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 316407000122 Sugar (and other) transporter; Region: Sugar_tr; pfam00083 316407000123 putative substrate translocation pore; other site 316407000124 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 316407000125 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 316407000126 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 316407000127 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407000128 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 5,10-...; Region: DHFR; cd00209 316407000129 folate binding site; other site 316407000130 NADP+ binding site; other site 316407000131 bis(5'-nucleosyl)-tetraphosphatase (symmetrical); Region: apaH; TIGR00668 316407000132 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 316407000133 active site 316407000134 metal-binding site 316407000135 Protein of unknown function (DUF525); Region: DUF525; cl01119 316407000136 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; cl12011 316407000137 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 316407000138 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 316407000139 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 316407000140 SurA N-terminal domain; Region: SurA_N; pfam09312 316407000141 PPIC-type PPIASE domain; Region: Rotamase; cl08278 316407000142 PPIC-type PPIASE domain; Region: Rotamase; cl08278 316407000143 LPS assembly outer membrane complex protein LptD; Provisional; Region: PRK03761 316407000144 OstA-like protein; Region: OstA; cl00844 316407000145 Organic solvent tolerance protein; Region: OstA_C; pfam04453 316407000146 Dna-J like membrane chaperone protein; Provisional; Region: djlA; PRK09430 316407000147 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 316407000148 putative metal binding site; other site 316407000149 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...; Region: DnaJ; cd06257 316407000150 HSP70 interaction site; other site 316407000151 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 316407000152 active site 316407000153 ATP-dependent helicase HepA; Validated; Region: PRK04914 316407000154 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 316407000155 ATP binding site; other site 316407000156 putative Mg++ binding site; other site 316407000157 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 316407000158 nucleotide binding region; other site 316407000159 ATP-binding site; other site 316407000160 DNA polymerase II; Reviewed; Region: PRK05762 316407000161 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases; Region: DNA_polB_II_exo; cd05784 316407000162 active site 316407000163 catalytic site; other site 316407000164 substrate binding site; other site 316407000165 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 316407000166 active site 316407000167 metal-binding site 316407000168 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; cd00398 316407000169 intersubunit interface; other site 316407000170 active site 316407000171 Zn2+ binding site; other site 316407000172 L-arabinose isomerase; Provisional; Region: PRK02929 316407000173 L-Arabinose isomerase (AI) catalyzes the isomerization of L-arabinose to L-ribulose, the first reaction in its conversion into D-xylulose-5-phosphate, an intermediate in the pentose phosphate pathway, which allows L-arabinose to be used as a carbon...; Region: L-arabinose_isomerase; cd03557 316407000174 putative hexamer (dimer of trimers) interface; other site 316407000175 trimer interface; other site 316407000176 putative substrate binding site; other site 316407000177 putative metal binding site; other site 316407000178 ribulokinase; Provisional; Region: PRK04123 316407000179 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; pfam00370 316407000180 FGGY family of carbohydrate kinases, C-terminal domain; Region: FGGY_C; pfam02782 316407000181 DNA-binding transcriptional regulator AraC; Provisional; Region: PRK10572 316407000182 Cupin domain; Region: Cupin_2; cl09118 316407000183 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407000184 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407000185 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 316407000186 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 316407000187 thiamine transporter ATP-binding subunit; Provisional; Region: thiQ; PRK10771 316407000188 ABC-type thiamine tranport system; part of the binding-protein-dependent transport system tbpA-thiPQ for thiamine and TPP. Probably responsible for the translocation of thiamine across the membrane. ABC transporters are a large family of proteins...; Region: ABC_ThiQ_thiamine_transporter; cd03298 316407000189 Walker A/P-loop; other site 316407000190 ATP binding site; other site 316407000191 Q-loop/lid; other site 316407000192 ABC transporter signature motif; other site 316407000193 Walker B; other site 316407000194 D-loop; other site 316407000195 H-loop/switch region; other site 316407000196 thiamine transporter membrane protein; Reviewed; Region: thiP; PRK09433 316407000197 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...; Region: TM_PBP2; cd06261 316407000198 dimer interface; other site 316407000199 conserved gate region; other site 316407000200 putative PBP binding loops; other site 316407000201 ABC-ATPase subunit interface; other site 316407000202 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...; Region: TM_PBP2; cd06261 316407000203 dimer interface; other site 316407000204 conserved gate region; other site 316407000205 putative PBP binding loops; other site 316407000206 ABC-ATPase subunit interface; other site 316407000207 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 316407000208 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 316407000209 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG4533 316407000210 The C-terminal solute-binding domain of DNA-binding transcriptional regulator SgrR is related to the ABC-type oligopeptide-binding proteins and contains the type 2 periplasmic-binding fold; Region: PBP2_SgrR_like; cd08507 316407000211 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 316407000212 sugar efflux transporter; Region: 2A0120; TIGR00899 316407000213 putative substrate translocation pore; other site 316407000214 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 3-...; Region: IPMI_Swivel; cd01577 316407000215 substrate binding site; other site 316407000216 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 316407000217 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 316407000218 substrate binding site; other site 316407000219 ligand binding site; other site 316407000220 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 316407000221 isocitrate dehydrogenase; Validated; Region: PRK06451 316407000222 2-isopropylmalate synthase; Validated; Region: PRK00915 316407000223 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 316407000224 active site 316407000225 catalytic residues; other site 316407000226 metal-binding site 316407000227 LeuA allosteric (dimerization) domain; Region: LeuA_dimer; pfam08502 316407000228 leu operon leader peptide; Provisional; Region: PRK09925 316407000229 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 316407000230 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407000231 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 316407000232 putative substrate binding pocket; other site 316407000233 putative dimerization interface; other site 316407000234 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK07979 316407000235 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 316407000236 PYR/PP interface; other site 316407000237 dimer interface; other site 316407000238 TPP binding site; other site 316407000239 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 316407000240 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 316407000241 TPP-binding site; other site 316407000242 dimer interface; other site 316407000243 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 316407000244 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 316407000245 putative valine binding site; other site 316407000246 dimer interface; other site 316407000247 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 316407000248 DNA-binding transcriptional regulator FruR; Provisional; Region: PRK11303 316407000249 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 316407000250 DNA binding site 316407000251 domain linker motif; other site 316407000252 Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs; Region: PBP1_FruR; cd06274 316407000253 dimerization interface; other site 316407000254 ligand binding site; other site 316407000255 mraZ protein; Region: TIGR00242 316407000256 MraZ protein; Region: MraZ; pfam02381 316407000257 MraZ protein; Region: MraZ; pfam02381 316407000258 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; cl12011 316407000259 Septum formation initiator; Region: DivIC; cl11433 316407000260 peptidoglycan synthase FtsI; Provisional; Region: PRK15105 316407000261 Penicillin-binding Protein dimerization domain; Region: PBP_dimer; pfam03717 316407000262 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 316407000263 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 316407000264 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 316407000265 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 316407000266 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 316407000267 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed; Region: murF; PRK10773 316407000268 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 316407000269 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 316407000270 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 316407000271 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 316407000272 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 undecaprenyl-pyrophosphoryl-N-...; Region: GT_MraY; cd06852 316407000273 Mg++ binding site; other site 316407000274 putative catalytic motif; other site 316407000275 putative substrate binding site; other site 316407000276 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03806 316407000277 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 316407000278 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 316407000279 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 316407000280 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 316407000281 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...; Region: GT1_MurG; cd03785 316407000282 active site 316407000283 homodimer interface; other site 316407000284 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 316407000285 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 316407000286 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 316407000287 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 316407000288 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 316407000289 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 316407000290 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 316407000291 cell division protein FtsQ; Provisional; Region: PRK10775 316407000292 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 316407000293 Cell division protein FtsQ; Region: FtsQ; pfam03799 316407000294 cell division protein FtsA; Reviewed; Region: ftsA; PRK09472 316407000295 Cell division protein FtsA; Region: FtsA; cl11496 316407000296 Cell division protein FtsA; Region: FtsA; cl11496 316407000297 cell division protein FtsZ; Validated; Region: PRK09330 316407000298 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...; Region: FtsZ_type1; cd02201 316407000299 nucleotide binding site; other site 316407000300 SulA interaction site; other site 316407000301 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 316407000302 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 316407000303 Secretion monitor precursor protein (SecM); Region: SecM; cl11636 316407000304 SecA DEAD-like domain; Region: SecA_DEAD; pfam07517 316407000305 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; cl12029 316407000306 SecA preprotein cross-linking domain; Region: SecA_PP_bind; pfam01043 316407000307 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 316407000308 nucleotide binding region; other site 316407000309 ATP-binding site; other site 316407000310 SecA Wing and Scaffold domain; Region: SecA_SW; pfam07516 316407000311 hypothetical protein; Provisional; Region: PRK10396 316407000312 SEC-C motif; Region: SEC-C; cl12132 316407000313 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 316407000314 active site 316407000315 8-oxo-dGMP binding site; other site 316407000316 nudix motif; other site 316407000317 metal-binding site 316407000318 Domain of unknown function (DUF329); Region: DUF329; cl01144 316407000319 Protein of unknown function (DUF1342); Region: DUF1342; cl01892 316407000320 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 316407000321 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 316407000322 CoA-binding site; other site 316407000323 ATP-binding; other site 316407000324 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05096 316407000325 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 the...; Region: IMPDH; cd00381 316407000326 active site 316407000327 type IV pilin biogenesis protein; Provisional; Region: PRK10573 316407000328 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 316407000329 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 316407000330 hypothetical protein; Provisional; Region: PRK10436 316407000331 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 316407000332 Walker A motif; other site 316407000333 ATP binding site; other site 316407000334 Walker B motif; other site 316407000335 putative major pilin subunit; Provisional; Region: PRK10574 316407000336 Pilin (bacterial filament); Region: Pilin; pfam00114 316407000337 quinolinate phosphoribosyltransferase; Validated; Region: PRK09016 316407000338 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 5-...; Region: QPRTase; cd01572 316407000339 dimerization interface; other site 316407000340 active site 316407000341 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 316407000342 amidase catalytic site; other site 316407000343 Zn binding residues; other site 316407000344 substrate binding site; other site 316407000345 CobD/Cbib protein; Region: CobD_Cbib; cl00561 316407000346 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407000347 Amino acid permease; Region: AA_permease; pfam00324 316407000348 Transcriptional regulators [Transcription]; Region: FadR; COG2186 316407000349 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407000350 DNA binding site 316407000351 FCD domain; Region: FCD; cl11656 316407000352 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 316407000353 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 316407000354 dimer interface; other site 316407000355 TPP-binding site; other site 316407000356 pyruvate dehydrogenase dihydrolipoyltransacetylase; Validated; Region: aceF; PRK11854 316407000357 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 316407000358 E3 interaction surface; other site 316407000359 lipoyl attachment site; other site 316407000360 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 316407000361 E3 interaction surface; other site 316407000362 lipoyl attachment site; other site 316407000363 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 316407000364 E3 interaction surface; other site 316407000365 lipoyl attachment site; other site 316407000366 e3 binding domain; Region: E3_binding; pfam02817 316407000367 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 316407000368 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 316407000369 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407000370 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407000371 Pyridine nucleotide-disulphide oxidoreductase, dimerization domain; Region: Pyr_redox_dim; pfam02852 316407000372 Protein of unknown function (DUF3300); Region: DUF3300; pfam11737 316407000373 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 316407000374 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 316407000375 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...; Region: AcnB_Swivel; cd01576 316407000376 substrate binding site; other site 316407000377 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 316407000378 substrate binding site; other site 316407000379 ligand binding site; other site 316407000380 Uncharacterized protein family (UPF0231); Region: UPF0231; cl11474 316407000381 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; cl00687 316407000382 spermidine synthase; Provisional; Region: PRK00811 316407000383 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 316407000384 S-adenosylmethionine binding site; other site 316407000385 Bacterial chaperone lipoprotein (PulS_OutS); Region: PulS_OutS; cl09898 316407000386 multicopper oxidase; Provisional; Region: PRK10965 316407000387 Multicopper oxidase; Region: Cu-oxidase; cl14658 316407000388 Multicopper oxidase; Region: Cu-oxidase; cl14658 316407000389 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family; Region: PQQ_membr_DH; TIGR03074 316407000390 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 316407000391 Trp docking motif; other site 316407000392 active site 316407000393 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 316407000394 Trp docking motif; other site 316407000395 active site 316407000396 'Velcro' closure; other site 316407000397 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 316407000398 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 316407000399 active site clefts 316407000400 zinc binding site; other site 316407000401 dimer interface; other site 316407000402 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 316407000403 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407000404 Walker A/P-loop; other site 316407000405 ATP binding site; other site 316407000406 Q-loop/lid; other site 316407000407 ABC transporter signature motif; other site 316407000408 Walker B; other site 316407000409 D-loop; other site 316407000410 H-loop/switch region; other site 316407000411 ABC-2 type transporter; Region: ABC2_membrane; cl11417 316407000412 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_man; cd00006 316407000413 active pocket/dimerization site; other site 316407000414 active site 316407000415 phosphorylation site 316407000416 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 316407000417 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 316407000418 tetramerization interface; other site 316407000419 active site 316407000420 hypothetical protein; Provisional; Region: PRK09956 316407000421 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 316407000422 pantoate--beta-alanine ligase; Region: panC; TIGR00018 316407000423 Pantoate-beta-alanine ligase; Region: PanC; cd00560 316407000424 active site 316407000425 ATP-binding site; other site 316407000426 pantoate-binding site; other site 316407000427 HXXH motif; other site 316407000428 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 316407000429 oligomerization interface; other site 316407000430 active site 316407000431 metal-binding site 316407000432 Fimbrial protein; Region: Fimbrial; cl01416 316407000433 Fimbrial protein; Region: Fimbrial; cl01416 316407000434 putative fimbrial protein StaE; Provisional; Region: PRK15263 316407000435 putative fimbrial protein StkD; Provisional; Region: PRK15306; cl14700 316407000436 putative fimbrial outer membrane usher protein; Provisional; Region: PRK09828 316407000437 pilin outer membrane usher protein SafC; Provisional; Region: PRK15223; cl14650 316407000438 putative chaperone protein EcpD; Provisional; Region: PRK09926 316407000439 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 316407000440 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 316407000441 Fimbrial protein; Region: Fimbrial; cl01416 316407000442 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 316407000443 catalytic center binding site; other site 316407000444 ATP binding site; other site 316407000445 poly(A) polymerase I; Provisional; Region: pcnB; PRK11623 316407000446 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 316407000447 active site 316407000448 NTP binding site; other site 316407000449 metal binding triad; metal-binding site 316407000450 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 316407000451 active site 316407000452 nucleotide binding site; other site 316407000453 HIGH motif; other site 316407000454 KMSKS motif; other site 316407000455 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 316407000456 Sugar fermentation stimulation protein; Region: SfsA; cl00647 316407000457 2'-5' RNA ligase; Provisional; Region: PRK15124 316407000458 2',5' RNA ligase family; Region: 2_5_RNA_ligase; pfam02834 316407000459 2',5' RNA ligase family; Region: 2_5_RNA_ligase; pfam02834 316407000460 ATP-dependent RNA helicase HrpB; Provisional; Region: PRK11664 316407000461 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 316407000462 ATP binding site; other site 316407000463 putative Mg++ binding site; other site 316407000464 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; cl12029 316407000465 Helicase associated domain (HA2); Region: HA2; cl04503 316407000466 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 316407000467 bifunctional glycosyl transferase/transpeptidase; Reviewed; Region: mrcB; PRK09506 316407000468 Transglycosylase; Region: Transgly; cl07896 316407000469 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 316407000470 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 316407000471 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 316407000472 N-terminal plug; other site 316407000473 ligand-binding site; other site 316407000474 iron-hydroxamate transporter ATP-binding subunit; Provisional; Region: PRK10575 316407000475 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 316407000476 Walker A/P-loop; other site 316407000477 ATP binding site; other site 316407000478 Q-loop/lid; other site 316407000479 ABC transporter signature motif; other site 316407000480 Walker B; other site 316407000481 D-loop; other site 316407000482 H-loop/switch region; other site 316407000483 Fe3+-siderophore binding domain FhuD. These proteins have been shown to function as initial receptors in ABC transport of Fe3+-siderophores in many eubacterial species. They belong to the TroA-like superfamily of helical backbone metal receptor...; Region: FhuD; cd01146 316407000484 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 316407000485 siderophore binding site; other site 316407000486 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 316407000487 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...; Region: TM_ABC_iron-siderophores_like; cd06550 316407000488 ABC-ATPase subunit interface; other site 316407000489 dimer interface; other site 316407000490 putative PBP binding regions; other site 316407000491 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...; Region: TM_ABC_iron-siderophores_like; cd06550 316407000492 ABC-ATPase subunit interface; other site 316407000493 dimer interface; other site 316407000494 putative PBP binding regions; other site 316407000495 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 316407000496 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 316407000497 inhibitor-cofactor binding pocket; inhibition site 316407000498 pyridoxal 5'-phosphate binding site; other site 316407000499 catalytic residue; other site 316407000500 ClC chloride channel EriC. This domain is found in the EriC chloride transporters that mediate the extreme acid resistance response in eubacteria and archaea. This response allows bacteria to survive in the acidic environments by decarboxylation-...; Region: EriC; cd01031 316407000501 Voltage gated chloride channel; Region: Voltage_CLC; pfam00654 316407000502 Cl- selectivity filter; other site 316407000503 Cl- binding residues; other site 316407000504 pore gating glutamate residue; other site 316407000505 dimer interface; other site 316407000506 H+/Cl- coupling transport residue; other site 316407000507 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 316407000508 hypothetical protein; Provisional; Region: PRK10578 316407000509 UPF0126 domain; Region: UPF0126; pfam03458 316407000510 UPF0126 domain; Region: UPF0126; pfam03458 316407000511 vitamin B12-transporter protein BtuF; Provisional; Region: PRK03379 316407000512 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...; Region: BtuF; cd01144 316407000513 cobalamin binding residues; other site 316407000514 putative BtuC binding residues; other site 316407000515 dimer interface; other site 316407000516 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 316407000517 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 316407000518 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01096 316407000519 serine endoprotease; Provisional; Region: PRK10942 316407000520 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...; Region: Tryp_SPc; cl00149 316407000521 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 C-...; Region: PDZ_serine_protease; cd00987 316407000522 protein binding site; other site 316407000523 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 C-...; Region: PDZ_serine_protease; cd00987 316407000524 carbohydrate diacid transcriptional activator CdaR; Provisional; Region: PRK11477 316407000525 Putative sugar diacid recognition; Region: Diacid_rec; pfam05651 316407000526 Protein of unknown function (DUF3461); Region: DUF3461; cl10125 316407000527 Predicted phosphohydrolases [General function prediction only]; Region: COG1408 316407000528 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 316407000529 putative active site; other site 316407000530 putative metal binding site; other site 316407000531 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 316407000532 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 316407000533 trimer interface; other site 316407000534 active site 316407000535 substrate binding site; other site 316407000536 CoA binding site; other site 316407000537 PII uridylyl-transferase; Provisional; Region: PRK05007 316407000538 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 316407000539 metal binding triad; other site 316407000540 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 316407000541 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 316407000542 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 316407000543 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 316407000544 methionine aminopeptidase; Reviewed; Region: PRK07281 316407000545 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 316407000546 active site 316407000547 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 316407000548 rRNA interaction site; other site 316407000549 S8 interaction site; other site 316407000550 putative laminin-1 binding site; other site 316407000551 elongation factor Ts; Provisional; Region: tsf; PRK09377 316407000552 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 316407000553 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 316407000554 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...; Region: AAK_UMPK-PyrH-Ec; cd04254 316407000555 putative nucleotide binding site; other site 316407000556 uridine monophosphate binding site; other site 316407000557 homohexameric interface; other site 316407000558 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 round of...; Region: RRF; cd00520 316407000559 hinge region; other site 316407000560 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 316407000561 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 316407000562 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 316407000563 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; cd00475 316407000564 catalytic residue; other site 316407000565 putative FPP diphosphate binding site; other site 316407000566 putative FPP binding hydrophobic cleft; other site 316407000567 dimer interface; other site 316407000568 putative IPP diphosphate binding site; other site 316407000569 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 316407000570 zinc metallopeptidase RseP; Provisional; Region: PRK10779 316407000571 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 316407000572 active site 316407000573 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...; Region: PDZ_metalloprotease; cd00989 316407000574 protein binding site; other site 316407000575 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 316407000576 putative substrate binding region; other site 316407000577 outer membrane protein assembly factor YaeT; Provisional; Region: PRK11067 316407000578 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 316407000579 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 316407000580 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 316407000581 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 316407000582 Surface antigen; Region: Bac_surface_Ag; cl03097 316407000583 Outer membrane protein (OmpH-like); Region: OmpH; cl08146 316407000584 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 316407000585 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 316407000586 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-2,3-...; Region: LbH_LpxD; cd03352 316407000587 trimer interface; other site 316407000588 active site 316407000589 UDP-GlcNAc binding site; other site 316407000590 lipid-binding site 316407000591 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 316407000592 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 316407000593 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...; Region: LbH_UDP-GlcNAc_AT; cd03351 316407000594 active site 316407000595 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 316407000596 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 316407000597 bacterial Ribonuclease HII-like; Region: RNaseH_typeII_bacteria_HII_like; cd07182 316407000598 active site 316407000599 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 316407000600 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 316407000601 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 316407000602 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...; Region: DnaE_OBF; cd04485 316407000603 generic binding surface II; other site 316407000604 generic binding surface I; other site 316407000605 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 316407000606 lysine decarboxylase LdcC; Provisional; Region: PRK15399 316407000607 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; cl09944 316407000608 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...; Region: Orn_deC_like; cd00615 316407000609 homodimer interface; other site 316407000610 pyridoxal 5'-phosphate binding site; other site 316407000611 catalytic residue; other site 316407000612 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 316407000613 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 316407000614 putative metal binding site; other site 316407000615 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 316407000616 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 316407000617 Ligand Binding Site; other site 316407000618 TilS substrate binding domain; Region: TilS; pfam09179 316407000619 B3/4 domain; Region: B3_4; cl11458 316407000620 Modulator of Rho-dependent transcription termination (ROF); Region: ROF; cl09210 316407000621 Uncharacterized protein family (UPF0253); Region: UPF0253; cl11640 316407000622 YaeQ protein; Region: YaeQ; cl01913 316407000623 RF-1 domain; Region: RF-1; cl02875 316407000624 Uncharacterized lipoprotein NlpE involved in copper resistance; Region: NlpE; cl01138 316407000625 hypothetical protein; Provisional; Region: PRK11479 316407000626 Orthopoxvirus protein of unknown function (DUF830); Region: DUF830; cl13998 316407000627 prolyl-tRNA synthetase; Provisional; Region: PRK09194 316407000628 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 formation...; Region: ProRS_core_prok; cd00779 316407000629 dimer interface; other site 316407000630 motif 1; other site 316407000631 active site 316407000632 motif 2; other site 316407000633 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 single-...; Region: ProRS-INS; cd04334 316407000634 putative deacylase active site; other site 316407000635 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 316407000636 active site 316407000637 motif 3; other site 316407000638 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-...; Region: ProRS_anticodon_short; cd00861 316407000639 anticodon binding site; other site 316407000640 Uncharacterized protein family UPF0066; Region: UPF0066; cl00749 316407000641 outer membrane lipoprotein; Reviewed; Region: rcsF; PRK10781 316407000642 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 316407000643 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...; Region: TM_PBP2; cd06261 316407000644 dimer interface; other site 316407000645 conserved gate region; other site 316407000646 ABC-ATPase subunit interface; other site 316407000647 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 316407000648 MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport. Other members of this system include the MetP permease and the MetQ substrate binding protein; Region: ABC_MetN_methionine_transporter; cd03258 316407000649 Walker A/P-loop; other site 316407000650 ATP binding site; other site 316407000651 Q-loop/lid; other site 316407000652 ABC transporter signature motif; other site 316407000653 Walker B; other site 316407000654 D-loop; other site 316407000655 H-loop/switch region; other site 316407000656 NIL domain; Region: NIL; pfam09383 316407000657 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 316407000658 active site 316407000659 motif I; other site 316407000660 motif II; other site 316407000661 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...; Region: Aldo_ket_red; cd06660 316407000662 active site 316407000663 catalytic tetrad; other site 316407000664 Transcriptional regulator [Transcription]; Region: LysR; COG0583 316407000665 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407000666 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA; cd08478 316407000667 putative effector binding pocket; other site 316407000668 dimerization interface; other site 316407000669 Endonuclease/Exonuclease/phosphatase family; Region: Exo_endo_phos; cl00490 316407000670 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 316407000671 S-adenosylmethionine binding site; other site 316407000672 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 316407000673 MLTD_N; Region: MLTD_N; pfam06474 316407000674 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 catalyze...; Region: LT_GEWL; cd00254 316407000675 N-acetyl-D-glucosamine binding site; other site 316407000676 catalytic residue; other site 316407000677 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 316407000678 putative peptidoglycan binding site; other site 316407000679 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 316407000680 putative peptidoglycan binding site; other site 316407000681 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 316407000682 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; cl12011 316407000683 RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack...; Region: RnaseH; cd06222 316407000684 RNA/DNA hybrid binding site; other site 316407000685 active site 316407000686 Proteobacterial; Region: dnaQ_proteo; TIGR01406 316407000687 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 316407000688 active site 316407000689 substrate binding site; other site 316407000690 catalytic site; other site 316407000691 Transposase [DNA replication, recombination, and repair]; Region: COG5433 316407000692 Predicted amidohydrolase [General function prediction only]; Region: COG0388 316407000693 Xanthomonas campestris XC1258 and related proteins, members of the nitrilase superfamily (putative class 13 nitrilases); Region: Xc-1258_like; cd07575 316407000694 putative active site; other site 316407000695 catalytic triad; other site 316407000696 multimer interface; other site 316407000697 dimer interface; other site 316407000698 Inhibitor of vertebrate lysozyme (Ivy); Region: Ivy; cl07428 316407000699 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 316407000700 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 316407000701 active site 316407000702 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 316407000703 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 316407000704 dimer interface; other site 316407000705 active site 316407000706 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 316407000707 putative active site; other site 316407000708 putative dimer interface; other site 316407000709 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 316407000710 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 316407000711 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 316407000712 RelB antitoxin; Region: RelB; cl01171 316407000713 NlpC/P60 family; Region: NLPC_P60; cl11438 316407000714 Transposase IS200 like; Region: Transposase_17; cl00848 316407000715 ECK0230:JW5811:b0229; flagellar system protein, promoterless fragment 316407000716 ECK0231:JW5812:b0230; flagellar system protein, promoterless fragment 316407000717 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 316407000718 active site 316407000719 DNA polymerase IV; Validated; Region: PRK02406 316407000720 DNA binding site 316407000721 Phd_YefM; Region: PhdYeFM; cl09153 316407000722 putative toxin YafO; Provisional; Region: PRK09885 316407000723 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 316407000724 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 316407000725 Coenzyme A binding pocket; other site 316407000726 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a...; Region: Hint; cl12032 316407000727 RF-1 domain; Region: RF-1; cl02875 316407000728 Peptidase dimerization domain; Region: M20_dimer; cl09126 316407000729 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 316407000730 fermentation/respiration switch protein; Reviewed; Region: frsA; PRK05077 316407000731 Periplasmic glucan biosynthesis protein, MdoG; Region: MdoG; cl01208 316407000732 Transcriptional regulator Crl; Region: Crl; cl11653 316407000733 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...; Region: gram_neg_porins; cd00342 316407000734 trimer interface; other site 316407000735 eyelet of channel; other site 316407000736 gamma-glutamyl kinase; Provisional; Region: PRK05429 316407000737 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 316407000738 nucleotide binding site; other site 316407000739 homotetrameric interface; other site 316407000740 putative phosphate binding site; other site 316407000741 putative allosteric binding site; other site 316407000742 PUA domain; Region: PUA; cl00607 316407000743 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 316407000744 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 316407000745 putative catalytic cysteine; other site 316407000746 Protein of unknown function (DUF1219); Region: DUF1219; pfam06755 316407000747 YagB/YeeU/YfjZ family; Region: YagB_YeeU_YfjZ; pfam06154 316407000748 Protein of unknown function (DUF987); Region: DUF987; pfam06174 316407000749 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 316407000750 MPN+ (JAMM) motif; other site 316407000751 Zinc-binding site; other site 316407000752 Antirestriction protein; Region: Antirestrict; pfam03230 316407000753 Bacterial protein of unknown function (DUF905); Region: DUF905; pfam06006 316407000754 Predicted transcriptional regulator [Transcription]; Region: COG2378 316407000755 Domain of unknown function (DUF932); Region: DUF932; cl12129 316407000756 Predicted GTPase [General function prediction only]; Region: COG3596 316407000757 Era (E. coli Ras-like protein)-like. This family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngG), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs)...; Region: Era_like; cd00880 316407000758 G1 box; other site 316407000759 GTP/Mg2+ binding site; other site 316407000760 Switch I region; other site 316407000761 G2 box; other site 316407000762 Switch II region; other site 316407000763 G3 box; other site 316407000764 G4 box; other site 316407000765 G5 box; other site 316407000766 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 316407000767 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407000768 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 316407000769 dimerization interface; other site 316407000770 substrate binding pocket; other site 316407000771 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 316407000772 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; cl01116 316407000773 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 316407000774 Integrase core domain; Region: rve; cl01316 316407000775 putative transposase OrfB; Reviewed; Region: PHA02517 316407000776 Retron-type reverse transcriptase [DNA replication, recombination, and repair]; Region: COG3344 316407000777 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 316407000778 putative active site; other site 316407000779 putative NTP binding site; other site 316407000780 putative nucleic acid binding site; other site 316407000781 Transposase domain (DUF772); Region: DUF772; cl12084 316407000782 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 316407000783 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407000784 Amino acid permease; Region: AA_permease; pfam00324 316407000785 Homocysteine/selenocysteine methylase (S-methylmethionine-dependent) [Amino acid transport and metabolism]; Region: MHT1; cl14105 316407000786 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 316407000787 ferric transporter ATP-binding subunit; Provisional; Region: fbpC; PRK11432 316407000788 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407000789 Walker A/P-loop; other site 316407000790 ATP binding site; other site 316407000791 Q-loop/lid; other site 316407000792 ABC transporter signature motif; other site 316407000793 Walker B; other site 316407000794 D-loop; other site 316407000795 H-loop/switch region; other site 316407000796 TOBE domain; Region: TOBE_2; cl01440 316407000797 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...; Region: TM_PBP2; cd06261 316407000798 ABC-ATPase subunit interface; other site 316407000799 putative PBP binding loops; other site 316407000800 IS1 transposase; Region: Transposase_27; cl00721 316407000801 Insertion element protein; Region: Ins_element1; pfam03811 316407000802 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 316407000803 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; cl01116 316407000804 YagB/YeeU/YfjZ family; Region: YagB_YeeU_YfjZ; pfam06154 316407000805 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; cl01116 316407000806 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 316407000807 Integrase core domain; Region: rve; cl01316 316407000808 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 316407000809 Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family...; Region: DHDPS-like; cd00408 316407000810 inhibitor site; inhibition site 316407000811 active site 316407000812 dimer interface; other site 316407000813 catalytic residue; other site 316407000814 Dehydratase family; Region: ILVD_EDD; cl00340 316407000815 probable dehydratase, YjhG/YagF family; Region: yjhG_yagF; TIGR03432 316407000816 putative symporter YagG; Provisional; Region: PRK09669 316407000817 putative transporter; Provisional; Region: PRK11462 316407000818 Beta-xylosidase [Carbohydrate transport and metabolism]; Region: XynB; COG3507 316407000819 Glycosyl hydrolase family 43, beta-D-xylosidase; Region: GH43_XYL_1; cd09000 316407000820 inhibitor binding site; inhibition site 316407000821 active site 316407000822 Protein of unknown function (DUF1349); Region: DUF1349; cl01397 316407000823 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407000824 Transcriptional regulator [Transcription]; Region: IclR; COG1414 316407000825 Bacterial transcriptional regulator; Region: IclR; pfam01614 316407000826 ornithine carbamoyltransferase subunit I; Provisional; Region: PRK03515 316407000827 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 316407000828 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 316407000829 IS1 transposase; Region: Transposase_27; cl00721 316407000830 Insertion element protein; Region: Ins_element1; pfam03811 316407000831 Protein of unknown function (DUF3296); Region: DUF3296; pfam11726 316407000832 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 316407000833 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 316407000834 Phage integrase family; Region: Phage_integrase; pfam00589 316407000835 DNA binding site 316407000836 Int/Topo IB signature motif; other site 316407000837 active site 316407000838 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 316407000839 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 316407000840 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 316407000841 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 316407000842 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; pfam01315 316407000843 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 316407000844 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 316407000845 FAD binding domain; Region: FAD_binding_4; cl10516 316407000846 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; pfam03450 316407000847 aldehyde oxidoreductase 2Fe-2S subunit; Provisional; Region: PRK11433 316407000848 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; cl00159 316407000849 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 316407000850 Protein of unknown function (DUF1440); Region: DUF1440; cl01380 316407000851 Uncharacterized protein family (UPF0153); Region: UPF0153; cl00497 316407000852 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 316407000853 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...; Region: LuxR_C_like; cd06170 316407000854 DNA binding residues 316407000855 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 316407000856 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 316407000857 Protein of unknown function (DUF3442); Region: DUF3442; pfam11924 316407000858 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; cl01116 316407000859 putative transposase OrfB; Reviewed; Region: PHA02517 316407000860 Integrase core domain; Region: rve; cl01316 316407000861 right oriC-binding transcriptional activator; Provisional; Region: PRK15121 316407000862 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407000863 Protein of unknown function, DUF417; Region: DUF417; cl01162 316407000864 Protein of unknown function (DUF1471); Region: DUF1471; cl11507 316407000865 pyridine nucleotide-disulfide oxidoreductase; Provisional; Region: PRK08010 316407000866 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407000867 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407000868 Pyridine nucleotide-disulphide oxidoreductase, dimerization domain; Region: Pyr_redox_dim; pfam02852 316407000869 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 316407000870 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407000871 C subunit; Region: glycerol3P_GlpC; TIGR03379 316407000872 Cysteine-rich domain; Region: CCG; pfam02754 316407000873 Cysteine-rich domain; Region: CCG; pfam02754 316407000874 iron-sulfur cluster-binding protein; Region: TIGR00273 316407000875 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; cl00674 316407000876 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 alpha-; Region: HCP_like; cl14655 316407000877 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 316407000878 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; cl00674 316407000879 choline dehydrogenase; Validated; Region: PRK02106 316407000880 GMC oxidoreductase; Region: GMC_oxred_N; pfam00732 316407000881 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 316407000882 NAD+-dependent 4-trimethylaminobutyraldehyde dehydrogenase, ALDH family 9A1; Region: ALDH_F9_TMBADH; cd07090 316407000883 tetrameric interface; other site 316407000884 NAD binding site; other site 316407000885 catalytic residues; other site 316407000886 transcriptional regulator BetI; Validated; Region: PRK00767 316407000887 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316407000888 choline transport protein BetT; Provisional; Region: PRK09928 316407000889 BCCT family transporter; Region: BCCT; cl00569 316407000890 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...; Region: LuxR_C_like; cd06170 316407000891 DNA binding residues 316407000892 dimerization interface; other site 316407000893 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 316407000894 DNA-binding transcriptional activator AllS; Provisional; Region: PRK10094 316407000895 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407000896 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 316407000897 dimerization interface; other site 316407000898 Protein of unknown function (DUF1097); Region: DUF1097; pfam06496 316407000899 Voltage-dependent potassium channel; Provisional; Region: PLN03192 316407000900 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 316407000901 Protein of unknown function (DUF2877); Region: DUF2877; pfam11392 316407000902 Succinyl-CoA synthetase, alpha subunit [Energy production and conversion]; Region: SucD; COG0074 316407000903 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407000904 CoA-ligase; Region: Ligase_CoA; pfam00549 316407000905 membrane protein FdrA; Validated; Region: PRK06091 316407000906 Protein of unknown function (DUF1116); Region: DUF1116; pfam06545 316407000907 carbamate kinase; Reviewed; Region: PRK12686 316407000908 AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an...; Region: AAK_CK; cd04235 316407000909 putative substrate binding site; other site 316407000910 nucleotide binding site; other site 316407000911 nucleotide binding site; other site 316407000912 homodimer interface; other site 316407000913 Bacterial cytosine deaminase and related metal-dependent hydrolases. Cytosine deaminases (CDs) catalyze the deamination of cytosine, producing uracil and ammonia. They play an important role in pyrimidine salvage. CDs are present in prokaryotes and...; Region: Bact_CD; cd01293 316407000914 cytosine deaminase; Provisional; Region: PRK05985 316407000915 active site 316407000916 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 316407000917 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 316407000918 putative NAD(P) binding site; other site 316407000919 putative substrate binding site; other site 316407000920 catalytic Zn binding site; other site 316407000921 structural Zn binding site; other site 316407000922 dimer interface; other site 316407000923 LysE type translocator; Region: LysE; cl00565 316407000924 Protein of unknown function (DUF1471); Region: DUF1471; cl11507 316407000925 propionate catabolism operon regulatory protein PrpR; Provisional; Region: PRK15424 316407000926 Propionate catabolism activator; Region: PrpR_N; pfam06506 316407000927 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...; Region: AAA; cd00009 316407000928 Walker A motif; other site 316407000929 ATP binding site; other site 316407000930 Walker B motif; other site 316407000931 arginine finger; other site 316407000932 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 316407000933 PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]; Region: PrpB; COG2513 316407000934 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 316407000935 tetramer interface; other site 316407000936 active site 316407000937 Mg2+/Mn2+ binding site; other site 316407000938 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 316407000939 Subgroup of 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 (...; Region: Ec2MCS_like_1; cd06117 316407000940 dimer interface; other site 316407000941 active site 316407000942 citrylCoA binding site; other site 316407000943 oxalacetate/citrate binding site; other site 316407000944 coenzyme A binding site; other site 316407000945 catalytic triad; other site 316407000946 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 316407000947 2-methylcitrate dehydratase; Region: prpD; TIGR02330 316407000948 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 316407000949 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 316407000950 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 316407000951 Purine-cytosine permease and related proteins [Nucleotide transport and metabolism]; Region: CodB; COG1457 316407000952 Sodium:solute symporter family; Region: SSF; cl00456 316407000953 Cytosine deaminase and related metal-dependent hydrolases [Nucleotide transport and metabolism / General function prediction only]; Region: SsnA; COG0402 316407000954 Bacterial cytosine deaminase and related metal-dependent hydrolases. Cytosine deaminases (CDs) catalyze the deamination of cytosine, producing uracil and ammonia. They play an important role in pyrimidine salvage. CDs are present in prokaryotes and...; Region: Bact_CD; cd01293 316407000955 active site 316407000956 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 316407000957 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407000958 The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold; Region: PBP2_CynR; cd08425 316407000959 dimerization interface; other site 316407000960 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeB; cd00884 316407000961 active site clefts 316407000962 zinc binding site; other site 316407000963 dimer interface; other site 316407000964 cyanate hydratase; Validated; Region: PRK02866 316407000965 Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the...; Region: Cyanase_C; cd00559 316407000966 oligomer interface; other site 316407000967 active site 316407000968 putative cyanate transporter; Provisional; Region: cynX; PRK09705 316407000969 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 316407000970 galactoside O-acetyltransferase; Reviewed; Region: lacA; PRK09527 316407000971 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 316407000972 active site 316407000973 substrate binding site; other site 316407000974 trimer interface; other site 316407000975 CoA binding site; other site 316407000976 LacY proton/sugar symporter; Region: LacY_symp; pfam01306 316407000977 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 316407000978 putative substrate translocation pore; other site 316407000979 beta-D-galactosidase; Reviewed; Region: lacZ; PRK09525 316407000980 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 316407000981 domain; Region: Glyco_hydro_2; pfam00703 316407000982 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 316407000983 Beta galactosidase small chain; Region: Bgal_small_N; pfam02929 316407000984 lac repressor; Reviewed; Region: lacI; PRK09526 316407000985 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 316407000986 DNA binding site 316407000987 domain linker motif; other site 316407000988 Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_LacI; cd01574 316407000989 ligand binding site; other site 316407000990 dimerization interface (open form); other site 316407000991 dimerization interface (closed form); other site 316407000992 DNA-binding transcriptional activator MhpR; Provisional; Region: PRK09834 316407000993 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407000994 Bacterial transcriptional regulator; Region: IclR; pfam01614 316407000995 3-(3-hydroxyphenyl)propionate hydroxylase; Validated; Region: mhpA; PRK06183 316407000996 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407000997 Subunit B of the Class III Extradiol ring-cleavage dioxygenase, 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB), which catalyzes the oxidization and subsequent ring-opening of 2,3-dihydroxyphenylpropionate; Region: MhpB_like; cd07365 316407000998 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 316407000999 putative active site; other site 316407001000 Fe(II) binding site; other site 316407001001 putative dimer interface; other site 316407001002 putative tetramer interface; other site 316407001003 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 316407001004 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; cl12031 316407001005 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 316407001006 acetaldehyde dehydrogenase; Validated; Region: PRK08300 316407001007 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407001008 Prokaryotic acetaldehyde dehydrogenase, dimerization; Region: AcetDehyd-dimer; pfam09290 316407001009 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 316407001010 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 316407001011 active site 316407001012 catalytic residues; other site 316407001013 metal-binding site 316407001014 DmpG-like communication domain; Region: DmpG_comm; pfam07836 316407001015 putative 3-hydroxyphenylpropionic transporter MhpT; Provisional; Region: PRK11551 316407001016 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 316407001017 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 316407001018 Uncharacterized protein conserved in bacteria (DUF2058); Region: DUF2058; cl01201 316407001019 Predicted esterase [General function prediction only]; Region: COG0627 316407001020 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; cl12031 316407001021 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 316407001022 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 316407001023 substrate binding site; other site 316407001024 catalytic Zn binding site; other site 316407001025 NAD binding site; other site 316407001026 structural Zn binding site; other site 316407001027 dimer interface; other site 316407001028 Uncharacterized BCR, COG1937; Region: DUF156; cl00846 316407001029 ECK0356:JW0350:b0359; predicted acyl transferase 316407001030 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; cl01116 316407001031 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 316407001032 IS2 transposase TnpB; Reviewed; Region: PRK09409 316407001033 Integrase core domain; Region: rve; cl01316 316407001034 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 316407001035 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 316407001036 putative trimer interface; other site 316407001037 putative CoA binding site; other site 316407001038 Glycosyltransferases, probably involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG1215 316407001039 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 316407001040 DXD motif; other site 316407001041 GlcNAc-PI de-N-acetylase; Region: PIG-L; cl00929 316407001042 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 316407001043 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...; Region: PBPb; cd00134 316407001044 substrate binding pocket; other site 316407001045 membrane-bound complex binding site; other site 316407001046 hinge residues; other site 316407001047 taurine transporter ATP-binding subunit; Provisional; Region: tauB; PRK11248 316407001048 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 316407001049 Walker A/P-loop; other site 316407001050 ATP binding site; other site 316407001051 Q-loop/lid; other site 316407001052 ABC transporter signature motif; other site 316407001053 Walker B; other site 316407001054 D-loop; other site 316407001055 H-loop/switch region; other site 316407001056 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...; Region: TM_PBP2; cd06261 316407001057 dimer interface; other site 316407001058 conserved gate region; other site 316407001059 putative PBP binding loops; other site 316407001060 ABC-ATPase subunit interface; other site 316407001061 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 316407001062 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG...; Region: CAS_like; cl00184 316407001063 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 316407001064 dimer interface; other site 316407001065 active site 316407001066 Schiff base residues; other site 316407001067 putative transposase OrfB; Reviewed; Region: PHA02517 316407001068 Integrase core domain; Region: rve; cl01316 316407001069 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; cl01116 316407001070 Pertactin-like passenger domains (virulence factors) of autotransporter proteins of the type V secretion system. Autotransporters are proteins used by Gram-negative bacteria to transport proteins across their outer membranes. The C-terminal (beta)...; Region: PL_Passenger_AT; cd00253 316407001071 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 316407001072 Autotransporter beta-domain; Region: Autotransporter; cl02365 316407001073 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11832 316407001074 Beta-lactamase; Region: Beta-lactamase; cl01009 316407001075 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 316407001076 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 316407001077 Protein of unknown function (DUF1615); Region: DUF1615; pfam07759 316407001078 Protein of unknown function (DUF2755); Region: DUF2755; pfam10954 316407001079 Protein of unknown function (DUF2754); Region: DUF2754; pfam10953 316407001080 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 316407001081 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 316407001082 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 316407001083 Sigma-S stabilisation anti-adaptor protein; Region: Anti-adapt_IraP; cl11681 316407001084 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 316407001085 dimer interface; other site 316407001086 Alkaline phosphatase homologues; Region: alkPPc; smart00098 316407001087 active site 316407001088 psiF repeat; Region: PsiF_repeat; pfam07769 316407001089 psiF repeat; Region: PsiF_repeat; pfam07769 316407001090 diguanylate cyclase AdrA; Provisional; Region: adrA; PRK10245 316407001091 MASE2 domain; Region: MASE2; pfam05230 316407001092 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316407001093 metal-binding site 316407001094 active site 316407001095 I-site; other site 316407001096 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 316407001097 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407001098 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; cl00727 316407001099 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...; Region: SK; cd00464 316407001100 shikimate kinase; Reviewed; Region: aroK; PRK00131 316407001101 ADP binding site; other site 316407001102 magnesium binding site; other site 316407001103 putative shikimate binding site; other site 316407001104 hypothetical protein; Provisional; Region: PRK10380 316407001105 AroM protein; Region: AroM; cl06364 316407001106 Protein of unknown function (DUF1255); Region: DUF1255; cl01202 316407001107 Protein of unknown function (DUF2773); Region: DUF2773; pfam10971 316407001108 Putative exonuclease, RdgC; Region: RdgC; cl01122 316407001109 fructokinase; Reviewed; Region: PRK09557 316407001110 ROK family; Region: ROK; cl09121 316407001111 MFS transport protein AraJ; Provisional; Region: PRK10091 316407001112 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 316407001113 putative substrate translocation pore; other site 316407001114 exonuclease subunit SbcC; Provisional; Region: PRK10246 316407001115 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407001116 Walker A/P-loop; other site 316407001117 ATP binding site; other site 316407001118 Q-loop/lid; other site 316407001119 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407001120 ABC transporter signature motif; other site 316407001121 Walker B; other site 316407001122 D-loop; other site 316407001123 H-loop/switch region; other site 316407001124 exonuclease subunit SbcD; Provisional; Region: PRK10966 316407001125 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 316407001126 active site 316407001127 metal-binding site 316407001128 DNA binding site 316407001129 Type 5 capsule protein repressor C terminal; Region: SbcD_C; pfam12320 316407001130 transcriptional regulator PhoB; Provisional; Region: PRK10161 316407001131 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 316407001132 active site 316407001133 phosphorylation site 316407001134 intermolecular recognition site; other site 316407001135 dimerization interface; other site 316407001136 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...; Region: trans_reg_C; cd00383 316407001137 DNA binding site 316407001138 phosphate regulon sensor protein; Provisional; Region: phoR; PRK11006 316407001139 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 316407001140 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 316407001141 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 trans-...; Region: HisKA; cd00082 316407001142 dimer interface; other site 316407001143 phosphorylation site 316407001144 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 316407001145 ATP binding site; other site 316407001146 Mg2+ binding site; other site 316407001147 G-X-G motif; other site 316407001148 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 316407001149 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407001150 Amino acid permease; Region: AA_permease; pfam00324 316407001151 maltodextrin glucosidase; Provisional; Region: PRK10785 316407001152 CD and pullulan-degrading enzymes N-terminus domain. Members of this subgroup include: Cyclomaltodextrinase (CDase), maltogenic amylase, and neopullulanase all of which are capable of hydrolyzing all or two of the following three types of substrates:...; Region: CD_pullulan_degrading_enzymes_N_term; cd02857 316407001153 homodimer; other site 316407001154 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 316407001155 Protein of unknown function, DUF479; Region: DUF479; cl01203 316407001156 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 316407001157 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 316407001158 Queuine tRNA-ribosyltransferase; Region: TGT; cl00409 316407001159 Preprotein translocase subunit; Region: YajC; cl00806 316407001160 EnvZ/OmpR regulon moderator; Provisional; Region: PRK10629 316407001161 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 316407001162 Protein export membrane protein; Region: SecD_SecF; cl14618 316407001163 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 316407001164 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 316407001165 Protein export membrane protein; Region: SecD_SecF; cl14618 316407001166 hypothetical protein; Provisional; Region: PRK11295 316407001167 Nucleoside-specific channel-forming protein, Tsx; Region: Channel_Tsx; cl04114 316407001168 Protein of unknown function (DUF3251); Region: DUF3251; cl08186 316407001169 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 316407001170 ATP cone domain; Region: ATP-cone; pfam03477 316407001171 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 316407001172 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 316407001173 catalytic motif; other site 316407001174 Zn binding site; other site 316407001175 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 5,10-...; Region: DHFR; cl00161 316407001176 6,7-dimethyl-8-ribityllumazine synthase; Region: DMRL_synthase; cl00317 316407001177 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 316407001178 putative RNA binding site; other site 316407001179 thiamine monophosphate kinase; Provisional; Region: PRK05731 316407001180 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 316407001181 ATP binding site; other site 316407001182 dimerization interface; other site 316407001183 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 316407001184 tetramer interfaces; other site 316407001185 binuclear metal-binding site; other site 316407001186 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...; Region: Aldo_ket_red; cd06660 316407001187 active site 316407001188 catalytic tetrad; other site 316407001189 1-deoxy-D-xylulose-5-phosphate synthase; Region: dxs; TIGR00204 316407001190 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 with important pharmaceutical activity. DXS...; Region: TPP_DXS; cd02007 316407001191 TPP-binding site; other site 316407001192 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 316407001193 PYR/PP interface; other site 316407001194 dimer interface; other site 316407001195 TPP binding site; other site 316407001196 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 316407001197 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 316407001198 substrate binding pocket; other site 316407001199 chain length determination region; other site 316407001200 substrate-Mg2+ binding site; other site 316407001201 catalytic residues; other site 316407001202 aspartate-rich region 1; other site 316407001203 active site lid residues 316407001204 aspartate-rich region 2; other site 316407001205 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 316407001206 tRNA s(4)U8 sulfurtransferase; Provisional; Region: PRK01269 316407001207 THUMP domain; Region: THUMP; cl12076 316407001208 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 316407001209 Ligand Binding Site; other site 316407001210 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 316407001211 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Region: GATase1_DJ-1; cd03135 316407001212 conserved cys residue; other site 316407001213 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 316407001214 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407001215 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 316407001216 Protein of unknown function (DUF520); Region: DUF520; cl00723 316407001217 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 316407001218 Major Facilitator Superfamily; Region: MFS_1; pfam07690 316407001219 putative substrate translocation pore; other site 316407001220 UbiA prenyltransferase family; Region: UbiA; cl00337 316407001221 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; cl01204 316407001222 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 316407001223 Subunit I/III interface; other site 316407001224 Subunit III/IV interface; other site 316407001225 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 316407001226 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 316407001227 D-pathway; other site 316407001228 Putative ubiquinol binding site; other site 316407001229 Low-spin heme (heme b) binding site; other site 316407001230 Putative water exit pathway; other site 316407001231 Binuclear center (heme o3/CuB); other site 316407001232 K-pathway; other site 316407001233 Putative proton exit pathway; other site 316407001234 cytochrome o ubiquinol oxidase subunit II; Provisional; Region: PRK10525 316407001235 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl10078 316407001236 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 316407001237 muropeptide transporter; Reviewed; Region: ampG; PRK11902 316407001238 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 316407001239 putative substrate translocation pore; other site 316407001240 hypothetical protein; Provisional; Region: PRK11627 316407001241 Uncharacterized lipoprotein; Region: Lipoprotein_16; pfam03923 316407001242 BolA-like protein; Region: BolA; cl00386 316407001243 trigger factor; Provisional; Region: tig; PRK01490 316407001244 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 316407001245 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 316407001246 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 316407001247 oligomer interface; other site 316407001248 active site residues 316407001249 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 316407001250 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 316407001251 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...; Region: AAA; cd00009 316407001252 Walker A motif; other site 316407001253 ATP binding site; other site 316407001254 Walker B motif; other site 316407001255 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 316407001256 DNA-binding ATP-dependent protease La; Provisional; Region: PRK10787 316407001257 Found in ATP-dependent protease La (LON); Region: LON; cl01056 316407001258 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...; Region: AAA; cd00009 316407001259 Walker A motif; other site 316407001260 ATP binding site; other site 316407001261 Walker B motif; other site 316407001262 arginine finger; other site 316407001263 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 316407001264 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 higher-...; Region: HU_IHF; cd00591 316407001265 IHF dimer interface; other site 316407001266 IHF - DNA interface; other site 316407001267 periplasmic folding chaperone; Provisional; Region: PRK10788 316407001268 SurA N-terminal domain; Region: SurA_N; pfam09312 316407001269 PPIC-type PPIASE domain; Region: Rotamase; cl08278 316407001270 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl11430 316407001271 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...; Region: 4HBT; cd00586 316407001272 active site 316407001273 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 316407001274 Ligand Binding Site; other site 316407001275 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG4533 316407001276 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cl01709 316407001277 thiamin pyrimidine pyrophosphate hydrolase; Provisional; Region: PRK15126 316407001278 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 316407001279 active site 316407001280 motif I; other site 316407001281 motif II; other site 316407001282 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; cl11391 316407001283 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 316407001284 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407001285 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 316407001286 putative multidrug transporter membrane\ATP-binding components; Provisional; Region: PRK10789 316407001287 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407001288 Walker A/P-loop; other site 316407001289 ATP binding site; other site 316407001290 Q-loop/lid; other site 316407001291 ABC transporter signature motif; other site 316407001292 Walker B; other site 316407001293 D-loop; other site 316407001294 H-loop/switch region; other site 316407001295 putative multidrug transporter membrane\ATP-binding components; Provisional; Region: PRK10790 316407001296 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 316407001297 Glucan exporter ATP-binding protein. In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide...; Region: ABCC_Glucan_exporter_like; cd03254 316407001298 Walker A/P-loop; other site 316407001299 ATP binding site; other site 316407001300 Q-loop/lid; other site 316407001301 ABC transporter signature motif; other site 316407001302 Walker B; other site 316407001303 D-loop; other site 316407001304 H-loop/switch region; other site 316407001305 Nitrogen regulatory protein P-II; Region: P-II; cl00412 316407001306 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 316407001307 acyl-CoA thioesterase II; Provisional; Region: PRK10526 316407001308 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 316407001309 active site 316407001310 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 316407001311 catalytic triad; other site 316407001312 dimer interface; other site 316407001313 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3126 316407001314 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 316407001315 DNA binding site 316407001316 active site 316407001317 Protein of unknown function (DUF1428); Region: DUF1428; cl02319 316407001318 Predicted signal transduction protein containing sensor and EAL domains [Signal transduction mechanisms]; Region: COG4943 316407001319 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 316407001320 Extracytoplasmic function sigma factor YlaC; Region: YlaC; pfam10777 316407001321 maltose O-acetyltransferase; Provisional; Region: PRK10092 316407001322 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 316407001323 active site 316407001324 substrate binding site; other site 316407001325 trimer interface; other site 316407001326 CoA binding site; other site 316407001327 Haemolysin expression modulating protein; Region: HHA; cl11501 316407001328 Biofilm formation regulator YbaJ; Region: YbaJ; cl11675 316407001329 multidrug efflux system protein AcrB; Provisional; Region: PRK15127 316407001330 Protein export membrane protein; Region: SecD_SecF; cl14618 316407001331 Protein export membrane protein; Region: SecD_SecF; cl14618 316407001332 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 316407001333 DNA-binding transcriptional repressor AcrR; Provisional; Region: PRK10668 316407001334 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316407001335 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 316407001336 hypothetical protein; Provisional; Region: PRK11281 316407001337 EXS family; Region: EXS; cl03905 316407001338 RnfE family; Region: NQR2_RnfD_RnfE; cl00779 316407001339 Mechanosensitive ion channel; Region: MS_channel; pfam00924 316407001340 Protein of unknown function (DUF2496); Region: DUF2496; cl11670 316407001341 Primosomal replication protein priB and priC; Region: priB_priC; cl11483 316407001342 Protein of unknown function (DUF454); Region: DUF454; cl01063 316407001343 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 316407001344 DNA polymerase III subunits gamma and tau; Validated; Region: PRK07994 316407001345 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...; Region: AAA; cd00009 316407001346 Walker A motif; other site 316407001347 ATP binding site; other site 316407001348 Walker B motif; other site 316407001349 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407001350 arginine finger; other site 316407001351 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 316407001352 DNA polymerase III subunits tau domain IV DnaB-binding; Region: DNA_pol3_tau_4; pfam12168 316407001353 DNA polymerase III tau subunit V interacting with alpha; Region: DNA_pol3_tau_5; pfam12170 316407001354 Uncharacterized BCR, YbaB family COG0718; Region: DUF149; cl00494 316407001355 recombination protein RecR; Reviewed; Region: recR; PRK00076 316407001356 RecR protein; Region: RecR; pfam02132 316407001357 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 316407001358 putative active site; other site 316407001359 putative metal-binding site; other site 316407001360 tetramer interface; other site 316407001361 heat shock protein 90; Provisional; Region: PRK05218 316407001362 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 316407001363 ATP binding site; other site 316407001364 Mg2+ binding site; other site 316407001365 G-X-G motif; other site 316407001366 adenylate kinase; Reviewed; Region: adk; PRK00279 316407001367 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 316407001368 AMP-binding site; other site 316407001369 ATP-AMP (Ap5A)-binding site; other site 316407001370 ferrochelatase; Region: hemH; TIGR00109 316407001371 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 316407001372 C-terminal domain interface; other site 316407001373 active site 316407001374 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 316407001375 active site 316407001376 N-terminal domain interface; other site 316407001377 acetyl esterase; Provisional; Region: PRK10162 316407001378 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, 2-...; Region: ribokinase_pfkB_like; cl00192 316407001379 putative cation:proton antiport protein; Provisional; Region: PRK10669 316407001380 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 316407001381 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407001382 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 316407001383 Major Facilitator Superfamily; Region: MFS_1; pfam07690 316407001384 putative substrate translocation pore; other site 316407001385 bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor; Reviewed; Region: ushA; PRK09558 316407001386 Escherichia coli UshA and related proteins, N-terminal metallophosphatase domain; Region: MPP_UshA_N; cd07405 316407001387 active site 316407001388 metal-binding site 316407001389 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 316407001390 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 316407001391 putative deacylase active site; other site 316407001392 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3735 316407001393 GumN protein; Region: GumN; cl12050 316407001394 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl09100 316407001395 copper exporting ATPase; Provisional; Region: copA; PRK10671 316407001396 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 316407001397 metal-binding site 316407001398 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 316407001399 metal-binding site 316407001400 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 316407001401 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 316407001402 motif II; other site 316407001403 Glutaminase; Region: Glutaminase; cl00907 316407001404 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407001405 DNA-binding transcriptional regulator CueR; Provisional; Region: PRK10227 316407001406 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 316407001407 DNA binding residues 316407001408 dimer interface; other site 316407001409 copper binding site; other site 316407001410 NfeD-like; Region: NfeD; cl00686 316407001411 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 316407001412 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 316407001413 putative ABC transporter ATP-binding protein YbbL; Provisional; Region: PRK10247 316407001414 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 316407001415 Walker A/P-loop; other site 316407001416 ATP binding site; other site 316407001417 Q-loop/lid; other site 316407001418 ABC transporter signature motif; other site 316407001419 Walker B; other site 316407001420 D-loop; other site 316407001421 H-loop/switch region; other site 316407001422 Uncharacterized protein family (UPF0014); Region: UPF0014; cl00424 316407001423 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 316407001424 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 316407001425 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 316407001426 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407001427 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 316407001428 active site 316407001429 catalytic triad; other site 316407001430 oxyanion hole; other site 316407001431 switch loop; other site 316407001432 putative ABC transporter ATP-binding protein YbbA; Provisional; Region: PRK10584 316407001433 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 316407001434 Walker A/P-loop; other site 316407001435 ATP binding site; other site 316407001436 Q-loop/lid; other site 316407001437 ABC transporter signature motif; other site 316407001438 Walker B; other site 316407001439 D-loop; other site 316407001440 H-loop/switch region; other site 316407001441 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 316407001442 Predicted permease; Region: FtsX; cl11418 316407001443 Predicted permease; Region: FtsX; cl11418 316407001444 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 316407001445 RHS Repeat; Region: RHS_repeat; cl11982 316407001446 RHS Repeat; Region: RHS_repeat; cl11982 316407001447 RHS Repeat; Region: RHS_repeat; cl11982 316407001448 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 316407001449 RHS Repeat; Region: RHS_repeat; cl11982 316407001450 RHS Repeat; Region: RHS_repeat; cl11982 316407001451 RHS protein; Region: RHS; pfam03527 316407001452 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 316407001453 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 316407001454 RHS protein; Region: RHS; pfam03527 316407001455 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 316407001456 hypothetical protein; Provisional; Region: PRK09781; cl08057 316407001457 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 316407001458 Member of the Rhodanese Homology Domain superfamily. This CD includes several putative ATP /GTP binding proteins including E. coli YbbB; Region: RHOD_YbbB; cd01520 316407001459 active site residue 316407001460 DNA-binding transcriptional activator AllS; Provisional; Region: PRK10094 316407001461 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407001462 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 316407001463 dimerization interface; other site 316407001464 Ureidoglycolate hydrolase [Nucleotide transport and metabolism]; Region: DAL3; COG3194 316407001465 Ureidoglycolate hydrolase; Region: Ureidogly_hydro; cl01250 316407001466 DNA-binding transcriptional repressor AllR; Provisional; Region: PRK10163 316407001467 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407001468 Bacterial transcriptional regulator; Region: IclR; pfam01614 316407001469 glyoxylate carboligase; Provisional; Region: PRK11269 316407001470 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 316407001471 PYR/PP interface; other site 316407001472 dimer interface; other site 316407001473 TPP binding site; other site 316407001474 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 316407001475 TPP-binding module; composed of proteins similar to Escherichia coli glyoxylate carboligase (Gcl). E. coli glyoxylate carboligase, plays a key role in glyoxylate metabolism where it catalyzes the condensation of two molecules of glyoxylate to give...; Region: TPP_Gcl; cd02006 316407001476 TPP-binding site; other site 316407001477 hydroxypyruvate isomerase; Provisional; Region: PRK09997 316407001478 tartronate semialdehyde reductase; Provisional; Region: PRK15059 316407001479 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407001480 Sodium:solute symporter family; Region: SSF; cl00456 316407001481 Purine-cytosine permease and related proteins [Nucleotide transport and metabolism]; Region: CodB; COG1457 316407001482 allantoinase; Provisional; Region: PRK08044 316407001483 L-Hydantoinases (L-HYDs) and Allantoinase (ALN); L-Hydantoinases are a member of the dihydropyrimidinase family, which catalyzes the reversible hydrolytic ring opening of dihydropyrimidines and hydantoins (five-membered cyclic diamides used in...; Region: L-HYD_ALN; cd01315 316407001484 active site 316407001485 Permease family; Region: Xan_ur_permease; cl00967 316407001486 Glycerate kinase family; Region: Gly_kinase; cl00841 316407001487 putative allantoin catabolism protein; Region: ura-cupin; TIGR03214 316407001488 Cupin domain; Region: Cupin_2; cl09118 316407001489 Cupin domain; Region: Cupin_2; cl09118 316407001490 allantoate amidohydrolase; Region: AllC; TIGR03176 316407001491 Peptidase dimerization domain; Region: M20_dimer; cl09126 316407001492 Peptidase dimerization domain; Region: M20_dimer; cl09126 316407001493 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 316407001494 membrane protein FdrA; Validated; Region: PRK06091 316407001495 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407001496 CoA-ligase; Region: Ligase_CoA; pfam00549 316407001497 ECK0512:JW0507:b4507; hypothetical protein, N-ter fragment 316407001498 ECK0512:JW0508+JW0507:b4572; hypothetical protein 316407001499 ECK0512:JW0508:b0519; hypothetical protein, C-ter fragment 316407001500 Protein of unknown function (DUF2877); Region: DUF2877; pfam11392 316407001501 carbamate kinase; Reviewed; Region: PRK09411 316407001502 AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an...; Region: AAK_CK; cd04235 316407001503 putative substrate binding site; other site 316407001504 nucleotide binding site; other site 316407001505 nucleotide binding site; other site 316407001506 homodimer interface; other site 316407001507 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 316407001508 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 316407001509 AIR carboxylase; Region: AIRC; cl00310 316407001510 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2908 316407001511 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 316407001512 putative active site; other site 316407001513 putative metal binding site; other site 316407001514 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 316407001515 substrate binding site; other site 316407001516 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 316407001517 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 316407001518 active site 316407001519 HIGH motif; other site 316407001520 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 316407001521 KMSKS motif; other site 316407001522 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 316407001523 tRNA binding surface; other site 316407001524 anticodon binding site; other site 316407001525 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; cl00868 316407001526 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 316407001527 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 316407001528 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 316407001529 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 316407001530 homodimer interface; other site 316407001531 NADP binding site; other site 316407001532 substrate binding site; other site 316407001533 Fimbrial protein; Region: Fimbrial; cl01416 316407001534 fimbrial chaperone protein FimC; Provisional; Region: PRK15195 316407001535 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 316407001536 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 316407001537 outer membrane usher protein FimD; Provisional; Region: PRK15198 316407001538 pilin outer membrane usher protein SafC; Provisional; Region: PRK15223; cl14650 316407001539 Fimbrial protein; Region: Fimbrial; cl01416 316407001540 Fimbrial protein; Region: Fimbrial; cl01416 316407001541 transcriptional regulator FimZ; Provisional; Region: PRK09935 316407001542 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 316407001543 active site 316407001544 phosphorylation site 316407001545 intermolecular recognition site; other site 316407001546 dimerization interface; other site 316407001547 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...; Region: LuxR_C_like; cd06170 316407001548 DNA binding residues 316407001549 dimerization interface; other site 316407001550 DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial and phage integrases, including those similar to phage P22-like integrases, DLP12 and APSE-1; Region: INT_P22_C; cd01192 316407001551 Phage integrase family; Region: Phage_integrase; pfam00589 316407001552 Int/Topo IB signature motif; other site 316407001553 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 316407001554 DLP12 prophage region; ECK0532:JW0527:b4508; predicted replication protein fragment 316407001555 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; cl01116 316407001556 putative transposase OrfB; Reviewed; Region: PHA02517 316407001557 Integrase core domain; Region: rve; cl01316 316407001558 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 316407001559 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 316407001560 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 316407001561 catalytic residues; other site 316407001562 catalytic nucleophile; other site 316407001563 Recombinase; Region: Recombinase; pfam07508 316407001564 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 316407001565 substrate binding site; other site 316407001566 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 316407001567 NinB protein; Region: NinB; cl14671 316407001568 prophage protein NinE; Provisional; Region: PRK09689 316407001569 Protein of unknown function (DUF1364); Region: DUF1364; pfam07102 316407001570 Endodeoxyribonuclease RusA; Region: RusA; cl01885 316407001571 Phage antitermination protein Q; Region: Phage_antitermQ; pfam06530 316407001572 Transposase domain (DUF772); Region: DUF772; cl12084 316407001573 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 316407001574 DLP12 prophage region; ECK0544:JW5078:b0553; truncated outer membrane porin 316407001575 Lysis protein S; Region: Lysis_S; pfam04971 316407001576 Endolysins and autolysins are found in viruses and bacteria, respectively. The ds DNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell...; Region: endolysin_autolysin; cd00737 316407001577 catalytic residues; other site 316407001578 Bacteriophage lysis protein; Region: Phage_lysis; pfam03245 316407001579 Lipoprotein Rz1 precursor; Region: Rz1; pfam06085 316407001580 Bor protein; Region: Lambda_Bor; pfam06291 316407001581 Protein of unknown function (DUF1398); Region: DUF1398; cl11576 316407001582 Phage DNA packaging protein Nu1; Region: Phage_Nu1; cl01720 316407001583 DLP12 prophage region; ECK0553:JW5815:b0561; predicted tail fiber assembly protein 316407001584 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; cl12011 316407001585 Caudovirales tail fibre assembly protein; Region: Caudo_TAP; pfam02413 316407001586 transcriptional regulator YdeO; Provisional; Region: PRK09940 316407001587 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407001588 Omptin family; Region: Omptin; cl01886 316407001589 DNA-binding transcriptional regulator GadX; Provisional; Region: PRK09978 316407001590 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407001591 hypothetical protein; Provisional; Region: PRK09936 316407001592 bacteriophage N4 receptor, outer membrane subunit; Provisional; Region: PRK09782 316407001593 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 316407001594 TPR motif; other site 316407001595 binding surface 316407001596 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 316407001597 bacteriophage N4 adsorption protein B; Provisional; Region: nfrB; PRK11234 316407001598 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 316407001599 sensor kinase CusS; Provisional; Region: PRK09835 316407001600 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 connected by an extended linker. The...; Region: HAMP; cd06225 316407001601 dimerization interface; other site 316407001602 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 trans-...; Region: HisKA; cd00082 316407001603 dimer interface; other site 316407001604 phosphorylation site 316407001605 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 316407001606 ATP binding site; other site 316407001607 Mg2+ binding site; other site 316407001608 G-X-G motif; other site 316407001609 DNA-binding transcriptional activator CusR; Provisional; Region: PRK09836 316407001610 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 316407001611 active site 316407001612 phosphorylation site 316407001613 intermolecular recognition site; other site 316407001614 dimerization interface; other site 316407001615 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...; Region: trans_reg_C; cd00383 316407001616 DNA binding site 316407001617 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 316407001618 Outer membrane efflux protein; Region: OEP; pfam02321 316407001619 Outer membrane efflux protein; Region: OEP; pfam02321 316407001620 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 316407001621 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 316407001622 heavy metal efflux pump (cobalt-zinc-cadmium); Region: 2A0601; TIGR00914 316407001623 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407001624 Mechanosensitive ion channel; Region: MS_channel; pfam00924 316407001625 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 316407001626 dimer interface; other site 316407001627 FMN binding site; other site 316407001628 Protein of unknown function (DUF419); Region: DUF419; cl09948 316407001629 Protein of unknown function (DUF1158); Region: DUF1158; pfam06643 316407001630 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 316407001631 uncharacterized enzyme; Region: gshA_cyan_rel; TIGR02050 316407001632 Hok/gef family; Region: HOK_GEF; cl11494 316407001633 Transposase DDE domain; Region: Transposase_11; pfam01609 316407001634 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 316407001635 phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex; Provisional; Region: PRK10251 316407001636 outer membrane receptor FepA; Provisional; Region: PRK13524 316407001637 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 316407001638 N-terminal plug; other site 316407001639 ligand-binding site; other site 316407001640 enterobactin/ferric enterobactin esterase; Provisional; Region: PRK10439 316407001641 Domain of unknown function (DUF3327); Region: DUF3327; pfam11806 316407001642 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; cl12031 316407001643 MbtH-like protein; Region: MbtH; cl01279 316407001644 enterobactin synthase subunit F; Provisional; Region: entF; PRK10252 316407001645 Condensation domain; Region: Condensation; cl09290 316407001646 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 316407001647 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 316407001648 Phosphopantetheine attachment site; Region: PP-binding; cl09936 316407001649 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; cl12031 316407001650 Chain length determinant protein; Region: Wzz; cl01623 316407001651 iron-enterobactin transporter ATP-binding protein; Provisional; Region: PRK10253 316407001652 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 316407001653 Walker A/P-loop; other site 316407001654 ATP binding site; other site 316407001655 Q-loop/lid; other site 316407001656 ABC transporter signature motif; other site 316407001657 Walker B; other site 316407001658 D-loop; other site 316407001659 H-loop/switch region; other site 316407001660 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 316407001661 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...; Region: TM_ABC_iron-siderophores_like; cd06550 316407001662 ABC-ATPase subunit interface; other site 316407001663 dimer interface; other site 316407001664 putative PBP binding regions; other site 316407001665 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...; Region: TM_ABC_iron-siderophores_like; cd06550 316407001666 ABC-ATPase subunit interface; other site 316407001667 dimer interface; other site 316407001668 putative PBP binding regions; other site 316407001669 enterobactin exporter EntS; Provisional; Region: PRK10489 316407001670 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 316407001671 putative substrate translocation pore; other site 316407001672 iron-enterobactin transporter periplasmic binding protein; Provisional; Region: PRK10957 316407001673 Fe3+-siderophore binding domain FhuD. These proteins have been shown to function as initial receptors in ABC transport of Fe3+-siderophores in many eubacterial species. They belong to the TroA-like superfamily of helical backbone metal receptor...; Region: FhuD; cd01146 316407001674 siderophore binding site; other site 316407001675 isochorismate synthase EntC; Provisional; Region: PRK15016 316407001676 chorismate binding enzyme; Region: Chorismate_bind; cl10555 316407001677 enterobactin synthase subunit E; Provisional; Region: entE; PRK10946 316407001678 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 316407001679 Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase, catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of a vinyl ether, an uncommon reaction in...; Region: isochorismatase; cd01013 316407001680 hydrophobic substrate binding pocket; other site 316407001681 Isochorismatase family; Region: Isochorismatase; pfam00857 316407001682 active site 316407001683 conserved cis-peptide bond; other site 316407001684 Phosphopantetheine attachment site; Region: PP-binding; cl09936 316407001685 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407001686 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 316407001687 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 316407001688 CoenzymeA binding site; other site 316407001689 subunit interaction site; other site 316407001690 PHB binding site; other site 316407001691 Carbon starvation protein CstA; Region: CstA; cl00856 316407001692 Protein of unknown function (DUF466); Region: DUF466; cl01082 316407001693 Glycerol dehydrogenases-like; Region: GlyDH-like1; cd08172 316407001694 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 316407001695 putative active site; other site 316407001696 metal-binding site 316407001697 methionine aminotransferase; Validated; Region: PRK09082 316407001698 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 316407001699 pyridoxal 5'-phosphate binding site; other site 316407001700 homodimer interface; other site 316407001701 catalytic residue; other site 316407001702 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 316407001703 ParB-like nuclease domain; Region: ParBc; cl02129 316407001704 Predicted phosphoadenosine phosphosulfate sulfotransferase [General function prediction only]; Region: COG3969 316407001705 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 316407001706 Active Sites; active site 316407001707 Domain of unknown function (DUF3440); Region: DUF3440; pfam11922 316407001708 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11482 316407001709 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407001710 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 316407001711 disulfide isomerase/thiol-disulfide oxidase; Provisional; Region: dsbG; PRK11657 316407001712 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...; Region: DsbA_DsbC_DsbG; cd03020 316407001713 dimerization domain; other site 316407001714 dimer interface; other site 316407001715 catalytic residues; other site 316407001716 alkyl hydroperoxide reductase subunit C; Provisional; Region: PRK10382 316407001717 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...; Region: PRX_Typ2cys; cd03015 316407001718 dimer interface; other site 316407001719 decamer (pentamer of dimers) interface; other site 316407001720 catalytic triad; other site 316407001721 peroxidatic and resolving cysteines; other site 316407001722 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 316407001723 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...; Region: AhpF_NTD_N; cd02974 316407001724 catalytic residue; other site 316407001725 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 316407001726 catalytic residues; other site 316407001727 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407001728 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 316407001729 Ligand Binding Site; other site 316407001730 Glutathione-dependent formaldehyde dehydrogenase related proteins, child 1; Region: FDH_like_1; cd08283 316407001731 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 316407001732 NAD binding site; other site 316407001733 catalytic Zn binding site; other site 316407001734 structural Zn binding site; other site 316407001735 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 316407001736 C-term; Region: GreA_GreB; pfam01272 316407001737 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 316407001738 B1 nucleotide binding pocket; other site 316407001739 B2 nucleotide binding pocket; other site 316407001740 CAS motifs; other site 316407001741 active site 316407001742 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 316407001743 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; cd00625 316407001744 transmembrane helices; other site 316407001745 ATP:dephospho-CoA triphosphoribosyl transferase; Region: CitG; cl00768 316407001746 Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase; Region: CitX; cl01498 316407001747 Citrate lyase, alpha subunit [Energy production and conversion]; Region: CitF; COG3051 316407001748 Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their...; Region: malate_synt; cl09155 316407001749 Malonate decarboxylase delta subunit (MdcD); Region: ACP; cl06082 316407001750 [citrate (pro-3S)-lyase] ligase; Region: cit_ly_ligase; TIGR00124 316407001751 Citrate lyase ligase; Region: Citrate_lyase_ligase; cd02169 316407001752 putative active site; other site 316407001753 (T/H)XGH motif; other site 316407001754 sensor histidine kinase DpiB; Provisional; Region: dpiB; PRK15053 316407001755 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 316407001756 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 316407001757 ATP binding site; other site 316407001758 Mg2+ binding site; other site 316407001759 G-X-G motif; other site 316407001760 two-component response regulator DpiA; Provisional; Region: dpiA; PRK10046 316407001761 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 316407001762 active site 316407001763 phosphorylation site 316407001764 intermolecular recognition site; other site 316407001765 dimerization interface; other site 316407001766 Transcriptional regulator; Region: CitT; pfam12431 316407001767 ECK0614:JW0613+JW0616:b0621; IS is inserted, intact dcuC is found in strain MG1655 316407001768 C4-dicarboxylate transporter [Energy production and conversion]; Region: DcuC; cl14617 316407001769 Transposase domain (DUF772); Region: DUF772; cl12084 316407001770 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 316407001771 C4-dicarboxylate transporter [Energy production and conversion]; Region: DcuC; cl14617 316407001772 Antimicrobial peptide resistance and lipid A acylation protein PagP; Region: PagP; cl06181 316407001773 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 protein...; Region: CSP_CDS; cd04458 316407001774 DNA binding site 316407001775 RNA-binding motif; other site 316407001776 CrcB-like protein; Region: CRCB; cl09114 316407001777 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 316407001778 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 316407001779 active site 316407001780 catalytic triad; other site 316407001781 dimer interface; other site 316407001782 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 316407001783 lipoyl synthase; Provisional; Region: PRK05481 316407001784 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; cl14056 316407001785 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11482 316407001786 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407001787 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 316407001788 substrate binding pocket; other site 316407001789 dimerization interface; other site 316407001790 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 316407001791 Protein of unknown function (DUF493); Region: DUF493; cl01102 316407001792 D-alanyl-D-alanine carboxypeptidase fraction A; Provisional; Region: PRK10793 316407001793 Beta-lactamase; Region: Beta-lactamase; cl01009 316407001794 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 316407001795 rare lipoprotein A; Provisional; Region: PRK10672 316407001796 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 316407001797 Sporulation related domain; Region: SPOR; cl10051 316407001798 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 316407001799 penicillin-binding protein 2; Provisional; Region: PRK10795 316407001800 Penicillin-binding Protein dimerization domain; Region: PBP_dimer; pfam03717 316407001801 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 316407001802 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; cl00679 316407001803 Domain of unknown function DUF143; Region: DUF143; cl00519 316407001804 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 316407001805 catalytic core; other site 316407001806 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 316407001807 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 316407001808 active site 316407001809 (T/H)XGH motif; other site 316407001810 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 316407001811 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 316407001812 Rare lipoprotein B family; Region: RplB; cl01125 316407001813 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 316407001814 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 316407001815 HIGH motif; other site 316407001816 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 316407001817 KMSKS motif; other site 316407001818 active site 316407001819 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 316407001820 tRNA binding surface; other site 316407001821 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 316407001822 hypothetical protein; Provisional; Region: PRK11032 316407001823 Protein of unknown function (DUF1451); Region: DUF1451; pfam07295 316407001824 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 316407001825 Sel1 repeat; Region: Sel1; cl02723 316407001826 Sel1 repeat; Region: Sel1; cl02723 316407001827 Sel1 repeat; Region: Sel1; cl02723 316407001828 Sel1 repeat; Region: Sel1; cl02723 316407001829 Sel1 repeat; Region: Sel1; cl02723 316407001830 Protein of unknown function (DUF1266); Region: DUF1266; cl14673 316407001831 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...; Region: DnaJ; cl02542 316407001832 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 316407001833 Sel1 repeat; Region: Sel1; cl02723 316407001834 Sel1 repeat; Region: Sel1; cl02723 316407001835 Protein of unknown function (DUF1266); Region: DUF1266; cl14673 316407001836 Molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: DnaK; COG0443 316407001837 Inosine-uridine preferring nucleoside hydrolase; Region: IU_nuc_hydro; pfam01156 316407001838 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 316407001839 active site 316407001840 tetramer interface; other site 316407001841 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 316407001842 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP; Region: ABC_HisP_GlnQ_permeases; cd03262 316407001843 Walker A/P-loop; other site 316407001844 ATP binding site; other site 316407001845 Q-loop/lid; other site 316407001846 ABC transporter signature motif; other site 316407001847 Walker B; other site 316407001848 D-loop; other site 316407001849 H-loop/switch region; other site 316407001850 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 316407001851 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...; Region: TM_PBP2; cd06261 316407001852 dimer interface; other site 316407001853 conserved gate region; other site 316407001854 putative PBP binding loops; other site 316407001855 ABC-ATPase subunit interface; other site 316407001856 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 316407001857 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...; Region: TM_PBP2; cd06261 316407001858 dimer interface; other site 316407001859 conserved gate region; other site 316407001860 putative PBP binding loops; other site 316407001861 ABC-ATPase subunit interface; other site 316407001862 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 316407001863 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...; Region: PBPb; cd00134 316407001864 substrate binding pocket; other site 316407001865 membrane-bound complex binding site; other site 316407001866 hinge residues; other site 316407001867 Transposase domain (DUF772); Region: DUF772; cl12084 316407001868 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 316407001869 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 316407001870 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 316407001871 putative active site; other site 316407001872 catalytic triad; other site 316407001873 putative dimer interface; other site 316407001874 magnesium/cobalt efflux protein CorC; Provisional; Region: PRK15094 316407001875 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 316407001876 Transporter associated domain; Region: CorC_HlyC; pfam03471 316407001877 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 316407001878 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 316407001879 PhoH-like protein; Region: PhoH; cl12134 316407001880 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 316407001881 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 316407001882 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 316407001883 FeS/SAM binding site; other site 316407001884 TRAM domain; Region: TRAM; cl01282 316407001885 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Reviewed; Region: ubiF; PRK08020 316407001886 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407001887 asparagine synthetase B; Provisional; Region: asnB; PRK09431 316407001888 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 316407001889 active site 316407001890 dimer interface; other site 316407001891 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...; Region: Asn_Synthase_B_C; cd01991 316407001892 Ligand Binding Site; other site 316407001893 Molecular Tunnel; other site 316407001894 UMP phosphatase; Provisional; Region: PRK10444 316407001895 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 316407001896 active site 316407001897 motif I; other site 316407001898 motif II; other site 316407001899 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 316407001900 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407001901 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 316407001902 ROK family; Region: ROK; cl09121 316407001903 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 316407001904 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 316407001905 active site 316407001906 dimer interface; other site 316407001907 GlcN6P_deaminase: Glucosamine-6-phosphate (GlcN6P) deaminase subfamily; GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium. The reaction is an aldo-keto isomerization coupled with an amination...; Region: GlcN6P_deaminase; cd01399 316407001908 active site 316407001909 trimer interface; other site 316407001910 allosteric site; other site 316407001911 active site lid 316407001912 hexamer (dimer of trimers) interface; other site 316407001913 PTS system N-acetyl glucosamine specific transporter subunits IIABC; Provisional; Region: PRK10255 316407001914 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 316407001915 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...; Region: PTS_IIB_glc; cd00212 316407001916 active site turn 316407001917 phosphorylation site 316407001918 PTS_IIA, PTS system, glucose/sucrose 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_glc; cd00210 316407001919 HPr interaction site; other site 316407001920 glycerol kinase (GK) interaction site; other site 316407001921 active site 316407001922 phosphorylation site 316407001923 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 316407001924 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 316407001925 HIGH motif; other site 316407001926 active site 316407001927 nucleotide binding site; other site 316407001928 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 316407001929 KMSKS motif; other site 316407001930 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 316407001931 outer membrane porin, OprD family; Region: OprD; pfam03573 316407001932 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 316407001933 metal binding site 2; metal-binding site 316407001934 putative DNA binding helix; other site 316407001935 metal binding site 1; metal-binding site 316407001936 dimer interface; other site 316407001937 structural Zn2+ binding site; other site 316407001938 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 316407001939 LexA regulated protein; Provisional; Region: PRK11675 316407001940 acyl-CoA esterase; Provisional; Region: PRK10673 316407001941 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; cl12031 316407001942 SeqA protein; Region: SeqA; cl11470 316407001943 phosphoglucomutase, alpha-D-glucose phosphate-specific; Region: pgm; TIGR01132 316407001944 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 316407001945 active site 316407001946 substrate binding site; other site 316407001947 metal-binding site 316407001948 Protein of unknown function DUF2625; Region: DUF2625; cl08177 316407001949 Protein of unknown function DUF2625; Region: DUF2625; cl08177 316407001950 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 316407001951 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407001952 ornithine decarboxylase; Provisional; Region: PRK13578 316407001953 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; cl09944 316407001954 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...; Region: Orn_deC_like; cd00615 316407001955 homodimer interface; other site 316407001956 pyridoxal 5'-phosphate binding site; other site 316407001957 catalytic residue; other site 316407001958 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 316407001959 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 316407001960 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 316407001961 active site 316407001962 phosphorylation site 316407001963 intermolecular recognition site; other site 316407001964 dimerization interface; other site 316407001965 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...; Region: trans_reg_C; cd00383 316407001966 DNA binding site 316407001967 sensor protein KdpD; Provisional; Region: PRK10490 316407001968 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 316407001969 USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium...; Region: USP_OKCHK; cd01987 316407001970 Ligand Binding Site; other site 316407001971 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 trans-...; Region: HisKA; cl00080 316407001972 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 316407001973 ATP binding site; other site 316407001974 Mg2+ binding site; other site 316407001975 G-X-G motif; other site 316407001976 K+-transporting ATPase, c chain; Region: KdpC; cl00944 316407001977 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 316407001978 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 316407001979 K+-transporting ATPase, A chain [Inorganic ion transport and metabolism]; Region: KdpA; cl00903 316407001980 Potassium-transporting ATPase A subunit; Region: KdpA; pfam03814 316407001981 Protein of unknown function (DUF2517); Region: DUF2517; pfam10725 316407001982 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 316407001983 RHS Repeat; Region: RHS_repeat; cl11982 316407001984 RHS Repeat; Region: RHS_repeat; cl11982 316407001985 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 316407001986 RHS Repeat; Region: RHS_repeat; cl11982 316407001987 RHS Repeat; Region: RHS_repeat; cl11982 316407001988 RHS protein; Region: RHS; pfam03527 316407001989 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 316407001990 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 316407001991 RHS protein; Region: RHS; pfam03527 316407001992 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 316407001993 Transposase [DNA replication, recombination, and repair]; Region: COG5433 316407001994 ECK0694:JW0695:b0705; predicted transposase 316407001995 Transposase [DNA replication, recombination, and repair]; Region: COG5433 316407001996 Transposase [DNA replication, recombination, and repair]; Region: COG5433 316407001997 Protein of unknown function (DUF1722); Region: DUF1722; cl01284 316407001998 deoxyribodipyrimidine photolyase; Provisional; Region: PRK10674 316407001999 DNA photolyase; Region: DNA_photolyase; pfam00875 316407002000 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 316407002001 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 316407002002 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 316407002003 putative substrate translocation pore; other site 316407002004 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; cl11420 316407002005 Uncharacterized conserved protein [Function unknown]; Region: COG0327 316407002006 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl01309 316407002007 Allophanate hydrolase subunit 1; Region: AHS1; pfam02682 316407002008 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 316407002009 Allophanate hydrolase subunit 2; Region: AHS2; cl00865 316407002010 Allophanate hydrolase subunit 2; Region: AHS2; pfam02626 316407002011 LamB/YcsF family; Region: LamB_YcsF; cl00664 316407002012 endonuclease VIII; Provisional; Region: PRK10445 316407002013 N-terminal domain of Escherichia coli Nei/endonuclease VIII and related DNA glycosylases; Region: EcNei-like_N; cd08965 316407002014 DNA binding site 316407002015 catalytic residue; other site 316407002016 H2TH interface; other site 316407002017 putative catalytic residues; other site 316407002018 intercalation triad; other site 316407002019 substrate specificity determining residue; other site 316407002020 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 316407002021 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 316407002022 membrane protein AbrB duplication; Region: Gneg_AbrB_dup; TIGR03082 316407002023 Putative ammonia monooxygenase; Region: AmoA; pfam05145 316407002024 membrane protein AbrB duplication; Region: Gneg_AbrB_dup; TIGR03082 316407002025 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 316407002026 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 316407002027 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 316407002028 pilin outer membrane usher protein SafC; Provisional; Region: PRK15223; cl14650 316407002029 Fimbrial Usher protein; Region: Usher; pfam00577 316407002030 Fimbrial protein; Region: Fimbrial; cl01416 316407002031 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 316407002032 dimer interface; other site 316407002033 Citrate synthase; Region: Citrate_synt; pfam00285 316407002034 active site 316407002035 citrylCoA binding site; other site 316407002036 NADH binding; other site 316407002037 cationic pore residues; other site 316407002038 oxalacetate/citrate binding site; other site 316407002039 coenzyme A binding site; other site 316407002040 catalytic triad; other site 316407002041 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 316407002042 Iron-sulfur protein interface; other site 316407002043 proximal quinone binding site; other site 316407002044 SdhD (CybS) interface; other site 316407002045 proximal heme binding site; other site 316407002046 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 316407002047 SdhC subunit interface; other site 316407002048 proximal heme binding site; other site 316407002049 cardiolipin binding site; other site 316407002050 Iron-sulfur protein interface; other site 316407002051 proximal quinone binding site; other site 316407002052 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK08958 316407002053 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407002054 domain; Region: Succ_DH_flav_C; pfam02910 316407002055 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 316407002056 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 316407002057 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 2-oxoglutarate to succinyl-CoA and carbon dioxide, a key reaction of...; Region: TPP_E1_OGDC_like; cd02016 316407002058 TPP-binding site; other site 316407002059 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 316407002060 dimer interface; other site 316407002061 PYR/PP interface; other site 316407002062 TPP binding site; other site 316407002063 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 316407002064 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 316407002065 E3 interaction surface; other site 316407002066 lipoyl attachment site; other site 316407002067 e3 binding domain; Region: E3_binding; pfam02817 316407002068 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 316407002069 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 316407002070 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 316407002071 CoA-ligase; Region: Ligase_CoA; pfam00549 316407002072 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 316407002073 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407002074 CoA-ligase; Region: Ligase_CoA; pfam00549 316407002075 DNA-binding transcriptional repressor MngR; Provisional; Region: PRK09764 316407002076 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407002077 DNA binding site 316407002078 UTRA domain; Region: UTRA; cl06649 316407002079 PTS system 2-O-a-mannosyl-D-glycerate specific transporter subunit IIABC; Provisional; Region: PRK09765 316407002080 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 316407002081 active site 316407002082 phosphorylation site 316407002083 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA...; Region: PTS_IIB_fructose; cd05569 316407002084 P-loop; other site 316407002085 active site 316407002086 phosphorylation site 316407002087 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 316407002088 alpha-mannosidase; Provisional; Region: PRK09819 316407002089 Glycosyl hydrolases family 38 N-terminal domain; Region: Glyco_hydro_38; pfam01074 316407002090 Alpha mannosidase, middle domain; Region: Alpha-mann_mid; cl08536 316407002091 Glycosyl hydrolases family 38 C-terminal domain; Region: Glyco_hydro_38C; pfam07748 316407002092 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 316407002093 cytochrome bd-II oxidase subunit 2; Provisional; Region: PRK15028; cl12219 316407002094 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 316407002095 Membrane bound YbgT-like protein; Region: YbgT_YccB; cl02039 316407002096 Cyd operon protein YbgE (Cyd_oper_YbgE); Region: Cyd_oper_YbgE; cl11451 316407002097 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...; Region: 4HBT; cd00586 316407002098 active site 316407002099 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 316407002100 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 316407002101 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 316407002102 cell envelope integrity inner membrane protein TolA; Provisional; Region: tolA; PRK09510 316407002103 TolA C-terminal; Region: TolA; pfam06519 316407002104 translocation protein TolB; Provisional; Region: tolB; PRK03629 316407002105 TolB amino-terminal domain; Region: TolB_N; pfam04052 316407002106 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 316407002107 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 316407002108 peptidoglycan-associated outer membrane lipoprotein; Provisional; Region: PRK10802 316407002109 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 316407002110 ligand binding site; other site 316407002111 tol-pal system protein YbgF; Provisional; Region: PRK10803 316407002112 Quinolinate synthetase A protein; Region: NadA; cl00420 316407002113 Nicotinamide mononucleotide transporter; Region: NMN_transporter; cl01256 316407002114 Cation efflux family; Region: Cation_efflux; cl00316 316407002115 NeuB family; Region: NeuB; cl00496 316407002116 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 316407002117 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 316407002118 catalytic core; other site 316407002119 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 316407002120 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 316407002121 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 316407002122 active site 316407002123 catalytic residues; other site 316407002124 galactokinase; Provisional; Region: PRK05101 316407002125 Galactokinase galactose-binding signature; Region: GalKase_gal_bdg; pfam10509 316407002126 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 316407002127 galactose-1-phosphate uridylyltransferase; Provisional; Region: PRK11720 316407002128 Galactose-1-phosphate uridyl transferase (GalT): This enzyme plays a key role in galactose metabolism by catalysing the transfer of a uridine 5'-phosphoryl group from UDP-galactose 1-phosphate. The structure of E.coli GalT reveals that the enzyme...; Region: GalT; cd00608 316407002129 dimer interface; other site 316407002130 active site 316407002131 UDP-galactose-4-epimerase; Provisional; Region: PRK10675 316407002132 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407002133 putative molybdenum transport ATP-binding protein ModF; Provisional; Region: PRK10938 316407002134 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407002135 Walker A/P-loop; other site 316407002136 ATP binding site; other site 316407002137 Q-loop/lid; other site 316407002138 ABC transporter signature motif; other site 316407002139 Walker B; other site 316407002140 D-loop; other site 316407002141 H-loop/switch region; other site 316407002142 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407002143 Walker A/P-loop; other site 316407002144 ATP binding site; other site 316407002145 Q-loop/lid; other site 316407002146 ABC transporter signature motif; other site 316407002147 Walker B; other site 316407002148 D-loop; other site 316407002149 H-loop/switch region; other site 316407002150 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 316407002151 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407002152 TOBE domain; Region: TOBE_2; cl01440 316407002153 TOBE domain; Region: TOBE_2; cl01440 316407002154 Protein of unknown function (DUF2592); Region: DUF2592; pfam10766 316407002155 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 316407002156 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...; Region: TM_PBP2; cd06261 316407002157 putative PBP binding loops; other site 316407002158 ABC-ATPase subunit interface; other site 316407002159 molybdate transporter ATP-binding protein; Provisional; Region: modC; PRK11144 316407002160 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407002161 Walker A/P-loop; other site 316407002162 ATP binding site; other site 316407002163 Q-loop/lid; other site 316407002164 ABC transporter signature motif; other site 316407002165 Walker B; other site 316407002166 D-loop; other site 316407002167 H-loop/switch region; other site 316407002168 TOBE domain; Region: TOBE_2; cl01440 316407002169 pyridoxal phosphate (PLP) phosphatase; Provisional; Region: PRK10530 316407002170 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 316407002171 motif II; other site 316407002172 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; cl11391 316407002173 6-phosphogluconolactonase; Provisional; Region: PRK11028 316407002174 Transcriptional regulator [Transcription]; Region: LysR; COG0583 316407002175 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407002176 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 316407002177 putative dimerization interface; other site 316407002178 PrpF protein; Region: PrpF; pfam04303 316407002179 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 316407002180 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; cl09110 316407002181 transmembrane helices; other site 316407002182 putative hydratase; Provisional; Region: PRK11413 316407002183 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 316407002184 substrate binding site; other site 316407002185 ligand binding site; other site 316407002186 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 316407002187 substrate binding site; other site 316407002188 Pectin methylesterase [Carbohydrate transport and metabolism]; Region: PemB; COG4677 316407002189 Pectinesterase; Region: Pectinesterase; cl01911 316407002190 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 316407002191 substrate binding site; other site 316407002192 adenosylmethionine--8-amino-7-oxononanoate transaminase; Validated; Region: PRK07986 316407002193 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 316407002194 inhibitor-cofactor binding pocket; inhibition site 316407002195 pyridoxal 5'-phosphate binding site; other site 316407002196 catalytic residue; other site 316407002197 biotin synthase; Provisional; Region: PRK15108 316407002198 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 316407002199 FeS/SAM binding site; other site 316407002200 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 316407002201 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 316407002202 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), 8-amino-7-...; Region: KBL_like; cd06454 316407002203 substrate-cofactor binding pocket; other site 316407002204 pyridoxal 5'-phosphate binding site; other site 316407002205 catalytic residue; other site 316407002206 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 316407002207 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 316407002208 S-adenosylmethionine binding site; other site 316407002209 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 316407002210 Dethiobiotin synthetase (DTBS) is the penultimate enzyme in the biotin biosynthesis pathway in Escherichia coli and other microorganisms. The enzyme catalyzes formation of the ureido ring of dethiobiotin from (7R,8S)-7,8-diaminononanoic acid (DAPA) and...; Region: DTBS; cd03109 316407002211 ADP binding site; other site 316407002212 excinuclease ABC subunit B; Provisional; Region: PRK05298 316407002213 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 316407002214 ATP binding site; other site 316407002215 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 316407002216 nucleotide binding region; other site 316407002217 ATP-binding site; other site 316407002218 Ultra-violet resistance protein B; Region: UvrB; pfam12344 316407002219 UvrB/uvrC motif; Region: UVR; pfam02151 316407002220 Uncharacterized protein family UPF0052; Region: UPF0052; pfam01933 316407002221 family of mostly uncharacterized proteins similar to B.subtilis YvcK; Region: YvcK_like; cd07187 316407002222 putative substrate binding pocket; other site 316407002223 dimer interface; other site 316407002224 phosphate binding site; other site 316407002225 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 316407002226 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 316407002227 FeS/SAM binding site; other site 316407002228 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 316407002229 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 316407002230 MPT binding site; other site 316407002231 trimer interface; other site 316407002232 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...; Region: MoaC_PE; cd01420 316407002233 trimer interface; other site 316407002234 dimer interface; other site 316407002235 putative active site; other site 316407002236 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 316407002237 MoaE interaction surface; other site 316407002238 MoeB interaction surface; other site 316407002239 thiocarboxylated glycine; other site 316407002240 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 316407002241 MoaE homodimer interface; other site 316407002242 MoaD interaction; other site 316407002243 active site residues 316407002244 BAX inhibitor (BI)-1 like protein family. Mammalian members of this family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well characterized oncogene, or...; Region: BI-1-like; cd06181 316407002245 BAX inhibitor (BI)-1 like protein family. Mammalian members of this family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well characterized oncogene, or...; Region: BI-1-like; cl00473 316407002246 Uncharacterized protein family (UPF0104); Region: UPF0104; cl04219 316407002247 cardiolipin synthase 2; Provisional; Region: PRK11263 316407002248 Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of...; Region: PLDc; cd00138 316407002249 active site 316407002250 signature motif; other site 316407002251 Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of...; Region: PLDc; cd00138 316407002252 active site 316407002253 signature motif; other site 316407002254 Endonuclease/Exonuclease/phosphatase family; Region: Exo_endo_phos; cl00490 316407002255 Putative inner membrane protein YbhQ; Region: YbhQ; pfam11076 316407002256 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 316407002257 ABC-2 type transporter; Region: ABC2_membrane; cl11417 316407002258 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 316407002259 ABC-2 type transporter; Region: ABC2_membrane; cl11417 316407002260 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 316407002261 The ABCA subfamily mediates the transport of a variety of lipid compounds. Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency...; Region: ABC_subfamily_A; cd03263 316407002262 Walker A/P-loop; other site 316407002263 ATP binding site; other site 316407002264 Q-loop/lid; other site 316407002265 ABC transporter signature motif; other site 316407002266 Walker B; other site 316407002267 D-loop; other site 316407002268 H-loop/switch region; other site 316407002269 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 316407002270 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407002271 Walker A/P-loop; other site 316407002272 ATP binding site; other site 316407002273 Q-loop/lid; other site 316407002274 ABC transporter signature motif; other site 316407002275 Walker B; other site 316407002276 D-loop; other site 316407002277 H-loop/switch region; other site 316407002278 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 316407002279 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11552 316407002280 Domain of unknown function (DUF1956); Region: DUF1956; pfam09209 316407002281 helicase 45; Provisional; Region: PTZ00424 316407002282 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 316407002283 ATP binding site; other site 316407002284 Mg++ binding site; other site 316407002285 motif III; other site 316407002286 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 316407002287 nucleotide binding region; other site 316407002288 ATP-binding site; other site 316407002289 Domain of unknown function (DUF1768); Region: DUF1768; cl01271 316407002290 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 316407002291 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; cl12029 316407002292 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; cl12029 316407002293 helicase superfamily c-terminal domain; Region: HELICc2; cl09250 316407002294 glycosyl transferase family protein; Provisional; Region: PRK08136 316407002295 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 316407002296 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 316407002297 Protein of unknown function (DUF1471); Region: DUF1471; cl11507 316407002298 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 316407002299 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 316407002300 catecholate siderophore receptor Fiu; Provisional; Region: PRK09840 316407002301 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 316407002302 N-terminal plug; other site 316407002303 ligand-binding site; other site 316407002304 Protein of unknown function (DUF1471); Region: DUF1471; cl11507 316407002305 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; cl12011 316407002306 Protein of unknown function (DUF890); Region: Methyltransf_10; pfam05971 316407002307 putative mechanosensitive channel protein; Provisional; Region: PRK11465 316407002308 Mechanosensitive ion channel; Region: MS_channel; pfam00924 316407002309 glutamine ABC transporter ATP-binding protein; Reviewed; Region: glnQ; PRK09493 316407002310 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP; Region: ABC_HisP_GlnQ_permeases; cd03262 316407002311 Walker A/P-loop; other site 316407002312 ATP binding site; other site 316407002313 Q-loop/lid; other site 316407002314 ABC transporter signature motif; other site 316407002315 Walker B; other site 316407002316 D-loop; other site 316407002317 H-loop/switch region; other site 316407002318 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 316407002319 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...; Region: TM_PBP2; cd06261 316407002320 dimer interface; other site 316407002321 conserved gate region; other site 316407002322 putative PBP binding loops; other site 316407002323 ABC-ATPase subunit interface; other site 316407002324 glutamine ABC transporter periplasmic protein; Reviewed; Region: glnH; PRK09495 316407002325 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...; Region: PBPb; cd00134 316407002326 substrate binding pocket; other site 316407002327 membrane-bound complex binding site; other site 316407002328 hinge residues; other site 316407002329 Ferritin-like domain; Region: Ferritin; pfam00210 316407002330 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 316407002331 dimerization interface; other site 316407002332 DPS ferroxidase diiron center; other site 316407002333 ion pore; other site 316407002334 threonine and homoserine efflux system; Provisional; Region: PRK10532 316407002335 EamA-like transporter family; Region: EamA; cl01037 316407002336 Surface antigen; Region: Surface_Ag_2; cl01155 316407002337 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 316407002338 Sulfatase; Region: Sulfatase; cl10460 316407002339 manganese transport regulator MntR; Provisional; Region: PRK11050 316407002340 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407002341 Iron dependent repressor, metal binding and dimerization domain; Region: Fe_dep_repr_C; pfam02742 316407002342 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 316407002343 Putative anion permease YbiR. Based on sequence similarity, YbiR proteins are predicted to function as anion translocating permeases in eubacteria, archaea and plants. They belong to ArsB/NhaD superfamily of permeases that have been shown to...; Region: YbiR_permease; cd01117 316407002344 transmembrane helices; other site 316407002345 L,D-transpeptidase; Provisional; Region: PRK10260 316407002346 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 316407002347 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 316407002348 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407002349 Walker A/P-loop; other site 316407002350 ATP binding site; other site 316407002351 Q-loop/lid; other site 316407002352 ABC transporter signature motif; other site 316407002353 Walker B; other site 316407002354 D-loop; other site 316407002355 H-loop/switch region; other site 316407002356 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 316407002357 Protein of unknown function (DUF1479); Region: DUF1479; pfam07350 316407002358 Cof subfamily of IIB subfamily of haloacid dehalogenase superfamily; Region: Cof-subfamily; TIGR00099 316407002359 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 316407002360 active site 316407002361 motif I; other site 316407002362 motif II; other site 316407002363 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 316407002364 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; cl11391 316407002365 pyruvate formate-lyase; Region: PFL2-3; TIGR01774 316407002366 Pyruvate formate lyase 2 and related enzymes; Region: PFL2_DhaB_BssA; cd01677 316407002367 dimer interface; other site 316407002368 active site 316407002369 glycine loop; other site 316407002370 glycyl-radical enzyme activating protein family; Region: PFLE_PFLC; TIGR02494 316407002371 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea, which are member of the MipB/TalC subfamily of class I aldolases. FSA catalyze an aldol cleavage of fructose 6-phosphate and do not utilize fructose, fructose 1-...; Region: Transaldolase_FSA; cd00956 316407002372 active site 316407002373 intersubunit interactions; other site 316407002374 catalytic residue; other site 316407002375 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 316407002376 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...; Region: ThiF_MoeB_HesA_family; cd00757 316407002377 ATP binding site; other site 316407002378 substrate interface; other site 316407002379 molybdopterin biosynthesis protein MoeA; Provisional; Region: PRK10680 316407002380 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 316407002381 dimer interface; other site 316407002382 putative functional site; other site 316407002383 putative MPT binding site; other site 316407002384 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 316407002385 catalytic nucleophile; other site 316407002386 glutathione transporter ATP-binding protein; Provisional; Region: PRK10261 316407002387 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 316407002388 Walker A/P-loop; other site 316407002389 ATP binding site; other site 316407002390 Q-loop/lid; other site 316407002391 ABC transporter signature motif; other site 316407002392 Walker B; other site 316407002393 D-loop; other site 316407002394 H-loop/switch region; other site 316407002395 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 316407002396 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 316407002397 Walker A/P-loop; other site 316407002398 ATP binding site; other site 316407002399 Q-loop/lid; other site 316407002400 ABC transporter signature motif; other site 316407002401 Walker B; other site 316407002402 D-loop; other site 316407002403 H-loop/switch region; other site 316407002404 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 316407002405 glutathione ABC transporter substrate-binding protein GsiB; Provisional; Region: PRK15413 316407002406 The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib contains the type 2 periplasmic binding fold; Region: PBP2_Ylib_like; cd08499 316407002407 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...; Region: TM_PBP2; cd06261 316407002408 dimer interface; other site 316407002409 conserved gate region; other site 316407002410 putative PBP binding loops; other site 316407002411 ABC-ATPase subunit interface; other site 316407002412 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...; Region: TM_PBP2; cd06261 316407002413 dimer interface; other site 316407002414 conserved gate region; other site 316407002415 putative PBP binding loops; other site 316407002416 ABC-ATPase subunit interface; other site 316407002417 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 316407002418 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316407002419 metal-binding site 316407002420 active site 316407002421 I-site; other site 316407002422 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 316407002423 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 316407002424 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 316407002425 FeS/SAM binding site; other site 316407002426 Biofilm formation protein (YliH/bssR); Region: YliH; cl08211 316407002427 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 316407002428 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 316407002429 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 316407002430 GST_N family, unknown subfamily 2; 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_2; cd03047 316407002431 putative C-terminal domain interface; other site 316407002432 putative GSH binding site (G-site); other site 316407002433 putative dimer interface; other site 316407002434 GST_C family, unknown subfamily 2; 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_C_2; cd03180 316407002435 putative N-terminal domain interface; other site 316407002436 putative dimer interface; other site 316407002437 putative substrate binding pocket (H-site); other site 316407002438 D-alanyl-D-alanine carboxypeptidase fraction C; Provisional; Region: PRK10001 316407002439 Beta-lactamase; Region: Beta-lactamase; cl01009 316407002440 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 316407002441 DNA-binding transcriptional repressor DeoR; Provisional; Region: PRK10681 316407002442 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407002443 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 316407002444 PAP2_like proteins, BcrC_like subfamily. Several members of this family have been annotated as bacitracin transport permeases, as it was suspected that they form the permease component of an ABC transporter system. It was shown, however, that BcrC from...; Region: PAP2_BcrC_like; cd03385 316407002445 active site 316407002446 multidrug efflux system translocase MdfA; Provisional; Region: PRK15402 316407002447 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 316407002448 putative substrate translocation pore; other site 316407002449 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 316407002450 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 316407002451 active site 316407002452 motif I; other site 316407002453 motif II; other site 316407002454 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; cl11391 316407002455 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 316407002456 putative substrate translocation pore; other site 316407002457 Major Facilitator Superfamily; Region: MFS_1; pfam07690 316407002458 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3226 316407002459 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316407002460 putative transporter; Provisional; Region: PRK04972 316407002461 Predicted Permease Membrane Region; Region: Asp-Al_Ex; cl06061 316407002462 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; cl09110 316407002463 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; cl09110 316407002464 Predicted Permease Membrane Region; Region: Asp-Al_Ex; cl06061 316407002465 Putative inner membrane protein of Enterobacteriaceae; Region: YbjM; pfam11045 316407002466 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 316407002467 GSH binding site; other site 316407002468 catalytic residues; other site 316407002469 Protein of unknown function (DUF1418); Region: DUF1418; cl11648 316407002470 This family contains NADPH-dependent flavin reductase and oxygen-insensitive nitroreductase. These enzymes are homodimeric flavoproteins that contain one FMN per monomer as a cofactor. Flavin reductase catalyzes the reduction of flavin by using NADPH...; Region: NfsA_FRP; cd02146 316407002471 dimer interface; other site 316407002472 FMN binding site; other site 316407002473 NADPH bind site; other site 316407002474 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 316407002475 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 316407002476 Putative bacterial sensory transduction regulator; Region: YbjN; pfam10722 316407002477 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 316407002478 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 316407002479 putrescine transporter ATP-binding subunit; Provisional; Region: potG; PRK11607 316407002480 PotA is an ABC-type transporter and the ATPase component of the spermidine/putrescine-preferential uptake system consisting of PotA, -B, -C, and -D. PotA has two domains with the N-terminal domain containing the ATPase activity and the residues...; Region: ABC_PotA_N; cd03300 316407002481 Walker A/P-loop; other site 316407002482 ATP binding site; other site 316407002483 Q-loop/lid; other site 316407002484 ABC transporter signature motif; other site 316407002485 Walker B; other site 316407002486 D-loop; other site 316407002487 H-loop/switch region; other site 316407002488 TOBE domain; Region: TOBE_2; cl01440 316407002489 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...; Region: TM_PBP2; cd06261 316407002490 dimer interface; other site 316407002491 conserved gate region; other site 316407002492 putative PBP binding loops; other site 316407002493 ABC-ATPase subunit interface; other site 316407002494 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...; Region: TM_PBP2; cd06261 316407002495 dimer interface; other site 316407002496 conserved gate region; other site 316407002497 putative PBP binding loops; other site 316407002498 ABC-ATPase subunit interface; other site 316407002499 Protein of unknown function (DUF2593); Region: DUF2593; pfam10767 316407002500 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; cl12011 316407002501 23S rRNA methyluridine methyltransferase; Reviewed; Region: rumB; PRK03522 316407002502 putative ABC transporter arginine-biding protein; Provisional; Region: PRK15007 316407002503 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...; Region: PBPb; cd00134 316407002504 substrate binding pocket; other site 316407002505 membrane-bound complex binding site; other site 316407002506 hinge residues; other site 316407002507 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...; Region: TM_PBP2; cd06261 316407002508 dimer interface; other site 316407002509 conserved gate region; other site 316407002510 putative PBP binding loops; other site 316407002511 ABC-ATPase subunit interface; other site 316407002512 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 316407002513 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...; Region: TM_PBP2; cd06261 316407002514 dimer interface; other site 316407002515 conserved gate region; other site 316407002516 putative PBP binding loops; other site 316407002517 ABC-ATPase subunit interface; other site 316407002518 putative ABC transporter arginine-biding protein; Provisional; Region: PRK15007 316407002519 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...; Region: PBPb; cd00134 316407002520 substrate binding pocket; other site 316407002521 membrane-bound complex binding site; other site 316407002522 hinge residues; other site 316407002523 arginine transporter ATP-binding subunit; Provisional; Region: artP; PRK11124 316407002524 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407002525 Walker A/P-loop; other site 316407002526 ATP binding site; other site 316407002527 Q-loop/lid; other site 316407002528 ABC transporter signature motif; other site 316407002529 Walker B; other site 316407002530 D-loop; other site 316407002531 H-loop/switch region; other site 316407002532 putative lipoprotein; Provisional; Region: PRK10533 316407002533 Domain of unknown function (DUF74); Region: DUF74; cl00426 316407002534 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 316407002535 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 316407002536 amidase catalytic site; other site 316407002537 Zn binding residues; other site 316407002538 substrate binding site; other site 316407002539 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 316407002540 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407002541 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 316407002542 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407002543 Protein of unknown function (DUF2867); Region: DUF2867; pfam11066 316407002544 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 316407002545 Beta-eliminating lyase; Region: Beta_elim_lyase; pfam01212 316407002546 tetramer interface; other site 316407002547 pyridoxal 5'-phosphate binding site; other site 316407002548 catalytic residue; other site 316407002549 pyruvate dehydrogenase; Provisional; Region: PRK09124 316407002550 Pyrimidine (PYR) binding domain of POX; Region: TPP_PYR_POX; cd07039 316407002551 PYR/PP interface; other site 316407002552 tetramer interface; other site 316407002553 dimer interface; other site 316407002554 TPP binding site; other site 316407002555 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 316407002556 Thiamine pyrophosphate (TPP) family, Pyruvate oxidase (POX) subfamily, TPP-binding module; composed of proteins similar to Lactobacillus plantarum POX, which plays a key role in controlling acetate production under aerobic conditions. POX...; Region: TPP_POX; cd02014 316407002557 TPP-binding site; other site 316407002558 HCP oxidoreductase, NADH-dependent; Provisional; Region: PRK10684 316407002559 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 316407002560 FAD binding pocket; other site 316407002561 FAD binding motif; other site 316407002562 phosphate binding motif; other site 316407002563 beta-alpha-beta structure motif; other site 316407002564 NAD binding pocket; other site 316407002565 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 316407002566 catalytic loop; other site 316407002567 iron binding site; other site 316407002568 hybrid cluster protein; Provisional; Region: PRK05290 316407002569 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 alpha-; Region: HCP_like; cl14655 316407002570 ACS interaction site; other site 316407002571 CODH interaction site; other site 316407002572 Hybrid cluster protein (HCP), formerly known as prismane, is thought to play a role in nitrogen metabolism but its specific function is unknown. HCP has three structural domains, an N-terminal alpha-helical domain, and two similar domains comprising a...; Region: HCP; cd01914 316407002573 hybrid metal cluster; other site 316407002574 Membrane protein of unknown function (DUF340); Region: DUF340; cl01028 316407002575 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-...; Region: MIP; cd00333 316407002576 amphipathic channel; other site 316407002577 Asn-Pro-Ala signature motifs; other site 316407002578 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]; Region: COG3593 316407002579 TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as...; Region: TOPRIM_OLD; cd01026 316407002580 putative active site; other site 316407002581 putative metal-binding site; other site 316407002582 Protein of unknown function (DUF535); Region: DUF535; cl01128 316407002583 macrolide transporter subunit MacA; Provisional; Region: PRK11578 316407002584 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 316407002585 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 316407002586 Walker A/P-loop; other site 316407002587 ATP binding site; other site 316407002588 Q-loop/lid; other site 316407002589 ABC transporter signature motif; other site 316407002590 Walker B; other site 316407002591 D-loop; other site 316407002592 H-loop/switch region; other site 316407002593 Predicted permease; Region: FtsX; cl11418 316407002594 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 protein...; Region: CSP_CDS; cd04458 316407002595 DNA binding site 316407002596 RNA-binding motif; other site 316407002597 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; cl00933 316407002598 ATP-dependent Clp protease ATP-binding subunit; Provisional; Region: clpA; PRK11034 316407002599 Clp amino terminal domain; Region: Clp_N; pfam02861 316407002600 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...; Region: AAA; cd00009 316407002601 Walker A motif; other site 316407002602 ATP binding site; other site 316407002603 Walker B motif; other site 316407002604 arginine finger; other site 316407002605 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...; Region: AAA; cd00009 316407002606 Walker A motif; other site 316407002607 ATP binding site; other site 316407002608 Walker B motif; other site 316407002609 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 316407002610 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 316407002611 rRNA binding site; other site 316407002612 predicted 30S ribosome binding site; other site 316407002613 Leucyl/phenylalanyl-tRNA protein transferase; Region: Leu_Phe_trans; cl01006 316407002614 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11160 316407002615 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 316407002616 The CYD subfamily implicated in cytochrome bd biogenesis. The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd...; Region: ABCC_cytochrome_bd; cd03247 316407002617 Walker A/P-loop; other site 316407002618 ATP binding site; other site 316407002619 Q-loop/lid; other site 316407002620 ABC transporter signature motif; other site 316407002621 Walker B; other site 316407002622 D-loop; other site 316407002623 H-loop/switch region; other site 316407002624 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11174 316407002625 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 316407002626 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407002627 Walker A/P-loop; other site 316407002628 ATP binding site; other site 316407002629 Q-loop/lid; other site 316407002630 ABC transporter signature motif; other site 316407002631 Walker B; other site 316407002632 D-loop; other site 316407002633 H-loop/switch region; other site 316407002634 thioredoxin reductase; Provisional; Region: PRK10262 316407002635 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407002636 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 316407002637 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407002638 DNA translocase FtsK; Provisional; Region: PRK10263 316407002639 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]; Region: VirB11; COG0630 316407002640 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407002641 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 316407002642 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 316407002643 recombination factor protein RarA; Reviewed; Region: PRK13342 316407002644 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...; Region: AAA; cd00009 316407002645 Walker A motif; other site 316407002646 ATP binding site; other site 316407002647 Walker B motif; other site 316407002648 arginine finger; other site 316407002649 MgsA AAA+ ATPase C terminal; Region: MgsA_C; cl13440 316407002650 seryl-tRNA synthetase; Provisional; Region: PRK05431 316407002651 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 316407002652 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 316407002653 dimer interface; other site 316407002654 active site 316407002655 motif 1; other site 316407002656 motif 2; other site 316407002657 motif 3; other site 316407002658 anaerobic dimethyl sulfoxide reductase subunit A; Provisional; Region: PRK14990 316407002659 This CD (MopB_DmsA-EC) includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-...; Region: MopB_DmsA-EC; cd02770 316407002660 putative [Fe4-S4] binding site; other site 316407002661 putative molybdopterin cofactor binding site; other site 316407002662 The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-...; Region: MopB_CT_DmsA-EC; cd02794 316407002663 putative molybdopterin cofactor binding site; other site 316407002664 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 316407002665 DMSO reductase anchor subunit (DmsC); Region: DmsC; cl04869 316407002666 Isochorismatase family; Region: Isochorismatase; pfam00857 316407002667 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 316407002668 catalytic triad; other site 316407002669 dimer interface; other site 316407002670 conserved cis-peptide bond; other site 316407002671 putative MFS family transporter protein; Provisional; Region: PRK03633 316407002672 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 316407002673 putative substrate translocation pore; other site 316407002674 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 316407002675 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407002676 Transcriptional regulator [Transcription]; Region: LysR; COG0583 316407002677 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407002678 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_5; cd08474 316407002679 putative effector binding pocket; other site 316407002680 putative dimerization interface; other site 316407002681 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 316407002682 pyruvate formate lyase-activating enzyme 1; Provisional; Region: pflA; PRK11145 316407002683 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 316407002684 FeS/SAM binding site; other site 316407002685 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 316407002686 Pyruvate formate lyase 1; Region: PFL1; cd01678 316407002687 coenzyme A binding site; other site 316407002688 active site 316407002689 catalytic residues; other site 316407002690 glycine loop; other site 316407002691 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 316407002692 YcaO-like family; Region: YcaO; cl09146 316407002693 Protein of unknown function (DUF421); Region: DUF421; cl00990 316407002694 Phosphoserine aminotransferase (PSAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major group in this CD corresponds to phosphoserine aminotransferase (PSAT). PSAT is active...; Region: PSAT_like; cd00611 316407002695 homodimer interface; other site 316407002696 substrate-cofactor binding pocket; other site 316407002697 pyridoxal 5'-phosphate binding site; other site 316407002698 catalytic residue; other site 316407002699 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 316407002700 Enol pyruvate transferases family includes EPSP synthases and UDP-N-acetylglucosamine enolpyruvyl transferase. Both enzymes catalyze the reaction of enolpyruvyl transfer; Region: EPT-like; cd01554 316407002701 hinge; other site 316407002702 active site 316407002703 Peptidase family M48; Region: Peptidase_M48; cl12018 316407002704 cytidylate kinase; Provisional; Region: cmk; PRK00023 316407002705 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 316407002706 CMP-binding site; other site 316407002707 The sites determining sugar specificity; other site 316407002708 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 316407002709 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 316407002710 RNA binding site; other site 316407002711 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 of...; Region: S1_RPS1_repeat_ec3; cd05688 316407002712 RNA binding site; other site 316407002713 S1_RPS1_repeat_ec4: 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 of...; Region: S1_RPS1_repeat_ec4; cd05689 316407002714 RNA binding site; other site 316407002715 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec5; cd05690 316407002716 RNA binding site; other site 316407002717 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 of...; Region: S1_RPS1_repeat_ec6; cd05691 316407002718 RNA binding site; other site 316407002719 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 higher-...; Region: HU_IHF; cd00591 316407002720 IHF dimer interface; other site 316407002721 IHF - DNA interface; other site 316407002722 ComEC family competence protein; Provisional; Region: PRK11539 316407002723 Competence protein; Region: Competence; cl00471 316407002724 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 316407002725 lipid transporter ATP-binding/permease protein; Provisional; Region: PRK11176 316407002726 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 316407002727 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 316407002728 Walker A/P-loop; other site 316407002729 ATP binding site; other site 316407002730 Q-loop/lid; other site 316407002731 ABC transporter signature motif; other site 316407002732 Walker B; other site 316407002733 D-loop; other site 316407002734 H-loop/switch region; other site 316407002735 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 316407002736 tetraacyldisaccharide 4'-kinase; Region: lpxK; TIGR00682 316407002737 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3214 316407002738 Protein of unknown function (DUF1006); Region: DUF1006; pfam06224 316407002739 Trm112p-like protein; Region: Trm112p; cl01066 316407002740 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 316407002741 Ligand binding site; other site 316407002742 oligomer interface; other site 316407002743 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 316407002744 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 316407002745 putative active site; other site 316407002746 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1, 4-benzoquinol methylase [Coenzyme metabolism]; Region: UbiG; COG2227 316407002747 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 316407002748 S-adenosylmethionine binding site; other site 316407002749 KicB killing factor; Region: KicB; cl11468 316407002750 MukE-like family; Region: MukE; cl11471 316407002751 cell division protein MukB; Provisional; Region: mukB; PRK04863 316407002752 MukB N-terminal; Region: MukB; pfam04310 316407002753 murein L,D-transpeptidase; Provisional; Region: PRK10594 316407002754 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 316407002755 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 316407002756 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 316407002757 Peptidase M15; Region: Peptidase_M15_3; cl01194 316407002758 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 316407002759 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 316407002760 pyridoxal 5'-phosphate binding site; other site 316407002761 homodimer interface; other site 316407002762 catalytic residue; other site 316407002763 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...; Region: gram_neg_porins; cd00342 316407002764 trimer interface; other site 316407002765 eyelet of channel; other site 316407002766 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 316407002767 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 (...; Region: EcAsnRS_like_N; cd04318 316407002768 putative dimer interface; other site 316407002769 putative anticodon binding site; other site 316407002770 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...; Region: AsxRS_core; cd00776 316407002771 homodimer interface; other site 316407002772 motif 1; other site 316407002773 motif 2; other site 316407002774 active site 316407002775 motif 3; other site 316407002776 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 316407002777 Nicotinate phosphoribosyltransferase (NAPRTase), related to PncB. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting...; Region: PncB_like; cd01401 316407002778 active site 316407002779 aminopeptidase N; Provisional; Region: pepN; PRK14015 316407002780 Peptidase family M1; Region: Peptidase_M1; pfam01433 316407002781 aliphatic sulfonates transport ATP-binding subunit; Provisional; Region: ssuB; PRK11247 316407002782 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 316407002783 Walker A/P-loop; other site 316407002784 ATP binding site; other site 316407002785 Q-loop/lid; other site 316407002786 ABC transporter signature motif; other site 316407002787 Walker B; other site 316407002788 D-loop; other site 316407002789 H-loop/switch region; other site 316407002790 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...; Region: TM_PBP2; cd06261 316407002791 dimer interface; other site 316407002792 conserved gate region; other site 316407002793 putative PBP binding loops; other site 316407002794 ABC-ATPase subunit interface; other site 316407002795 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 316407002796 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 316407002797 active site 316407002798 dimer interface; other site 316407002799 non-prolyl cis peptide bond; other site 316407002800 insertion regions; other site 316407002801 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...; Region: PBPb; cd00134 316407002802 substrate binding pocket; other site 316407002803 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 316407002804 membrane-bound complex binding site; other site 316407002805 hinge residues; other site 316407002806 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 316407002807 Fimbrial protein; Region: Fimbrial; cl01416 316407002808 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 316407002809 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 316407002810 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 316407002811 pilin outer membrane usher protein SafC; Provisional; Region: PRK15223; cl14650 316407002812 Fimbrial Usher protein; Region: Usher; pfam00577 316407002813 Fimbrial protein; Region: Fimbrial; cl01416 316407002814 Fimbrial protein; Region: Fimbrial; cl01416 316407002815 Fimbrial protein; Region: Fimbrial; cl01416 316407002816 putativi pili assembly chaperone; Provisional; Region: PRK11385 316407002817 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 316407002818 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 316407002819 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...; Region: DHOD_2_like; cd04738 316407002820 quinone interaction residues; other site 316407002821 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 316407002822 active site 316407002823 catalytic residues; other site 316407002824 FMN binding site; other site 316407002825 substrate binding site; other site 316407002826 Protein of unknown function (DUF1379); Region: DUF1379; pfam07126 316407002827 Uncharacterized Fe-S protein [General function prediction only]; Region: COG3217 316407002828 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 316407002829 MOSC domain; Region: MOSC; pfam03473 316407002830 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 316407002831 catalytic loop; other site 316407002832 iron binding site; other site 316407002833 23S rRNA m(2)G2445 methyltransferase; Provisional; Region: rlmL; PRK11783 316407002834 THUMP domain; Region: THUMP; cl12076 316407002835 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; cl12011 316407002836 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 316407002837 S-adenosylmethionine binding site; other site 316407002838 ABC transporter ATPase component; Reviewed; Region: PRK11147 316407002839 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407002840 Walker A/P-loop; other site 316407002841 ATP binding site; other site 316407002842 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407002843 Q-loop/lid; other site 316407002844 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 316407002845 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 316407002846 paraquat-inducible membrane protein A; Provisional; Region: PRK15103 316407002847 Paraquat-inducible protein A; Region: PqiA; pfam04403 316407002848 Paraquat-inducible protein A; Region: PqiA; pfam04403 316407002849 paraquat-inducible protein B; Provisional; Region: PRK10807 316407002850 mce related protein; Region: MCE; cl03606 316407002851 mce related protein; Region: MCE; cl03606 316407002852 mce related protein; Region: MCE; cl03606 316407002853 Protein of unknown function (DUF330); Region: DUF330; cl01135 316407002854 Ribosome modulation factor; Region: RMF; cl01207 316407002855 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 316407002856 active site 1 316407002857 dimer interface; other site 316407002858 active site 2 316407002859 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 316407002860 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 316407002861 Organiser of macrodomain of Terminus of chromosome; Region: MatP; cl11476 316407002862 outer membrane protein A; Reviewed; Region: PRK10808 316407002863 Surface antigen; Region: Surface_Ag_2; cl01155 316407002864 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 316407002865 ligand binding site; other site 316407002866 Cell division inhibitor SulA; Region: SulA; cl01880 316407002867 TfoX N-terminal domain; Region: TfoX_N; cl01167 316407002868 TfoX N-terminal domain; Region: TfoX_N; cl01167 316407002869 hypothetical membrane protein, TIGR01666; Region: YCCS 316407002870 integral membrane protein, YccS/YhfK family; Region: YCCS_YHJK; TIGR01667 316407002871 hypothetical protein; Provisional; Region: PRK11770 316407002872 Domain of unknown function (DUF307); Region: DUF307; pfam03733 316407002873 Domain of unknown function (DUF307); Region: DUF307; pfam03733 316407002874 DNA helicase IV; Provisional; Region: helD; PRK11054 316407002875 DNA helicase IV / RNA helicase N terminal; Region: Nucleolin_N; pfam12462 316407002876 UvrD/REP helicase; Region: UvrD-helicase; cl14126 316407002877 Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to...; Region: MGS; cd01422 316407002878 active site 316407002879 dimer interfaces; other site 316407002880 catalytic residues; other site 316407002881 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; cl11437 316407002882 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407002883 Hemimethylated DNA-binding protein YccV like; Region: YccV-like; cl01548 316407002884 23S rRNA m(5)C1962 methyltransferase; Provisional; Region: PRK15128 316407002885 PUA domain; Region: PUA; cl00607 316407002886 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 316407002887 S-adenosylmethionine binding site; other site 316407002888 Acylphosphatase; Region: Acylphosphatase; cl00551 316407002889 DsrC like protein; Region: DsrC; cl01101 316407002890 BAX inhibitor (BI)-1 like protein family. Mammalian members of this family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well characterized oncogene, or...; Region: BI-1-like; cd06181 316407002891 hydrogenase (NiFe) small subunit (hydA); Region: hydA; TIGR00391 316407002892 Tat (twin-arginine translocation) pathway signal sequence; Region: TAT_signal_seq; TIGR01409 316407002893 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 316407002894 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; cl00417 316407002895 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 316407002896 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...; Region: H2MP_MemB-H2up; cd06062 316407002897 putative substrate-binding site; other site 316407002898 nickel binding site; other site 316407002899 HyaE family; HyaE is also called HupG and HoxO. They are proteins serving a critical role in the assembly of multimeric [NiFe] hydrogenases, the enzymes that catalyze the oxidation of molecular hydrogen to enable microorganisms to utilize hydrogen as...; Region: HyaE; cd02965 316407002900 HupH hydrogenase expression protein, C-terminal conserved region; Region: HupH_C; pfam04809 316407002901 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 316407002902 cytochrome bd-II oxidase subunit 2; Provisional; Region: PRK15028; cl12219 316407002903 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 316407002904 phosphoanhydride phosphorylase; Provisional; Region: PRK10172 316407002905 Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction; Region: HP_HAP_like; cd07061 316407002906 catalytic core; other site 316407002907 Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction; Region: HP_HAP_like; cd07061 316407002908 cryptic autophosphorylating protein tyrosine kinase Etk; Provisional; Region: PRK09841 316407002909 Chain length determinant protein; Region: Wzz; cl01623 316407002910 Chain length determinant protein; Region: Wzz; cl01623 316407002911 Chain length determinant protein; Region: Wzz; cl01623 316407002912 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 316407002913 Nucleotide binding site; other site 316407002914 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 316407002915 Low molecular weight phosphatase family; Region: LMWPc; cd00115 316407002916 active site 316407002917 polysaccharide export protein Wza; Provisional; Region: PRK15078 316407002918 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 316407002919 Bacterial putative lipoprotein (DUF940); Region: DUF940; pfam06082 316407002920 SLBB-domain like (DUF1017); Region: DUF1017; pfam06251 316407002921 Protein of unknown function (DUF2886); Region: DUF2886; pfam11102 316407002922 Protein of unknown function (DUF2886); Region: DUF2886; pfam11102 316407002923 Insertion element protein; Region: Ins_element1; pfam03811 316407002924 IS1 transposase; Region: Transposase_27; cl00721 316407002925 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 protein...; Region: CSP_CDS; cd04458 316407002926 DNA binding site 316407002927 RNA-binding motif; other site 316407002928 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 protein...; Region: CSP_CDS; cd04458 316407002929 DNA binding site 316407002930 RNA-binding motif; other site 316407002931 cold shock gene; Provisional; Region: PRK09891 316407002932 GnsA/GnsB family; Region: GnsAB; pfam08178 316407002933 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 316407002934 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 alpha-; Region: HCP_like; cl14655 316407002935 hybrid sensory histidine kinase TorS; Provisional; Region: PRK11466 316407002936 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 connected by an extended linker. The...; Region: HAMP; cl01054 316407002937 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 trans-...; Region: HisKA; cd00082 316407002938 dimer interface; other site 316407002939 phosphorylation site 316407002940 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 316407002941 ATP binding site; other site 316407002942 Mg2+ binding site; other site 316407002943 G-X-G motif; other site 316407002944 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 316407002945 active site 316407002946 phosphorylation site 316407002947 intermolecular recognition site; other site 316407002948 dimerization interface; other site 316407002949 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 316407002950 putative binding surface; other site 316407002951 active site 316407002952 TMAO reductase system periplasmic protein TorT; Provisional; Region: PRK10936 316407002953 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 316407002954 putative ligand binding site; other site 316407002955 DNA-binding transcriptional regulator TorR; Provisional; Region: PRK10766 316407002956 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 316407002957 active site 316407002958 phosphorylation site 316407002959 intermolecular recognition site; other site 316407002960 dimerization interface; other site 316407002961 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...; Region: trans_reg_C; cd00383 316407002962 DNA binding site 316407002963 trimethylamine N-oxide reductase cytochrome c-type subunit; Provisional; Region: PRK15032 316407002964 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl09485 316407002965 trimethylamine N-oxide reductase I catalytic subunit; Provisional; Region: PRK15102 316407002966 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 316407002967 molybdopterin cofactor binding site; other site 316407002968 substrate binding site; other site 316407002969 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 316407002970 molybdopterin cofactor binding site; other site 316407002971 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 316407002972 chaperone-modulator protein CbpM; Provisional; Region: PRK10265 316407002973 curved DNA-binding protein CbpA; Provisional; Region: PRK10266 316407002974 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...; Region: DnaJ; cd06257 316407002975 HSP70 interaction site; other site 316407002976 DnaJ C terminal region; Region: DnaJ_C; pfam01556 316407002977 DnaJ C terminal region; Region: DnaJ_C; pfam01556 316407002978 hypothetical protein; Provisional; Region: PRK09784 316407002979 glucose-1-phosphatase/inositol phosphatase; Provisional; Region: PRK10173 316407002980 Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction; Region: HP_HAP_like; cd07061 316407002981 catalytic core; other site 316407002982 Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction; Region: HP_HAP_like; cd07061 316407002983 hypothetical protein; Provisional; Region: PRK10174 316407002984 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 316407002985 Permease family; Region: Xan_ur_permease; cl00967 316407002986 Flavin Reductases; Region: FlaRed; cl00801 316407002987 Nitroreductase-like family 5. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_5; cd02148 316407002988 putative FMN binding site; other site 316407002989 pyrimidine utilization protein D; Region: RutD; TIGR03611 316407002990 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; cl12031 316407002991 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 316407002992 homotrimer interaction site; other site 316407002993 putative active site; other site 316407002994 Isochorismatase family; Region: Isochorismatase; pfam00857 316407002995 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 316407002996 catalytic triad; other site 316407002997 conserved cis-peptide bond; other site 316407002998 pyrimidine utilization protein A; Region: RutA; TIGR03612 316407002999 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 316407003000 active site 316407003001 dimer interface; other site 316407003002 non-prolyl cis peptide bond; other site 316407003003 insertion regions; other site 316407003004 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl14614 316407003005 HTH-type transcriptional regulator RutR; Provisional; Region: PRK15008 316407003006 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316407003007 YcdC-like protein, C-terminal region; Region: TetR_C_3; pfam08362 316407003008 trifunctional transcriptional regulator/proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: putA; PRK11809 316407003009 Predicted transcriptional regulator [Transcription]; Region: COG3905 316407003010 Proline dehydrogenase; Region: Pro_dh; cl03282 316407003011 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 316407003012 Glutamate binding site; other site 316407003013 NAD binding site; other site 316407003014 catalytic residues; other site 316407003015 Sodium:solute symporter family; Region: SSF; cl00456 316407003016 ECK1007:JW1002:b1017; hypothetical protein, C-ter fragment 316407003017 ECK1007:JW5141+JW1002:b4490; predicted membrane protein 316407003018 ECK1007:JW5141:b1016; hypothetical protein, N-ter fragment 316407003019 Imelysin; Region: Peptidase_M75; cl09159 316407003020 Dyp-type peroxidase family; Region: Dyp_perox; cl01067 316407003021 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 316407003022 PhoH-like protein; Region: PhoH; cl12134 316407003023 hemin storage system protein; Provisional; Region: hmsS; cl14676 316407003024 N-glycosyltransferase; Provisional; Region: PRK11204 316407003025 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 316407003026 DXD motif; other site 316407003027 outer membrane N-deacetylase; Provisional; Region: pgaB; PRK14582 316407003028 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 316407003029 outer membrane protein PgaA; Provisional; Region: pgaA; PRK10049 316407003030 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316407003031 metal-binding site 316407003032 active site 316407003033 I-site; other site 316407003034 putative transposase OrfB; Reviewed; Region: PHA02517 316407003035 Integrase core domain; Region: rve; cl01316 316407003036 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; cl01116 316407003037 ECK1016:JW5145:b1028; hypothetical protein 316407003038 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407003039 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 316407003040 putative hydrolase; Validated; Region: PRK09248 316407003041 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 316407003042 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 316407003043 Protein of unknown function (DUF1097); Region: DUF1097; pfam06496 316407003044 Curli production assembly/transport component CsgG; Region: CsgG; cl00639 316407003045 Curli production assembly/transport component CsgF; Region: Tafi-CsgF; cl08082 316407003046 Curli assembly protein CsgE; Region: CsgE; cl08115 316407003047 DNA-binding transcriptional regulator CsgD; Provisional; Region: PRK10100 316407003048 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...; Region: LuxR_C_like; cd06170 316407003049 DNA binding residues 316407003050 dimerization interface; other site 316407003051 curlin minor subunit CsgB; Provisional; Region: csgB; PRK10101 316407003052 Curlin associated repeat; Region: Curlin_rpt; pfam07012 316407003053 Curlin associated repeat; Region: Curlin_rpt; pfam07012 316407003054 major curlin subunit; Provisional; Region: csgA; PRK10051 316407003055 Curlin associated repeat; Region: Curlin_rpt; pfam07012 316407003056 Thin aggregative fimbriae synthesis protein; Region: Tafi-CsgC; cl11667 316407003057 IS2 transposase TnpB; Reviewed; Region: PRK09409 316407003058 Integrase core domain; Region: rve; cl01316 316407003059 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; cl01116 316407003060 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 316407003061 Fimbrial protein; Region: Fimbrial; cl01416 316407003062 Macro domain, Appr-1'-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose...; Region: Macro_Appr_pase_like; cd02908 316407003063 putative ADP-ribose binding site; other site 316407003064 putative active site; other site 316407003065 Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of...; Region: PLDc; cd00138 316407003066 active site 316407003067 signature motif; other site 316407003068 Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of...; Region: PLDc; cd00138 316407003069 active site 316407003070 signature motif; other site 316407003071 Predicted acyltransferases [Lipid metabolism]; Region: COG1835; cl00792 316407003072 Acyltransferase family; Region: Acyl_transf_3; pfam01757 316407003073 Periplasmic glucan biosynthesis protein, MdoG; Region: MdoG; cl01208 316407003074 Glucan_BSP_ModH catalyzes the elongation of beta-1,2 polyglucose chains of glucan; Region: Glucan_BSP_ModH; cd04191 316407003075 Ligand binding site; other site 316407003076 DXD motif; other site 316407003077 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 316407003078 Protein of unknown function (DUF1375); Region: DUF1375; cl11456 316407003079 secY/secA suppressor protein; Provisional; Region: PRK11467 316407003080 drug efflux system protein MdtG; Provisional; Region: PRK09874 316407003081 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 316407003082 putative substrate translocation pore; other site 316407003083 lipid A biosynthesis lauroyl acyltransferase; Provisional; Region: PRK08734 316407003084 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 316407003085 putative acyl-acceptor binding pocket; other site 316407003086 putative rhodanese-related sulfurtransferase; Provisional; Region: PRK00142 316407003087 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 316407003088 active site residue 316407003089 YceI-like domain; Region: YceI; cl01001 316407003090 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 316407003091 Protein of unknown function (DUF2770); Region: DUF2770; pfam10968 316407003092 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407003093 sarcosine oxidase, monomeric form; Region: soxA_mon; TIGR01377 316407003094 biofilm formation regulatory protein BssS; Reviewed; Region: bssS; PRK12301 316407003095 DinI-like family; Region: DinI; cl11630 316407003096 Dihydroorotase [Nucleotide transport and metabolism]; Region: PyrC; COG0418 316407003097 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 316407003098 active site 316407003099 substrate binding pocket; other site 316407003100 dimer interface; other site 316407003101 Protein of unknown function (DUF1439); Region: DUF1439; cl06345 316407003102 glutaredoxin 2; Provisional; Region: PRK10387 316407003103 GST_N family, Glutaredoxin 2 (GRX2) subfamily; composed of bacterial proteins similar to E. coli GRX2, an atypical GRX with a molecular mass of about 24kD, compared with other GRXs which are 9-12kD in size. GRX2 adopts a GST fold containing an N-...; Region: GST_N_GRX2; cd03037 316407003104 C-terminal domain interface; other site 316407003105 GSH binding site (G-site); other site 316407003106 catalytic residues; other site 316407003107 putative dimer interface; other site 316407003108 GST_C family, Glutaredoxin 2 (GRX2) subfamily; composed of bacterial proteins similar to E. coli GRX2, an atypical GRX with a molecular mass of about 24kD (most GRXs range from 9-12kD). GRX2 adopts a GST fold containing an N-terminal thioredoxin-fold...; Region: GST_C_GRX2; cd03199 316407003109 putative dimer interface; other site 316407003110 putative substrate binding pocket (H-site); other site 316407003111 N-terminal domain interface; other site 316407003112 multidrug resistance protein MdtH; Provisional; Region: PRK11646 316407003113 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 316407003114 putative substrate translocation pore; other site 316407003115 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 316407003116 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 316407003117 hypothetical protein; Provisional; Region: PRK11239 316407003118 Protein of unknown function, DUF480; Region: DUF480; cl01209 316407003119 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 316407003120 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407003121 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 316407003122 integral membrane protein MviN; Region: mviN; TIGR01695 316407003123 FlgN protein; Region: FlgN; cl09176 316407003124 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 316407003125 SAF domain; Region: SAF; cl00555 316407003126 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 316407003127 flagellar basal body rod protein FlgB; Provisional; Region: flgB; cl09471 316407003128 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 316407003129 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 316407003130 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 316407003131 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK06655 316407003132 Flagellar hook capping protein; Region: FlgD; cl04347 316407003133 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 316407003134 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 316407003135 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 316407003136 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 316407003137 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 316407003138 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 316407003139 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 316407003140 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 316407003141 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 316407003142 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 316407003143 Flagellar L-ring protein; Region: FlgH; cl00905 316407003144 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 316407003145 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 316407003146 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 316407003147 Rod binding protein; Region: Rod-binding; cl01626 316407003148 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; cl00743 316407003149 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK08147 316407003150 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 316407003151 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08027 316407003152 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 316407003153 ribonuclease E; Reviewed; Region: rne; PRK10811 316407003154 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 316407003155 homodimer interface; other site 316407003156 oligonucleotide binding site; other site 316407003157 Polyribonucleotide phosphorylase C terminal; Region: PNPase_C; pfam12111 316407003158 Protein of unknown function (DUF2655); Region: DUF2655; pfam10848 316407003159 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 316407003160 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 316407003161 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 316407003162 active site 316407003163 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 316407003164 active site 316407003165 dimer interface; other site 316407003166 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 316407003167 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 316407003168 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 316407003169 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 316407003170 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 316407003171 dimer interface; other site 316407003172 active site 316407003173 CoA binding pocket; other site 316407003174 Acyl transferase domain; Region: Acyl_transf_1; cl08282 316407003175 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 316407003176 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407003177 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 316407003178 Phosphopantetheine attachment site; Region: PP-binding; cl09936 316407003179 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 316407003180 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 316407003181 dimer interface; other site 316407003182 active site 316407003183 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 316407003184 Aminotransferase class IV; Region: Aminotran_4; pfam01063 316407003185 pyridoxal 5'-phosphate binding site; other site 316407003186 catalytic residue; other site 316407003187 YceG-like family; Region: YceG; pfam02618 316407003188 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 316407003189 dimerization interface; other site 316407003190 thymidylate kinase; Validated; Region: tmk; PRK00698 316407003191 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...; Region: TMPK; cd01672 316407003192 TMP-binding site; other site 316407003193 ATP-binding site; other site 316407003194 DNA polymerase III subunit delta'; Validated; Region: PRK07993 316407003195 C terminal; Region: DNApol3-delta_C; pfam09115 316407003196 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 316407003197 active site 316407003198 PTS system glucose-specific transporter subunits IIBC; Provisional; Region: PRK11089 316407003199 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 316407003200 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...; Region: PTS_IIB_glc; cd00212 316407003201 active site turn 316407003202 phosphorylation site 316407003203 ferric-rhodotorulic acid outer membrane transporter; Provisional; Region: PRK10003 316407003204 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 316407003205 N-terminal plug; other site 316407003206 ligand-binding site; other site 316407003207 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 316407003208 nucleotide binding site/active site; other site 316407003209 HIT family signature motif; other site 316407003210 catalytic residue; other site 316407003211 Predicted periplasmic lipoprotein [General function prediction only]; Region: COG5633 316407003212 Putative periplasmic lipoprotein; Region: DUF1425; cd09030 316407003213 putative dimer interface; other site 316407003214 Collagen-binding surface adhesin SpaP (antigen I/II family) [General function prediction only]; Region: FlgN; cl01354 316407003215 Phosphotransferase enzyme family; Region: APH; pfam01636 316407003216 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 316407003217 active site 316407003218 substrate binding site; other site 316407003219 ATP binding site; other site 316407003220 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 316407003221 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; cl12031 316407003222 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 316407003223 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407003224 Rickettsia 17 kDa surface antigen; Region: Rick_17kDa_Anti; cl10470 316407003225 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 316407003226 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316407003227 Protein of unknown function (DUF1471); Region: DUF1471; cl11507 316407003228 L,D-transpeptidase; Provisional; Region: PRK10190 316407003229 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 316407003230 putative peptidoglycan binding site; other site 316407003231 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 316407003232 transcription-repair coupling factor; Provisional; Region: PRK10689 316407003233 CarD-like/TRCF domain; Region: CarD_TRCF; cl00588 316407003234 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 316407003235 ATP binding site; other site 316407003236 putative Mg++ binding site; other site 316407003237 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 316407003238 nucleotide binding region; other site 316407003239 ATP-binding site; other site 316407003240 TRCF domain; Region: TRCF; pfam03461 316407003241 Predicted acyltransferases [Lipid metabolism]; Region: COG1835; cl00792 316407003242 Acyltransferase family; Region: Acyl_transf_3; pfam01757 316407003243 Predicted permease; Region: FtsX; cl11418 316407003244 LolC/E family; Region: lolCE; TIGR02212 316407003245 lipoprotein transporter ATP-binding subunit; Provisional; Region: lolD; PRK11629 316407003246 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 316407003247 Walker A/P-loop; other site 316407003248 ATP binding site; other site 316407003249 Q-loop/lid; other site 316407003250 ABC transporter signature motif; other site 316407003251 Walker B; other site 316407003252 D-loop; other site 316407003253 H-loop/switch region; other site 316407003254 Predicted permease; Region: FtsX; cl11418 316407003255 LolC/E family; Region: lolCE; TIGR02212 316407003256 ROK family; Region: ROK; cl09121 316407003257 fructokinase; Reviewed; Region: PRK09557 316407003258 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...; Region: SIRT5_Af1_CobB; cd01412 316407003259 NAD+ binding site; other site 316407003260 substrate binding site; other site 316407003261 Zn binding site; other site 316407003262 Domain of unknown function (DUF477); Region: DUF477; cl01535 316407003263 Protein of unknown function (DUF3592); Region: DUF3592; pfam12158 316407003264 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 316407003265 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 316407003266 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...; Region: TM_PBP2; cd06261 316407003267 dimer interface; other site 316407003268 conserved gate region; other site 316407003269 putative PBP binding loops; other site 316407003270 ABC-ATPase subunit interface; other site 316407003271 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...; Region: TM_PBP2; cd06261 316407003272 dimer interface; other site 316407003273 conserved gate region; other site 316407003274 putative PBP binding loops; other site 316407003275 ABC-ATPase subunit interface; other site 316407003276 putrescine/spermidine ABC transporter ATPase protein; Reviewed; Region: potA; PRK09452 316407003277 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407003278 Walker A/P-loop; other site 316407003279 ATP binding site; other site 316407003280 Q-loop/lid; other site 316407003281 ABC transporter signature motif; other site 316407003282 Walker B; other site 316407003283 D-loop; other site 316407003284 H-loop/switch region; other site 316407003285 TOBE domain; Region: TOBE_2; cl01440 316407003286 Peptidase dimerization domain; Region: M20_dimer; cl09126 316407003287 peptidase T; Region: peptidase-T; TIGR01882 316407003288 Uncharacterized conserved protein [Function unknown]; Region: COG2850 316407003289 sensor protein PhoQ; Provisional; Region: PRK10815 316407003290 PhoQ Sensor; Region: PhoQ_Sensor; pfam08918 316407003291 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 trans-...; Region: HisKA; cl00080 316407003292 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 316407003293 ATP binding site; other site 316407003294 Mg2+ binding site; other site 316407003295 G-X-G motif; other site 316407003296 DNA-binding transcriptional regulator PhoP; Provisional; Region: PRK10816 316407003297 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 316407003298 active site 316407003299 phosphorylation site 316407003300 intermolecular recognition site; other site 316407003301 dimerization interface; other site 316407003302 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...; Region: trans_reg_C; cd00383 316407003303 DNA binding site 316407003304 adenylosuccinate lyase; Provisional; Region: PRK09285 316407003305 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 316407003306 tetramer interface; other site 316407003307 active site 316407003308 Protein of unknown function (DUF489); Region: DUF489; cl01097 316407003309 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 316407003310 tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase; Region: trmU; TIGR00420 316407003311 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...; Region: Nudix_Hydrolase_2; cd03675 316407003312 nudix motif; other site 316407003313 23S rRNA pseudouridine synthase E; Provisional; Region: PRK11394 316407003314 PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE. This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-...; Region: PseudoU_synth_RluE; cd02566 316407003315 probable active site; other site 316407003316 isocitrate dehydrogenase; Validated; Region: PRK07362 316407003317 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 316407003318 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; cl12011 316407003319 phage exclusion protein Lit; Provisional; Region: PRK09672 316407003320 Peptidase U49; Region: Peptidase_U49; pfam10463 316407003321 Bacteriophage lambda integrase, N-terminal domain; Region: Phage_integ_N; pfam09003 316407003322 Lambda integrase, C-terminal catalytic domain. Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome. They belong to the...; Region: INT_Lambda_C; cd00800 316407003323 Phage integrase family; Region: Phage_integrase; pfam00589 316407003324 dimer interface; other site 316407003325 Int/Topo IB signature motif; other site 316407003326 active site 316407003327 Excisionase-like protein; Region: Exc; pfam07825 316407003328 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 316407003329 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 (...; Region: S24_LexA-like; cd06529 316407003330 Catalytic site; other site 316407003331 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407003332 DNA binding site 316407003333 Phage Terminase; Region: Terminase_1; pfam03354 316407003334 Phage portal protein; Region: Phage_portal; cl01923 316407003335 Baseplate J-like protein; Region: Baseplate_J; cl01294 316407003336 Uncharacterized protein conserved in bacteria (DUF2313); Region: DUF2313; cl01542 316407003337 Caudovirales tail fibre assembly protein; Region: Caudo_TAP; pfam02413 316407003338 Caudovirales tail fibre assembly protein; Region: Caudo_TAP; pfam02413 316407003339 ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment 316407003340 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 316407003341 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 316407003342 catalytic residues; other site 316407003343 catalytic nucleophile; other site 316407003344 Presynaptic Site I dimer interface; other site 316407003345 Synaptic Antiparallel dimer interface; other site 316407003346 Synaptic Flat tetramer interface; other site 316407003347 Synaptic Site I dimer interface; other site 316407003348 DNA binding site 316407003349 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 316407003350 DNA-binding interface; DNA binding site 316407003351 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...; Region: HNHc; cd00085 316407003352 active site 316407003353 ECK1146:JW5173:b4519; conserved hypothetical protein 316407003354 anti-adapter protein IraM; Provisional; Region: PRK09919 316407003355 Protein of unknown function (DUF1398); Region: DUF1398; cl11576 316407003356 transcriptional regulator MirA; Provisional; Region: PRK15043 316407003357 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 316407003358 DNA binding residues 316407003359 Sensors of blue-light using FAD; Region: BLUF; pfam04940 316407003360 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 316407003361 Biofilm development protein YmgB/AriR; Region: YmgB; pfam10798 316407003362 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 316407003363 ECK1157:JW5176:b1170; hypothetical protein, C-ter fragment 316407003364 ECK1157:JW5901+JW5176:b4491; hypothetical protein 316407003365 ECK1157:JW5901:b1169; hypothetical protein, N-ter fragment 316407003366 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 316407003367 Septum formation topological specificity factor MinE; Region: MinE; cl00538 316407003368 cell division inhibitor MinD; Provisional; Region: PRK10818 316407003369 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...; Region: MinD; cd02036 316407003370 Switch I; other site 316407003371 Switch II; other site 316407003372 septum formation inhibitor; Reviewed; Region: minC; PRK03511 316407003373 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 316407003374 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 316407003375 Fels-1 Prophage Protein-like; Region: Fels1; pfam05666 316407003376 Fels-1 Prophage Protein-like; Region: Fels1; pfam05666 316407003377 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 316407003378 YcgL domain; Region: YcgL; cl01189 316407003379 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 316407003380 Uncharacterized protein family (UPF0153); Region: UPF0153; cl00497 316407003381 Haemolysin E (HlyE); Region: HlyE; cl11627 316407003382 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 316407003383 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 (...; Region: S24_LexA-like; cd06529 316407003384 Catalytic site; other site 316407003385 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 316407003386 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 316407003387 active site 316407003388 DNA binding site 316407003389 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 316407003390 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; cd00625 316407003391 transmembrane helices; other site 316407003392 fatty acid metabolism regulator; Provisional; Region: PRK04984 316407003393 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407003394 DNA binding site 316407003395 FCD domain; Region: FCD; cl11656 316407003396 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; cl01044 316407003397 SpoVR like protein; Region: SpoVR; pfam04293 316407003398 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407003399 D-amino acid dehydrogenase small subunit; Provisional; Region: PRK12409 316407003400 alanine racemase; Reviewed; Region: dadX; PRK03646 316407003401 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 316407003402 active site 316407003403 pyridoxal 5'-phosphate (PLP) binding site; other site 316407003404 substrate binding site; other site 316407003405 catalytic residues; other site 316407003406 dimer interface; other site 316407003407 NhaP-type Na+/H+ and K+/H+ antiporters with a unique C-terminal domain [Inorganic ion transport and metabolism]; Region: COG3263 316407003408 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 316407003409 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; cl09110 316407003410 Transporter associated domain; Region: CorC_HlyC; pfam03471 316407003411 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 316407003412 dimer interface; other site 316407003413 catalytic triad; other site 316407003414 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 catalyze...; Region: LT_GEWL; cd00254 316407003415 N-acetyl-D-glucosamine binding site; other site 316407003416 catalytic residue; other site 316407003417 c-di-GMP-binding protein [Signal transduction mechanisms]; Region: COG5581 316407003418 YcgR protein; Region: YcgR; pfam07317 316407003419 PilZ domain; Region: PilZ; cl01260 316407003420 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 316407003421 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; cl01801 316407003422 Neutral trehalase [Carbohydrate transport and metabolism]; Region: TreA; COG1626 316407003423 dihydroxyacetone kinase subunit M; Provisional; Region: PRK11377 316407003424 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_man; cl00025 316407003425 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 316407003426 dimerization domain swap beta strand; other site 316407003427 regulatory protein interface; other site 316407003428 active site 316407003429 regulatory phosphorylation site; other site 316407003430 PEP-utilising enzyme, N-terminal; Region: PEP-utilizers_N; pfam05524 316407003431 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 316407003432 DAK2 domain; Region: Dak2; cl03685 316407003433 dihydroxyacetone kinase subunit DhaK; Provisional; Region: PRK14481; cl10557 316407003434 Dak1 domain; Region: Dak1; pfam02733 316407003435 DNA-binding transcriptional regulator DhaR; Provisional; Region: PRK11388 316407003436 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 316407003437 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...; Region: AAA; cd00009 316407003438 Walker A motif; other site 316407003439 ATP binding site; other site 316407003440 Walker B motif; other site 316407003441 arginine finger; other site 316407003442 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 316407003443 autotransport protein MisL; Provisional; Region: PRK15313 316407003444 Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 1, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of Neisseria and Haemophilus IgA1 proteases...; Region: PL1_Passenger_AT; cd01343 316407003445 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 316407003446 Autotransporter beta-domain; Region: Autotransporter; cl02365 316407003447 GTP-binding protein YchF; Reviewed; Region: PRK09601 316407003448 YchF subfamily. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated...; Region: YchF; cd01900 316407003449 G1 box; other site 316407003450 GTP/Mg2+ binding site; other site 316407003451 Switch I region; other site 316407003452 G2 box; other site 316407003453 Switch II region; other site 316407003454 G3 box; other site 316407003455 G4 box; other site 316407003456 G5 box; other site 316407003457 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 316407003458 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 316407003459 putative active site; other site 316407003460 catalytic residue; other site 316407003461 Protein of unknown function (DUF2583); Region: DUF2583; cl11676 316407003462 putative transporter; Provisional; Region: PRK11660 316407003463 Permease family; Region: Xan_ur_permease; cl00967 316407003464 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 316407003465 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 316407003466 ribose-phosphate pyrophosphokinase; Region: ribP_PPkin; TIGR01251 316407003467 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 316407003468 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 316407003469 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 316407003470 outer membrane lipoprotein LolB; Region: lolB; TIGR00548 316407003471 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 316407003472 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 316407003473 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 316407003474 tRNA; other site 316407003475 putative tRNA binding site; other site 316407003476 putative NADP binding site; other site 316407003477 Glutamyl-tRNAGlu reductase, dimerization domain; Region: GlutR_dimer; pfam00745 316407003478 peptide chain release factor 1; Validated; Region: prfA; PRK00591 316407003479 RF-1 domain; Region: RF-1; cl02875 316407003480 RF-1 domain; Region: RF-1; cl02875 316407003481 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 316407003482 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 316407003483 Invasion gene expression up-regulator, SirB; Region: SirB; cl01184 316407003484 Uncharacterized conserved protein [Function unknown]; Region: COG2912 316407003485 hypothetical protein; Provisional; Region: PRK10941 316407003486 NeuB family; Region: NeuB; cl00496 316407003487 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 316407003488 calcium/sodium:proton antiporter; Provisional; Region: PRK10599 316407003489 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 316407003490 ChaB; Region: ChaB; cl01887 316407003491 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 316407003492 putative active site pocket; other site 316407003493 dimerization interface; other site 316407003494 putative catalytic residue; other site 316407003495 DsrE/DsrF-like family; Region: DrsE; cl00672 316407003496 Protein of unknown function (DUF3442); Region: DUF3442; pfam11924 316407003497 transcriptional regulator NarL; Provisional; Region: PRK10651 316407003498 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 316407003499 active site 316407003500 phosphorylation site 316407003501 intermolecular recognition site; other site 316407003502 dimerization interface; other site 316407003503 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...; Region: LuxR_C_like; cd06170 316407003504 DNA binding residues 316407003505 dimerization interface; other site 316407003506 nitrate/nitrite sensor protein NarX; Provisional; Region: PRK10600 316407003507 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 connected by an extended linker. The...; Region: HAMP; cl01054 316407003508 Histidine kinase; Region: HisKA_3; pfam07730 316407003509 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 316407003510 ATP binding site; other site 316407003511 Mg2+ binding site; other site 316407003512 G-X-G motif; other site 316407003513 nitrate/nitrite transport protein NarU; Provisional; Region: PRK15034 316407003514 nitrite extrusion protein (nitrite facilitator); Region: 2A0108; TIGR00886 316407003515 respiratory nitrate reductase, alpha subunit; Region: narG; TIGR01580 316407003516 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate...; Region: MopB_Nitrate-R-NarG-like; cd02750 316407003517 [4Fe-4S] binding site; other site 316407003518 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 tungsten-...; Region: Molybdopterin-Binding; cl09928 316407003519 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 tungsten-...; Region: Molybdopterin-Binding; cl09928 316407003520 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 tungsten-...; Region: Molybdopterin-Binding; cl09928 316407003521 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate...; Region: MopB_CT_Nitrate-R-NarG-like; cd02776 316407003522 molybdopterin cofactor binding site; other site 316407003523 nitrate reductase, beta subunit; Region: narH; TIGR01660 316407003524 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 316407003525 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; cl00959 316407003526 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 316407003527 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 316407003528 Formyl transferase; Region: Formyl_trans_N; cl00395 316407003529 hypothetical protein; Provisional; Region: PRK01617 316407003530 SEC-C motif; Region: SEC-C; cl12132 316407003531 hypothetical protein; Provisional; Region: PRK10279 316407003532 Bacterial patatin-like phospholipase domain containing protein 6; Region: Pat_NTE_like_bacteria; cd07228 316407003533 active site 316407003534 nucleophile elbow; other site 316407003535 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 316407003536 active site 316407003537 response regulator of RpoS; Provisional; Region: PRK10693 316407003538 phosphorylation site 316407003539 intermolecular recognition site; other site 316407003540 dimerization interface; other site 316407003541 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 316407003542 active site 316407003543 tetramer interface; other site 316407003544 Domain in histone-like proteins of HNS family; Region: HNS; cl09251 316407003545 DNA binding protein, nucleoid-associated; Provisional; Region: PRK10328 316407003546 Thymidine kinase; Region: TK; cl00631 316407003547 ECK1234:JW1227:b1239; hypothetical protein, C-ter fragment 316407003548 ECK1234:JW5883+JW1227:b4573; hypothetical protein 316407003549 ECK1234:JW5883:b1240; hypothetical protein, N-ter fragment 316407003550 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional; Region: PRK13805 316407003551 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 316407003552 putative catalytic cysteine; other site 316407003553 C-terminal alcohol dehydrogenase domain of the acetaldehyde dehydrogenase-alcohol dehydrogenase bifunctional two-domain protein (AAD); Region: AAD_C; cd08178 316407003554 putative active site; other site 316407003555 metal-binding site 316407003556 MarC family integral membrane protein; Region: MarC; cl00919 316407003557 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; cl01116 316407003558 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 316407003559 IS2 transposase TnpB; Reviewed; Region: PRK09409 316407003560 Integrase core domain; Region: rve; cl01316 316407003561 oligopeptide ABC transporter substrate-binding protein OppA; Provisional; Region: PRK15104 316407003562 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 316407003563 peptide binding site; other site 316407003564 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...; Region: TM_PBP2; cd06261 316407003565 dimer interface; other site 316407003566 conserved gate region; other site 316407003567 putative PBP binding loops; other site 316407003568 ABC-ATPase subunit interface; other site 316407003569 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...; Region: TM_PBP2; cd06261 316407003570 dimer interface; other site 316407003571 conserved gate region; other site 316407003572 putative PBP binding loops; other site 316407003573 ABC-ATPase subunit interface; other site 316407003574 oligopeptide transporter ATP-binding component; Provisional; Region: oppD; PRK09473 316407003575 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 316407003576 Walker A/P-loop; other site 316407003577 ATP binding site; other site 316407003578 Q-loop/lid; other site 316407003579 ABC transporter signature motif; other site 316407003580 Walker B; other site 316407003581 D-loop; other site 316407003582 H-loop/switch region; other site 316407003583 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 316407003584 oligopeptide ABC transporter ATP-binding protein OppF; Provisional; Region: PRK15079 316407003585 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 316407003586 Walker A/P-loop; other site 316407003587 ATP binding site; other site 316407003588 Q-loop/lid; other site 316407003589 ABC transporter signature motif; other site 316407003590 Walker B; other site 316407003591 D-loop; other site 316407003592 H-loop/switch region; other site 316407003593 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 316407003594 Protein of unknown function, DUF440; Region: DUF440; cl11472 316407003595 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 316407003596 Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of...; Region: PLDc; cd00138 316407003597 active site 316407003598 signature motif; other site 316407003599 Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of...; Region: PLDc; cd00138 316407003600 active site 316407003601 signature motif; other site 316407003602 voltage-gated potassium channel; Provisional; Region: PRK10537 316407003603 Ion channel; Region: Ion_trans_2; cl11596 316407003604 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407003605 YCII-related domain; Region: YCII; cl00999 316407003606 transport protein TonB; Provisional; Region: PRK10819 316407003607 Gram-negative bacterial tonB protein; Region: TonB; cl10048 316407003608 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...; Region: BFIT_BACH; cd03442 316407003609 Intracellular septation protein A; Region: IspA; cl01098 316407003610 Uncharacterized protein family (UPF0259); Region: UPF0259; cl11642 316407003611 Surface antigen; Region: Surface_Ag_2; cl01155 316407003612 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 316407003613 dinuclear metal binding motif; other site 316407003614 YciF bacterial stress response protein, ferritin-like iron-binding domain; Region: YciF; cd07909 316407003615 dimerization interface; other site 316407003616 metal-binding site 316407003617 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 316407003618 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...; Region: Tryptophan_synthase_alpha; cd04724 316407003619 substrate binding site; other site 316407003620 active site 316407003621 catalytic residues; other site 316407003622 heterodimer interface; other site 316407003623 tryptophan synthase, beta chain; Region: PLN02618 316407003624 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 316407003625 pyridoxal 5'-phosphate binding site; other site 316407003626 catalytic residue; other site 316407003627 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional; Region: PRK09427 316407003628 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 316407003629 active site 316407003630 ribulose/triose binding site; other site 316407003631 phosphate binding site; other site 316407003632 substrate (anthranilate) binding pocket; other site 316407003633 product (indole) binding pocket; other site 316407003634 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 monomeric...; Region: PRAI; cd00405 316407003635 active site 316407003636 bifunctional glutamine amidotransferase/anthranilate phosphoribosyltransferase; Provisional; Region: PRK09522 316407003637 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 316407003638 glutamine binding; other site 316407003639 catalytic triad; other site 316407003640 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 316407003641 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 316407003642 anthranilate synthase component I; Provisional; Region: PRK13564 316407003643 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 316407003644 chorismate binding enzyme; Region: Chorismate_bind; cl10555 316407003645 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 316407003646 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 316407003647 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 316407003648 Predicted membrane protein (DUF2207); Region: DUF2207; pfam09972 316407003649 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 316407003650 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 316407003651 RNA binding surface; other site 316407003652 PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_RluB; cd02556 316407003653 probable active site; other site 316407003654 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 316407003655 Cob(I)alamin adenosyltransferase N terminal; Region: Co_AT_N; pfam12557 316407003656 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...; Region: CobA_CobO_BtuR; cd00561 316407003657 homodimer interface; other site 316407003658 Walker A motif; other site 316407003659 ATP binding site; other site 316407003660 hydroxycobalamin binding site; other site 316407003661 Walker B motif; other site 316407003662 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407003663 3-ketoacyl-(acyl-carrier-protein) reductase; Reviewed; Region: PRK12826 316407003664 Peptidase family S49 N-terminal; Region: Peptidase_S49_N; pfam08496 316407003665 putative inner membrane peptidase; Provisional; Region: PRK11778 316407003666 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 316407003667 tandem repeat interface; other site 316407003668 oligomer interface; other site 316407003669 active site residues 316407003670 Protein of unknown function (DUF2498); Region: DUF2498; cl11671 316407003671 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 316407003672 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...; Region: TOPRIM_TopoIA_TopoI; cd03363 316407003673 active site 316407003674 interdomain interaction site; other site 316407003675 putative metal-binding site; other site 316407003676 nucleotide binding site; other site 316407003677 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...; Region: TOP1Ac; cd00186 316407003678 domain I; other site 316407003679 DNA binding groove 316407003680 phosphate binding site; other site 316407003681 domain II; other site 316407003682 domain III; other site 316407003683 nucleotide binding site; other site 316407003684 catalytic site; other site 316407003685 domain IV; other site 316407003686 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 316407003687 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 316407003688 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 316407003689 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 316407003690 transcriptional regulator CysB; Reviewed; Region: cysB; PRK12681 316407003691 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407003692 The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold; Region: PBP2_CysB; cd08443 316407003693 substrate binding site; other site 316407003694 putative dimerization interface; other site 316407003695 ECK1270:JW5198+JW5199:b4574; hypothetical protein 316407003696 ECK1270:JW5198:b4522; hypothetical protein, N-ter fragment 316407003697 ECK1270:JW5199:b4523; hypothetical protein, C-ter fragment 316407003698 aconitate hydratase; Validated; Region: PRK09277 316407003699 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 316407003700 substrate binding site; other site 316407003701 ligand binding site; other site 316407003702 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 316407003703 substrate binding site; other site 316407003704 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 316407003705 dimerization interface; other site 316407003706 active site 316407003707 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 316407003708 active site 316407003709 Protein of unknown function (DUF1049); Region: DUF1049; cl01539 316407003710 tetratricopeptide repeat protein; Provisional; Region: PRK11788 316407003711 Quinolinate synthetase A protein; Region: NadA; cl00420 316407003712 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 contains two...; Region: OMP_decarboxylase_like; cd04725 316407003713 active site 316407003714 dimer interface; other site 316407003715 translation initiation factor Sui1; Validated; Region: PRK06824 316407003716 The SUI1/eIF1 (eukaryotic initiation factor 1) fold is found in eukaryotes, archaea, and some bacteria and is thought to play an important role in accurate initiator codon recognition during translation initiation. This fold, which includes two...; Region: SUI1_eIF1; cl00229 316407003717 Predicted RNA interaction site; other site 316407003718 putative binding site; other site 316407003719 Mutations affecting start-site selection; other site 316407003720 lipoprotein; Provisional; Region: PRK10540 316407003721 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 316407003722 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407003723 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 316407003724 RNase II stability modulator; Provisional; Region: PRK10060 316407003725 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 316407003726 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316407003727 metal-binding site 316407003728 active site 316407003729 I-site; other site 316407003730 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 316407003731 exoribonuclease II; Provisional; Region: PRK05054 316407003732 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 316407003733 RNB domain; Region: RNB; pfam00773 316407003734 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 316407003735 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 316407003736 Uncharacterized conserved protein [Function unknown]; Region: COG2128 316407003737 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407003738 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 316407003739 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 316407003740 putative active site; other site 316407003741 antimicrobial peptide ABC system ATP-binding protein SapF; Provisional; Region: PRK15112 316407003742 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 316407003743 Walker A/P-loop; other site 316407003744 ATP binding site; other site 316407003745 Q-loop/lid; other site 316407003746 ABC transporter signature motif; other site 316407003747 Walker B; other site 316407003748 D-loop; other site 316407003749 H-loop/switch region; other site 316407003750 antimicrobial peptide ABC transporter ATP-binding protein; Provisional; Region: PRK15093 316407003751 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 316407003752 Walker A/P-loop; other site 316407003753 ATP binding site; other site 316407003754 Q-loop/lid; other site 316407003755 ABC transporter signature motif; other site 316407003756 Walker B; other site 316407003757 D-loop; other site 316407003758 H-loop/switch region; other site 316407003759 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 316407003760 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...; Region: TM_PBP2; cd06261 316407003761 dimer interface; other site 316407003762 conserved gate region; other site 316407003763 putative PBP binding loops; other site 316407003764 ABC-ATPase subunit interface; other site 316407003765 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...; Region: TM_PBP2; cd06261 316407003766 dimer interface; other site 316407003767 conserved gate region; other site 316407003768 putative PBP binding loops; other site 316407003769 ABC-ATPase subunit interface; other site 316407003770 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 316407003771 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 316407003772 peptide binding site; other site 316407003773 Protein of unknown function (DUF2543); Region: DUF2543; pfam10820 316407003774 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 316407003775 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407003776 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 316407003777 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 316407003778 gamma-glutamyl-gamma-aminobutyrate hydrolase; Provisional; Region: puuD; PRK11366 316407003779 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 316407003780 catalytic triad; other site 316407003781 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 316407003782 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 316407003783 non-specific DNA binding site; other site 316407003784 salt bridge; other site 316407003785 sequence-specific DNA binding site; other site 316407003786 Cupin domain; Region: Cupin_2; cl09118 316407003787 1-pyrroline-5-carboxylate dehydrogenase; Provisional; Region: PRK03137 316407003788 Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like; Region: ALDH_GABALDH-PuuC; cd07112 316407003789 NAD(P) binding site; other site 316407003790 catalytic residues; other site 316407003791 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407003792 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 316407003793 4-aminobutyrate transaminase; Provisional; Region: PRK09792 316407003794 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 316407003795 inhibitor-cofactor binding pocket; inhibition site 316407003796 pyridoxal 5'-phosphate binding site; other site 316407003797 catalytic residue; other site 316407003798 phage shock protein operon transcriptional activator; Provisional; Region: pspF; PRK11608 316407003799 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...; Region: AAA; cd00009 316407003800 Walker A motif; other site 316407003801 ATP binding site; other site 316407003802 Walker B motif; other site 316407003803 arginine finger; other site 316407003804 phage shock protein PspA; Provisional; Region: PRK10698 316407003805 phage shock protein A; Region: phageshock_pspA; TIGR02977 316407003806 Phage shock protein B; Region: PspB; cl05946 316407003807 PspC domain; Region: PspC; cl00864 316407003808 phage shock protein C; Region: phageshock_pspC; TIGR02978 316407003809 Phage shock protein PspD (Phageshock_PspD); Region: Phageshock_PspD; cl11512 316407003810 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 316407003811 active site residue 316407003812 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 316407003813 sucrose phosphorylase; Provisional; Region: PRK13840 316407003814 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 316407003815 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 316407003816 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...; Region: TM_PBP2; cd06261 316407003817 dimer interface; other site 316407003818 conserved gate region; other site 316407003819 putative PBP binding loops; other site 316407003820 ABC-ATPase subunit interface; other site 316407003821 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...; Region: TM_PBP2; cd06261 316407003822 dimer interface; other site 316407003823 conserved gate region; other site 316407003824 putative PBP binding loops; other site 316407003825 ABC-ATPase subunit interface; other site 316407003826 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 316407003827 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide and other MDR family members; Region: 2-desacetyl-2-hydroxyethyl_bacteriochlorophyllide_; cd08255 316407003828 putative NAD(P) binding site; other site 316407003829 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 316407003830 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of D-arabino-6-...; Region: AP2Ec; cl12060 316407003831 Metal-binding active site; metal-binding site 316407003832 AP (apurinic/apyrimidinic) site pocket; other site 316407003833 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 316407003834 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407003835 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 316407003836 Trehalose and maltose hydrolases (possible phosphorylases) [Carbohydrate transport and metabolism]; Region: ATH1; COG1554 316407003837 Glycosyl hydrolase family 65, N-terminal domain; Region: Glyco_hydro_65N; pfam03636 316407003838 Glycosyl hydrolase family 65, C-terminal domain; Region: Glyco_hydro_65C; pfam03633 316407003839 beta-phosphoglucomutase; Region: bPGM; TIGR01990 316407003840 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 316407003841 motif II; other site 316407003842 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 316407003843 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 316407003844 Walker A/P-loop; other site 316407003845 ATP binding site; other site 316407003846 Q-loop/lid; other site 316407003847 ABC transporter signature motif; other site 316407003848 Walker B; other site 316407003849 D-loop; other site 316407003850 H-loop/switch region; other site 316407003851 Outer membrane protein G (OmpG); Region: Porin_OmpG; pfam09381 316407003852 Protein of unknown function, DUF481; Region: DUF481; cl01213 316407003853 Transcriptional regulators [Transcription]; Region: PurR; COG1609 316407003854 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 316407003855 DNA binding site 316407003856 domain linker motif; other site 316407003857 Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors; Region: PBP1_ycjW_transcription_regulator_like; cd06294 316407003858 putative dimerization interface; other site 316407003859 putative ligand binding site; other site 316407003860 YcjX-like family, DUF463; Region: DUF463; cl01193 316407003861 hypothetical protein; Provisional; Region: PRK05415 316407003862 Domain of unknown function (DUF697); Region: DUF697; cl12064 316407003863 DNA-binding transcriptional regulator TyrR; Provisional; Region: PRK10820 316407003864 N-terminal ACT domain of the TyrR protein; Region: ACT_TyrR; cd04877 316407003865 putative aromatic amino acid binding site; other site 316407003866 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...; Region: AAA; cd00009 316407003867 Walker A motif; other site 316407003868 ATP binding site; other site 316407003869 Walker B motif; other site 316407003870 arginine finger; other site 316407003871 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 316407003872 dimer interface; other site 316407003873 catalytic triad; other site 316407003874 peroxidatic and resolving cysteines; other site 316407003875 L-Ala-D/L-Glu epimerase; Provisional; Region: PRK15129 316407003876 L-Ala-D/L-Glu epimerase catalyzes the epimerization of L-Ala-D/L-Glu and other dipeptides. The genomic context and the substrate specificity of characterized members of this family from E.coli and B.subtilis indicates a possible role in the metabolism...; Region: L-Ala-DL-Glu_epimerase; cd03319 316407003877 active site 316407003878 Peptidase M14-like domain of Escherichia coli Murein Peptide Amidase A (MpaA) and related proteins. MpaA is a member of the M14 family of metallocarboxypeptidases (MCPs), however it has an exceptional type of activity, it hydrolyzes the gamma-D-...; Region: M14_MpaA_like; cd06904 316407003879 putative active site; other site 316407003880 Zn-binding site; other site 316407003881 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407003882 NAD(P) binding pocket; other site 316407003883 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 316407003884 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; cl12031 316407003885 Transcriptional regulator [Transcription]; Region: LysR; COG0583 316407003886 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407003887 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_5; cd08474 316407003888 putative effector binding pocket; other site 316407003889 putative dimerization interface; other site 316407003890 oligopeptide ABC transporter substrate-binding protein OppA; Provisional; Region: PRK15104 316407003891 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 316407003892 peptide binding site; other site 316407003893 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 316407003894 Mechanosensitive ion channel; Region: MS_channel; pfam00924 316407003895 Transposase domain (DUF772); Region: DUF772; cl12084 316407003896 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 316407003897 Protein of unknown function (DUF2534); Region: DUF2534; pfam10749 316407003898 universal stress protein UspE; Provisional; Region: PRK11175 316407003899 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 316407003900 Ligand Binding Site; other site 316407003901 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 316407003902 Ligand Binding Site; other site 316407003903 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 316407003904 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 316407003905 ligand binding site; other site 316407003906 flexible hinge region; other site 316407003907 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 316407003908 putative switch regulator; other site 316407003909 non-specific DNA interactions; other site 316407003910 DNA binding site 316407003911 sequence specific DNA binding site; other site 316407003912 putative cAMP binding site; other site 316407003913 O-6-alkylguanine-DNA:cysteine-protein methyltransferase; Provisional; Region: PRK10286 316407003914 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 316407003915 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 316407003916 DNA binding site 316407003917 active site 316407003918 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; cl09110 316407003919 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 316407003920 amidohydrolase; Region: amidohydrolases; TIGR01891 316407003921 Peptidase dimerization domain; Region: M20_dimer; cl09126 316407003922 Peptidase dimerization domain; Region: M20_dimer; cl09126 316407003923 amidohydrolase; Region: amidohydrolases; TIGR01891 316407003924 Peptidase dimerization domain; Region: M20_dimer; cl09126 316407003925 putative DNA-binding transcriptional regulator; Provisional; Region: PRK09791 316407003926 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407003927 The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold; Region: PBP2_TdcA; cd08418 316407003928 putative substrate binding pocket; other site 316407003929 putative dimerization interface; other site 316407003930 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 316407003931 Smr domain; Region: Smr; cl02619 316407003932 PAS domain S-box; Region: sensory_box; TIGR00229 316407003933 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 316407003934 putative active site; other site 316407003935 heme pocket; other site 316407003936 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316407003937 metal-binding site 316407003938 active site 316407003939 I-site; other site 316407003940 CorA-like Mg2+ transporter protein; Region: CorA; cl00459 316407003941 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 316407003942 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 316407003943 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 316407003944 ATP binding site; other site 316407003945 Mg++ binding site; other site 316407003946 motif III; other site 316407003947 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 316407003948 nucleotide binding region; other site 316407003949 ATP-binding site; other site 316407003950 DbpA RNA binding domain; Region: DbpA; pfam03880 316407003951 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 316407003952 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...; Region: Alpha_ANH_like_II; cd01993 316407003953 Ligand Binding Site; other site 316407003954 Domain of unknown function (DUF3596); Region: DUF3596; pfam12167 316407003955 phiCTX phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various phage and bacterial integrases, including those similar to phage integrases: Bordetella and...; Region: INT_phiCTX_C; cd01191 316407003956 Int/Topo IB signature motif; other site 316407003957 Putative excisionase (DUF1233); Region: DUF1233; pfam06806 316407003958 Protein of unknown function (DUF1187); Region: DUF1187; cl11638 316407003959 restriction alleviation and modification protein; Reviewed; Region: lar; cl08047 316407003960 RecT family; Region: RecT; cl04285 316407003961 exonuclease VIII; Reviewed; Region: PRK09709 316407003962 Enterobacterial exodeoxyribonuclease VIII; Region: Exonuc_VIII; pfam06630 316407003963 hypothetical protein; Reviewed; Region: PRK09790 316407003964 FtsZ inhibitor protein; Reviewed; Region: kil; PRK11354 316407003965 Protein of unknown function (DUF1391); Region: DUF1391; pfam07151 316407003966 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]; Region: COG4197 316407003967 Protein of unknown function (DUF1019); Region: DUF1019; pfam06254 316407003968 Protein of unknown function (DUF1376); Region: DUF1376; cl01531 316407003969 Phd_YefM; Region: PhdYeFM; cl09153 316407003970 putative replication protein; Provisional; Region: PRK12377 316407003971 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407003972 Mn-dependent transcriptional regulator [Transcription]; Region: TroR; COG1321 316407003973 Protein of unknown function (DUF1627); Region: DUF1627; pfam07789 316407003974 Bacteriophage lysis protein; Region: Phage_lysis; pfam03245 316407003975 Lipoprotein Rz1 precursor; Region: Rz1; pfam06085 316407003976 Cation transport protein; Region: TrkH; cl10514 316407003977 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 316407003978 ParB-like nuclease domain; Region: ParBc; cl02129 316407003979 Phage-related minor tail protein [Function unknown]; Region: COG5281 316407003980 Prophage tail length tape measure protein; Region: TMP_2; pfam06791 316407003981 ECK1366:JW5884+JW5904:b4570; Rac prophage region; hypothetical protein 316407003982 ECK1366:JW5884:b1369; Rac prophage region; hypothetical protein, N-ter fragment 316407003983 ECK1366:JW5904:b1371; Rac prophage region; hypothetical protein, C-ter fragment 316407003984 Transposase domain (DUF772); Region: DUF772; cl12084 316407003985 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 316407003986 Prophage tail fibre N-terminal; Region: phage_tail_N; pfam08400 316407003987 Phage tail fibre repeat; Region: Phage_fiber_2; pfam03406 316407003988 long tail fiber, proximal subunit; Provisional; Region: 34; PHA02584 316407003989 Phage Tail Collar Domain; Region: Collar; pfam07484 316407003990 Caudovirales tail fibre assembly protein; Region: Caudo_TAP; pfam02413 316407003991 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 316407003992 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 316407003993 catalytic residues; other site 316407003994 catalytic nucleophile; other site 316407003995 Presynaptic Site I dimer interface; other site 316407003996 Synaptic Antiparallel dimer interface; other site 316407003997 Synaptic Flat tetramer interface; other site 316407003998 Synaptic Site I dimer interface; other site 316407003999 DNA binding site 316407004000 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 316407004001 DNA-binding interface; DNA binding site 316407004002 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 316407004003 Ligand Binding Site; other site 316407004004 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...; Region: gram_neg_porins; cd00342 316407004005 trimer interface; other site 316407004006 eyelet of channel; other site 316407004007 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 316407004008 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 316407004009 dimer interface; other site 316407004010 PYR/PP interface; other site 316407004011 TPP binding site; other site 316407004012 substrate binding site; other site 316407004013 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 316407004014 Domain of unknown function; Region: EKR; pfam10371 316407004015 4Fe-4S binding domain; Region: Fer4; pfam00037 316407004016 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 alpha-; Region: HCP_like; cl14655 316407004017 TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This subfamily also includes proteins characterized as...; Region: TPP_PFOR_PNO; cd03377 316407004018 TPP-binding site; other site 316407004019 dimer interface; other site 316407004020 Domain of unknown function (DUF333); Region: DUF333; pfam03891 316407004021 META domain; Region: META; cl01245 316407004022 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 316407004023 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407004024 Dicarboxylate transport; Region: DctA-YdbH; cl14674 316407004025 Protein of unknown function (DUF1318); Region: DUF1318; cl01547 316407004026 DNA-binding transcriptional activator FeaR; Provisional; Region: PRK09685 316407004027 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407004028 delta-1-pyrroline-5-carboxylate dehydrogenase, group 2, putative; Region: D1pyr5carbox2; TIGR01237 316407004029 Escherichia coli NAD+-dependent phenylacetaldehyde dehydrogenase PadA-like; Region: ALDH_PADH_NahF; cd07113 316407004030 NAD(P) binding site; other site 316407004031 catalytic residues; other site 316407004032 Cu2+-containing amine oxidase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TynA; COG3733 316407004033 tyramine oxidase; Provisional; Region: tynA; PRK14696 316407004034 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 316407004035 Copper amine oxidase, N2 domain; Region: Cu_amine_oxidN2; pfam02727 316407004036 Copper amine oxidase, N3 domain; Region: Cu_amine_oxidN3; pfam02728 316407004037 Copper amine oxidase, enzyme domain; Region: Cu_amine_oxid; pfam01179 316407004038 bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase; Provisional; Region: PRK11563 316407004039 N-terminal domain of the monoamine oxidase C dehydratase; Region: ALDH_MaoC-N; cd07128 316407004040 substrate binding site; other site 316407004041 dimer interface; other site 316407004042 NADP binding site; other site 316407004043 catalytic residues; other site 316407004044 MaoC_C The C-terminal hot dog fold of the MaoC (monoamine oxidase C) dehydratase regulatory protein. Orthologs of MaoC include PaaZ [Escherichia coli] and PaaN [Pseudomonas putida], which are putative ring-opening enzymes involved in phenylacetic acid...; Region: MaoC_C; cd03452 316407004045 substrate binding site; other site 316407004046 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; cl01346 316407004047 phenylacetate-CoA oxygenase, PaaG subunit; Region: PA_CoA_Oxy1; TIGR02156 316407004048 Phenylacetic acid degradation B; Region: PaaB; cl01371 316407004049 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; cl01346 316407004050 Domain of unknown function DUF59; Region: DUF59; cl00941 316407004051 phenylacetate-CoA oxygenase, PaaJ subunit; Region: PA_CoA_Oxy4; TIGR02159 316407004052 phenylacetate-CoA oxygenase/reductase, PaaK subunit; Region: PA_CoA_Oxy5; TIGR02160 316407004053 NAD(P) binding domain of ferredoxin reductase like phenylacetic acid (PA) degradation oxidoreductase. PA oxidoreductases of E. coli hydroxylate PA-CoA in the second step of PA degradation. Members of this group typically fuse a ferredoxin reductase-...; Region: PA_degradation_oxidoreductase_like; cd06214 316407004054 FAD binding pocket; other site 316407004055 FAD binding motif; other site 316407004056 phosphate binding motif; other site 316407004057 beta-alpha-beta structure motif; other site 316407004058 NAD(p) ribose binding residues; other site 316407004059 NAD binding pocket; other site 316407004060 NAD(P)-pyrophosphate-nicotinamide binding residues; other site 316407004061 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 316407004062 catalytic loop; other site 316407004063 iron binding site; other site 316407004064 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 316407004065 substrate binding site; other site 316407004066 oxyanion hole (OAH) forming residues; other site 316407004067 trimer interface; other site 316407004068 enoyl-CoA hydratase; Provisional; Region: PRK06688 316407004069 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 316407004070 substrate binding site; other site 316407004071 oxyanion hole (OAH) forming residues; other site 316407004072 trimer interface; other site 316407004073 3-hydroxyacyl-CoA dehydrogenase PaaC; Region: PaaC-3OHAcCoADH; TIGR02279 316407004074 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407004075 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 316407004076 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 316407004077 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 316407004078 CoenzymeA binding site; other site 316407004079 subunit interaction site; other site 316407004080 PHB binding site; other site 316407004081 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 316407004082 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 316407004083 dimer interface; other site 316407004084 active site 316407004085 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 316407004086 PaaX-like protein; Region: PaaX; pfam07848 316407004087 phenylacetic acid degradation operon negative regulatory protein PaaX; Region: PaaX_trns_reg; TIGR02277 316407004088 PaaX-like protein C-terminal domain; Region: PaaX_C; pfam08223 316407004089 phenylacetic acid degradation protein PaaY; Region: PaaY; TIGR02287 316407004090 paaY-like: This group is composed by uncharacterized proteins with similarity to the protein product of the E. coli paaY gene, which is part of the paa gene cluster responsible for phenylacetic acid degradation. Proteins in this group are expected to...; Region: LbH_paaY_like; cd04745 316407004091 putative trimer interface; other site 316407004092 putative metal binding site; other site 316407004093 ECK1398:JW1402:b1405; predicted outer membrane protein, C-ter fragment 316407004094 ECK1398:JW5802+JW1402:b4492; predicted outer membrane protein 316407004095 ECK1398:JW5802:b1401; predicted outer membrane protein, N-ter fragment 316407004096 IS2 transposase TnpB; Reviewed; Region: PRK09409 316407004097 Integrase core domain; Region: rve; cl01316 316407004098 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; cl01116 316407004099 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 316407004100 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 316407004101 Integrase core domain; Region: rve; cl01316 316407004102 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...; Region: Aldo_ket_red; cd06660 316407004103 active site 316407004104 catalytic tetrad; other site 316407004105 Protein of unknown function (DUF2773); Region: DUF2773; pfam10971 316407004106 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 316407004107 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 316407004108 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 316407004109 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; cl12031 316407004110 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; cl12031 316407004111 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; cl12011 316407004112 PAP2_like proteins, Aur1_like subfamily. Yeast Aur1p or Ipc1p is necessary for the addition of inositol phosphate to ceramide, an essential step in yeast sphingolipid synthesis, and is the target of several antifungal compounds such as aureobasidin; Region: PAP2_Aur1_like; cd03386 316407004113 active site 316407004114 Dual specificity phosphatases (DSP); Ser/Thr and Tyr protein phosphatases. Structurally similar to tyrosine-specific phosphatases but with a shallower active site cleft and a distinctive active site signature motif, HCxxGxxR. Characterized as VHR- or...; Region: DSPc; cd00127 316407004115 active site 316407004116 catalytic residues; other site 316407004117 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 316407004118 ATP-dependent RNA helicase HrpA; Provisional; Region: PRK11131 316407004119 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 316407004120 ATP binding site; other site 316407004121 putative Mg++ binding site; other site 316407004122 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 316407004123 nucleotide binding region; other site 316407004124 ATP-binding site; other site 316407004125 Helicase associated domain (HA2); Region: HA2; cl04503 316407004126 Domain of unknown function (DUF1605); Region: DUF1605; pfam07717 316407004127 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 316407004128 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 316407004129 putative active site; other site 316407004130 1-pyrroline-5-carboxylate dehydrogenase; Provisional; Region: PRK03137 316407004131 Escherichia coli lactaldehyde dehydrogenase AldA-like; Region: ALDH_LactADH-AldA; cd07088 316407004132 NAD binding site; other site 316407004133 catalytic residues; other site 316407004134 substrate binding site; other site 316407004135 ECK1409:JW1413:b1416; glyceraldehyde-3-phosphate dehydrogenase C, N-ter fragment 316407004136 ECK1409:JW5906+JW1413:b4493; glyceraldehyde-3-phosphate dehydrogenase C 316407004137 ECK1409:JW5906:b1417; glyceraldehyde-3-phosphate dehydrogenase C, C-ter fragment 316407004138 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 316407004139 hypothetical protein; Provisional; Region: PRK10040 316407004140 Hok/gef family; Region: HOK_GEF; cl11494 316407004141 methyl-accepting chemotaxis protein II; Provisional; Region: PRK15048 316407004142 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 316407004143 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 connected by an extended linker. The...; Region: HAMP; cd06225 316407004144 dimerization interface; other site 316407004145 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 316407004146 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 316407004147 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407004148 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 316407004149 dimerization interface; other site 316407004150 Protein of unknown function (DUF1338); Region: DUF1338; cl02226 316407004151 Protein of unknown function (DUF1338); Region: DUF1338; cl02226 316407004152 Periplasmic glucan biosynthesis protein, MdoG; Region: MdoG; cl01208 316407004153 Protein of unknown function (DUF465); Region: DUF465; cl01070 316407004154 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 316407004155 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 316407004156 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; cd00208 316407004157 putative trimer interface; other site 316407004158 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 316407004159 putative CoA binding site; other site 316407004160 putative trimer interface; other site 316407004161 putative CoA binding site; other site 316407004162 C4-dicarboxylate transporter/malic acid transport protein; Region: C4dic_mal_tran; cl04176 316407004163 tellurite resistance protein TehB; Provisional; Region: PRK12335 316407004164 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 316407004165 S-adenosylmethionine binding site; other site 316407004166 Protein of unknown function (DUF3313); Region: DUF3313; pfam11769 316407004167 ECK1425:JW5227+JW5961:b4578; predicted transposase 316407004168 ECK1425:JW5227:b4530; predicted transposase, N-ter fragment 316407004169 ECK1425:JW5961:b4531; predicted transposase, C-ter fragment 316407004170 Helix-turn-helix domain; Region: HTH_14; pfam12323 316407004171 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 316407004172 Probable transposase; Region: Transposase_2; pfam01385 316407004173 Putative transposase DNA-binding domain; Region: Transposase_35; pfam07282 316407004174 Uncharacterized protein involved in benzoate metabolism [Secondary metabolites biosynthesis, transport, and catabolism]; Region: BenE; COG3135 316407004175 Permease family; Region: Xan_ur_permease; cl00967 316407004176 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 316407004177 non-specific DNA binding site; other site 316407004178 salt bridge; other site 316407004179 sequence-specific DNA binding site; other site 316407004180 Cupin domain; Region: Cupin_2; cl09118 316407004181 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 316407004182 Peptidase family U32; Region: Peptidase_U32; cl03113 316407004183 Collagenase; Region: DUF3656; pfam12392 316407004184 Protein of unknown function (DUF2554); Region: DUF2554; pfam10829 316407004185 YcfA-like protein; Region: YcfA; cl00752 316407004186 Uncharacterized protein family (UPF0150); Region: UPF0150; cl00691 316407004187 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl09100 316407004188 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 316407004189 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407004190 DNA binding site 316407004191 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 316407004192 pyridoxal 5'-phosphate binding site; other site 316407004193 homodimer interface; other site 316407004194 catalytic residue; other site 316407004195 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 316407004196 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 316407004197 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407004198 Walker A/P-loop; other site 316407004199 ATP binding site; other site 316407004200 Q-loop/lid; other site 316407004201 ABC transporter signature motif; other site 316407004202 Walker B; other site 316407004203 D-loop; other site 316407004204 H-loop/switch region; other site 316407004205 TOBE domain; Region: TOBE_2; cl01440 316407004206 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...; Region: TM_PBP2; cd06261 316407004207 dimer interface; other site 316407004208 conserved gate region; other site 316407004209 putative PBP binding loops; other site 316407004210 ABC-ATPase subunit interface; other site 316407004211 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...; Region: TM_PBP2; cl00427 316407004212 delta-1-pyrroline-5-carboxylate dehydrogenase, group 2, putative; Region: D1pyr5carbox2; TIGR01237 316407004213 Escherichia coli NAD+-dependent gamma-aminobutyraldehyde dehydrogenase YdcW-like; Region: ALDH_ABALDH-YdcW; cd07092 316407004214 tetrameric interface; other site 316407004215 NAD binding site; other site 316407004216 catalytic residues; other site 316407004217 substrate binding site; other site 316407004218 Protein of unknown function (DUF2566); Region: DUF2566; pfam10753 316407004219 Protein of unknown function (DUF2526); Region: DUF2526; pfam10735 316407004220 Protein of unknown function, DUF606; Region: DUF606; cl01273 316407004221 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 316407004222 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 316407004223 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 316407004224 Prostaglandin dehydrogenases; Region: PGDH; cd05288 316407004225 NAD(P) binding site; other site 316407004226 substrate binding site; other site 316407004227 dimer interface; other site 316407004228 colanic acid/biofilm transcriptional regulator; Provisional; Region: PRK11414 316407004229 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407004230 DNA binding site 316407004231 FCD domain; Region: FCD; cl11656 316407004232 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 316407004233 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 316407004234 N-terminal plug; other site 316407004235 ligand-binding site; other site 316407004236 Uncharacterized conserved protein [Function unknown]; Region: COG3391 316407004237 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407004238 Amino acid permease; Region: AA_permease; pfam00324 316407004239 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 316407004240 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens...; Region: GST_N_Beta; cd03057 316407004241 C-terminal domain interface; other site 316407004242 GSH binding site (G-site); other site 316407004243 dimer interface; other site 316407004244 GST_C family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens...; Region: GST_C_Beta; cd03188 316407004245 dimer interface; other site 316407004246 N-terminal domain interface; other site 316407004247 substrate binding pocket (H-site); other site 316407004248 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 316407004249 RHS protein; Region: RHS; pfam03527 316407004250 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 316407004251 Transposase [DNA replication, recombination, and repair]; Region: COG5433 316407004252 Transposase [DNA replication, recombination, and repair]; Region: COG5433 316407004253 Transposase [DNA replication, recombination, and repair]; Region: COG5433 316407004254 Transposase [DNA replication, recombination, and repair]; Region: COG5433 316407004255 Transposase [DNA replication, recombination, and repair]; Region: COG5433 316407004256 Transposase [DNA replication, recombination, and repair]; Region: COG5433 316407004257 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 316407004258 Flavin Reductases; Region: FlaRed; cl00801 316407004259 N-acetyltransferase; Region: Acetyltransf_2; cl00949 316407004260 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 316407004261 phenazine biosynthesis protein PhzF family; Region: PhzF_family; TIGR00654 316407004262 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; cl00959 316407004263 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 316407004264 Nitrate reductase beta subunit [Energy production and conversion]; Region: NarY; COG1140 316407004265 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 316407004266 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate...; Region: MopB_Nitrate-R-NarG-like; cd02750 316407004267 [4Fe-4S] binding site; other site 316407004268 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 tungsten-...; Region: Molybdopterin-Binding; cl09928 316407004269 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 tungsten-...; Region: Molybdopterin-Binding; cl09928 316407004270 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 tungsten-...; Region: Molybdopterin-Binding; cl09928 316407004271 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate...; Region: MopB_CT_Nitrate-R-NarG-like; cd02776 316407004272 molybdopterin cofactor binding site; other site 316407004273 nitrate/nitrite transport protein NarU; Provisional; Region: PRK15034 316407004274 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 316407004275 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...; Region: OM_channels; cl00284 316407004276 aromatic amino acid exporter; Provisional; Region: PRK11689 316407004277 formate dehydrogenase, alpha subunit, proteobacterial-type; Region: formate-DH-alph; TIGR01553 316407004278 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 316407004279 [4Fe-4S] binding site; other site 316407004280 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 tungsten-...; Region: Molybdopterin-Binding; cl09928 316407004281 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 316407004282 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 316407004283 molybdopterin cofactor binding site; other site 316407004284 Fe-S containing; Region: FDH-beta; TIGR01582 316407004285 Formate dehydrogenase N, transmembrane; Region: Form-deh_trans; pfam09163 316407004286 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 316407004287 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl09100 316407004288 ethanol-active dehydrogenase/acetaldehyde-active reductase; Provisional; Region: PRK09422 316407004289 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD3; cd08297 316407004290 NAD binding site; other site 316407004291 substrate binding site; other site 316407004292 catalytic Zn binding site; other site 316407004293 tetramer interface; other site 316407004294 structural Zn binding site; other site 316407004295 malate dehydrogenase; Provisional; Region: PRK13529 316407004296 Malic enzyme, N-terminal domain; Region: malic; pfam00390 316407004297 NAD(P) binding domain of malic enzyme (ME), subgroup 1; Region: NAD_bind_1_malic_enz; cd05312 316407004298 NAD(P) binding site; other site 316407004299 30S ribosomal protein subunit S22 family; Region: Ribosomal_S22; cl11579 316407004300 Putative biofilm-dependent modulation protein; Region: BDM; cl11581 316407004301 OsmC-like protein; Region: OsmC; cl00767 316407004302 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 316407004303 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 316407004304 Walker A/P-loop; other site 316407004305 ATP binding site; other site 316407004306 Q-loop/lid; other site 316407004307 ABC transporter signature motif; other site 316407004308 Walker B; other site 316407004309 D-loop; other site 316407004310 H-loop/switch region; other site 316407004311 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 316407004312 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 316407004313 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 316407004314 Walker A/P-loop; other site 316407004315 ATP binding site; other site 316407004316 Q-loop/lid; other site 316407004317 ABC transporter signature motif; other site 316407004318 Walker B; other site 316407004319 D-loop; other site 316407004320 H-loop/switch region; other site 316407004321 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 316407004322 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...; Region: TM_PBP2; cd06261 316407004323 dimer interface; other site 316407004324 conserved gate region; other site 316407004325 putative PBP binding loops; other site 316407004326 ABC-ATPase subunit interface; other site 316407004327 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...; Region: TM_PBP2; cd06261 316407004328 dimer interface; other site 316407004329 conserved gate region; other site 316407004330 putative PBP binding loops; other site 316407004331 ABC-ATPase subunit interface; other site 316407004332 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_7; cd08512 316407004333 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 316407004334 D-alanyl-D-alanine carboxypeptidase; Region: VanY; cl00813 316407004335 cyclic-di-GMP phosphodiesterase; Provisional; Region: PRK11359 316407004336 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 316407004337 putative active site; other site 316407004338 heme pocket; other site 316407004339 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 316407004340 putative active site; other site 316407004341 heme pocket; other site 316407004342 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316407004343 metal-binding site 316407004344 active site 316407004345 I-site; other site 316407004346 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 316407004347 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316407004348 metal-binding site 316407004349 active site 316407004350 I-site; other site 316407004351 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1649 316407004352 Uncharacterized BCR, COG1649; Region: DUF187; pfam02638 316407004353 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407004354 Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism]; Region: GadB; COG0076 316407004355 DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to DOPA/tyrosine decarboxylase (DDC), histidine decarboxylase (HDC), and...; Region: DOPA_deC_like; cd06450 316407004356 pyridoxal 5'-phosphate binding site; other site 316407004357 catalytic residue; other site 316407004358 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 316407004359 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 316407004360 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 316407004361 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 316407004362 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 316407004363 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 316407004364 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...; Region: OM_channels; cl00284 316407004365 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]; Region: COG4178 316407004366 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 316407004367 Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed...; Region: ABCD_peroxisomal_ALDP; cd03223 316407004368 Arylsulfatase regulator (Fe-S oxidoreductase) [General function prediction only]; Region: AslB; COG0641 316407004369 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 316407004370 FeS/SAM binding site; other site 316407004371 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 316407004372 Sulfatase; Region: Sulfatase; cl10460 316407004373 transcriptional regulator YdeO; Provisional; Region: PRK09940 316407004374 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407004375 putative oxidoreductase; Provisional; Region: PRK09939 316407004376 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 316407004377 putative molybdopterin cofactor binding site; other site 316407004378 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: MopB_CT_ydeP; cd02787 316407004379 putative molybdopterin cofactor binding site; other site 316407004380 FimH, mannose binding; Region: FimH_man-bind; pfam09160 316407004381 Fimbrial protein; Region: Fimbrial; cl01416 316407004382 Fimbrial protein; Region: Fimbrial; cl01416 316407004383 Fimbrial protein; Region: Fimbrial; cl01416 316407004384 pilin outer membrane usher protein SafC; Provisional; Region: PRK15223; cl14650 316407004385 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 316407004386 HipA N-terminal domain; Region: couple_hipA; TIGR03071 316407004387 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 316407004388 HipA-like N-terminal domain; Region: HipA_N; pfam07805 316407004389 HipA-like C-terminal domain; Region: HipA_C; pfam07804 316407004390 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 316407004391 non-specific DNA binding site; other site 316407004392 salt bridge; other site 316407004393 sequence-specific DNA binding site; other site 316407004394 ECK1502:JW1502:b1509; conserved hypothetical protein 316407004395 putative lipoprotein/autotransporter domain-containing protein; Provisional; Region: PRK14849 316407004396 autoinducer-2 (AI-2) kinase; Provisional; Region: PRK10939 316407004397 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; pfam00370 316407004398 FGGY family of carbohydrate kinases, C-terminal domain; Region: FGGY_C; pfam02782 316407004399 transcriptional regulator LsrR; Provisional; Region: PRK15418 316407004400 Putative sugar-binding domain; Region: Sugar-bind; pfam04198 316407004401 autoinducer 2 ABC transporter ATP-binding protein LsrA; Provisional; Region: PRK15439 316407004402 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and...; Region: ABC_Carb_Monos_I; cd03216 316407004403 Walker A/P-loop; other site 316407004404 ATP binding site; other site 316407004405 Q-loop/lid; other site 316407004406 ABC transporter signature motif; other site 316407004407 Walker B; other site 316407004408 D-loop; other site 316407004409 H-loop/switch region; other site 316407004410 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (; Region: ABC_Carb_Monos_II; cd03215 316407004411 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 316407004412 TM-ABC transporter signature motif; other site 316407004413 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 316407004414 TM-ABC transporter signature motif; other site 316407004415 autoinducer 2-binding protein lsrB; Provisional; Region: PRK15408 316407004416 Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs; Region: PBP1_LsrB_Quorum_Sensing; cd06302 316407004417 ligand binding site; other site 316407004418 DhnA-type fructose-1,6-bisphosphate aldolase and related enzymes [Carbohydrate transport and metabolism]; Region: FbaB; COG1830 316407004419 Class I fructose-1,6-bisphosphate (FBP) aldolases of the archaeal type (DhnA homologs) found in bacteria and archaea. Catalysis of the enzymes proceeds via a Schiff-base mechanism like other class I aldolases, although this subfamily is clearly...; Region: DhnA; cd00958 316407004420 putative active site; other site 316407004421 catalytic residue; other site 316407004422 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 316407004423 trans-aconitate 2-methyltransferase; Provisional; Region: PRK01683 316407004424 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 316407004425 S-adenosylmethionine binding site; other site 316407004426 Bestrophin; Region: Bestrophin; cl01544 316407004427 altronate oxidoreductase; Provisional; Region: PRK03643 316407004428 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 316407004429 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 316407004430 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316407004431 metal-binding site 316407004432 active site 316407004433 I-site; other site 316407004434 Glutaminase; Region: Glutaminase; cl00907 316407004435 Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 1-like; Region: ALDH_SSADH1_GabD1; cd07100 316407004436 NAD(P) binding site; other site 316407004437 catalytic residues; other site 316407004438 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 316407004439 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407004440 The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; Region: PBP2_YofA_SoxR_like; cd08442 316407004441 putative dimerization interface; other site 316407004442 putative arabinose transporter; Provisional; Region: PRK03545 316407004443 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 316407004444 putative substrate translocation pore; other site 316407004445 MarC family integral membrane protein; Region: MarC; cl00919 316407004446 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407004447 Transcriptional regulators [Transcription]; Region: MarR; COG1846 316407004448 DNA-binding transcriptional activator MarA; Provisional; Region: PRK11511 316407004449 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407004450 hypothetical protein; Provisional; Region: PRK10106 316407004451 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 316407004452 EamA-like transporter family; Region: EamA; cl01037 316407004453 putative transporter; Provisional; Region: PRK10054 316407004454 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 316407004455 putative substrate translocation pore; other site 316407004456 diguanylate cyclase; Provisional; Region: PRK09894 316407004457 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316407004458 metal-binding site 316407004459 active site 316407004460 I-site; other site 316407004461 Bacterial OB fold (BOF) protein; Region: BOF; cl01196 316407004462 Competence-damaged protein; Region: CinA; cl00666 316407004463 dipeptidyl carboxypeptidase II; Provisional; Region: PRK10280 316407004464 Peptidase family M3 dipeptidyl carboxypeptidase (DCP; Dcp II; peptidyl dipeptidase; EC 3.4.15.5). This metal-binding M3A family also includes oligopeptidase A (OpdA; EC 3.4.24.70) enzyme. DCP cleaves dipeptides off the C-termini of various peptides and...; Region: M3A_DCP_Oligopeptidase_A; cd06456 316407004465 active site 316407004466 zinc binding site; other site 316407004467 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407004468 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 316407004469 Transcriptional regulators [Transcription]; Region: GntR; COG1802 316407004470 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407004471 DNA binding site 316407004472 FCD domain; Region: FCD; cl11656 316407004473 putative selenium-binding protein YdfZ; Region: YdfZ_fam; TIGR03318 316407004474 D-mannonate oxidoreductase; Provisional; Region: PRK15037 316407004475 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 316407004476 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 316407004477 metabolite-proton symporter; Region: 2A0106; TIGR00883 316407004478 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 316407004479 putative substrate translocation pore; other site 316407004480 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 316407004481 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 316407004482 catalytic residues; other site 316407004483 catalytic nucleophile; other site 316407004484 Presynaptic Site I dimer interface; other site 316407004485 Synaptic Antiparallel dimer interface; other site 316407004486 Synaptic Flat tetramer interface; other site 316407004487 Synaptic Site I dimer interface; other site 316407004488 DNA binding site 316407004489 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 316407004490 DNA-binding interface; DNA binding site 316407004491 Caudovirales tail fibre assembly protein; Region: Caudo_TAP; pfam02413 316407004492 Phage Tail Collar Domain; Region: Collar; pfam07484 316407004493 Phage DNA packaging protein Nu1; Region: Phage_Nu1; cl01720 316407004494 Protein of unknown function (DUF1398); Region: DUF1398; cl11576 316407004495 GnsA/GnsB family; Region: GnsAB; pfam08178 316407004496 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 protein...; Region: CSP_CDS; cd04458 316407004497 DNA binding site 316407004498 RNA-binding motif; other site 316407004499 Protein of unknown function (DUF2514); Region: DUF2514; pfam10721 316407004500 Endolysins and autolysins are found in viruses and bacteria, respectively. The ds DNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell...; Region: endolysin_autolysin; cd00737 316407004501 catalytic residues; other site 316407004502 Protein of unknown function (DUF1327); Region: DUF1327; pfam07041 316407004503 Lysis protein S; Region: Lysis_S; pfam04971 316407004504 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 protein...; Region: CSP_CDS; cd04458 316407004505 DNA binding site 316407004506 RNA-binding motif; other site 316407004507 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 protein...; Region: CSP_CDS; cd04458 316407004508 DNA binding site 316407004509 RNA-binding motif; other site 316407004510 Antitermination protein; Region: Antiterm; pfam03589 316407004511 chaperone protein DnaJ; Region: DnaJ_bact; TIGR02349 316407004512 Antitermination protein; Region: Antiterm; pfam03589 316407004513 Protein of unknown function (DUF968); Region: DUF968; pfam06147 316407004514 Hok/gef family; Region: HOK_GEF; cl11494 316407004515 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 316407004516 RelB antitoxin; Region: RelB; cl01171 316407004517 Protein of unknown function (DUF1019); Region: DUF1019; pfam06254 316407004518 DNA-binding transcriptional regulator DicC; Provisional; Region: PRK09744 316407004519 transcriptional repressor DicA; Reviewed; Region: PRK09706 316407004520 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 316407004521 non-specific DNA binding site; other site 316407004522 salt bridge; other site 316407004523 sequence-specific DNA binding site; other site 316407004524 Protein of unknown function (DUF1391); Region: DUF1391; pfam07151 316407004525 DicB protein; Region: DicB; pfam05358 316407004526 Protein of unknown function (DUF1482); Region: DUF1482; pfam07358 316407004527 Integrase core domain; Region: rve; cl01316 316407004528 Domain of unknown function (DUF3596); Region: DUF3596; pfam12167 316407004529 phiCTX phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various phage and bacterial integrases, including those similar to phage integrases: Bordetella and...; Region: INT_phiCTX_C; cd01191 316407004530 Phage integrase family; Region: Phage_integrase; pfam00589 316407004531 Int/Topo IB signature motif; other site 316407004532 ECK1574:JW5257:b4534; hypothetical protein 316407004533 putative oxidoreductase; Provisional; Region: PRK10083 316407004534 Alcohol dehydrogenases of the MDR family; Region: Zn_ADH7; cd08261 316407004535 putative NAD(P) binding site; other site 316407004536 catalytic Zn binding site; other site 316407004537 structural Zn binding site; other site 316407004538 bifunctional D-altronate/D-mannonate dehydratase; Provisional; Region: PRK15072 316407004539 The starvation sensing protein RpsA from E.coli and its homologs are lactonizing enzymes whose putative targets are homoserine lactone (HSL)-derivative. They are part of the mandelate racemase (MR)-like subfamily of the enolase superfamily. Enzymes of...; Region: rpsA; cd03322 316407004540 putative active site pocket; other site 316407004541 putative metal binding site; other site 316407004542 Uncharacterized BCR, YnfA/UPF0060 family; Region: UPF0060; cl00757 316407004543 Protein of unknown function (DUF1283); Region: DUF1283; cl11644 316407004544 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 316407004545 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 316407004546 Uncharacterized protein family (UPF0257); Region: UPF0257; cl14672 316407004547 Protein of unknown function (DUF1161); Region: DUF1161; pfam06649 316407004548 DmsA/YnfE family; Region: dmsA_ynfE; TIGR02166 316407004549 This CD (MopB_DmsA-EC) includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-...; Region: MopB_DmsA-EC; cd02770 316407004550 putative [Fe4-S4] binding site; other site 316407004551 putative molybdopterin cofactor binding site; other site 316407004552 The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-...; Region: MopB_CT_DmsA-EC; cd02794 316407004553 putative molybdopterin cofactor binding site; other site 316407004554 DmsA/YnfE family; Region: dmsA_ynfE; TIGR02166 316407004555 This CD (MopB_DmsA-EC) includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-...; Region: MopB_DmsA-EC; cd02770 316407004556 putative [Fe4-S4] binding site; other site 316407004557 putative molybdopterin cofactor binding site; other site 316407004558 The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-...; Region: MopB_CT_DmsA-EC; cd02794 316407004559 putative molybdopterin cofactor binding site; other site 316407004560 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 316407004561 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 alpha-; Region: HCP_like; cl14655 316407004562 DMSO reductase anchor subunit (DmsC); Region: DmsC; cl04869 316407004563 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 316407004564 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 316407004565 Cl- selectivity filter; other site 316407004566 Cl- binding residues; other site 316407004567 pore gating glutamate residue; other site 316407004568 dimer interface; other site 316407004569 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 316407004570 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 316407004571 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 316407004572 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 316407004573 ROK family; Region: ROK; cl09121 316407004574 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 316407004575 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407004576 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 316407004577 dimerization interface; other site 316407004578 substrate binding pocket; other site 316407004579 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 316407004580 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 316407004581 putative substrate translocation pore; other site 316407004582 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...; Region: Tryp_SPc; cl00149 316407004583 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 316407004584 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 316407004585 Domain of unknown function DUF20; Region: UPF0118; cl00465 316407004586 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 316407004587 NAD(P) transhydrogenase beta subunit; Region: PNTB; cl00566 316407004588 NAD(P) transhydrogenase subunit alpha; Provisional; Region: pntA; PRK09424 316407004589 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; pfam05222 316407004590 Protein of unknown function (DUF1471); Region: DUF1471; cl11507 316407004591 Protein of unknown function (DUF1471); Region: DUF1471; cl11507 316407004592 Protein of unknown function (DUF1471); Region: DUF1471; cl11507 316407004593 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407004594 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 316407004595 dihydromonapterin reductase; Provisional; Region: PRK06483 316407004596 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407004597 GlpM protein; Region: GlpM; cl01212 316407004598 DNA-binding transcriptional regulator RstA; Provisional; Region: PRK10701 316407004599 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 316407004600 active site 316407004601 phosphorylation site 316407004602 intermolecular recognition site; other site 316407004603 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...; Region: trans_reg_C; cd00383 316407004604 DNA binding site 316407004605 sensor protein RstB; Provisional; Region: PRK10604 316407004606 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 connected by an extended linker. The...; Region: HAMP; cl01054 316407004607 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 trans-...; Region: HisKA; cl00080 316407004608 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 316407004609 ATP binding site; other site 316407004610 Mg2+ binding site; other site 316407004611 G-X-G motif; other site 316407004612 DNA replication terminus site-binding protein (Ter protein); Region: Ter; cl11502 316407004613 fumarate hydratase; Reviewed; Region: fumC; PRK00485 316407004614 Class II fumarases; Region: Fumarase_classII; cd01362 316407004615 active site 316407004616 tetramer interface; other site 316407004617 fumarate hydratase; Provisional; Region: PRK15389 316407004618 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 316407004619 Fumarase C-terminus; Region: Fumerase_C; cl00795 316407004620 mannose-6-phosphate isomerase; Provisional; Region: PRK15131; cl14659 316407004621 Phosphomannose isomerase type I; Region: PMI_typeI; pfam01238 316407004622 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5339 316407004623 hypothetical protein; Provisional; Region: PRK11367 316407004624 putative outer membrane porin protein; Provisional; Region: PRK11379 316407004625 glucuronide transporter; Provisional; Region: PRK09848 316407004626 putative transporter; Provisional; Region: PRK11462 316407004627 beta-D-glucuronidase; Provisional; Region: PRK10150 316407004628 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 316407004629 domain; Region: Glyco_hydro_2; pfam00703 316407004630 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 316407004631 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 316407004632 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316407004633 7-alpha-hydroxysteroid dehydrogenase; Validated; Region: PRK06113 316407004634 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407004635 DNA-binding transcriptional repressor MalI; Provisional; Region: PRK10014 316407004636 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cl02583 316407004637 Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria; Region: PBP1_MalI_like; cd06289 316407004638 putative dimerization interface; other site 316407004639 putative ligand binding site; other site 316407004640 bifunctional PTS system maltose and glucose-specific transporter subunits IICB; Provisional; Region: PRK10110 316407004641 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 316407004642 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...; Region: PTS_IIB_glc; cd00212 316407004643 active site turn 316407004644 phosphorylation site 316407004645 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 316407004646 pyridoxal 5'-phosphate binding site; other site 316407004647 homodimer interface; other site 316407004648 catalytic residue; other site 316407004649 Adenosine deaminase (ADA) is a monomeric zinc dependent enzyme which catalyzes the irreversible hydrolytic deamination of both adenosine, as well as desoxyadenosine, to ammonia and inosine or desoxyinosine, respectively. ADA plays an important role in...; Region: ADA; cd01320 316407004650 active site 316407004651 purine riboside binding site; other site 316407004652 putative oxidoreductase; Provisional; Region: PRK11579 316407004653 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407004654 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 316407004655 Haemolysin expression modulating protein; Region: HHA; cl11501 316407004656 Protein of unknown function (DUF2569); Region: DUF2569; pfam10754 316407004657 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 316407004658 electron transport complex protein RnfB; Provisional; Region: PRK05113 316407004659 Putative Fe-S cluster; Region: FeS; pfam04060 316407004660 4Fe-4S binding domain; Region: Fer4; pfam00037 316407004661 Predicted NADH:ubiquinone oxidoreductase, subunit RnfC [Energy production and conversion]; Region: RnfC; COG4656 316407004662 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 316407004663 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl11430 316407004664 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 alpha-; Region: HCP_like; cl14655 316407004665 RnfE family; Region: NQR2_RnfD_RnfE; cl00779 316407004666 FMN-binding domain; Region: FMN_bind; cl01081 316407004667 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 316407004668 endonuclease III; Provisional; Region: PRK10702 316407004669 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 316407004670 minor groove reading motif; other site 316407004671 helix-hairpin-helix signature motif; other site 316407004672 substrate binding pocket; other site 316407004673 active site 316407004674 FES domain; Region: FES; smart00525 316407004675 dipeptide/tripeptide permease B; Provisional; Region: PRK10207 316407004676 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 316407004677 putative substrate translocation pore; other site 316407004678 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; cl11420 316407004679 glutathionine S-transferase; Provisional; Region: PRK10542 316407004680 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens...; Region: GST_N_Beta; cd03057 316407004681 C-terminal domain interface; other site 316407004682 GSH binding site (G-site); other site 316407004683 dimer interface; other site 316407004684 GST_C family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens...; Region: GST_C_Beta; cd03188 316407004685 N-terminal domain interface; other site 316407004686 dimer interface; other site 316407004687 substrate binding pocket (H-site); other site 316407004688 Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and...; Region: pyridoxal_pyridoxamine_kinase; cd01173 316407004689 dimer interface; other site 316407004690 pyridoxal binding site; other site 316407004691 ATP binding site; other site 316407004692 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 316407004693 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 316407004694 active site 316407004695 HIGH motif; other site 316407004696 dimer interface; other site 316407004697 KMSKS motif; other site 316407004698 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 316407004699 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 316407004700 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 316407004701 Pyridoxine 5'-phosphate oxidase C-terminal dimerization region; Region: PNPOx_C; pfam10590 316407004702 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; cl01604 316407004703 Uncharacterized protein family (UPF0075); Region: UPF0075; cl04217 316407004704 Rickettsia 17 kDa surface antigen; Region: Rick_17kDa_Anti; cl10470 316407004705 transcriptional regulator SlyA; Provisional; Region: PRK03573 316407004706 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407004707 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 316407004708 Fusaric acid resistance protein family; Region: FUSC; pfam04632 316407004709 Bacterial protein of unknown function (DUF939); Region: DUF939; cl12136 316407004710 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 316407004711 E-class dimer interface; other site 316407004712 P-class dimer interface; other site 316407004713 active site 316407004714 Cu2+ binding site; other site 316407004715 Zn2+ binding site; other site 316407004716 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...; Region: Aldo_ket_red; cd06660 316407004717 active site 316407004718 catalytic tetrad; other site 316407004719 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 316407004720 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 316407004721 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316407004722 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 316407004723 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 316407004724 FMN binding site; other site 316407004725 active site 316407004726 substrate binding site; other site 316407004727 catalytic residue; other site 316407004728 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 316407004729 dimer interface; other site 316407004730 active site 316407004731 metal-binding site 316407004732 glutathione binding site; other site 316407004733 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 316407004734 DEDDh 3'-5' exonuclease domain of RNase T; Region: RNaseT; cd06134 316407004735 dimer interface; other site 316407004736 putative active site; other site 316407004737 putative substrate binding site; other site 316407004738 catalytic site; other site 316407004739 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 316407004740 putative ATP-dependent helicase Lhr; Provisional; Region: PRK09751 316407004741 ATP binding site; other site 316407004742 putative Mg++ binding site; other site 316407004743 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 316407004744 nucleotide binding region; other site 316407004745 ATP-binding site; other site 316407004746 DEAD/H associated; Region: DEAD_assoc; pfam08494 316407004747 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 316407004748 putative GSH binding site; other site 316407004749 catalytic residues; other site 316407004750 NlpC/P60 family; Region: NLPC_P60; cl11438 316407004751 superoxide dismutase; Provisional; Region: PRK10543 316407004752 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 316407004753 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 316407004754 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 316407004755 Major Facilitator Superfamily; Region: MFS_1; pfam07690 316407004756 putative substrate translocation pore; other site 316407004757 DNA-binding transcriptional repressor PurR; Provisional; Region: PRK10703 316407004758 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 316407004759 DNA binding site 316407004760 domain linker motif; other site 316407004761 Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli; Region: PBP1_PurR; cd06275 316407004762 dimerization interface; other site 316407004763 ligand binding site; other site 316407004764 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 316407004765 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407004766 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 316407004767 dimerization interface; other site 316407004768 putative transporter; Provisional; Region: PRK11043 316407004769 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 316407004770 putative substrate translocation pore; other site 316407004771 cyclopropane fatty acyl phospholipid synthase; Provisional; Region: PRK11705 316407004772 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; cl12011 316407004773 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 316407004774 S-adenosylmethionine binding site; other site 316407004775 riboflavin synthase subunit alpha; Provisional; Region: PRK13020 316407004776 Lumazine binding domain; Region: Lum_binding; pfam00677 316407004777 Lumazine binding domain; Region: Lum_binding; pfam00677 316407004778 multidrug efflux protein; Reviewed; Region: PRK01766 316407004779 MatE; Region: MatE; pfam01554 316407004780 MatE; Region: MatE; pfam01554 316407004781 hypothetical protein; Provisional; Region: PRK09945 316407004782 Putative mono-oxygenase ydhR; Region: ydhR; cl07420 316407004783 hypothetical protein; Provisional; Region: PRK09897 316407004784 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4529 316407004785 hypothetical protein; Provisional; Region: PRK09946 316407004786 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 316407004787 cytochrome c nitrite reductase, Fe-S protein; Region: cyt_nit_nrfC; TIGR03149 316407004788 hypothetical protein; Provisional; Region: PRK09947 316407004789 putative oxidoreductase; Provisional; Region: PRK09849 316407004790 Aldehyde ferredoxin oxidoreductase, N-terminal domain; Region: AFOR_N; cl08354 316407004791 Aldehyde ferredoxin oxidoreductase, domains 2 & 3; Region: AFOR_C; pfam01314 316407004792 hypothetical protein; Provisional; Region: PRK09898 316407004793 Protein of unknown function (DUF2767); Region: DUF2767; cl08104 316407004794 pyruvate kinase; Provisional; Region: PRK09206 316407004795 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; cd00288 316407004796 domain interfaces; other site 316407004797 active site 316407004798 Murein lipoprotein [Cell envelope biogenesis, outer membrane]; Region: COG4238; cl11539 316407004799 L,D-transpeptidase; Provisional; Region: PRK10190 316407004800 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 316407004801 putative peptidoglycan binding site; other site 316407004802 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 316407004803 Fe-S metabolism associated domain; Region: SufE; cl00951 316407004804 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 316407004805 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 316407004806 pyridoxal 5'-phosphate binding pocket; other site 316407004807 catalytic residue; other site 316407004808 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 316407004809 FeS assembly protein SufD, group 1; Region: sufD; TIGR01981 316407004810 cysteine desulfurase ATPase component; Reviewed; Region: sufC; PRK09580 316407004811 ABC-type transport system involved in Fe-S cluster assembly, ATPase component. Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under...; Region: ABC_FeS_Assembly; cd03217 316407004812 Walker A/P-loop; other site 316407004813 ATP binding site; other site 316407004814 Q-loop/lid; other site 316407004815 ABC transporter signature motif; other site 316407004816 Walker B; other site 316407004817 D-loop; other site 316407004818 H-loop/switch region; other site 316407004819 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 316407004820 putative ABC transporter; Region: ycf24; CHL00085 316407004821 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 316407004822 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 316407004823 CoenzymeA binding site; other site 316407004824 subunit interaction site; other site 316407004825 PHB binding site; other site 316407004826 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 316407004827 FAD binding domain; Region: FAD_binding_4; cl10516 316407004828 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 316407004829 Domain of unknown function DUF20; Region: UPF0118; cl00465 316407004830 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 316407004831 Domain of unknown function (DUF1870); Region: DUF1870; pfam08965 316407004832 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 316407004833 Major Facilitator Superfamily; Region: MFS_1; pfam07690 316407004834 putative substrate translocation pore; other site 316407004835 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 316407004836 putative substrate translocation pore; other site 316407004837 quinate/shikimate dehydrogenase; Reviewed; Region: PRK12749 316407004838 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 316407004839 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 316407004840 shikimate binding site; other site 316407004841 NAD(P) binding site; other site 316407004842 Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase.) Catalyzes the cis-dehydration of 3-dehydroquinate via a covalent imine intermediate to produce dehydroshikimate. Dehydroquinase is the third enzyme in the shikimate pathway, which is...; Region: DHQase_I; cd00502 316407004843 3-dehydroquinate dehydratase, type I; Region: aroD; TIGR01093 316407004844 active site 316407004845 catalytic residue; other site 316407004846 dimer interface; other site 316407004847 Acyl CoA:acetate/3-ketoacid CoA transferase [Lipid metabolism]; Region: COG4670 316407004848 Coenzyme A transferase; Region: CoA_trans; cl00773 316407004849 Coenzyme A transferase; Region: CoA_trans; cl00773 316407004850 putative acyl-CoA dehydrogenase; Provisional; Region: PRK12341 316407004851 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 316407004852 active site 316407004853 Cupin domain; Region: Cupin_2; cl09118 316407004854 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 316407004855 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 316407004856 Ligand binding site; other site 316407004857 electron transfer flavoprotein subunit YdiR; Provisional; Region: PRK11916 316407004858 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 316407004859 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 316407004860 putative oxidoreductase FixC; Provisional; Region: PRK10157 316407004861 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407004862 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 316407004863 ferredoxin-like protein FixX; Provisional; Region: PRK15449 316407004864 short chain acyl-CoA synthetase; Reviewed; Region: PRK06087 316407004865 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 316407004866 phosphoenolpyruvate synthase; Validated; Region: PRK06464 316407004867 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 316407004868 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 316407004869 Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their...; Region: malate_synt; cl09155 316407004870 Domain of unknown function (DUF299); Region: DUF299; cl00780 316407004871 NeuB family; Region: NeuB; cl00496 316407004872 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 316407004873 Hemin uptake protein hemP; Region: hemP; cl10043 316407004874 Uncharacterized ACR, YdiU/UPF0061 family; Region: UPF0061; cl00428 316407004875 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; cl00290 316407004876 NlpC/P60 family; Region: NLPC_P60; cl11438 316407004877 vitamin B12-transporter ATPase; Provisional; Region: PRK03695 316407004878 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 316407004879 Walker A/P-loop; other site 316407004880 ATP binding site; other site 316407004881 Q-loop/lid; other site 316407004882 ABC transporter signature motif; other site 316407004883 Walker B; other site 316407004884 D-loop; other site 316407004885 H-loop/switch region; other site 316407004886 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...; Region: GSH_Peroxidase; cd00340 316407004887 catalytic residues; other site 316407004888 dimer interface; other site 316407004889 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...; Region: TM_ABC_iron-siderophores_like; cd06550 316407004890 ABC-ATPase subunit interface; other site 316407004891 dimer interface; other site 316407004892 putative PBP binding regions; other site 316407004893 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 higher-...; Region: HU_IHF; cd00591 316407004894 IHF dimer interface; other site 316407004895 IHF - DNA interface; other site 316407004896 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 316407004897 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 316407004898 putative tRNA-binding site; other site 316407004899 B3/4 domain; Region: B3_4; cl11458 316407004900 tRNA synthetase B5 domain; Region: B5; cl08394 316407004901 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 316407004902 dimer interface; other site 316407004903 motif 1; other site 316407004904 motif 3; other site 316407004905 motif 2; other site 316407004906 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 316407004907 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 316407004908 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 316407004909 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 316407004910 dimer interface; other site 316407004911 motif 1; other site 316407004912 active site 316407004913 motif 2; other site 316407004914 motif 3; other site 316407004915 Ribosomal protein L20; Region: Ribosomal_L20; cl00393 316407004916 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 316407004917 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 316407004918 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 316407004919 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 316407004920 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 316407004921 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...; Region: TGS_ThrRS_N; cd01667 316407004922 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 316407004923 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 316407004924 active site 316407004925 dimer interface; other site 316407004926 motif 1; other site 316407004927 motif 2; other site 316407004928 motif 3; other site 316407004929 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 316407004930 anticodon binding site; other site 316407004931 ECK1718:JW1710:b1721; hypothetical protein, C-ter fragment 316407004932 ECK1718:JW5278+JW1710:b4494; hypothetical protein 316407004933 ECK1718:JW5278:b1720; hypothetical protein, N-ter fragment 316407004934 Protein of unknown function, DUF481; Region: DUF481; cl01213 316407004935 6-phosphofructokinase 2; Provisional; Region: PRK10294 316407004936 1-phosphofructokinase (FruK), minor 6-phosphofructokinase (pfkB) and related sugar kinases. FruK plays an important role in the predominant pathway for fructose utilisation.This group also contains tagatose-6-phophate kinase, an enzyme of the tagatose...; Region: FruK_PfkB_like; cd01164 316407004937 putative substrate binding site; other site 316407004938 putative ATP binding site; other site 316407004939 Protein of unknown function (DUF2622); Region: DUF2622; pfam11080 316407004940 Phosphotransferase enzyme family; Region: APH; pfam01636 316407004941 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cd05120 316407004942 active site 316407004943 ATP binding site; other site 316407004944 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 316407004945 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 316407004946 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; cl11391 316407004947 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 316407004948 motif II; other site 316407004949 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; cl00868 316407004950 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 316407004951 Cell division activator CedA; Region: CedA; cl11674 316407004952 hydroperoxidase II; Provisional; Region: katE; PRK11249 316407004953 Clade 2 of the heme-binding enzyme catalase; Region: catalase_clade_2; cd08155 316407004954 tetramer interface; other site 316407004955 heme binding pocket; other site 316407004956 Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases; Region: GATase1_catalase; cd03132 316407004957 domain interactions; other site 316407004958 YdjC-like protein; Region: YdjC; cl01344 316407004959 Alpha-galactosidases/6-phospho-beta-glucosidases, family 4 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: CelF; COG1486 316407004960 Glycoside Hydrolases Family 4; Phospho-beta-glucosidase; Region: GH4_P_beta_glucosidase; cd05296 316407004961 NAD binding site; other site 316407004962 sugar binding site; other site 316407004963 divalent metal binding site; other site 316407004964 tetramer (dimer of dimers) interface; other site 316407004965 dimer interface; other site 316407004966 DNA-binding transcriptional regulator ChbR; Provisional; Region: PRK10296 316407004967 Cupin domain; Region: Cupin_2; cl09118 316407004968 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407004969 PTS_IIA, PTS system, lactose/cellobiose 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_lac; cd00215 316407004970 methionine cluster; other site 316407004971 active site 316407004972 phosphorylation site 316407004973 metal-binding site 316407004974 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 316407004975 PTS_IIB_chitobiose_lichenan: subunit IIB of enzyme II (EII) of the N,N-diacetylchitobiose-specific and lichenan-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In these systems, EII is either a lichenan- or an N,N-...; Region: PTS_IIB_chitobiose_lichenan; cd05564 316407004976 active site 316407004977 P-loop; other site 316407004978 phosphorylation site 316407004979 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 316407004980 NAD+ synthetase; Region: nadE; TIGR00552 316407004981 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...; Region: NAD_synthase; cd00553 316407004982 homodimer interface; other site 316407004983 NAD binding pocket; other site 316407004984 ATP binding pocket; other site 316407004985 Mg binding site; other site 316407004986 active-site loop 316407004987 nucleotide excision repair endonuclease; Provisional; Region: PRK10545 316407004988 GIY-YIG catalytic domain; Region: GIY-YIG; cl01061 316407004989 HutD; Region: HutD; cl01532 316407004990 P pilus assembly/Cpx signaling pathway, periplasmic inhibitor/zinc-resistance associated protein [Intracellular trafficking and secretion / Cell motility and secretio / Signal transduction mechanisms / Inorganic ion transport and metabolism]; Region: CpxP; cl01482 316407004991 Peptidase M14 Succinylglutamate desuccinylase (ASTE, also known as N-succinyl-L-glutamate amidohydrolase, N2-succinylglutamate desuccinylase, and SGDS; EC 3.5.1.96) belongs to the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily...; Region: M14_ASTE; cd03855 316407004992 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 316407004993 putative active site; other site 316407004994 Zn-binding site; other site 316407004995 Succinylarginine dihydrolase; Region: AstB; cl01511 316407004996 N-succinylglutamate 5-semialdehyde dehydrogenase, AstD-like; Region: ALDH_SGSD_AstD; cd07095 316407004997 NAD(P) binding site; other site 316407004998 catalytic residues; other site 316407004999 Arginine N-succinyltransferase beta subunit; Region: AstA; cl11440 316407005000 Arginine/ornithine N-succinyltransferase beta subunit [Amino acid transport and metabolism]; Region: AstA; COG3138 316407005001 bifunctional succinylornithine transaminase/acetylornithine transaminase; Provisional; Region: PRK12381 316407005002 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 316407005003 inhibitor-cofactor binding pocket; inhibition site 316407005004 pyridoxal 5'-phosphate binding site; other site 316407005005 catalytic residue; other site 316407005006 Endonuclease/Exonuclease/phosphatase family; Region: Exo_endo_phos; cl00490 316407005007 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 316407005008 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 316407005009 Uncharacterized conserved protein [Function unknown]; Region: COG2128 316407005010 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 316407005011 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG4134 316407005012 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 316407005013 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4135 316407005014 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...; Region: TM_PBP2; cl00427 316407005015 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: COG4136 316407005016 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407005017 Walker A/P-loop; other site 316407005018 ATP binding site; other site 316407005019 Q-loop/lid; other site 316407005020 ABC transporter signature motif; other site 316407005021 Walker B; other site 316407005022 D-loop; other site 316407005023 H-loop/switch region; other site 316407005024 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 316407005025 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...; Region: TST_Repeat_1; cd01448 316407005026 active site residue 316407005027 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 316407005028 active site residue 316407005029 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 316407005030 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 316407005031 active site 316407005032 8-oxo-dGMP binding site; other site 316407005033 nudix motif; other site 316407005034 metal-binding site 316407005035 Protein of unknown function (DUF1496); Region: DUF1496; pfam07383 316407005036 glutamate dehydrogenase; Provisional; Region: PRK09414 316407005037 Glu/Leu/Phe/Val dehydrogenase, dimerization domain; Region: ELFV_dehydrog_N; pfam02812 316407005038 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 316407005039 NAD(P) binding site; other site 316407005040 Protein of unknown function (DUF1266); Region: DUF1266; cl14673 316407005041 DNA topoisomerase III; Provisional; Region: PRK07726 316407005042 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:...; Region: TOPRIM_TopoIA_TopoIII; cd03362 316407005043 active site 316407005044 putative interdomain interaction site; other site 316407005045 putative metal-binding site; other site 316407005046 putative nucleotide binding site; other site 316407005047 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...; Region: TOP1Ac; cd00186 316407005048 domain I; other site 316407005049 DNA binding groove 316407005050 phosphate binding site; other site 316407005051 domain II; other site 316407005052 domain III; other site 316407005053 nucleotide binding site; other site 316407005054 catalytic site; other site 316407005055 domain IV; other site 316407005056 selenophosphate synthetase; Provisional; Region: PRK00943 316407005057 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 316407005058 dimerization interface; other site 316407005059 putative ATP binding site; other site 316407005060 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 beta-...; Region: Arsenite_oxidase; cd02135 316407005061 putative FMN binding site; other site 316407005062 protease 4; Provisional; Region: PRK10949 316407005063 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 316407005064 tandem repeat interface; other site 316407005065 oligomer interface; other site 316407005066 active site residues 316407005067 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_1; cd07019 316407005068 tandem repeat interface; other site 316407005069 oligomer interface; other site 316407005070 active site residues 316407005071 Asparaginase (amidohydrolase): Asparaginases are tetrameric enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases, one highly specific for asparagine and localised to the...; Region: Asparaginase; cd00411 316407005072 active site/substrate binding site 316407005073 tetramer interface; other site 316407005074 Nicotinamidase/pyrazinamidase (PZase). Nicotinamidase, a ubiquitous enzyme in prokaryotes, converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD). The same enzyme is...; Region: nicotinamidase; cd01011 316407005075 Isochorismatase family; Region: Isochorismatase; pfam00857 316407005076 catalytic triad; other site 316407005077 metal-binding site 316407005078 conserved cis-peptide bond; other site 316407005079 Sugar (and other) transporter; Region: Sugar_tr; pfam00083 316407005080 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 316407005081 putative substrate translocation pore; other site 316407005082 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 316407005083 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 316407005084 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407005085 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 316407005086 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...; Region: Aldo_ket_red; cd06660 316407005087 active site 316407005088 catalytic tetrad; other site 316407005089 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 316407005090 substrate binding site; other site 316407005091 ATP binding site; other site 316407005092 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...; Region: TBP_aldolase_IIB; cd00947 316407005093 hypothetical protein; Provisional; Region: PRK08185 316407005094 intersubunit interface; other site 316407005095 active site 316407005096 zinc binding site; other site 316407005097 Na+ binding site; other site 316407005098 Sorbitol dehydrogenase; Region: sorbitol_DH; cd05285 316407005099 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 316407005100 inhibitor binding site; inhibition site 316407005101 catalytic Zn binding site; other site 316407005102 structural Zn binding site; other site 316407005103 NADP binding site; other site 316407005104 tetramer interface; other site 316407005105 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 316407005106 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 316407005107 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 316407005108 Alcohol dehydrogenases of the MDR family; Region: Zn_ADH4; cd08258 316407005109 putative NAD(P) binding site; other site 316407005110 catalytic Zn binding site; other site 316407005111 structural Zn binding site; other site 316407005112 Protein of unknown function (DUF1315); Region: DUF1315; cl01215 316407005113 SelR domain; Region: SelR; cl00369 316407005114 glyceraldehyde-3-phosphate dehydrogenase A; Provisional; Region: gapA; PRK15425 316407005115 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407005116 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 316407005117 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 316407005118 active site 316407005119 phosphate binding residues; other site 316407005120 catalytic residues; other site 316407005121 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...; Region: Aldo_ket_red; cd06660 316407005122 active site 316407005123 catalytic tetrad; other site 316407005124 MltA-interacting protein MipA; Region: MipA; cl01504 316407005125 PrkA family serine protein kinase; Provisional; Region: PRK15455 316407005126 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407005127 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 316407005128 Protein of unknown function (DUF444); Region: DUF444; pfam04285 316407005129 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 316407005130 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316407005131 metal-binding site 316407005132 active site 316407005133 I-site; other site 316407005134 putative diguanylate cyclase YedQ; Provisional; Region: PRK15426 316407005135 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316407005136 metal-binding site 316407005137 active site 316407005138 I-site; other site 316407005139 YeaK is an uncharacterized Echerichia coli protein with a YbaK-like domain of unknown function. The YbaK-like domain family includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting...; Region: YeaK; cd04336 316407005140 putative deacylase active site; other site 316407005141 Protein of unknown function (DUF441); Region: DUF441; cl01041 316407005142 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 316407005143 cyanate transporter; Region: CynX; TIGR00896 316407005144 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 316407005145 Protein of unknown function, DUF488; Region: DUF488; cl01246 316407005146 Putative hemolysin [General function prediction only]; Region: Hlx; COG3042 316407005147 Flagellar L-ring protein; Region: FlgH; cl00905 316407005148 Domain of unknown function (DUF333); Region: DUF333; pfam03891 316407005149 GAF domain; Region: GAF; cl00853 316407005150 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316407005151 metal-binding site 316407005152 active site 316407005153 I-site; other site 316407005154 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 316407005155 Domain of unknown function (DUF1869); Region: DUF1869; pfam08956 316407005156 Domain of unknown function (DUF1971); Region: DUF1971; cl01451 316407005157 LysE type translocator; Region: LysE; cl00565 316407005158 transcriptional activator TtdR; Provisional; Region: PRK09801 316407005159 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407005160 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_9; cd08479 316407005161 putative effector binding pocket; other site 316407005162 putative dimerization interface; other site 316407005163 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 316407005164 BCCT family transporter; Region: BCCT; cl00569 316407005165 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 316407005166 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 316407005167 [2Fe-2S] cluster binding site; other site 316407005168 C-terminal catalytic domain of the oxygenase alpha subunit of an uncharacterized subgroup of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C_2; cd08886 316407005169 putative alpha subunit interface; other site 316407005170 putative active site; other site 316407005171 putative substrate binding site; other site 316407005172 Fe binding site; other site 316407005173 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 316407005174 Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-...; Region: PDR_like; cd06185 316407005175 FMN-binding pocket; other site 316407005176 flavin binding motif; other site 316407005177 phosphate binding motif; other site 316407005178 beta-alpha-beta structure motif; other site 316407005179 NAD binding pocket; other site 316407005180 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 316407005181 catalytic loop; other site 316407005182 iron binding site; other site 316407005183 ribonuclease D; Provisional; Region: PRK10829 316407005184 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 316407005185 putative active site; other site 316407005186 catalytic site; other site 316407005187 putative substrate binding site; other site 316407005188 HRDC domain; Region: HRDC; cl02578 316407005189 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08974 316407005190 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 316407005191 Outer membrane lipoprotein Slp family; Region: Slp; cl01164 316407005192 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 316407005193 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 316407005194 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; cl12029 316407005195 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; cl12029 316407005196 helicase superfamily c-terminal domain; Region: HELICc2; cl09250 316407005197 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 316407005198 homotrimer interaction site; other site 316407005199 putative active site; other site 316407005200 Domain of unknown function (DUF1889); Region: DUF1889; pfam08986 316407005201 Uncharacterized protein family (UPF0181); Region: UPF0181; cl11477 316407005202 aminodeoxychorismate synthase subunit I; Provisional; Region: pabB; PRK15465 316407005203 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 316407005204 chorismate binding enzyme; Region: Chorismate_bind; cl10555 316407005205 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 316407005206 putative active site; other site 316407005207 putative CoA binding site; other site 316407005208 nudix motif; other site 316407005209 metal-binding site 316407005210 L-serine deaminase; Provisional; Region: PRK15023 316407005211 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 316407005212 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 316407005213 phage resistance protein; Provisional; Region: PRK10551 316407005214 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 316407005215 Integral membrane protein TerC family; Region: TerC; cl10468 316407005216 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 316407005217 Transporter associated domain; Region: CorC_HlyC; pfam03471 316407005218 PTS system mannose-specific transporter subunits IIAB; Provisional; Region: PRK15088 316407005219 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_man; cd00006 316407005220 active pocket/dimerization site; other site 316407005221 active site 316407005222 phosphorylation site 316407005223 Mannose/sorbose 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 is one of four...; Region: PTS_IIB_man; cd00001 316407005224 active site 316407005225 phosphorylation site 316407005226 PTS system sorbose-specific iic component; Region: EII-Sor; cl01506 316407005227 PTS system mannose/fructose/sorbose family IID component; Region: EIID-AGA; cl01507 316407005228 Protein of unknown function (DUF986); Region: DUF986; cl01983 316407005229 hypothetical protein; Provisional; Region: PRK11469 316407005230 Domain of unknown function DUF; Region: DUF204; pfam02659 316407005231 Domain of unknown function DUF; Region: DUF204; pfam02659 316407005232 SAM-dependent methyltransferases [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: SmtA; COG0500 316407005233 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 316407005234 S-adenosylmethionine binding site; other site 316407005235 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 protein...; Region: CSP_CDS; cd04458 316407005236 DNA binding site 316407005237 RNA-binding motif; other site 316407005238 Protein of unknown function (DUF2627); Region: DUF2527; pfam10736 316407005239 PhoPQ regulatory protein; Provisional; Region: PRK10299 316407005240 DNA-binding transcriptional regulator KdgR; Provisional; Region: PRK15090 316407005241 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407005242 Bacterial transcriptional regulator; Region: IclR; pfam01614 316407005243 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 316407005244 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 316407005245 putative substrate translocation pore; other site 316407005246 Peptidase family M48; Region: Peptidase_M48; cl12018 316407005247 carboxy-terminal protease; Provisional; Region: PRK11186 316407005248 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 316407005249 protein binding site; other site 316407005250 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 316407005251 Catalytic dyad; other site 316407005252 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 316407005253 FinO bacterial conjugation repressor domain; the basic protein FinO is part of the the two component FinOP system which is responsible for repressing bacterial conjugation; the FinOP system represses the transfer (tra) operon of the F-plasmid which...; Region: FinO_conjug_rep; cl00174 316407005254 GAF domain; Region: GAF; cl00853 316407005255 integral membrane protein, PqiA family; Region: pqiA_fam; TIGR00155 316407005256 Paraquat-inducible protein A; Region: PqiA; pfam04403 316407005257 Paraquat-inducible protein A; Region: PqiA; pfam04403 316407005258 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 316407005259 mce related protein; Region: MCE; cl03606 316407005260 mce related protein; Region: MCE; cl03606 316407005261 mce related protein; Region: MCE; cl03606 316407005262 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 316407005263 mce related protein; Region: MCE; cl03606 316407005264 mce related protein; Region: MCE; cl03606 316407005265 rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed; Region: yebU; PRK11933 316407005266 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; cl12011 316407005267 Uncharacterized conserved protein [Function unknown]; Region: COG3270 316407005268 Protein of unknown function (DUF1480); Region: DUF1480; pfam07351 316407005269 Protein of unknown function (DUF1482); Region: DUF1482; pfam07358 316407005270 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 316407005271 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 316407005272 active site 316407005273 metal-binding site 316407005274 Protein of unknown function (DUF2511); Region: DUF2511; pfam10709 316407005275 Copper resistance protein D; Region: CopD; cl00563 316407005276 Copper resistance protein CopC; Region: CopC; cl01012 316407005277 DNA polymerase III, theta subunit; Region: DNA_pol3_theta; cl11635 316407005278 Predicted amidohydrolase [General function prediction only]; Region: COG0388 316407005279 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 316407005280 exodeoxyribonuclease X; Provisional; Region: PRK07983 316407005281 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 316407005282 active site 316407005283 substrate binding site; other site 316407005284 catalytic site; other site 316407005285 protease 2; Provisional; Region: PRK10115 316407005286 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; cl12031 316407005287 tellurium resistance terB-like protein, subgroup 3; Region: terB_like_YebE; cd07178 316407005288 putative metal binding site; other site 316407005289 hypothetical protein; Provisional; Region: PRK13680 316407005290 YebG protein; Region: YebG; cl01217 316407005291 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 316407005292 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 316407005293 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 316407005294 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 316407005295 KDPG and KHG aldolase. This family belongs to the class I adolases whose reaction mechanism involves Schiff base formation between a substrate carbonyl and lysine residue in the active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, is best...; Region: KDPG_aldolase; cd00452 316407005296 active site 316407005297 intersubunit interface; other site 316407005298 catalytic residue; other site 316407005299 Dehydratase family; Region: ILVD_EDD; cl00340 316407005300 6-phosphogluconate dehydratase; Region: edd; TIGR01196 316407005301 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 316407005302 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 316407005303 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 316407005304 DNA-binding transcriptional regulator HexR; Provisional; Region: PRK11302 316407005305 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...; Region: SIS_RpiR; cd05013 316407005306 putative active site; other site 316407005307 pyruvate kinase; Provisional; Region: PRK05826 316407005308 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; cd00288 316407005309 domain interfaces; other site 316407005310 active site 316407005311 lipid A biosynthesis lauroyl acyltransferase; Provisional; Region: PRK08734 316407005312 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 316407005313 putative acyl-acceptor binding pocket; other site 316407005314 putative peptidase; Provisional; Region: PRK11649 316407005315 Opacity-associated protein A N-terminal motif; Region: OapA_N; pfam08525 316407005316 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 316407005317 Peptidase family M23; Region: Peptidase_M23; pfam01551 316407005318 Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism; Region: ZnuA; cd01019 316407005319 metal-binding site 316407005320 high-affinity zinc transporter ATPase; Reviewed; Region: znuC; PRK09544 316407005321 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-...; Region: ABC_Metallic_Cations; cd03235 316407005322 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...; Region: TM_ABC_iron-siderophores_like; cd06550 316407005323 ABC-ATPase subunit interface; other site 316407005324 dimer interface; other site 316407005325 putative PBP binding regions; other site 316407005326 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 316407005327 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...; Region: AAA; cd00009 316407005328 Walker A motif; other site 316407005329 ATP binding site; other site 316407005330 Walker B motif; other site 316407005331 arginine finger; other site 316407005332 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 316407005333 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 316407005334 RuvA N terminal domain; Region: RuvA_N; pfam01330 316407005335 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 316407005336 Orthopoxvirus protein of unknown function (DUF830); Region: DUF830; cl13998 316407005337 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 includes...; Region: RuvC_resolvase; cd00529 316407005338 active site 316407005339 putative DNA-binding cleft; other site 316407005340 dimer interface; other site 316407005341 Domain of unknown function DUF28; Region: DUF28; cl00361 316407005342 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_7; cd04664 316407005343 nudix motif; other site 316407005344 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 316407005345 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 316407005346 dimer interface; other site 316407005347 anticodon binding site; other site 316407005348 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 the...; Region: AspRS_core; cd00777 316407005349 homodimer interface; other site 316407005350 motif 1; other site 316407005351 active site 316407005352 motif 2; other site 316407005353 GAD domain; Region: GAD; pfam02938 316407005354 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 the...; Region: AspRS_core; cd00777 316407005355 motif 3; other site 316407005356 Isochorismatase family; Region: Isochorismatase; pfam00857 316407005357 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 316407005358 catalytic triad; other site 316407005359 conserved cis-peptide bond; other site 316407005360 Protein of unknown function DUF72; Region: DUF72; cl00777 316407005361 MAPEG family; Region: MAPEG; cl09190 316407005362 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 316407005363 S-adenosylmethionine binding site; other site 316407005364 tRNA mo(5)U34 methyltransferase; Provisional; Region: PRK15068 316407005365 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; cl12011 316407005366 Tat (twin-arginine translocation) pathway signal sequence; Region: TAT_signal_seq; TIGR01409 316407005367 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 316407005368 molybdopterin guanine dinucleotide-containing S/N-oxide reductases; Region: bisC_fam; TIGR00509 316407005369 molybdopterin cofactor binding site; other site 316407005370 substrate binding site; other site 316407005371 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 316407005372 molybdopterin cofactor binding site; other site 316407005373 trimethylamine-N-oxide reductase c-type cytochrome TorC; Region: torC; TIGR02162 316407005374 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl09485 316407005375 CutC family; Region: CutC; cl01218 316407005376 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 316407005377 putative metal binding site; other site 316407005378 arginyl-tRNA synthetase; Region: argS; TIGR00456 316407005379 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 316407005380 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 316407005381 active site 316407005382 HIGH motif; other site 316407005383 KMSK motif region; other site 316407005384 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 316407005385 tRNA binding surface; other site 316407005386 anticodon binding site; other site 316407005387 Protein of unknown function (DUF1311); Region: DUF1311; cl01530 316407005388 Flagellar protein FlhE; Region: FlhE; pfam06366 316407005389 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 316407005390 FHIPEP family; Region: FHIPEP; cl07980 316407005391 Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhB; cl12017 316407005392 FlhB HrpN YscU SpaS Family; Region: Bac_export_2; pfam01312 316407005393 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 316407005394 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 316407005395 active site 316407005396 phosphorylation site 316407005397 intermolecular recognition site; other site 316407005398 dimerization interface; other site 316407005399 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 316407005400 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 316407005401 active site 316407005402 phosphorylation site 316407005403 intermolecular recognition site; other site 316407005404 dimerization interface; other site 316407005405 CheB methylesterase; Region: CheB_methylest; pfam01339 316407005406 chemotaxis methyltransferase CheR; Provisional; Region: PRK10611 316407005407 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 316407005408 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; cl12011 316407005409 methyl-accepting protein IV; Provisional; Region: PRK09793 316407005410 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cd00181 316407005411 dimerization interface; other site 316407005412 ligand (aspartate) binding pocket; other site 316407005413 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 connected by an extended linker. The...; Region: HAMP; cl01054 316407005414 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 316407005415 methyl-accepting chemotaxis protein II; Provisional; Region: PRK15048 316407005416 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cd00181 316407005417 dimerization interface; other site 316407005418 ligand (aspartate) binding pocket; other site 316407005419 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 connected by an extended linker. The...; Region: HAMP; cl01054 316407005420 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 316407005421 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 316407005422 putative CheA interaction surface; other site 316407005423 chemotaxis protein CheA; Provisional; Region: PRK10547 316407005424 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 316407005425 putative binding surface; other site 316407005426 active site 316407005427 CheY binding; Region: CheY-binding; pfam09078 316407005428 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 316407005429 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 316407005430 ATP binding site; other site 316407005431 Mg2+ binding site; other site 316407005432 G-X-G motif; other site 316407005433 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 316407005434 flagellar motor protein MotB; Validated; Region: motB; PRK09041 316407005435 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 316407005436 ligand binding site; other site 316407005437 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 316407005438 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 316407005439 Flagellar transcriptional activator (FlhC); Region: FlhC; cl05036 316407005440 Flagellar transcriptional activator (FlhD); Region: FlhD; cl05012 316407005441 Transposase domain (DUF772); Region: DUF772; cl12084 316407005442 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 316407005443 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 316407005444 Ligand Binding Site; other site 316407005445 alpha,alpha-trehalose-phosphate synthase [UDP-forming]; Region: trehalose_OtsA; TIGR02400 316407005446 Trehalose-6-Phosphate Synthase (TPS) is a glycosyltransferase that catalyses the synthesis of alpha,alpha-1,1-trehalose-6-phosphate from glucose-6-phosphate using a UDP-glucose donor. It is a key enzyme in the trehalose synthesis pathway. Trehalose is...; Region: GT1_TPS; cd03788 316407005447 active site 316407005448 homotetramer interface; other site 316407005449 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; cl11391 316407005450 HAD-superfamily hydrolase, subfamily IIB; Region: HAD-SF-IIB; TIGR01484 316407005451 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 316407005452 TM-ABC transporter signature motif; other site 316407005453 L-arabinose transporter ATP-binding protein; Provisional; Region: araG; PRK11288 316407005454 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and...; Region: ABC_Carb_Monos_I; cd03216 316407005455 Walker A/P-loop; other site 316407005456 ATP binding site; other site 316407005457 Q-loop/lid; other site 316407005458 ABC transporter signature motif; other site 316407005459 Walker B; other site 316407005460 D-loop; other site 316407005461 H-loop/switch region; other site 316407005462 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (; Region: ABC_Carb_Monos_II; cd03215 316407005463 family; Region: Peripla_BP_1; pfam00532 316407005464 Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily; Region: PBP1_arabinose_binding; cd01540 316407005465 ligand binding site; other site 316407005466 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 316407005467 Ferritin-like domain; Region: Ferritin; pfam00210 316407005468 ferroxidase diiron center; other site 316407005469 Protein of unknown function (DUF2766); Region: DUF2766; pfam10964 316407005470 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 316407005471 Ferritin-like domain; Region: Ferritin; pfam00210 316407005472 ferroxidase diiron center; other site 316407005473 Protein of unknown function (DUF2492); Region: DUF2492; cl11278 316407005474 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407005475 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 316407005476 hypothetical protein; Provisional; Region: PRK10396 316407005477 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 316407005478 SEC-C motif; Region: SEC-C; cl12132 316407005479 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 316407005480 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 316407005481 GIY-YIG catalytic domain; Region: GIY-YIG; cl01061 316407005482 UvrB/uvrC motif; Region: UVR; pfam02151 316407005483 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 316407005484 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl11430 316407005485 response regulator; Provisional; Region: PRK09483 316407005486 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 316407005487 active site 316407005488 phosphorylation site 316407005489 intermolecular recognition site; other site 316407005490 dimerization interface; other site 316407005491 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...; Region: LuxR_C_like; cd06170 316407005492 DNA binding residues 316407005493 dimerization interface; other site 316407005494 Protein of unknown function (DUF2594); Region: DUF2594; cl11678 316407005495 DNA-binding transcriptional activator SdiA; Provisional; Region: PRK10188 316407005496 Autoinducer binding domain; Region: Autoind_bind; pfam03472 316407005497 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...; Region: LuxR_C_like; cd06170 316407005498 DNA binding residues 316407005499 dimerization interface; other site 316407005500 putative amino-acid ABC transporter ATP-binding protein YecC; Provisional; Region: PRK11264 316407005501 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP; Region: ABC_HisP_GlnQ_permeases; cd03262 316407005502 Walker A/P-loop; other site 316407005503 ATP binding site; other site 316407005504 Q-loop/lid; other site 316407005505 ABC transporter signature motif; other site 316407005506 Walker B; other site 316407005507 D-loop; other site 316407005508 H-loop/switch region; other site 316407005509 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 316407005510 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...; Region: TM_PBP2; cd06261 316407005511 dimer interface; other site 316407005512 conserved gate region; other site 316407005513 putative PBP binding loops; other site 316407005514 ABC-ATPase subunit interface; other site 316407005515 D-cysteine desulfhydrase; Validated; Region: PRK03910 316407005516 Aminocyclopropane-1-carboxylate deaminase (ACCD): Pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of 1-aminocyclopropane-L-carboxylate (ACC), a precursor of the plant hormone ethylene, to alpha-ketobutyrate and ammonia; Region: ACCD; cd06449 316407005517 pyridoxal 5'-phosphate binding site; other site 316407005518 catalytic residue; other site 316407005519 cystine transporter subunit; Provisional; Region: PRK11260 316407005520 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...; Region: PBPb; cd00134 316407005521 substrate binding pocket; other site 316407005522 membrane-bound complex binding site; other site 316407005523 hinge residues; other site 316407005524 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N; cl12235 316407005525 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 316407005526 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 316407005527 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 316407005528 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...; Region: Sigma70_r4; cd06171 316407005529 DNA binding residues 316407005530 flagellin; Validated; Region: PRK08026 316407005531 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 316407005532 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 316407005533 flagellar capping protein; Reviewed; Region: fliD; PRK08032 316407005534 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 316407005535 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 316407005536 Flagellar protein FliS; Region: FliS; cl00654 316407005537 Flagellar protein FliT; Region: FliT; cl05125 316407005538 cytoplasmic alpha-amylase; Reviewed; Region: PRK09441 316407005539 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 316407005540 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 316407005541 lipoprotein; Provisional; Region: PRK10397 316407005542 putative inner membrane protein; Provisional; Region: PRK11099 316407005543 YeeE/YedE family (DUF395); Region: DUF395; cl01018 316407005544 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 316407005545 CPxP motif; other site 316407005546 Uncharacterized ACR, COG2135; Region: DUF159; cl03646 316407005547 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 316407005548 Coenzyme A binding pocket; other site 316407005549 ECK1932:JW1918:b1933; hypothetical protein, N-ter fragment 316407005550 ECK1932:JW5912+JW1918:b4495; hypothetical protein 316407005551 ECK1932:JW5912:b1934; hypothetical protein, C-ter fragment 316407005552 ECK1934:JW5913:b1936; predicted defective phage integrase 316407005553 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 316407005554 flagellar basal-body M-ring protein/flagellar hook-basal body protein (fliF); Region: fliF; TIGR00206 316407005555 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 316407005556 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 316407005557 flagellar motor switch protein FliG; Region: fliG; TIGR00207 316407005558 FliG C-terminal domain; Region: FliG_C; pfam01706 316407005559 flagellar assembly protein H; Validated; Region: fliH; PRK05687 316407005560 Essential protein Yae1, N terminal; Region: Yae1_N; pfam09811 316407005561 Flagellar assembly protein FliH; Region: FliH; pfam02108 316407005562 flagellum-specific ATP synthase; Validated; Region: fliI; PRK07960 316407005563 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 316407005564 Walker A motif/ATP binding site; other site 316407005565 Walker B motif; other site 316407005566 Flagellar FliJ protein; Region: FliJ; cl09161 316407005567 flagellar export protein FliJ; Region: flagell_FliJ; TIGR02473 316407005568 Flagellar hook-length control protein FliK; Region: Flg_hook; cl14669 316407005569 Flagellar hook-length control protein [Cell motility and secretion]; Region: FliK; COG3144 316407005570 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 316407005571 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 316407005572 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 316407005573 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 316407005574 flagellar motor switch protein; Validated; Region: fliN; PRK05698 316407005575 Flagellar biosynthesis protein, FliO; Region: FliO; cl01247 316407005576 FliP family; Region: FliP; cl00593 316407005577 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 316407005578 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 316407005579 colanic acid capsular biosynthesis activation protein A; Provisional; Region: rcsA; PRK15411 316407005580 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...; Region: LuxR_C_like; cd06170 316407005581 DNA binding residues 316407005582 dimerization interface; other site 316407005583 Dextransucrase DSRB; Region: DSRB; cl11680 316407005584 Protein of unknown function (DUF2525); Region: DUF2525; pfam10733 316407005585 mannosyl-3-phosphoglycerate phosphatase; Reviewed; Region: PRK03669 316407005586 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 316407005587 active site 316407005588 motif I; other site 316407005589 motif II; other site 316407005590 putative diguanylate cyclase YedQ; Provisional; Region: PRK15426 316407005591 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316407005592 metal-binding site 316407005593 active site 316407005594 I-site; other site 316407005595 Uncharacterized small protein (DUF2158); Region: DUF2158; cl02293 316407005596 Protein of unknown function (DUF808); Region: DUF808; cl01002 316407005597 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 316407005598 EamA-like transporter family; Region: EamA; cl01037 316407005599 Very Short Patch Repair (Vsr) Endonuclease. Endonucleases in DNA repair that recognize damaged DNA and cleave the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches; Region: Vsr; cd00221 316407005600 additional DNA contacts; other site 316407005601 mismatch recognition site; other site 316407005602 active site 316407005603 zinc binding site; other site 316407005604 DNA intercalation site; other site 316407005605 DNA cytosine methylase; Provisional; Region: PRK10458 316407005606 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 316407005607 cofactor binding site; other site 316407005608 DNA binding site 316407005609 substrate interaction site; other site 316407005610 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 316407005611 Predicted HD superfamily hydrolase [General function prediction only]; Region: COG1418 316407005612 ECK1962:JW1948:b1965; hypothetical protein, middle fragment 316407005613 ECK1962:JW1949:b1966; hypothetical protein, C-ter fragment 316407005614 ECK1962:JW5319+JW1948+JW1949:b4496; hypothetical protein 316407005615 ECK1962:JW5319:b1964; hypothetical protein, N-ter fragment 316407005616 Type 1 glutamine amidotransferase (GATase1)-like domain found in Escherichia coli Hsp31 protein (EcHsp31); Region: GATase1_EcHsp31_like; cd03148 316407005617 dimer interface; other site 316407005618 metal-binding site 316407005619 potential oxyanion hole; other site 316407005620 potential catalytic triad; other site 316407005621 conserved cys residue; other site 316407005622 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 316407005623 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 trans-...; Region: HisKA; cd00082 316407005624 dimer interface; other site 316407005625 phosphorylation site 316407005626 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 316407005627 ATP binding site; other site 316407005628 Mg2+ binding site; other site 316407005629 G-X-G motif; other site 316407005630 transcriptional regulatory protein YedW; Provisional; Region: PRK11517 316407005631 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 316407005632 active site 316407005633 phosphorylation site 316407005634 intermolecular recognition site; other site 316407005635 dimerization interface; other site 316407005636 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...; Region: trans_reg_C; cd00383 316407005637 DNA binding site 316407005638 HIUase (5-hydroxyisourate hydrolase) catalyzes the second step in a three-step ureide pathway in which 5-hydroxyisourate (HIU), a product of the uricase (urate oxidase) reaction, is hydrolyzed to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU)...; Region: TLP_HIUase; cd05822 316407005639 active site 316407005640 homotetramer interface; other site 316407005641 Sulfite oxidase and related enzymes [General function prediction only]; Region: COG2041 316407005642 YedY_like molybdopterin cofactor (Moco) binding domain, a subgroup of the sulfite oxidase (SO) family of molybdopterin binding domains. Escherichia coli YedY has been propsed to form a heterodimer, consisting of a soluble catalytic subunit termed YedY...; Region: YedY_like_Moco; cd02107 316407005643 Moco binding site; other site 316407005644 metal coordination site; other site 316407005645 Ferric reductase like transmembrane component; Region: Ferric_reduct; cl01043 316407005646 YodA; Region: YodA; cl01365 316407005647 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 316407005648 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; cl01267 316407005649 putative invasin; Provisional; Region: PRK10177 316407005650 Protein of unknown function (DUF3442); Region: DUF3442; pfam11924 316407005651 Bacterial Ig-like domain (group 1); Region: Big_1; cl10510 316407005652 Bacterial Ig-like domain (group 1); Region: Big_1; cl10510 316407005653 Bacterial Ig-like domain (group 1); Region: Big_1; cl10510 316407005654 Bacterial Ig-like domain (group 1); Region: Big_1; cl10510 316407005655 Bacterial Ig-like domain (group 1); Region: Big_1; cl10510 316407005656 Bacterial Ig-like domain (group 1); Region: Big_1; cl10510 316407005657 Bacterial Ig-like domain (group 1); Region: Big_1; cl10510 316407005658 Bacterial Ig-like domain (group 1); Region: Big_1; cl10510 316407005659 Bacterial Ig-like domain (group 1); Region: Big_1; cl10510 316407005660 Bacterial Ig-like domain (group 1); Region: Big_1; cl10510 316407005661 Bacterial Ig-like domain (group 1); Region: Big_1; cl10510 316407005662 Bacterial Ig-like domain (group 1); Region: Big_1; cl10510 316407005663 Bacterial Ig-like domain (group 1); Region: Big_1; cl10510 316407005664 ECK1975:JW1961+JW5325:b4497; hypothetical protein 316407005665 ECK1975:JW1961:b1980; hypothetical protein, N-ter fragment 316407005666 ECK1975:JW5325:b1979; hypothetical protein, C-ter fragment 316407005667 shikimate transporter; Provisional; Region: PRK09952 316407005668 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 316407005669 putative substrate translocation pore; other site 316407005670 AMP nucleosidase; Provisional; Region: PRK08292 316407005671 Bacterial AMP nucleoside phosphorylase N-terminus; Region: AMNp_N; pfam10423 316407005672 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 316407005673 Domain of unknown function DUF28; Region: DUF28; cl00361 316407005674 MATE family multidrug exporter; Provisional; Region: PRK10189 316407005675 MatE; Region: MatE; pfam01554 316407005676 MatE; Region: MatE; pfam01554 316407005677 transcriptional regulator Cbl; Reviewed; Region: cbl; PRK12679 316407005678 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407005679 The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold; Region: PBP2_Cbl; cd08444 316407005680 putative substrate binding site; other site 316407005681 dimerization interface; other site 316407005682 nitrogen assimilation transcriptional regulator; Provisional; Region: PRK11233 316407005683 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407005684 The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; Region: PBP2_Nac; cd08433 316407005685 putative dimerization interface; other site 316407005686 L,D-transpeptidase; Provisional; Region: PRK10190 316407005687 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 316407005688 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 316407005689 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 316407005690 putative dimer interface; other site 316407005691 active site pocket 316407005692 putative cataytic base; other site 316407005693 Cobalamin-5-phosphate synthase; Region: CobS; cl00415 316407005694 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is...; Region: CobU; cd00544 316407005695 homotrimer interface; other site 316407005696 Walker A motif; other site 316407005697 GTP binding site; other site 316407005698 Walker B motif; other site 316407005699 Transposase domain (DUF772); Region: DUF772; cl12084 316407005700 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 316407005701 CP4-44 prophage region; ECK1989:JW5326:b1995; predicted disrupted hemin or colicin receptor 316407005702 IS2 transposase TnpB; Reviewed; Region: PRK09409 316407005703 Integrase core domain; Region: rve; cl01316 316407005704 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; cl01116 316407005705 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 316407005706 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...; Region: OM_channels; cl00284 316407005707 CP4-44 prophage region; ECK1991:JW5327:b1999; predicted GTP-binding protein 316407005708 Type V secretory pathway, adhesin AidA [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: AidA; COG3468 316407005709 Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 2, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of the nonprotease autotransporters, Ag43...; Region: PL2_Passenger_AT; cd01344 316407005710 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 316407005711 Autotransporter beta-domain; Region: Autotransporter; cl02365 316407005712 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 316407005713 MPN+ (JAMM) motif; other site 316407005714 Zinc-binding site; other site 316407005715 Protein of unknown function (DUF987); Region: DUF987; pfam06174 316407005716 YagB/YeeU/YfjZ family; Region: YagB_YeeU_YfjZ; pfam06154 316407005717 Protein of unknown function (DUF1219); Region: DUF1219; pfam06755 316407005718 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 316407005719 Protein of unknown function (DUF496); Region: DUF496; cl09955 316407005720 Predicted membrane protein [Function unknown]; Region: COG1289 316407005721 Bacterial protein of unknown function (DUF939); Region: DUF939; cl12136 316407005722 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; cl01368 316407005723 D-alanyl-D-alanine carboxypeptidase; Provisional; Region: dacD; PRK11397 316407005724 Beta-lactamase; Region: Beta-lactamase; cl01009 316407005725 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 316407005726 exonuclease I; Provisional; Region: sbcB; PRK11779 316407005727 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 316407005728 active site 316407005729 substrate binding site; other site 316407005730 catalytic site; other site 316407005731 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 316407005732 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 two-...; Region: SirA_YedF_YeeD; cd00291 316407005733 CPxP motif; other site 316407005734 YeeE/YedE family (DUF395); Region: DUF395; cl01018 316407005735 putative inner membrane protein; Provisional; Region: PRK11099 316407005736 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407005737 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407005738 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 316407005739 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 316407005740 dimerization interface; other site 316407005741 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 316407005742 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 316407005743 Phd_YefM; Region: PhdYeFM; cl09153 316407005744 ATP phosphoribosyltransferase; Reviewed; Region: hisG; PRK00489 316407005745 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 316407005746 HisG, C-terminal domain; Region: HisG_C; cl06867 316407005747 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 316407005748 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 oxidation of L-histidinol to L-...; Region: Histidinol_dh; cd06572 316407005749 NAD binding site; other site 316407005750 dimerization interface; other site 316407005751 product binding site; other site 316407005752 substrate binding site; other site 316407005753 zinc binding site; other site 316407005754 catalytic residues; other site 316407005755 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 316407005756 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 316407005757 pyridoxal 5'-phosphate binding site; other site 316407005758 homodimer interface; other site 316407005759 catalytic residue; other site 316407005760 imidazole glycerol-phosphate dehydratase/histidinol phosphatase; Provisional; Region: PRK05446 316407005761 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 316407005762 active site 316407005763 motif I; other site 316407005764 motif II; other site 316407005765 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 316407005766 putative active site pocket; other site 316407005767 4-fold oligomerization interface; other site 316407005768 metal binding residues; metal-binding site 316407005769 3-fold/trimer interface; other site 316407005770 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13170 316407005771 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 316407005772 putative active site; other site 316407005773 oxyanion strand; other site 316407005774 catalytic triad; other site 316407005775 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 316407005776 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 316407005777 catalytic residues; other site 316407005778 Imidazoleglycerol-phosphate synthase [Amino acid transport and metabolism]; Region: HisF; COG0107 316407005779 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)-formimino-5-; Region: HisF; cd04731 316407005780 substrate binding site; other site 316407005781 glutamase interaction surface; other site 316407005782 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; cl00344 316407005783 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 316407005784 Phosphoribosyl-ATP pyrophosphohydrolase; Region: PRA-PH; cl00345 316407005785 Chain length determinant protein; Region: Wzz; cl01623 316407005786 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 316407005787 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407005788 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 316407005789 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 316407005790 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407005791 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 316407005792 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 316407005793 ECK2025:JW2012:b4540; lipopolysaccharide biosynthesis protein, C-ter fragment 316407005794 ECK2025:JW2016+JW2012:b4571; lipopolysaccharide biosynthesis protein 316407005795 ECK2025:JW2016:b2031; lipopolysaccharide biosynthesis protein, N-ter fragment 316407005796 Transposase domain (DUF772); Region: DUF772; cl12084 316407005797 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 316407005798 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 316407005799 putative lipopolysaccharide biosynthesis O-acetyl transferase WbbJ; Provisional; Region: PRK09677 316407005800 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 6-...; Region: LbH_MAT_like; cd04647 316407005801 trimer interface; other site 316407005802 active site 316407005803 substrate binding site; other site 316407005804 CoA binding site; other site 316407005805 Glycosyl transferases group 1; Region: Glycos_transf_1; cl12012 316407005806 UDP-galactopyranose mutase; Region: UDP-GALP_mutase; TIGR00031 316407005807 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407005808 Polysaccharide biosynthesis protein; Region: Polysacc_synt; cl10513 316407005809 Cupin domain; Region: Cupin_2; cl09118 316407005810 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 316407005811 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 316407005812 substrate binding site; other site 316407005813 tetramer interface; other site 316407005814 dTDP-4-dehydrorhamnose reductase; Provisional; Region: PRK09987 316407005815 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407005816 dTDP-glucose 4,6 dehydratase; Provisional; Region: PRK10084 316407005817 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407005818 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 316407005819 active site 316407005820 tetramer interface; other site 316407005821 putative colanic acid biosynthesis protein; Provisional; Region: wcaM; PRK10123 316407005822 colanic acid biosynthesis glycosyltransferase WcaL; Provisional; Region: PRK15427 316407005823 This is a family of GT1 glycosyltransferases found specifically in certain bacteria. amsK in Erwinia amylovora, has been reported to be involved in the biosynthesis of amylovoran, a exopolysaccharide acting as a virulence factor; Region: GT1_amsK_like; cd03799 316407005824 putative ADP-binding pocket; other site 316407005825 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; cl09156 316407005826 Polysaccharide biosynthesis protein; Region: Polysacc_synt; cl10513 316407005827 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 316407005828 putative UDP-glucose lipid carrier transferase; Provisional; Region: PRK10124 316407005829 Bacterial sugar transferase; Region: Bac_transf; cl00939 316407005830 phosphomannomutase CpsG; Provisional; Region: PRK15414 316407005831 The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a...; Region: PMM_PGM; cd03089 316407005832 active site 316407005833 substrate binding site; other site 316407005834 metal-binding site 316407005835 mannose-1-phosphate guanyltransferase; Provisional; Region: cpsB; PRK15460 316407005836 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 316407005837 Substrate binding site; other site 316407005838 Cupin domain; Region: Cupin_2; cl09118 316407005839 putative glycosyl transferase; Provisional; Region: PRK10307 316407005840 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 316407005841 GDP-mannose glycosyl hydrolase (AKA GDP-mannose mannosyl hydrolase (GDPMH)) is a member of the Nudix hydrolase superfamily. This class of enzymes is unique from other members of the superfamily in two aspects. First, it contains a modified Nudix...; Region: GDPMH; cd03430 316407005842 active site 316407005843 GDP-Mannose binding site; other site 316407005844 dimer interface; other site 316407005845 modified nudix motif 316407005846 metal-binding site 316407005847 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 316407005848 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 316407005849 putative acyl transferase; Provisional; Region: PRK10502 316407005850 wcaF-like: This group is composed of the protein product of the E. coli wcaF gene and similar proteins. WcaF is part of the gene cluster responsible for the biosynthesis of the extracellular polysaccharide colanic acid. The wcaF protein is predicted to...; Region: LbH_wcaF_like; cd05825 316407005851 putative trimer interface; other site 316407005852 putative active site; other site 316407005853 putative substrate binding site; other site 316407005854 putative CoA binding site; other site 316407005855 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 316407005856 metal-binding site 316407005857 putative colanic acid biosynthesis protein; Provisional; Region: wcaD; PRK09953 316407005858 putative glycosyl transferase; Provisional; Region: PRK10125 316407005859 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 316407005860 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 316407005861 putative acyl transferase; Provisional; Region: PRK10191 316407005862 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 L-...; Region: LbH_SAT; cd03354 316407005863 trimer interface; other site 316407005864 active site 316407005865 substrate binding site; other site 316407005866 CoA binding site; other site 316407005867 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 316407005868 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 316407005869 active site 316407005870 tyrosine kinase; Provisional; Region: PRK11519 316407005871 Chain length determinant protein; Region: Wzz; cl01623 316407005872 Chain length determinant protein; Region: Wzz; cl01623 316407005873 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 316407005874 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 316407005875 Low molecular weight phosphatase family; Region: LMWPc; cd00115 316407005876 active site 316407005877 polysaccharide export protein Wza; Provisional; Region: PRK15078 316407005878 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 316407005879 Integral membrane protein TerC family; Region: TerC; cl10468 316407005880 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 316407005881 Transporter associated domain; Region: CorC_HlyC; pfam03471 316407005882 putative assembly protein; Provisional; Region: PRK10833 316407005883 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 316407005884 trimer interface; other site 316407005885 active site 316407005886 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 316407005887 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...; Region: UMPK; cd02023 316407005888 ATP-binding site; other site 316407005889 Sugar specificity; other site 316407005890 Pyrimidine base specificity; other site 316407005891 MASE1; Region: MASE1; cl01367 316407005892 putative diguanylate cyclase; Provisional; Region: PRK09776 316407005893 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 316407005894 putative active site; other site 316407005895 heme pocket; other site 316407005896 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 316407005897 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 316407005898 putative active site; other site 316407005899 heme pocket; other site 316407005900 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316407005901 metal-binding site 316407005902 active site 316407005903 I-site; other site 316407005904 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 316407005905 3-methyl-adenine DNA glycosylase II; Provisional; Region: PRK10308 316407005906 AlkA N-terminal domain; Region: AlkA_N; pfam06029 316407005907 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 316407005908 minor groove reading motif; other site 316407005909 helix-hairpin-helix signature motif; other site 316407005910 substrate binding pocket; other site 316407005911 active site 316407005912 putative chaperone; Provisional; Region: PRK11678 316407005913 Uncharacterized protein with protein kinase and helix-hairpin-helix DNA-binding domains [General function prediction only]; Region: COG4248 316407005914 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 316407005915 substrate binding site; other site 316407005916 activation loop (A-loop); other site 316407005917 Y-family of DNA polymerases; Region: PolY; cl12025 316407005918 Uncharacterized protein conserved in bacteria (DUF2314); Region: DUF2314; cl01543 316407005919 VWA subfamily: 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-...; Region: vWA_subfamily; cd01464 316407005920 metal ion-dependent adhesion site (MIDAS); other site 316407005921 multidrug efflux system subunit MdtA; Provisional; Region: PRK11556 316407005922 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2...; Region: Biotinyl_lipoyl_domains; cl11404 316407005923 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 316407005924 Protein export membrane protein; Region: SecD_SecF; cl14618 316407005925 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 316407005926 putative transporter; Provisional; Region: PRK10504 316407005927 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 316407005928 putative substrate translocation pore; other site 316407005929 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 316407005930 signal transduction histidine-protein kinase BaeS; Provisional; Region: PRK10549 316407005931 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 connected by an extended linker. The...; Region: HAMP; cd06225 316407005932 dimerization interface; other site 316407005933 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 trans-...; Region: HisKA; cd00082 316407005934 dimer interface; other site 316407005935 phosphorylation site 316407005936 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 316407005937 ATP binding site; other site 316407005938 Mg2+ binding site; other site 316407005939 G-X-G motif; other site 316407005940 DNA-binding transcriptional regulator BaeR; Provisional; Region: PRK10710 316407005941 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 316407005942 active site 316407005943 phosphorylation site 316407005944 intermolecular recognition site; other site 316407005945 dimerization interface; other site 316407005946 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...; Region: trans_reg_C; cd00383 316407005947 DNA binding site 316407005948 Domain of unknown function (DUF1508); Region: DUF1508; cl01356 316407005949 Domain of unknown function (DUF1508); Region: DUF1508; cl01356 316407005950 putative protease; Provisional; Region: PRK15452 316407005951 Peptidase family U32; Region: Peptidase_U32; cl03113 316407005952 Ogr/Delta-like zinc finger; Region: Ogr_Delta; cl04623 316407005953 ECK2080:JW5886:b2083; hypothetical protein fragment 316407005954 lipid kinase; Reviewed; Region: PRK13054 316407005955 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 316407005956 DNA-binding transcriptional regulator, C-ter fragment; ECK2083:JW2074:b2090 316407005957 DNA-binding transcriptional regulator, N-ter fragment; ECK2083:JW5340:b2087 316407005958 DNA-binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 316407005959 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; cl01116 316407005960 putative transposase OrfB; Reviewed; Region: PHA02517 316407005961 Integrase core domain; Region: rve; cl01316 316407005962 galactitol-1-phosphate dehydrogenase; Provisional; Region: PRK10309 316407005963 NAD(P)-dependent sugar dehydrogenases; Region: sugar_DH; cd08236 316407005964 putative NAD(P) binding site; other site 316407005965 catalytic Zn binding site; other site 316407005966 PTS system sugar-specific permease component; Region: EIIC-GAT; cl04451 316407005967 PTS_IIB_galactitol: subunit IIB of enzyme II (EII) of the galactitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is a galactitol-specific permease with two cytoplasmic domains (IIA and IIB) and a...; Region: PTS_IIB_galactitol; cd05566 316407005968 P-loop; other site 316407005969 active site 316407005970 phosphorylation site 316407005971 ECK2087:JW2078+JW2081:b2094; IS is inserted, intact gatA is found in strain MG1655 316407005972 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; cl00163 316407005973 Transposase domain (DUF772); Region: DUF772; cl12084 316407005974 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 316407005975 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; cl00163 316407005976 active site 316407005977 phosphorylation site 316407005978 Tagatose 6 phosphate kinase; Region: Tagatose_6_P_K; cl09211 316407005979 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...; Region: TBP_aldolase_IIB; cd00947 316407005980 hypothetical protein; Provisional; Region: PRK08185 316407005981 intersubunit interface; other site 316407005982 active site 316407005983 zinc binding site; other site 316407005984 Na+ binding site; other site 316407005985 DhnA-type fructose-1,6-bisphosphate aldolase and related enzymes [Carbohydrate transport and metabolism]; Region: FbaB; COG1830 316407005986 Class I fructose-1,6-bisphosphate (FBP) aldolases of the archaeal type (DhnA homologs) found in bacteria and archaea. Catalysis of the enzymes proceeds via a Schiff-base mechanism like other class I aldolases, although this subfamily is clearly...; Region: DhnA; cd00958 316407005987 putative active site; other site 316407005988 catalytic residue; other site 316407005989 Nucleoside H+ symporter; Region: Nuc_H_symport; pfam03825 316407005990 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 316407005991 putative substrate translocation pore; other site 316407005992 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; cl00614 316407005993 YegV-like sugar kinase. Found only in bacteria, YegV-like kinase is part of the ribokinase/pfkB sugar kinase superfamily. Its oligomerization state is unknown at this time; Region: YegV_kinase_like; cd01944 316407005994 substrate binding site; other site 316407005995 ATP binding site; other site 316407005996 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 316407005997 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407005998 DNA binding site 316407005999 UTRA domain; Region: UTRA; cl06649 316407006000 Lyzozyme M1 (1,4-beta-N-acetylmuramidase) [Cell envelope biogenesis, outer membrane]; Region: Acm; COG3757 316407006001 YegX is an uncharacterized bacterial protein with a glycosyl hydrolase family 25 (GH25) catalytic domain that is similar in sequence to the CH-type (Chalaropsis-type) lysozymes of the GH25 family of endolysins; Region: GH25_YegX-like; cd06524 316407006002 active site 316407006003 bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed; Region: PRK06427 316407006004 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 316407006005 dimer interface; other site 316407006006 substrate binding site; other site 316407006007 ATP binding site; other site 316407006008 4-methyl-5-beta-hydroxyethylthiazole (Thz) kinase catalyzes the phosphorylation of the hydroxylgroup of Thz. A reaction that allows cells to recycle Thz into the thiamine biosynthesis pathway, as an alternative to its synthesis from cysteine, tyrosine...; Region: THZ_kinase; cd01170 316407006009 substrate binding site; other site 316407006010 multimerization interface; other site 316407006011 ATP binding site; other site 316407006012 Uncharacterized BCR, COG1937; Region: DUF156; cl00846 316407006013 High-affinity nickel-transport protein; Region: NicO; cl00964 316407006014 Domain of unknown function (DUF3315); Region: DUF3315; cl02275 316407006015 putative fimbrial-like adhesin protein StcD; Provisional; Region: PRK15252; cl14699 316407006016 pilin outer membrane usher protein SafC; Provisional; Region: PRK15223; cl14650 316407006017 Fimbrial Usher protein; Region: Usher; pfam00577 316407006018 putative fimbrial assembly chaperone protein StcB; Provisional; Region: PRK15253 316407006019 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 316407006020 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 316407006021 Fimbrial protein; Region: Fimbrial; cl01416 316407006022 Protein of unknown function (DUF2574); Region: DUF2574; pfam10836 316407006023 antiporter inner membrane protein; Provisional; Region: PRK11670 316407006024 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 316407006025 Walker A motif; other site 316407006026 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 316407006027 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 316407006028 active site 316407006029 HIGH motif; other site 316407006030 KMSKS motif; other site 316407006031 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 316407006032 tRNA binding surface; other site 316407006033 anticodon binding site; other site 316407006034 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 316407006035 dimer interface; other site 316407006036 putative tRNA-binding site; other site 316407006037 DNA-binding transcriptional regulator, C-ter fragment; ECK2108:JW5916:b2117 316407006038 DNA-binding transcriptional regulator, N-ter fragment; ECK2108:JW2102:b2115 316407006039 DNA-binding transcriptional regulator, middle fragment; ECK2108:JW5915:b2116 316407006040 DNA-binding transcriptional regulator; ECK2108:JW2102+JW5915+JW5916:b4499 316407006041 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...; Region: AAA; cd00009 316407006042 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 316407006043 Walker A motif; other site 316407006044 ATP binding site; other site 316407006045 Walker B motif; other site 316407006046 arginine finger; other site 316407006047 VWA YIEM 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 para-...; Region: VWA_YIEM_type; cd01462 316407006048 metal ion-dependent adhesion site (MIDAS); other site 316407006049 Protein of unknown function (DUF1307); Region: DUF1307; cl01981 316407006050 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4807 316407006051 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 316407006052 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 316407006053 putative two-component response-regulatory protein YehT; Provisional; Region: PRK11697 316407006054 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 316407006055 active site 316407006056 phosphorylation site 316407006057 intermolecular recognition site; other site 316407006058 dimerization interface; other site 316407006059 LytTr DNA-binding domain; Region: LytTR; cl04498 316407006060 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 316407006061 Protein of unknown function (DUF1393); Region: DUF1393; cl01942 316407006062 GAF domain; Region: GAF; cl00853 316407006063 Histidine kinase; Region: His_kinase; pfam06580 316407006064 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 316407006065 transcriptional regulator MirA; Provisional; Region: PRK15043 316407006066 Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators; Region: HTH_MlrA-like; cd04763 316407006067 DNA binding residues 316407006068 hypothetical protein; Provisional; Region: PRK13681 316407006069 Uncharacterized protein family (UPF0182); Region: UPF0182; pfam03699 316407006070 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...; Region: TM_PBP2; cd06261 316407006071 dimer interface; other site 316407006072 conserved gate region; other site 316407006073 putative PBP binding loops; other site 316407006074 ABC-ATPase subunit interface; other site 316407006075 ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]; Region: OpuBA; COG1125 316407006076 OpuCA is a the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment. ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family...; Region: ABC_OpuCA_Osmoprotection; cd03295 316407006077 Walker A/P-loop; other site 316407006078 ATP binding site; other site 316407006079 Q-loop/lid; other site 316407006080 ABC transporter signature motif; other site 316407006081 Walker B; other site 316407006082 D-loop; other site 316407006083 H-loop/switch region; other site 316407006084 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; cl09108 316407006085 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...; Region: TM_PBP2; cl00427 316407006086 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 316407006087 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 316407006088 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 316407006089 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 316407006090 Glycosyl hydrolase family 3 C terminal domain; Region: Glyco_hydro_3_C; pfam01915 316407006091 D-lactate dehydrogenase; Provisional; Region: PRK11183 316407006092 FAD binding domain; Region: FAD_binding_4; cl10516 316407006093 D-lactate dehydrogenase, membrane binding; Region: Lact-deh-memb; pfam09330 316407006094 Beta-lactamase; Region: Beta-lactamase; cl01009 316407006095 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 316407006096 Yip1 domain; Region: Yip1; cl12048 316407006097 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 316407006098 oxidoreductase; Provisional; Region: PRK12743 316407006099 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407006100 Outer membrane efflux protein; Region: OEP; pfam02321 316407006101 Outer membrane efflux protein; Region: OEP; pfam02321 316407006102 multidrug resistance outer membrane protein MdtQ; Provisional; Region: PRK11459 316407006103 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...; Region: DUS_like_FMN; cd02801 316407006104 Dihydrouridine synthase (Dus); Region: Dus; pfam01207 316407006105 FMN binding site; other site 316407006106 active site 316407006107 catalytic residues; other site 316407006108 substrate binding site; other site 316407006109 LrgA family; Region: LrgA; cl00608 316407006110 LrgB-like family; Region: LrgB; cl00596 316407006111 cytidine deaminase; Provisional; Region: PRK09027 316407006112 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 316407006113 active site 316407006114 catalytic motif; other site 316407006115 Zn binding site; other site 316407006116 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 316407006117 active site 316407006118 catalytic motif; other site 316407006119 Zn binding site; other site 316407006120 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 316407006121 putative active site; other site 316407006122 Protein of unknown function (DUF2542); Region: DUF2542; pfam10808 316407006123 dihydropyrimidine dehydrogenase subunit A; Provisional; Region: PRK11749 316407006124 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407006125 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407006126 dihydropyrimidine dehydrogenase subunit B; Validated; Region: PRK08318 316407006127 Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN, and...; Region: DHPD_FMN; cd02940 316407006128 homodimer interface; other site 316407006129 active site 316407006130 FMN binding site; other site 316407006131 substrate binding site; other site 316407006132 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 316407006133 TM-ABC transporter signature motif; other site 316407006134 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and...; Region: ABC_Carb_Monos_I; cd03216 316407006135 galactose/methyl galaxtoside transporter ATP-binding protein; Provisional; Region: PRK10982 316407006136 Walker A/P-loop; other site 316407006137 ATP binding site; other site 316407006138 Q-loop/lid; other site 316407006139 ABC transporter signature motif; other site 316407006140 Walker B; other site 316407006141 D-loop; other site 316407006142 H-loop/switch region; other site 316407006143 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (; Region: ABC_Carb_Monos_II; cd03215 316407006144 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 316407006145 Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species; Region: PBP1_GGBP; cd01539 316407006146 ligand binding site; other site 316407006147 calcium binding site; other site 316407006148 DNA-binding transcriptional regulator GalS; Provisional; Region: PRK10401 316407006149 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 316407006150 DNA binding site 316407006151 domain linker motif; other site 316407006152 Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism; Region: PBP1_GalS_like; cd06270 316407006153 dimerization interface (closed form); other site 316407006154 ligand binding site; other site 316407006155 Predicted membrane protein [Function unknown]; Region: COG2311 316407006156 Protein of unknown function (DUF418); Region: DUF418; cl12135 316407006157 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In...; Region: GTP_cyclohydro1; cd00642 316407006158 homodecamer interface; other site 316407006159 GTP cyclohydrolase I; Provisional; Region: PLN03044 316407006160 active site 316407006161 putative catalytic site residues; other site 316407006162 zinc binding site; other site 316407006163 GTP-CH-I/GFRP interaction surface; other site 316407006164 Predicted esterase [General function prediction only]; Region: COG0627 316407006165 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; cl12031 316407006166 catecholate siderophore receptor CirA; Provisional; Region: PRK10064 316407006167 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 316407006168 N-terminal plug; other site 316407006169 ligand-binding site; other site 316407006170 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407006171 Amino acid permease; Region: AA_permease; pfam00324 316407006172 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 316407006173 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407006174 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 316407006175 putative dimerization interface; other site 316407006176 Conserved hypothetical protein 698; Region: Cons_hypoth698; cl01075 316407006177 endonuclease IV; Provisional; Region: PRK01060 316407006178 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of D-arabino-6-...; Region: AP2Ec; cd00019 316407006179 AP (apurinic/apyrimidinic) site pocket; other site 316407006180 DNA interaction; other site 316407006181 Metal-binding active site; metal-binding site 316407006182 putative kinase; Provisional; Region: PRK09954 316407006183 YeiC-like sugar kinase. Found in eukaryotes and bacteria, YeiC-like kinase is part of the ribokinase/pfkB sugar kinase superfamily. Its oligomerization state is unknown at this time; Region: YeiC_kinase_like; cd01941 316407006184 substrate binding site; other site 316407006185 ATP binding site; other site 316407006186 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 316407006187 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 316407006188 Nucleoside recognition; Region: Gate; cl00486 316407006189 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 316407006190 Inosine-uridine preferring nucleoside hydrolase; Region: IU_nuc_hydro; pfam01156 316407006191 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 316407006192 active site 316407006193 tetramer interface; other site 316407006194 DNA-binding transcriptional activator YeiL; Provisional; Region: PRK10402 316407006195 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 316407006196 ligand binding site; other site 316407006197 flexible hinge region; other site 316407006198 nucleoside transporter; Region: nupC; TIGR00804 316407006199 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 316407006200 Nucleoside recognition; Region: Gate; cl00486 316407006201 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 316407006202 Indigoidine synthase A like protein; Region: Indigoidine_A; cl00983 316407006203 YeiC-like sugar kinase. Found in eukaryotes and bacteria, YeiC-like kinase is part of the ribokinase/pfkB sugar kinase superfamily. Its oligomerization state is unknown at this time; Region: YeiC_kinase_like; cd01941 316407006204 substrate binding site; other site 316407006205 ATP binding site; other site 316407006206 PTS system fructose-specific transporter subunits IIBC; Provisional; Region: PRK10712 316407006207 N-terminal domain of the phosphotransferase system fructose-specific component IIB [Carbohydrate transport and metabolism]; Region: COG3925 316407006208 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA...; Region: PTS_IIB_fructose; cd05569 316407006209 P-loop; other site 316407006210 active site 316407006211 phosphorylation site 316407006212 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 316407006213 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 316407006214 1-phosphofructokinase (FruK), minor 6-phosphofructokinase (pfkB) and related sugar kinases. FruK plays an important role in the predominant pathway for fructose utilisation.This group also contains tagatose-6-phophate kinase, an enzyme of the tagatose...; Region: FruK_PfkB_like; cd01164 316407006215 putative substrate binding site; other site 316407006216 putative ATP binding site; other site 316407006217 bifunctional PTS system fructose-specific transporter subunit IIA/HPr protein; Provisional; Region: PRK11109 316407006218 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 316407006219 active site 316407006220 phosphorylation site 316407006221 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 316407006222 dimerization domain swap beta strand; other site 316407006223 regulatory protein interface; other site 316407006224 active site 316407006225 regulatory phosphorylation site; other site 316407006226 sugar efflux transporter B; Provisional; Region: PRK15011 316407006227 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 316407006228 putative substrate translocation pore; other site 316407006229 Uncharacterized protein family (UPF0153); Region: UPF0153; cl00497 316407006230 elongation factor P; Provisional; Region: PRK04542 316407006231 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 316407006232 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 N-formylmethionyl-...; Region: S1_EF-P_repeat_1; cd04470 316407006233 RNA binding site; other site 316407006234 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 N-formylmethionyl-...; Region: S1_EF-P_repeat_2; cd05794 316407006235 RNA binding site; other site 316407006236 D-mannonate oxidoreductase; Provisional; Region: PRK15037 316407006237 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 316407006238 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 316407006239 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 316407006240 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 316407006241 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 316407006242 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 316407006243 outer membrane lipoprotein; Provisional; Region: spr; PRK10838 316407006244 NlpC/P60 family; Region: NLPC_P60; cl11438 316407006245 phage resistance protein; Provisional; Region: PRK10551 316407006246 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 316407006247 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 316407006248 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_14; cd08497 316407006249 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...; Region: TM_PBP2; cd06261 316407006250 dimer interface; other site 316407006251 conserved gate region; other site 316407006252 putative PBP binding loops; other site 316407006253 ABC-ATPase subunit interface; other site 316407006254 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...; Region: TM_PBP2; cd06261 316407006255 dimer interface; other site 316407006256 conserved gate region; other site 316407006257 ABC-ATPase subunit interface; other site 316407006258 microcin C ABC transporter ATP-binding protein YejF; Provisional; Region: PRK15134 316407006259 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 316407006260 Walker A/P-loop; other site 316407006261 ATP binding site; other site 316407006262 Q-loop/lid; other site 316407006263 ABC transporter signature motif; other site 316407006264 Walker B; other site 316407006265 D-loop; other site 316407006266 H-loop/switch region; other site 316407006267 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 316407006268 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 316407006269 Walker A/P-loop; other site 316407006270 ATP binding site; other site 316407006271 Q-loop/lid; other site 316407006272 ABC transporter signature motif; other site 316407006273 Walker B; other site 316407006274 D-loop; other site 316407006275 H-loop/switch region; other site 316407006276 hypothetical protein; Provisional; Region: PRK11835 316407006277 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 316407006278 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 316407006279 putative substrate translocation pore; other site 316407006280 16S rRNA pseudouridylate synthase A; Provisional; Region: PRK10839 316407006281 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 316407006282 RNA binding surface; other site 316407006283 PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PseudoU_synth_RsuA; cd02553 316407006284 active site 316407006285 uracil binding; other site 316407006286 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; cl12029 316407006287 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 316407006288 nucleotide binding region; other site 316407006289 ATP-binding site; other site 316407006290 Ribosomal_L25_TL5_CTC: Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain. L25 is a single-domain protein, homologous to the N-terminal domain of TL5 and CTC, which each contain two domains. CTC is a known stress protein, and proteins of this...; Region: Ribosomal_L25_TL5_CTC; cd00495 316407006291 5S rRNA interface; other site 316407006292 CTC domain interface; other site 316407006293 L16 interface; other site 316407006294 37-kD nucleoid-associated bacterial protein; Region: NA37; cl01174 316407006295 Protein of unknown function (DUF1414); Region: DUF1414; cl01175 316407006296 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 316407006297 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 316407006298 Sulfatase; Region: Sulfatase; cl10460 316407006299 Type V secretory pathway, adhesin AidA [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: AidA; COG3468 316407006300 Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 1, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of Neisseria and Haemophilus IgA1 proteases...; Region: PL1_Passenger_AT; cd01343 316407006301 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 316407006302 Autotransporter beta-domain; Region: Autotransporter; cl02365 316407006303 Transposase domain (DUF772); Region: DUF772; cl12084 316407006304 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 316407006305 transcriptional regulator NarP; Provisional; Region: PRK10403 316407006306 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 316407006307 active site 316407006308 phosphorylation site 316407006309 intermolecular recognition site; other site 316407006310 dimerization interface; other site 316407006311 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...; Region: LuxR_C_like; cd06170 316407006312 DNA binding residues 316407006313 dimerization interface; other site 316407006314 Cytochrome C biogenesis protein; Region: CcmH; cl01179 316407006315 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 316407006316 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 316407006317 binding surface 316407006318 TPR motif; other site 316407006319 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 316407006320 catalytic residues; other site 316407006321 central insert; other site 316407006322 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 316407006323 CcmE; Region: CcmE; cl00994 316407006324 Heme exporter protein D (CcmD); Region: CcmD; cl11475 316407006325 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 316407006326 CcmB protein; Region: CcmB; cl01016 316407006327 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 316407006328 CcmA, the ATP-binding component of the bacterial CcmAB transporter. The CCM family is involved in bacterial cytochrome c biogenesis. Cytochrome c maturation in E. coli requires the ccm operon, which encodes eight membrane proteins (CcmABCDEFGH); Region: ABC_CcmA_heme_exporter; cd03231 316407006329 Walker A/P-loop; other site 316407006330 ATP binding site; other site 316407006331 Q-loop/lid; other site 316407006332 ABC transporter signature motif; other site 316407006333 Walker B; other site 316407006334 D-loop; other site 316407006335 H-loop/switch region; other site 316407006336 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl09485 316407006337 Nitrate/TMAO reductases, membrane-bound tetraheme cytochrome c subunit [Energy production and conversion]; Region: TorC; COG3005 316407006338 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; cl01153 316407006339 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 316407006340 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 alpha-; Region: HCP_like; cl14655 316407006341 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 316407006342 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 316407006343 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 oxidation via a membrane-anchored...; Region: MopB_Nitrate-R-NapA-like; cd02754 316407006344 [4Fe-4S] binding site; other site 316407006345 molybdopterin cofactor binding site; other site 316407006346 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 oxidation via a membrane-anchored...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 316407006347 molybdopterin cofactor binding site; other site 316407006348 NapD protein; Region: NapD; cl01163 316407006349 ferredoxin-type protein; Provisional; Region: PRK10194 316407006350 Protease Inhibitor Ecotin; homodimeric protease inhibitor; Region: Ecotin; cd00242 316407006351 secondary substrate binding site; other site 316407006352 primary substrate binding site; other site 316407006353 inhibition loop; other site 316407006354 dimerization interface; other site 316407006355 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407006356 Predicted dehydrogenase [General function prediction only]; Region: COG0579 316407006357 multidrug transporter membrane component/ATP-binding component; Provisional; Region: PRK10522 316407006358 The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export. They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with...; Region: ABCC_MRP_Like; cd03228 316407006359 Walker A/P-loop; other site 316407006360 ATP binding site; other site 316407006361 Q-loop/lid; other site 316407006362 ABC transporter signature motif; other site 316407006363 Walker B; other site 316407006364 D-loop; other site 316407006365 H-loop/switch region; other site 316407006366 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 316407006367 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional; Region: PRK15435 316407006368 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 316407006369 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407006370 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407006371 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 316407006372 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 316407006373 DNA binding site 316407006374 active site 316407006375 ApbE family; Region: ApbE; cl00643 316407006376 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...; Region: OM_channels; cl00284 316407006377 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional; Region: PRK10618 316407006378 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 316407006379 ATP binding site; other site 316407006380 G-X-G motif; other site 316407006381 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 316407006382 transcriptional regulator RcsB; Provisional; Region: PRK10840 316407006383 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 316407006384 active site 316407006385 phosphorylation site 316407006386 intermolecular recognition site; other site 316407006387 dimerization interface; other site 316407006388 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...; Region: LuxR_C_like; cd06170 316407006389 DNA binding residues 316407006390 dimerization interface; other site 316407006391 ECK2211:JW5920+JW5917:b2218; IS is inserted, intact rcsC is found in strain MG1655 316407006392 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 316407006393 active site 316407006394 phosphorylation site 316407006395 intermolecular recognition site; other site 316407006396 dimerization interface; other site 316407006397 IS2 transposase TnpB; Reviewed; Region: PRK09409 316407006398 Integrase core domain; Region: rve; cl01316 316407006399 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; cl01116 316407006400 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 316407006401 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional; Region: PRK10841 316407006402 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 trans-...; Region: HisKA; cl00080 316407006403 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 316407006404 ATP binding site; other site 316407006405 Mg2+ binding site; other site 316407006406 G-X-G motif; other site 316407006407 RcsC Alpha-Beta-Loop (ABL); Region: RcsC; pfam09456 316407006408 sensory histidine kinase AtoS; Provisional; Region: PRK11360 316407006409 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 316407006410 putative active site; other site 316407006411 heme pocket; other site 316407006412 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 trans-...; Region: HisKA; cd00082 316407006413 dimer interface; other site 316407006414 phosphorylation site 316407006415 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 316407006416 ATP binding site; other site 316407006417 Mg2+ binding site; other site 316407006418 G-X-G motif; other site 316407006419 acetoacetate metabolism regulatory protein AtoC; Provisional; Region: PRK11361 316407006420 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 316407006421 active site 316407006422 phosphorylation site 316407006423 intermolecular recognition site; other site 316407006424 dimerization interface; other site 316407006425 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...; Region: AAA; cd00009 316407006426 Walker A motif; other site 316407006427 ATP binding site; other site 316407006428 Walker B motif; other site 316407006429 arginine finger; other site 316407006430 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 316407006431 Coenzyme A transferase; Region: CoA_trans; cl00773 316407006432 Coenzyme A transferase; Region: CoA_trans; cl00773 316407006433 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; cl09110 316407006434 putative acyltransferase; Provisional; Region: PRK05790 316407006435 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 316407006436 dimer interface; other site 316407006437 active site 316407006438 Uncharacterized protein conserved in bacteria (DUF2135); Region: DUF2135; cl01910 316407006439 Predicted secreted protein [Function unknown]; Region: COG5445 316407006440 Predicted secreted protein (DUF2300); Region: DUF2300; pfam10062 316407006441 Predicted secreted protein [Function unknown]; Region: COG5445 316407006442 Stage II sporulation protein; Region: SpoIID; cl07201 316407006443 Predicted secreted protein (DUF2300); Region: DUF2300; pfam10062 316407006444 ECK2220:JW2221:b2227; hypothetical protein, C-ter fragment 316407006445 ECK2220:JW2222+JW2221:b4500; hypothetical protein 316407006446 ECK2220:JW2222:b2228; hypothetical protein, N-ter fragment 316407006447 NlpC/P60 family; Region: NLPC_P60; cl11438 316407006448 Uncharacterized protein conserved in bacteria (DUF2138); Region: DUF2138; cl01916 316407006449 DNA gyrase subunit A; Validated; Region: PRK05560 316407006450 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 in...; Region: TOP4c; cd00187 316407006451 CAP-like domain; other site 316407006452 active site 316407006453 primary dimer interface; other site 316407006454 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 316407006455 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 316407006456 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 316407006457 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 316407006458 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 316407006459 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 316407006460 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 316407006461 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 316407006462 S-adenosylmethionine binding site; other site 316407006463 adhesin; Provisional; Region: PRK09752 316407006464 Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 2, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of the nonprotease autotransporters, Ag43...; Region: PL2_Passenger_AT; cd01344 316407006465 Autotransporter beta-domain; Region: Autotransporter; cl02365 316407006466 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09103 316407006467 ATP cone domain; Region: ATP-cone; pfam03477 316407006468 Class I ribonucleotide reductase; Region: RNR_I; cd01679 316407006469 active site 316407006470 dimer interface; other site 316407006471 catalytic residues; other site 316407006472 effector binding site; other site 316407006473 R2 peptide binding site; other site 316407006474 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 316407006475 dimer interface; other site 316407006476 putative radical transfer pathway; other site 316407006477 diiron center; other site 316407006478 tyrosyl radical; other site 316407006479 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 316407006480 catalytic loop; other site 316407006481 iron binding site; other site 316407006482 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 316407006483 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 316407006484 Glycerophosphodiester phosphodiesterase domain of Escherichia coli (GlpQ) and similar proteins; Region: GDPD_EcGlpQ_like; cd08600 316407006485 Glycerophosphoryl diester phosphodiesterase family; Region: GDPD; pfam03009 316407006486 active site 316407006487 catalytic site; other site 316407006488 metal-binding site 316407006489 sn-glycerol-3-phosphate transporter; Provisional; Region: glpT; PRK11273 316407006490 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 316407006491 putative substrate translocation pore; other site 316407006492 sn-glycerol-3-phosphate dehydrogenase subunit A; Provisional; Region: glpA; PRK11101 316407006493 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407006494 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 316407006495 anaerobic glycerol-3-phosphate dehydrogenase subunit B; Validated; Region: PRK05329 316407006496 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl10040 316407006497 C subunit; Region: glycerol3P_GlpC; TIGR03379 316407006498 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 alpha-; Region: HCP_like; cl14655 316407006499 Cysteine-rich domain; Region: CCG; pfam02754 316407006500 Cysteine-rich domain; Region: CCG; pfam02754 316407006501 hypothetical protein; Provisional; Region: PRK09956 316407006502 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 316407006503 ECK2237:JW5964:b4543; hypothetical protein 316407006504 Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their...; Region: malate_synt; cl09155 316407006505 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [Carbohydrate transport and metabolism]; Region: HpcH; COG3836 316407006506 4-hydroxyphenylacetate permease; Region: HpaX; TIGR02332 316407006507 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 316407006508 putative substrate translocation pore; other site 316407006509 L-rhamnonate dehydratase; Provisional; Region: PRK15440 316407006510 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 2. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved...; Region: MR_like_2; cd03327 316407006511 putative active site pocket; other site 316407006512 putative metal binding site; other site 316407006513 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407006514 Transcriptional regulator [Transcription]; Region: IclR; COG1414 316407006515 Bacterial transcriptional regulator; Region: IclR; pfam01614 316407006516 hypothetical protein; Provisional; Region: PRK03673 316407006517 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 316407006518 putative MPT binding site; other site 316407006519 Competence-damaged protein; Region: CinA; cl00666 316407006520 YfaZ precursor; Region: YfaZ; pfam07437 316407006521 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or...; Region: Nudix_Hydrolase; cl00447 316407006522 nudix motif; other site 316407006523 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cd07040 316407006524 catalytic core; other site 316407006525 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 316407006526 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 316407006527 inhibitor-cofactor binding pocket; inhibition site 316407006528 pyridoxal 5'-phosphate binding site; other site 316407006529 catalytic residue; other site 316407006530 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 316407006531 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 316407006532 Ligand binding site; other site 316407006533 Putative Catalytic site; other site 316407006534 DXD motif; other site 316407006535 bifunctional UDP-glucuronic acid decarboxylase/UDP-4-amino-4-deoxy-L-arabinose formyltransferase; Validated; Region: PRK08125 316407006536 Formyl transferase; Region: Formyl_trans_N; cl00395 316407006537 Formyl transferase, C-terminal domain; Region: Formyl_trans_C; pfam02911 316407006538 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407006539 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional; Region: PRK15394 316407006540 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 316407006541 4-amino-4-deoxy-L-arabinose transferase; Provisional; Region: arnT; PRK13279 316407006542 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT; cl01961 316407006543 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 316407006544 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 316407006545 Polymyxin resistance protein PmrD; Region: PmrD; cl12732 316407006546 O-succinylbenzoic acid--CoA ligase; Provisional; Region: PRK09029 316407006547 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 316407006548 O-succinylbenzoate synthase; Provisional; Region: PRK05105 316407006549 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 316407006550 active site 316407006551 enoyl-CoA hydratase; Provisional; Region: PRK06688 316407006552 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 316407006553 substrate binding site; other site 316407006554 oxyanion hole (OAH) forming residues; other site 316407006555 trimer interface; other site 316407006556 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; cl12031 316407006557 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase; Region: menH_SHCHC; TIGR03695 316407006558 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase; Validated; Region: PRK07449 316407006559 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 316407006560 dimer interface; other site 316407006561 tetramer interface; other site 316407006562 PYR/PP interface; other site 316407006563 TPP binding site; other site 316407006564 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 role in the menaquinone biosynthetic pathway, converting...; Region: TPP_SHCHC_synthase; cd02009 316407006565 TPP-binding site; other site 316407006566 menaquinone-specific isochorismate synthase; Provisional; Region: PRK15012 316407006567 chorismate binding enzyme; Region: Chorismate_bind; cl10555 316407006568 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 316407006569 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 316407006570 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 316407006571 deubiquitinase; Provisional; Region: PRK11836; cl08202 316407006572 von Willebrand factor; Region: vWF_A; pfam12450 316407006573 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG2304 316407006574 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 para-...; Region: vWA_subgroup; cd01465 316407006575 metal ion-dependent adhesion site (MIDAS); other site 316407006576 Domain of unknown function (DUF3520); Region: DUF3520; pfam12034 316407006577 Peptidase dimerization domain; Region: M20_dimer; cl09126 316407006578 Domain of unknown function (DUF1877); Region: DUF1877; pfam08974 316407006579 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 316407006580 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 316407006581 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 316407006582 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 316407006583 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 316407006584 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 316407006585 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 316407006586 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 316407006587 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 316407006588 4Fe-4S binding domain; Region: Fer4; pfam00037 316407006589 4Fe-4S binding domain; Region: Fer4; pfam00037 316407006590 NADH dehydrogenase; Region: NADHdh; cl00469 316407006591 NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75 kD subunit (chain G) [Energy production and conversion]; Region: NuoG; COG1034 316407006592 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 316407006593 catalytic loop; other site 316407006594 iron binding site; other site 316407006595 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 316407006596 MopB_NDH-1_NuoG2-N7: The second domain of the NuoG subunit (with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory...; Region: MopB_NDH-1_NuoG2-N7; cd02771 316407006597 [4Fe-4S] binding site; other site 316407006598 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting...; Region: MopB_CT_NDH-1_NuoG2-N7; cd02788 316407006599 NADH dehydrogenase I subunit F; Provisional; Region: PRK11278 316407006600 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 316407006601 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl11430 316407006602 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 316407006603 NADH-quinone oxidoreductase, E subunit; Region: nuoE_fam; TIGR01958 316407006604 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of...; Region: TRX_Fd_NuoE; cd03064 316407006605 putative dimer interface; other site 316407006606 [2Fe-2S] cluster binding site; other site 316407006607 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl00539 316407006608 bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional; Region: PRK11742 316407006609 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; cl00417 316407006610 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 316407006611 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 316407006612 DNA-binding transcriptional repressor LrhA; Provisional; Region: PRK15092 316407006613 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407006614 The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; Region: PBP2_LrhA_like; cd08439 316407006615 putative dimerization interface; other site 316407006616 IS1 transposase; Region: Transposase_27; cl00721 316407006617 Insertion element protein; Region: Ins_element1; pfam03811 316407006618 tyrosine aminotransferase, eukaryotic; Region: tyr_amTase_E; TIGR01264 316407006619 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 316407006620 pyridoxal 5'-phosphate binding site; other site 316407006621 homodimer interface; other site 316407006622 catalytic residue; other site 316407006623 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 316407006624 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 316407006625 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 316407006626 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; cl09110 316407006627 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; cl09110 316407006628 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 316407006629 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 316407006630 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 316407006631 motif II; other site 316407006632 YfbU domain; Region: YfbU; cl01137 316407006633 Protein of unknown function, DUF412; Region: DUF412; cl01183 316407006634 Acetokinase family; Region: Acetate_kinase; cl01029 316407006635 phosphate acetyltransferase; Reviewed; Region: PRK05632 316407006636 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 316407006637 DRTGG domain; Region: DRTGG; cl12147 316407006638 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 316407006639 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; cl09110 316407006640 Predicted membrane protein [Function unknown]; Region: COG1288 316407006641 NUDIX hydrolase YfcD; Provisional; Region: PRK15393 316407006642 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_38; cd04697 316407006643 nudix motif; other site 316407006644 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 316407006645 active site 316407006646 metal-binding site 316407006647 homotetramer interface; other site 316407006648 glutathione S-transferase; Provisional; Region: PRK15113 316407006649 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 316407006650 C-terminal domain interface; other site 316407006651 GSH binding site (G-site); other site 316407006652 dimer interface; other site 316407006653 GST_C family, unknown subfamily 4; composed of uncharacterized 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 endogenous...; Region: GST_C_4; cd03195 316407006654 putative N-terminal domain interface; other site 316407006655 putative dimer interface; other site 316407006656 putative substrate binding pocket (H-site); other site 316407006657 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 316407006658 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...; Region: GST_N_Ure2p_like; cd03048 316407006659 C-terminal domain interface; other site 316407006660 GSH binding site (G-site); other site 316407006661 dimer interface; other site 316407006662 GST_C 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...; Region: GST_C_Ure2p_like; cd03178 316407006663 dimer interface; other site 316407006664 N-terminal domain interface; other site 316407006665 putative substrate binding pocket (H-site); other site 316407006666 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...; Region: DHNA_DHNTPE; cd00534 316407006667 homooctamer interface; other site 316407006668 active site 316407006669 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407006670 Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]; Region: COG1090 316407006671 Domain of unknown function (DUF1731); Region: DUF1731; pfam08338 316407006672 putative transposase; Provisional; Region: PRK09857 316407006673 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 316407006674 histidine/lysine/arginine/ornithine transporter subunit; Provisional; Region: PRK10619 316407006675 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP; Region: ABC_HisP_GlnQ_permeases; cd03262 316407006676 Walker A/P-loop; other site 316407006677 ATP binding site; other site 316407006678 Q-loop/lid; other site 316407006679 ABC transporter signature motif; other site 316407006680 Walker B; other site 316407006681 D-loop; other site 316407006682 H-loop/switch region; other site 316407006683 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...; Region: TM_PBP2; cd06261 316407006684 dimer interface; other site 316407006685 conserved gate region; other site 316407006686 putative PBP binding loops; other site 316407006687 ABC-ATPase subunit interface; other site 316407006688 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 316407006689 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...; Region: TM_PBP2; cd06261 316407006690 dimer interface; other site 316407006691 conserved gate region; other site 316407006692 putative PBP binding loops; other site 316407006693 ABC-ATPase subunit interface; other site 316407006694 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 316407006695 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...; Region: PBPb; cd00134 316407006696 substrate binding pocket; other site 316407006697 membrane-bound complex binding site; other site 316407006698 hinge residues; other site 316407006699 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 316407006700 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...; Region: PBPb; cd00134 316407006701 substrate binding pocket; other site 316407006702 membrane-bound complex binding site; other site 316407006703 hinge residues; other site 316407006704 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 316407006705 Flavoprotein; Region: Flavoprotein; cl08021 316407006706 amidophosphoribosyltransferase; Provisional; Region: PRK09246 316407006707 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 316407006708 active site 316407006709 tetramer interface; other site 316407006710 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 316407006711 Colicin V production protein; Region: Colicin_V; cl00567 316407006712 cell division protein DedD; Provisional; Region: PRK11633 316407006713 Sporulation related domain; Region: SPOR; cl10051 316407006714 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional; Region: PRK10846 316407006715 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 316407006716 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 316407006717 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 316407006718 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 316407006719 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 316407006720 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 316407006721 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1)...; Region: PseudoU_synth_EcTruA; cd02570 316407006722 dimerization interface 3.5A; other site 316407006723 active site 316407006724 putative semialdehyde dehydrogenase; Provisional; Region: PRK08040 316407006725 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407006726 Semialdehyde dehydrogenase, dimerization domain; Region: Semialdhyde_dhC; pfam02774 316407006727 erythronate-4-phosphate dehydrogenase PdxB; Provisional; Region: PRK15438 316407006728 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407006729 Domain of unknown function (DUF3410); Region: DUF3410; pfam11890 316407006730 flagella biosynthesis regulator; Provisional; Region: flk; PRK10715 316407006731 putative transporter; Provisional; Region: PRK12382 316407006732 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 316407006733 putative substrate translocation pore; other site 316407006734 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 316407006735 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 316407006736 dimer interface; other site 316407006737 active site 316407006738 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; cl12011 316407006739 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 316407006740 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407006741 YfcL protein; Region: YfcL; pfam08891 316407006742 Protein of unknown function, DUF462; Region: DUF462; cl01190 316407006743 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 316407006744 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 316407006745 Murein endopeptidase [Cell envelope biogenesis, outer membrane]; Region: MepA; COG3770 316407006746 Penicillin-insensitive murein endopeptidase; Region: Peptidase_M74; cl01538 316407006747 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 316407006748 Tetramer interface; other site 316407006749 active site 316407006750 FMN-binding site; other site 316407006751 HemK family putative methylases; Region: hemK_fam; TIGR00536 316407006752 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 316407006753 S-adenosylmethionine binding site; other site 316407006754 Smr domain; Region: Smr; cl02619 316407006755 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 316407006756 Protein of unknown function (DUF2544); Region: DUF2544; pfam11245 316407006757 Fimbrial protein; Region: Fimbrial; cl01416 316407006758 Fimbrial protein; Region: Fimbrial; cl01416 316407006759 Fimbrial protein; Region: Fimbrial; cl01416 316407006760 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 316407006761 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 316407006762 pilin outer membrane usher protein SafC; Provisional; Region: PRK15223; cl14650 316407006763 pilin outer membrane usher protein SafC; Provisional; Region: PRK15223; cl14650 316407006764 Fimbrial protein; Region: Fimbrial; cl01416 316407006765 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 316407006766 catalytic core; other site 316407006767 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 316407006768 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 316407006769 substrate binding site; other site 316407006770 oxyanion hole (OAH) forming residues; other site 316407006771 trimer interface; other site 316407006772 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407006773 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 316407006774 3-ketoacyl-CoA thiolase; Reviewed; Region: fadI; PRK08963 316407006775 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 316407006776 dimer interface; other site 316407006777 active site 316407006778 Protein of unknown function (DUF406); Region: DUF406; cl11449 316407006779 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl09488 316407006780 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 316407006781 VacJ like lipoprotein; Region: VacJ; cl01073 316407006782 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 316407006783 integrase; Provisional; Region: PRK09692 316407006784 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 316407006785 Int/Topo IB signature motif; other site 316407006786 active site 316407006787 GtrA-like protein; Region: GtrA; cl00971 316407006788 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 316407006789 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 316407006790 Ligand binding site; other site 316407006791 Putative Catalytic site; other site 316407006792 DXD motif; other site 316407006793 CPS-53 (KpLE1) prophage region; ECK2347:JW5383:b2353; tail fiber assembly protein fragment 316407006794 Caudovirales tail fibre assembly protein; Region: Caudo_TAP; pfam02413 316407006795 DNA N-6-adenine-methyltransferase (Dam); Region: Dam; cl05442 316407006796 PerC transcriptional activator; Region: PerC; pfam06069 316407006797 Uncharacterized conserved protein (DUF2303); Region: DUF2303; cl02338 316407006798 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 316407006799 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl01302 316407006800 DNA-binding transcriptional regulator DsdC; Provisional; Region: PRK10086 316407006801 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407006802 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 316407006803 dimerization interface; other site 316407006804 substrate binding pocket; other site 316407006805 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; cl09110 316407006806 gluconate transporter; Region: gntP; TIGR00791 316407006807 D-Serine dehydratase is a pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of L- or D-serine to pyruvate and ammonia. D-serine dehydratase serves as a detoxifying enzyme in most E. coli strains where D-serine is a competitive...; Region: D-Ser-dehyd; cd06447 316407006808 pyridoxal 5'-phosphate binding pocket; other site 316407006809 catalytic residue; other site 316407006810 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 316407006811 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 316407006812 putative substrate translocation pore; other site 316407006813 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 316407006814 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 316407006815 DNA-binding transcriptional activator EvgA; Provisional; Region: PRK09958 316407006816 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 316407006817 active site 316407006818 phosphorylation site 316407006819 intermolecular recognition site; other site 316407006820 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...; Region: LuxR_C_like; cd06170 316407006821 DNA binding residues 316407006822 dimerization interface; other site 316407006823 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional; Region: PRK09959 316407006824 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...; Region: PBPb; cd00134 316407006825 substrate binding pocket; other site 316407006826 membrane-bound complex binding site; other site 316407006827 hinge residues; other site 316407006828 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...; Region: PBPb; cd00134 316407006829 substrate binding pocket; other site 316407006830 membrane-bound complex binding site; other site 316407006831 hinge residues; other site 316407006832 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 trans-...; Region: HisKA; cd00082 316407006833 dimer interface; other site 316407006834 phosphorylation site 316407006835 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 316407006836 ATP binding site; other site 316407006837 Mg2+ binding site; other site 316407006838 G-X-G motif; other site 316407006839 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 316407006840 active site 316407006841 phosphorylation site 316407006842 intermolecular recognition site; other site 316407006843 dimerization interface; other site 316407006844 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 316407006845 putative binding surface; other site 316407006846 active site 316407006847 CoA-transferase family III; Region: CoA_transf_3; cl00778 316407006848 Membrane transport protein; Region: Mem_trans; cl09117 316407006849 putative oxalyl-CoA decarboxylase; Validated; Region: PRK09259 316407006850 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 316407006851 PYR/PP interface; other site 316407006852 dimer interface; other site 316407006853 TPP binding site; other site 316407006854 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 316407006855 TPP-binding module; composed of proteins similar to benzaldehyde lyase (BZL), oxalyl-CoA decarboxylase (OCoD) and 2-hydroxyphytanoyl-CoA lyase (2-HPCL). Pseudomonas fluorescens biovar I BZL cleaves the acyloin linkage of benzoin producing 2 molecules...; Region: TPP_BZL_OCoD_HPCL; cd02004 316407006856 TPP-binding site; other site 316407006857 dimer interface; other site 316407006858 CoA-transferase family III; Region: CoA_transf_3; cl00778 316407006859 hypothetical protein; Provisional; Region: PRK10316 316407006860 YfdX protein; Region: YfdX; pfam10938 316407006861 Protein of unknown function (DUF2545); Region: DUF2545; pfam10810 316407006862 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 316407006863 putative acyl-acceptor binding pocket; other site 316407006864 aspartate aminotransferase; Provisional; Region: PRK07681 316407006865 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 316407006866 pyridoxal 5'-phosphate binding site; other site 316407006867 homodimer interface; other site 316407006868 catalytic residue; other site 316407006869 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 316407006870 Protein of unknown function (DUF1393); Region: DUF1393; cl01942 316407006871 Histidine kinase; Region: His_kinase; pfam06580 316407006872 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 316407006873 ATP binding site; other site 316407006874 Mg2+ binding site; other site 316407006875 G-X-G motif; other site 316407006876 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 316407006877 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 316407006878 active site 316407006879 phosphorylation site 316407006880 intermolecular recognition site; other site 316407006881 dimerization interface; other site 316407006882 LytTr DNA-binding domain; Region: LytTR; cl04498 316407006883 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 316407006884 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407006885 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 316407006886 dimerization domain swap beta strand; other site 316407006887 regulatory protein interface; other site 316407006888 active site 316407006889 regulatory phosphorylation site; other site 316407006890 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 316407006891 PEP-utilising enzyme, N-terminal; Region: PEP-utilizers_N; pfam05524 316407006892 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 316407006893 Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their...; Region: malate_synt; cl09155 316407006894 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 316407006895 active site 316407006896 phosphorylation site 316407006897 Peptidase dimerization domain; Region: M20_dimer; cl09126 316407006898 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 316407006899 aminopeptidase; Provisional; Region: PRK09795 316407006900 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 316407006901 Similar to Prolidase and Aminopeptidase P. The members of this subfamily presumably catalyse hydrolysis of Xaa-Pro dipeptides and/or release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP-like; cd01092 316407006902 active site 316407006903 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 316407006904 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA...; Region: PTS_IIB_fructose; cd05569 316407006905 P-loop; other site 316407006906 active site 316407006907 phosphorylation site 316407006908 ROK family; Region: ROK; cl09121 316407006909 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 316407006910 Cl- selectivity filter; other site 316407006911 Cl- binding residues; other site 316407006912 pore gating glutamate residue; other site 316407006913 Protein of unknown function (DUF2502); Region: DUF2502; pfam10697 316407006914 Natural resistance-associated macrophage protein; Region: Nramp; cl00836 316407006915 nucleoside transporter; Region: nupC; TIGR00804 316407006916 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 316407006917 Nucleoside recognition; Region: Gate; cl00486 316407006918 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 316407006919 Transposase DDE domain; Region: Transposase_11; pfam01609 316407006920 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 316407006921 MASE1; Region: MASE1; cl01367 316407006922 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 316407006923 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 316407006924 Putative transcription regulator (DUF1323); Region: DUF1323; pfam07037 316407006925 Putative transcription regulator (DUF1323); Region: DUF1323; pfam07037 316407006926 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 316407006927 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 316407006928 active site 316407006929 HIGH motif; other site 316407006930 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 316407006931 active site 316407006932 KMSKS motif; other site 316407006933 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 316407006934 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407006935 The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold; Region: PBP2_XapR; cd08449 316407006936 putative dimerization interface; other site 316407006937 putative substrate binding pocket; other site 316407006938 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128; cl11521 316407006939 Nucleoside H+ symporter; Region: Nuc_H_symport; pfam03825 316407006940 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 316407006941 Nucleoside-specific channel-forming protein, Tsx; Region: Channel_Tsx; cl04114 316407006942 Transcriptional regulator [Transcription]; Region: LysR; COG0583 316407006943 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407006944 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 316407006945 putative dimerization interface; other site 316407006946 Membrane transport protein; Region: Mem_trans; cl09117 316407006947 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3530 316407006948 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 316407006949 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 316407006950 nucleotide binding pocket; other site 316407006951 K-X-D-G motif; other site 316407006952 catalytic site; other site 316407006953 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 316407006954 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 316407006955 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 316407006956 Dimer interface; other site 316407006957 BRCT sequence motif; other site 316407006958 cell division protein ZipA; Provisional; Region: PRK03427 316407006959 ZipA C-terminal domain. ZipA, a membrane-anchored protein, is one of at least nine essential gene products necessary for assembly of the septal ring which mediates cell division in E.coli. ZipA and FtsA directly bind FtsZ, a homolog of eukaryotic...; Region: ZipA; cd00231 316407006960 FtsZ protein binding site; other site 316407006961 Protein of unknown function (DUF540); Region: DUF540; cl01126 316407006962 cysteine synthases; Region: cysKM; TIGR01136 316407006963 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 316407006964 dimer interface; other site 316407006965 pyridoxal 5'-phosphate binding site; other site 316407006966 catalytic residue; other site 316407006967 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 316407006968 dimerization domain swap beta strand; other site 316407006969 regulatory protein interface; other site 316407006970 active site 316407006971 regulatory phosphorylation site; other site 316407006972 phosphoenolpyruvate-protein phosphotransferase; Provisional; Region: PRK11177 316407006973 PEP-utilising enzyme, N-terminal; Region: PEP-utilizers_N; pfam05524 316407006974 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 316407006975 Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their...; Region: malate_synt; cl09155 316407006976 PTS_IIA, PTS system, glucose/sucrose 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_glc; cd00210 316407006977 HPr interaction site; other site 316407006978 glycerol kinase (GK) interaction site; other site 316407006979 active site 316407006980 phosphorylation site 316407006981 Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and...; Region: pyridoxal_pyridoxamine_kinase; cd01173 316407006982 dimer interface; other site 316407006983 pyridoxal binding site; other site 316407006984 ATP binding site; other site 316407006985 hypothetical protein; Provisional; Region: PRK10318 316407006986 WGR domain of molybdate metabolism regulator and related proteins; Region: WGR_MMR_like; cd07996 316407006987 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4884 316407006988 cysteine synthases; Region: cysKM; TIGR01136 316407006989 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 316407006990 dimer interface; other site 316407006991 pyridoxal 5'-phosphate binding site; other site 316407006992 catalytic residue; other site 316407006993 sulfate/thiosulfate transporter subunit; Provisional; Region: PRK10851 316407006994 Part of the ABC transporter complex cysAWTP involved in sulfate import. Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a solute-...; Region: ABC_CysA_sulfate_importer; cd03296 316407006995 Walker A/P-loop; other site 316407006996 ATP binding site; other site 316407006997 Q-loop/lid; other site 316407006998 ABC transporter signature motif; other site 316407006999 Walker B; other site 316407007000 D-loop; other site 316407007001 H-loop/switch region; other site 316407007002 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...; Region: TM_PBP2; cd06261 316407007003 dimer interface; other site 316407007004 conserved gate region; other site 316407007005 putative PBP binding loops; other site 316407007006 ABC-ATPase subunit interface; other site 316407007007 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...; Region: TM_PBP2; cd06261 316407007008 dimer interface; other site 316407007009 conserved gate region; other site 316407007010 putative PBP binding loops; other site 316407007011 ABC-ATPase subunit interface; other site 316407007012 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 316407007013 short chain dehydrogenase; Provisional; Region: PRK08226 316407007014 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407007015 transcriptional regulator MurR; Provisional; Region: PRK15482 316407007016 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...; Region: SIS_RpiR; cd05013 316407007017 putative active site; other site 316407007018 N-acetylmuramic acid-6-phosphate etherase; Reviewed; Region: murQ; PRK05441 316407007019 N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid...; Region: SIS_Etherase; cd05007 316407007020 putative active site; other site 316407007021 PTS system N-acetylmuramic acid transporter subunits EIIBC; Reviewed; Region: murP; PRK09586 316407007022 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...; Region: PTS_IIB_glc; cd00212 316407007023 active site turn 316407007024 phosphorylation site 316407007025 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 316407007026 Beta-lactamase; Region: Beta-lactamase; cl01009 316407007027 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 316407007028 Dyp-type peroxidase family; Region: Dyp_perox; cl01067 316407007029 Protein of unknown function (DUF1131); Region: DUF1131; cl05867 316407007030 Protein of unknown function (DUF2919); Region: DUF2919; pfam11143 316407007031 GNAT-family acetyltransferase TIGR03103; Region: trio_acet_GNAT 316407007032 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 316407007033 Coenzyme A binding pocket; other site 316407007034 N-acetylmuramoyl-l-alanine amidase I; Provisional; Region: PRK10319 316407007035 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 316407007036 active site 316407007037 metal-binding site 316407007038 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 316407007039 transcriptional regulator EutR; Provisional; Region: PRK10130 316407007040 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407007041 carboxysome structural protein EutK; Provisional; Region: PRK15466 316407007042 Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment (BMC) domain; Region: BMC_CcmK_like; cd07045 316407007043 Hexamer interface; other site 316407007044 Hexagonal pore residue; other site 316407007045 ethanolamine utilization protein EutL; Provisional; Region: PRK15405 316407007046 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1; Region: BMC_EutL_repeat1; cd07049 316407007047 putative hexamer interface; other site 316407007048 putative hexagonal pore; other site 316407007049 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 2; Region: BMC_EutL_repeat2; cd07050 316407007050 putative hexamer interface; other site 316407007051 putative hexagonal pore; other site 316407007052 Ethanolamine ammonia-lyase light chain (EutC); Region: EutC; cl01762 316407007053 ethanolamine ammonia lyase large subunit; Provisional; Region: PRK15067 316407007054 Ethanolamine ammonia lyase large subunit (EutB); Region: EutB; cl09205 316407007055 reactivating factor for ethanolamine ammonia lyase; Provisional; Region: eutA; PRK10719 316407007056 Ethanolamine utilisation protein, EutH; Region: EutH; cl01248 316407007057 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 316407007058 iron-containing alcohol dehydrogenases (Fe-ADH)-like; Region: Fe-ADH; cd08551 316407007059 active site 316407007060 metal-binding site 316407007061 Ethanolamine utilization protein, possible chaperonin [Amino acid transport and metabolism]; Region: EutJ; COG4820 316407007062 aldehyde dehydrogenase EutE; Provisional; Region: PRK15398 316407007063 Ethanolamine utilization protein EutE-like; Region: ALDH_EutE; cd07121 316407007064 putative catalytic cysteine; other site 316407007065 Ethanolamine utilisation protein and carboxysome structural protein domain family; Region: EutN_CcmL; cd01614 316407007066 Hexamer/Pentamer interface; other site 316407007067 central pore; other site 316407007068 Bacterial Micro-Compartment (BMC) domain; Region: BMC_PduA; cd07059 316407007069 Hexamer interface; other site 316407007070 Putative hexagonal pore residue; other site 316407007071 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 316407007072 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; cl00920 316407007073 Cupin domain; Region: Cupin_2; cl09118 316407007074 Ethanolamine utilization protein [Amino acid transport and metabolism]; Region: EutQ; COG4766 316407007075 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cd00882 316407007076 G1 box; other site 316407007077 GTP/Mg2+ binding site; other site 316407007078 G2 box; other site 316407007079 Switch I region; other site 316407007080 G3 box; other site 316407007081 Switch II region; other site 316407007082 G4 box; other site 316407007083 G5 box; other site 316407007084 1,2-propanediol utilization protein U (PduU)/ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain; Region: BMC_PduU-EutS; cd07046 316407007085 putative hexamer interface; other site 316407007086 putative hexagonal pore; other site 316407007087 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 316407007088 Malic enzyme, N-terminal domain; Region: malic; pfam00390 316407007089 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 316407007090 putative NAD(P) binding site; other site 316407007091 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 316407007092 transaldolase-like protein; Provisional; Region: PTZ00411 316407007093 Transaldolases including both TalA and TalB. The enzyme catalyses the reversible transfer of a dyhydroxyacetone moiety, derived from fructose-6-phosphate to erythrose-4-phosphate yielding sedoheptulose-7-phosphate and glyceraldehyde-3-phosphate. The...; Region: Transaldolase_TalAB; cd00957 316407007094 active site 316407007095 dimer interface; other site 316407007096 catalytic residue; other site 316407007097 transketolase; Reviewed; Region: PRK12753 316407007098 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 316407007099 TPP-binding site; other site 316407007100 dimer interface; other site 316407007101 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 316407007102 PYR/PP interface; other site 316407007103 dimer interface; other site 316407007104 TPP binding site; other site 316407007105 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 316407007106 Protein of unknown function (DUF1176); Region: DUF1176; pfam06674 316407007107 GDP-mannose pyrophosphatase NudK; Provisional; Region: PRK15009 316407007108 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...; Region: ADPRase_NUDT5; cd03424 316407007109 dimer interface; other site 316407007110 ADP-ribose binding site; other site 316407007111 active site 316407007112 nudix motif; other site 316407007113 metal-binding site 316407007114 putative oxidoreductase Fe-S binding subunit; Reviewed; Region: PRK12769 316407007115 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407007116 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407007117 nitrate/nitrite sensor protein NarQ; Provisional; Region: PRK10935 316407007118 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 connected by an extended linker. The...; Region: HAMP; cl01054 316407007119 Histidine kinase; Region: HisKA_3; pfam07730 316407007120 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 316407007121 aminoglycoside/multidrug efflux system; Provisional; Region: PRK10555 316407007122 Protein export membrane protein; Region: SecD_SecF; cl14618 316407007123 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 316407007124 putative catalytic residues; other site 316407007125 Peptidase dimerization domain; Region: M20_dimer; cl09126 316407007126 succinyl-diaminopimelate desuccinylase, proteobacterial clade; Region: dapE_proteo; TIGR01246 316407007127 hypothetical protein; Provisional; Region: PRK13664 316407007128 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; cl12031 316407007129 Predicted esterase [General function prediction only]; Region: COG0400 316407007130 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]; Region: COG1444 316407007131 Putative ATPase (DUF699); Region: DUF699; pfam05127 316407007132 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; cl00988 316407007133 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 316407007134 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 316407007135 ATP binding site; other site 316407007136 active site 316407007137 substrate binding site; other site 316407007138 lipoprotein; Provisional; Region: PRK11679 316407007139 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 316407007140 Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue...; Region: DHDPS; cd00950 316407007141 dihydrodipicolinate synthase; Region: dapA; TIGR00674 316407007142 dimer interface; other site 316407007143 active site 316407007144 catalytic residue; other site 316407007145 glycine cleavage system transcriptional repressor; Provisional; Region: gcvR; PRK11589 316407007146 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; Region: ACT_GcvR_1; cd04893 316407007147 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 316407007148 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...; Region: PRX_BCP; cd03017 316407007149 catalytic triad; other site 316407007150 Fe-S-cluster-containing hydrogenase components 2 [Energy production and conversion]; Region: HycB; COG1142 316407007151 4Fe-4S binding domain; Region: Fer4; pfam00037 316407007152 hydrogenase 4 subunit B; Validated; Region: PRK06521 316407007153 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 316407007154 NADH dehydrogenase; Region: NADHdh; cl00469 316407007155 hydrogenase 4 subunit D; Validated; Region: PRK06525 316407007156 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 316407007157 Hydrogenase 4 membrane component (E) [Energy production and conversion]; Region: HyfE; cl12087 316407007158 hydrogenase 4 subunit F; Validated; Region: PRK06458 316407007159 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 316407007160 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl00539 316407007161 bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional; Region: PRK11742 316407007162 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; cl00417 316407007163 hydrogenase 4 subunit H; Validated; Region: PRK08222 316407007164 4Fe-4S binding domain; Region: Fer4; pfam00037 316407007165 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 316407007166 Formate hydrogenlyase maturation protein HycH; Region: HycH; cl06472 316407007167 Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]; Region: FhlA; COG3604 316407007168 GAF domain; Region: GAF; cl00853 316407007169 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...; Region: AAA; cd00009 316407007170 Walker A motif; other site 316407007171 ATP binding site; other site 316407007172 Walker B motif; other site 316407007173 arginine finger; other site 316407007174 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 316407007175 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 316407007176 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 316407007177 Domain of unknown function DUF20; Region: UPF0118; cl00465 316407007178 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 316407007179 Peptidase family M48; Region: Peptidase_M48; cl12018 316407007180 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 316407007181 catalytic residues; other site 316407007182 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407007183 Permease family; Region: Xan_ur_permease; cl00967 316407007184 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 316407007185 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 316407007186 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...; Region: PurM; cd02196 316407007187 dimerization interface; other site 316407007188 putative ATP binding site; other site 316407007189 Formyl transferase; Region: Formyl_trans_N; cl00395 316407007190 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 316407007191 polyphosphate kinase 1; Region: poly_P_kin; TIGR03705 316407007192 Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of...; Region: PLDc; cd00138 316407007193 active site 316407007194 signature motif; other site 316407007195 exopolyphosphatase; Provisional; Region: PRK10854 316407007196 exopolyphosphatase; Region: exo_poly_only; TIGR03706 316407007197 MASE1; Region: MASE1; cl01367 316407007198 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 316407007199 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 316407007200 Protein of unknown function (DUF2633); Region: DUF2633; pfam11119 316407007201 Rickettsia 17 kDa surface antigen; Region: Rick_17kDa_Anti; cl10470 316407007202 GMP synthase; Reviewed; Region: guaA; PRK00074 316407007203 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 316407007204 AMP/PPi binding site; other site 316407007205 candidate oxyanion hole; other site 316407007206 catalytic triad; other site 316407007207 potential glutamine specificity residues; other site 316407007208 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 316407007209 ATP Binding subdomain; other site 316407007210 Ligand Binding sites; other site 316407007211 Dimerization subdomain; other site 316407007212 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 316407007213 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; cl09108 316407007214 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 key...; Region: CBS_pair_IMPDH; cd04601 316407007215 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 the...; Region: IMPDH; cd00381 316407007216 active site 316407007217 exodeoxyribonuclease VII, large subunit; Region: xseA; TIGR00237 316407007218 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 single-strand-...; Region: ExoVII_LU_OBF; cd04489 316407007219 generic binding surface II; other site 316407007220 generic binding surface I; other site 316407007221 Protein of unknown function (DUF1407); Region: DUF1407; pfam07191 316407007222 GTP-binding protein Der; Reviewed; Region: PRK00093 316407007223 EngA1 subfamily. This CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that...; Region: EngA1; cd01894 316407007224 G1 box; other site 316407007225 GTP/Mg2+ binding site; other site 316407007226 Switch I region; other site 316407007227 G2 box; other site 316407007228 Switch II region; other site 316407007229 G3 box; other site 316407007230 G4 box; other site 316407007231 G5 box; other site 316407007232 EngA2 subfamily. This CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that...; Region: EngA2; cd01895 316407007233 G1 box; other site 316407007234 GTP/Mg2+ binding site; other site 316407007235 Switch I region; other site 316407007236 G2 box; other site 316407007237 G3 box; other site 316407007238 Switch II region; other site 316407007239 G4 box; other site 316407007240 G5 box; other site 316407007241 outer membrane biogenesis protein BamB; Provisional; Region: PRK11138 316407007242 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 316407007243 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 316407007244 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 316407007245 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 316407007246 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 ATP-dependent...; Region: HisRS-like_core; cd00773 316407007247 dimer interface; other site 316407007248 motif 1; other site 316407007249 active site 316407007250 motif 2; other site 316407007251 motif 3; other site 316407007252 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 316407007253 anticodon binding site; other site 316407007254 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 316407007255 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; Region: ispG_gcpE; TIGR00612 316407007256 cytoskeletal protein RodZ; Provisional; Region: PRK10856 316407007257 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl09100 316407007258 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 316407007259 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 316407007260 FeS/SAM binding site; other site 316407007261 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 316407007262 active site 316407007263 multimer interface; other site 316407007264 penicillin-binding protein 1C; Provisional; Region: PRK11240 316407007265 Transglycosylase; Region: Transgly; cl07896 316407007266 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 316407007267 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 316407007268 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 316407007269 MG2 domain; Region: A2M_N; pfam01835 316407007270 Alpha-2-macroglobulin family N-terminal region; Region: A2M_N_2; pfam07703 316407007271 Alpha-2-macroglobulin family; Region: A2M; pfam00207 316407007272 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 316407007273 surface patch; other site 316407007274 thioester region; other site 316407007275 specificity defining residues; other site 316407007276 3-mercaptopyruvate sulfurtransferase; Provisional; Region: sseA; PRK11493 316407007277 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...; Region: TST_Repeat_1; cd01448 316407007278 active site residue 316407007279 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 316407007280 active site residue 316407007281 SseB protein; Region: SseB; cl06279 316407007282 aminopeptidase B; Provisional; Region: PRK05015 316407007283 Peptidase; Region: DUF3663; pfam12404 316407007284 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...; Region: Peptidase_M17; cd00433 316407007285 interface (dimer of trimers); other site 316407007286 Substrate-binding/catalytic site; other site 316407007287 Zn-binding sites; other site 316407007288 Protein of unknown function (DUF528); Region: DUF528; cl01123 316407007289 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 316407007290 catalytic loop; other site 316407007291 iron binding site; other site 316407007292 chaperone protein HscA; Provisional; Region: hscA; PRK05183 316407007293 6,7-dimethyl-8-ribityllumazine synthase; Region: DMRL_synthase; cl00317 316407007294 co-chaperone HscB; Provisional; Region: hscB; PRK05014 316407007295 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...; Region: DnaJ; cd06257 316407007296 HSP70 interaction site; other site 316407007297 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 316407007298 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 316407007299 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 316407007300 trimerization site; other site 316407007301 active site 316407007302 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 316407007303 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 316407007304 pyridoxal 5'-phosphate binding pocket; other site 316407007305 catalytic residue; other site 316407007306 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407007307 rrf2 family protein (putative transcriptional regulator); Region: rrf2_super; TIGR00738 316407007308 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional; Region: PRK15114 316407007309 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 316407007310 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 316407007311 active site 316407007312 dimerization interface; other site 316407007313 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 316407007314 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; cl12031 316407007315 stationary phase inducible protein CsiE; Provisional; Region: PRK11564 316407007316 PRD domain; Region: PRD; pfam00874 316407007317 PRD domain; Region: PRD; pfam00874 316407007318 phenyl proprionate permease family protein; Region: 2A0127; TIGR00902 316407007319 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128; cl11521 316407007320 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 316407007321 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407007322 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 316407007323 dimerization interface; other site 316407007324 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 316407007325 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1)...; Region: Rieske; cl00938 316407007326 iron-sulfur cluster; other site 316407007327 [2Fe-2S] cluster binding site; other site 316407007328 C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_NDO-like; cd08881 316407007329 beta subunit interface; other site 316407007330 alpha subunit interface; other site 316407007331 active site 316407007332 substrate binding site; other site 316407007333 Fe binding site; other site 316407007334 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 316407007335 inter-subunit interface; other site 316407007336 Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise...; Region: Rieske_RO_ferredoxin; cd03528 316407007337 [2Fe-2S] cluster binding site; other site 316407007338 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407007339 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 316407007340 phenylpropionate dioxygenase ferredoxin reductase subunit; Provisional; Region: PRK09754 316407007341 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407007342 DoxX; Region: DoxX; cl00976 316407007343 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 316407007344 aldose 1-epimerase, similar to Escherichia coli YphB; Region: Aldose_epim_Ec_YphB; cd09021 316407007345 active site 316407007346 catalytic residues; other site 316407007347 L-threonine dehydrogenase (TDH)-like; Region: THR_DH_like; cd08239 316407007348 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 316407007349 putative NAD(P) binding site; other site 316407007350 catalytic Zn binding site; other site 316407007351 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 316407007352 TM-ABC transporter signature motif; other site 316407007353 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 316407007354 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and...; Region: ABC_Carb_Monos_I; cd03216 316407007355 Walker A/P-loop; other site 316407007356 ATP binding site; other site 316407007357 Q-loop/lid; other site 316407007358 ABC transporter signature motif; other site 316407007359 Walker B; other site 316407007360 D-loop; other site 316407007361 H-loop/switch region; other site 316407007362 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (; Region: ABC_Carb_Monos_II; cd03215 316407007363 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 316407007364 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 316407007365 ligand binding site; other site 316407007366 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 316407007367 TPR motif; other site 316407007368 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 316407007369 binding surface 316407007370 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 316407007371 TPR motif; other site 316407007372 binding surface 316407007373 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 316407007374 ROK family; Region: ROK; cl09121 316407007375 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...; Region: SHMT; cd00378 316407007376 dimer interface; other site 316407007377 glycine-pyridoxal phosphate binding site; other site 316407007378 active site 316407007379 folate binding site; other site 316407007380 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 316407007381 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 316407007382 heme-binding site; other site 316407007383 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 316407007384 FAD binding pocket; other site 316407007385 FAD binding motif; other site 316407007386 phosphate binding motif; other site 316407007387 beta-alpha-beta structure motif; other site 316407007388 NAD binding pocket; other site 316407007389 Heme binding pocket; other site 316407007390 Nitrogen regulatory protein P-II; Region: P-II; cl00412 316407007391 response regulator GlrR; Provisional; Region: PRK15115 316407007392 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 316407007393 active site 316407007394 phosphorylation site 316407007395 intermolecular recognition site; other site 316407007396 dimerization interface; other site 316407007397 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...; Region: AAA; cd00009 316407007398 Walker A motif; other site 316407007399 ATP binding site; other site 316407007400 Walker B motif; other site 316407007401 arginine finger; other site 316407007402 hypothetical protein; Provisional; Region: PRK10722 316407007403 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 trans-...; Region: HisKA; cd00082 316407007404 dimer interface; other site 316407007405 phosphorylation site 316407007406 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 316407007407 ATP binding site; other site 316407007408 Mg2+ binding site; other site 316407007409 G-X-G motif; other site 316407007410 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 316407007411 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 316407007412 dimerization interface; other site 316407007413 ATP binding site; other site 316407007414 AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal...; Region: PurM-like; cl10019 316407007415 dimerization interface; other site 316407007416 ATP binding site; other site 316407007417 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 316407007418 putative active site; other site 316407007419 catalytic triad; other site 316407007420 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 316407007421 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...; Region: PBPb; cd00134 316407007422 substrate binding pocket; other site 316407007423 membrane-bound complex binding site; other site 316407007424 hinge residues; other site 316407007425 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 catalyze...; Region: LT_GEWL; cd00254 316407007426 N-acetyl-D-glucosamine binding site; other site 316407007427 catalytic residue; other site 316407007428 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 316407007429 nucleoside/Zn binding site; other site 316407007430 dimer interface; other site 316407007431 catalytic motif; other site 316407007432 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; cl11391 316407007433 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11557 316407007434 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...; Region: SIS_RpiR; cd05013 316407007435 putative active site; other site 316407007436 ferredoxin; Validated; Region: PRK07118 316407007437 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 316407007438 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 the...; Region: PNPsynthase; cd00003 316407007439 active site 316407007440 hydrophilic channel; other site 316407007441 dimerization interface; other site 316407007442 catalytic residues; other site 316407007443 active site lid 316407007444 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 316407007445 Recombination protein O N terminal; Region: RecO_N; pfam11967 316407007446 Recombination protein O C terminal; Region: RecO_C; pfam02565 316407007447 GTPase Era; Reviewed; Region: era; PRK00089 316407007448 Era subfamily. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit...; Region: Era; cd04163 316407007449 G1 box; other site 316407007450 GTP/Mg2+ binding site; other site 316407007451 Switch I region; other site 316407007452 G2 box; other site 316407007453 Switch II region; other site 316407007454 G3 box; other site 316407007455 G4 box; other site 316407007456 G5 box; other site 316407007457 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains...; Region: KH-I; cl00098 316407007458 ribonuclease III; Reviewed; Region: rnc; PRK00102 316407007459 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 post-...; Region: RIBOc; cd00593 316407007460 dimerization interface; other site 316407007461 active site 316407007462 metal-binding site 316407007463 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...; Region: DSRM; cd00048 316407007464 dsRNA binding site; other site 316407007465 signal peptidase I; Provisional; Region: PRK10861 316407007466 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 316407007467 Catalytic site; other site 316407007468 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 316407007469 GTP-binding protein LepA; Provisional; Region: PRK05433 316407007470 LepA subfamily. LepA belongs to the GTPase family of and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and...; Region: LepA; cd01890 316407007471 G1 box; other site 316407007472 putative GEF interaction site; other site 316407007473 GTP/Mg2+ binding site; other site 316407007474 Switch I region; other site 316407007475 G2 box; other site 316407007476 G3 box; other site 316407007477 Switch II region; other site 316407007478 G4 box; other site 316407007479 G5 box; other site 316407007480 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-...; Region: lepA_II; cd03699 316407007481 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 316407007482 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 316407007483 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; cl01178 316407007484 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 316407007485 anti-RNA polymerase sigma factor SigE; Provisional; Region: PRK10863 316407007486 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 316407007487 Anti sigma-E protein RseA, C-terminal domain; Region: RseA_C; pfam03873 316407007488 RNA polymerase sigma factor RpoE; Region: RpoE_Sigma70; TIGR02939 316407007489 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 316407007490 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...; Region: Sigma70_r4; cd06171 316407007491 DNA binding residues 316407007492 L-aspartate oxidase; Provisional; Region: PRK09077 316407007493 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407007494 domain; Region: Succ_DH_flav_C; pfam02910 316407007495 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 316407007496 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; cl12011 316407007497 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 316407007498 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 316407007499 ATP binding site; other site 316407007500 Mg++ binding site; other site 316407007501 motif III; other site 316407007502 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 316407007503 nucleotide binding region; other site 316407007504 ATP-binding site; other site 316407007505 Transcriptional regulator [Transcription]; Region: LysR; COG0583 316407007506 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407007507 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 316407007508 dimerization interface; other site 316407007509 LysE type translocator; Region: LysE; cl00565 316407007510 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 316407007511 Uracil DNA glycosylase superfamily; Region: UDG; cl00483 316407007512 putative methyltransferase; Provisional; Region: PRK10864 316407007513 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 316407007514 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 316407007515 thioredoxin 2; Provisional; Region: PRK10996 316407007516 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 316407007517 catalytic residues; other site 316407007518 DTW domain; Region: DTW; cl01221 316407007519 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 316407007520 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407007521 Peptidase dimerization domain; Region: M20_dimer; cl09126 316407007522 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 316407007523 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 316407007524 phosphatidylserine synthase; Provisional; Region: pssA; PRK09428 316407007525 Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of...; Region: PLDc; cd00138 316407007526 active site 316407007527 signature motif; other site 316407007528 Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of...; Region: PLDc; cd00138 316407007529 active site 316407007530 signature motif; other site 316407007531 Predicted periplasmic lipoprotein (DUF2279); Region: DUF2279; cl11574 316407007532 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 316407007533 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 316407007534 putative substrate translocation pore; other site 316407007535 protein disaggregation chaperone; Provisional; Region: PRK10865 316407007536 Clp amino terminal domain; Region: Clp_N; pfam02861 316407007537 Clp amino terminal domain; Region: Clp_N; pfam02861 316407007538 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...; Region: AAA; cd00009 316407007539 Walker A motif; other site 316407007540 ATP binding site; other site 316407007541 Walker B motif; other site 316407007542 arginine finger; other site 316407007543 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...; Region: AAA; cd00009 316407007544 Walker A motif; other site 316407007545 ATP binding site; other site 316407007546 Walker B motif; other site 316407007547 arginine finger; other site 316407007548 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 316407007549 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 316407007550 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 316407007551 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 316407007552 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 316407007553 RNA binding surface; other site 316407007554 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 316407007555 active site 316407007556 outer membrane biogenesis protein BamD; Provisional; Region: PRK10866 316407007557 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 A site...; Region: RaiA; cd00552 316407007558 30S subunit binding site; other site 316407007559 bifunctional chorismate mutase/prephenate dehydratase; Provisional; Region: pheA; PRK10622 316407007560 Chorismate mutase type II; Region: CM_2; cl00693 316407007561 Prephenate dehydratase; Region: PDT; pfam00800 316407007562 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 316407007563 putative L-Phe binding site; other site 316407007564 bifunctional chorismate mutase/prephenate dehydrogenase; Provisional; Region: tyrA; PRK11199 316407007565 Chorismate mutase type II; Region: CM_2; cl00693 316407007566 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407007567 NeuB family; Region: NeuB; cl00496 316407007568 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 316407007569 lipoprotein; Provisional; Region: PRK11443 316407007570 Protein of unknown function (DUF2799); Region: DUF2799; pfam10973 316407007571 putative inner membrane diguanylate cyclase; Provisional; Region: PRK09966 316407007572 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316407007573 metal-binding site 316407007574 active site 316407007575 I-site; other site 316407007576 putative outer membrane lipoprotein; Provisional; Region: PRK09967 316407007577 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 316407007578 ligand binding site; other site 316407007579 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 316407007580 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 316407007581 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 316407007582 RimM N-terminal domain; Region: RimM; pfam01782 316407007583 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to...; Region: PRCH; cl09959 316407007584 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 316407007585 signal recognition particle protein; Provisional; Region: PRK10867 316407007586 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 316407007587 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 316407007588 P loop; other site 316407007589 GTP binding site; other site 316407007590 Signal peptide binding domain; Region: SRP_SPB; pfam02978 316407007591 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 316407007592 hypothetical protein; Provisional; Region: PRK11573 316407007593 Domain of unknown function DUF21; Region: DUF21; pfam01595 316407007594 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 316407007595 Transporter associated domain; Region: CorC_HlyC; pfam03471 316407007596 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 316407007597 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 316407007598 dimer interface; other site 316407007599 hsp70 (ATPase domain) interactions; other site 316407007600 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 316407007601 ATP-NAD kinase; Region: NAD_kinase; pfam01513 316407007602 recombination and repair protein; Provisional; Region: PRK10869 316407007603 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides...; Region: ABC_RecN; cd03241 316407007604 Walker A/P-loop; other site 316407007605 ATP binding site; other site 316407007606 Q-loop/lid; other site 316407007607 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides...; Region: ABC_RecN; cd03241 316407007608 Q-loop/lid; other site 316407007609 ABC transporter signature motif; other site 316407007610 Walker B; other site 316407007611 D-loop; other site 316407007612 H-loop/switch region; other site 316407007613 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 316407007614 Uncharacterized protein family (UPF0125); Region: UPF0125; cl01096 316407007615 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 316407007616 putative coenzyme Q binding site; other site 316407007617 SmpB protein; Region: SmpB; cl00482 316407007618 integrase; Provisional; Region: PRK09692 316407007619 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 316407007620 Int/Topo IB signature motif; other site 316407007621 active site 316407007622 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl01302 316407007623 Protein of unknown function (DUF3296); Region: DUF3296; pfam11726 316407007624 Superfamily II helicase [General function prediction only]; Region: COG1204 316407007625 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; cl12029 316407007626 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; cl12029 316407007627 Domain of unknown function (DUF1837); Region: DUF1837; pfam08878 316407007628 Predicted GTPase [General function prediction only]; Region: COG3596 316407007629 Era (E. coli Ras-like protein)-like. This family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngG), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs)...; Region: Era_like; cd00880 316407007630 G1 box; other site 316407007631 GTP/Mg2+ binding site; other site 316407007632 Switch I region; other site 316407007633 G2 box; other site 316407007634 Switch II region; other site 316407007635 G3 box; other site 316407007636 G4 box; other site 316407007637 G5 box; other site 316407007638 Domain of unknown function (DUF932); Region: DUF932; cl12129 316407007639 Predicted transcriptional regulator [Transcription]; Region: COG2378 316407007640 Predicted transcriptional regulator [Transcription]; Region: COG2378 316407007641 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 316407007642 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 316407007643 transmembrane helices; other site 316407007644 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; cl09110 316407007645 CP4-57 prophage region; ECK2637:JW5420:b2641; hypothetical protein 316407007646 Antirestriction protein; Region: Antirestrict; pfam03230 316407007647 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 316407007648 MPN+ (JAMM) motif; other site 316407007649 Zinc-binding site; other site 316407007650 Protein of unknown function (DUF987); Region: DUF987; pfam06174 316407007651 YagB/YeeU/YfjZ family; Region: YagB_YeeU_YfjZ; pfam06154 316407007652 Protein of unknown function (DUF1219); Region: DUF1219; pfam06755 316407007653 Type V secretory pathway, adhesin AidA [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: AidA; COG3468 316407007654 Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 1, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of Neisseria and Haemophilus IgA1 proteases...; Region: PL1_Passenger_AT; cd01343 316407007655 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 316407007656 Autotransporter beta-domain; Region: Autotransporter; cl02365 316407007657 ECK2645:JW5423:b2648; predicted invertase fragment 316407007658 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 316407007659 ECK2651:JW5426:b2657; conserved hypothetical protein 316407007660 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG...; Region: CAS_like; cd00250 316407007661 substrate binding pocket; other site 316407007662 active site 316407007663 iron coordination sites; other site 316407007664 Predicted dehydrogenase [General function prediction only]; Region: COG0579 316407007665 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407007666 delta-1-pyrroline-5-carboxylate dehydrogenase, group 2, putative; Region: D1pyr5carbox2; TIGR01237 316407007667 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 316407007668 tetramerization interface; other site 316407007669 NAD(P) binding site; other site 316407007670 catalytic residues; other site 316407007671 4-aminobutyrate aminotransferase; Validated; Region: PRK08088 316407007672 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 316407007673 inhibitor-cofactor binding pocket; inhibition site 316407007674 pyridoxal 5'-phosphate binding site; other site 316407007675 catalytic residue; other site 316407007676 Amino acid permease; Region: AA_permease; pfam00324 316407007677 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407007678 DNA-binding transcriptional regulator CsiR; Provisional; Region: PRK11534 316407007679 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407007680 DNA binding site 316407007681 FCD domain; Region: FCD; cl11656 316407007682 LysM domain/BON superfamily protein; Provisional; Region: PRK11198 316407007683 Putative phospholipid-binding domain; Region: BON; cl02771 316407007684 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 316407007685 putative peptidoglycan binding site; other site 316407007686 Uncharacterized protein family UPF0057; Region: UPF0057; cl00431 316407007687 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 316407007688 dimerization interface; other site 316407007689 putative DNA binding site; other site 316407007690 putative Zn2+ binding site; other site 316407007691 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YgaP, and similar uncharacterized putative rhodanese-related sulfurtransferases; Region: RHOD_YgaP; cd01527 316407007692 active site residue 316407007693 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 316407007694 Domain in histone-like proteins of HNS family; Region: HNS; cl09251 316407007695 DNA binding protein, nucleoid-associated; Provisional; Region: PRK10328 316407007696 Protein of unknown function (DUF1144); Region: DUF1144; pfam06610 316407007697 Protein of unknown function (DUF2002); Region: DUF2002; cl11580 316407007698 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 316407007699 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide...; Region: NrdH; cd02976 316407007700 catalytic residues; other site 316407007701 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 316407007702 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK08188 316407007703 Ribonucleotide reductase N-terminal; Region: RNR_N; pfam08343 316407007704 Class I ribonucleotide reductase; Region: RNR_I; cd01679 316407007705 active site 316407007706 dimer interface; other site 316407007707 catalytic residues; other site 316407007708 effector binding site; other site 316407007709 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 316407007710 ribonucleotide-diphosphate reductase subunit beta; Provisional; Region: nrdF2; PRK13966 316407007711 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 316407007712 dimer interface; other site 316407007713 putative radical transfer pathway; other site 316407007714 diiron center; other site 316407007715 tyrosyl radical; other site 316407007716 glycine betaine transporter ATP-binding subunit; Provisional; Region: PRK10070 316407007717 This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these...; Region: ABC_Pro_Gly_Bertaine; cd03294 316407007718 Walker A/P-loop; other site 316407007719 ATP binding site; other site 316407007720 Q-loop/lid; other site 316407007721 ABC transporter signature motif; other site 316407007722 Walker B; other site 316407007723 D-loop; other site 316407007724 H-loop/switch region; other site 316407007725 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the ABC transporter OpuCA. OpuCA is the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing...; Region: CBS_pair_ABC_OpuCA_assoc2; cd04583 316407007726 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...; Region: TM_PBP2; cd06261 316407007727 dimer interface; other site 316407007728 conserved gate region; other site 316407007729 putative PBP binding loops; other site 316407007730 ABC-ATPase subunit interface; other site 316407007731 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 316407007732 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 316407007733 benzoate transport; Region: 2A0115; TIGR00895 316407007734 ECK2675:JW5428:b2681; predicted transporter 316407007735 AzlC protein; Region: AzlC; cl00570 316407007736 putative L-valine exporter; Provisional; Region: PRK10408 316407007737 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407007738 Transcriptional regulators [Transcription]; Region: MarR; COG1846 316407007739 multidrug efflux system protein EmrA; Provisional; Region: PRK15136 316407007740 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 316407007741 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 316407007742 putative substrate translocation pore; other site 316407007743 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 316407007744 S-Ribosylhomocysteinase (LuxS); Region: LuxS; cl00802 316407007745 Glutamate-cysteine ligase; Region: Glu_cys_ligase; cl01099 316407007746 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 316407007747 beta-phosphoglucomutase family hydrolase; Region: PGMB-YQAB-SF; TIGR02009 316407007748 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 316407007749 motif II; other site 316407007750 Global regulator protein family; Region: CsrA; cl00670 316407007751 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 316407007752 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 formation...; Region: AlaRS_core; cd00673 316407007753 motif 1; other site 316407007754 active site 316407007755 motif 2; other site 316407007756 motif 3; other site 316407007757 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 316407007758 DHHA1 domain; Region: DHHA1; pfam02272 316407007759 RecX family; Region: RecX; cl00936 316407007760 recombinase A; Provisional; Region: recA; PRK09354 316407007761 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 316407007762 hexamer interface; other site 316407007763 Walker A motif; other site 316407007764 ATP binding site; other site 316407007765 Walker B motif; other site 316407007766 Competence-damaged protein; Region: CinA; cl00666 316407007767 lytic murein transglycosylase; Region: MltB_2; TIGR02283 316407007768 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 catalyze...; Region: LT_GEWL; cd00254 316407007769 N-acetyl-D-glucosamine binding site; other site 316407007770 catalytic residue; other site 316407007771 PTS system enzyme II sorbitol-specific factor; Region: EII-GUT; cl01515 316407007772 IIBC component; Region: EIIBC-GUT; TIGR00825 316407007773 Sorbitol phosphotransferase enzyme II N-terminus; Region: EIIBC-GUT_N; pfam03612 316407007774 Sorbitol phosphotransferase enzyme II C-terminus; Region: EIIBC-GUT_C; pfam07663 316407007775 PTS system glucitol/sorbitol-specific IIA component; Region: PTSIIA_gutA; cl01516 316407007776 sorbitol-6-phosphate dehydrogenase; Provisional; Region: PRK12384 316407007777 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407007778 Glucitol operon activator protein (GutM); Region: GutM; cl01890 316407007779 DNA-bindng transcriptional repressor SrlR; Provisional; Region: srlR; PRK10434 316407007780 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407007781 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 316407007782 D-arabinose 5-phosphate isomerase; Provisional; Region: gutQ; PRK11543 316407007783 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 5-...; Region: SIS_Kpsf; cd05014 316407007784 putative active site; other site 316407007785 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 316407007786 anaerobic nitric oxide reductase transcription regulator; Provisional; Region: PRK05022 316407007787 GAF domain; Region: GAF; cl00853 316407007788 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...; Region: AAA; cd00009 316407007789 Walker A motif; other site 316407007790 ATP binding site; other site 316407007791 Walker B motif; other site 316407007792 arginine finger; other site 316407007793 anaerobic nitric oxide reductase flavorubredoxin; Provisional; Region: PRK05452 316407007794 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 316407007795 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 316407007796 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They...; Region: rubredoxin; cd00730 316407007797 iron binding site; other site 316407007798 NADH:flavorubredoxin oxidoreductase; Provisional; Region: PRK04965 316407007799 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407007800 Acylphosphatase; Region: Acylphosphatase; cl00551 316407007801 [NiFe] hydrogenase maturation protein HypF; Region: hypF; TIGR00143 316407007802 HypF finger; Region: zf-HYPF; pfam07503 316407007803 HypF finger; Region: zf-HYPF; pfam07503 316407007804 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 316407007805 formate dehydrogenase-H ferredoxin subunit; Provisional; Region: PRK10330 316407007806 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 316407007807 Transcriptional regulators [Transcription]; Region: PurR; COG1609 316407007808 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 316407007809 DNA binding site 316407007810 domain linker motif; other site 316407007811 Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism; Region: PBP1_GalS_like; cd06270 316407007812 dimerization interface (closed form); other site 316407007813 ligand binding site; other site 316407007814 PTS system cellobiose/arbutin/salicin-specific transporter subunits IIBC; Provisional; Region: PRK09796 316407007815 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...; Region: PTS_IIB_glc; cd00212 316407007816 active site turn 316407007817 phosphorylation site 316407007818 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 316407007819 Glycosyl hydrolase family 1; Region: Glyco_hydro_1; cl01046 316407007820 Endopeptidases belonging to membrane-bound hydrogen evolving hydrogenase group. In hydrogenase 3 from E coli, the maturation of the large subunit (HycE) requires the cleavage of a C-terminal peptide by the endopeptidase HycI, before the final formation...; Region: H2MP_MemB-H2evol; cd06067 316407007821 nickel binding site; other site 316407007822 Formate hydrogenlyase maturation protein HycH; Region: HycH; cl06472 316407007823 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 316407007824 formate hydrogenlyase complex iron-sulfur subunit; Provisional; Region: PRK12387 316407007825 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 alpha-; Region: HCP_like; cl14655 316407007826 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl00539 316407007827 bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional; Region: PRK11742 316407007828 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; cl00417 316407007829 NADH dehydrogenase; Region: NADHdh; cl00469 316407007830 formate hydrogenlyase subunit 3; Reviewed; Region: PRK08042 316407007831 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 316407007832 Fe-S-cluster-containing hydrogenase components 2 [Energy production and conversion]; Region: HycB; COG1142 316407007833 Transcriptional repressor of hyc and hyp operons; Region: HycA_repressor; cl08095 316407007834 Hydrogenase expression/synthesis hypA family; Region: HypA; cl00418 316407007835 hydrogenase nickel incorporation protein HypB; Provisional; Region: PRK10463 316407007836 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 316407007837 HupF/HypC family; Region: HupF_HypC; cl00394 316407007838 Hydrogenase formation hypA family; Region: HypD; cl12072 316407007839 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 316407007840 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 316407007841 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 316407007842 dimerization interface; other site 316407007843 ATP binding site; other site 316407007844 formate hydrogenlyase transcriptional activator FhlA; Provisional; Region: PRK15429 316407007845 GAF domain; Region: GAF; cl00853 316407007846 GAF domain; Region: GAF; cl00853 316407007847 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...; Region: AAA; cd00009 316407007848 Walker A motif; other site 316407007849 ATP binding site; other site 316407007850 Walker B motif; other site 316407007851 arginine finger; other site 316407007852 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 316407007853 Nitrous oxide-stimulated promoter; Region: YgbA_NO; cl08119 316407007854 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 316407007855 MutS domain I; Region: MutS_I; pfam01624 316407007856 MutS domain II; Region: MutS_II; pfam05188 316407007857 MutS domain III; Region: MutS_III; cl04977 316407007858 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal...; Region: ABC_MutS1; cd03284 316407007859 Walker A/P-loop; other site 316407007860 ATP binding site; other site 316407007861 Q-loop/lid; other site 316407007862 ABC transporter signature motif; other site 316407007863 Walker B; other site 316407007864 D-loop; other site 316407007865 H-loop/switch region; other site 316407007866 PrpA and PrpB, metallophosphatase domain; Region: MPP_PrpA_PrpB; cd07424 316407007867 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 316407007868 active site 316407007869 metal-binding site 316407007870 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 316407007871 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407007872 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 316407007873 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 316407007874 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407007875 Protein of unknown function, DUF1537; Region: DUF1537; cl01345 316407007876 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 316407007877 active site 316407007878 intersubunit interface; other site 316407007879 Zn2+ binding site; other site 316407007880 hypothetical protein; Provisional; Region: PRK09989 316407007881 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; cl09110 316407007882 gluconate transporter; Region: gntP; TIGR00791 316407007883 RNA polymerase sigma factor RpoS; Region: rpoS_proteo; TIGR02394 316407007884 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 316407007885 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 316407007886 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 316407007887 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...; Region: Sigma70_r4; cd06171 316407007888 DNA binding residues 316407007889 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 316407007890 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 316407007891 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 316407007892 putative peptidoglycan binding site; other site 316407007893 Peptidase family M23; Region: Peptidase_M23; pfam01551 316407007894 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; cl12011 316407007895 Survival protein SurE; Region: SurE; cl00448 316407007896 tRNA pseudouridine synthase D; Reviewed; Region: truD; PRK00984 316407007897 PseudoU_synth_EcTruD: Pseudouridine synthase, TruD family. This group consists of bacterial pseudouridine synthases similar to Escherichia coli TruD. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_EcTruD; cd02575 316407007898 Permutation of conserved domain; other site 316407007899 active site 316407007900 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 316407007901 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...; Region: MECDP_synthase; cd00554 316407007902 homotrimer interaction site; other site 316407007903 zinc binding site; other site 316407007904 CDP-binding sites; other site 316407007905 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 316407007906 substrate binding site; other site 316407007907 dimer interface; other site 316407007908 Septum formation initiator; Region: DivIC; cl11433 316407007909 Protein of unknown function (DUF3561); Region: DUF3561; cl08142 316407007910 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 important for the assimilation...; Region: APSK; cd02027 316407007911 Gluconate kinase [Carbohydrate transport and metabolism]; Region: GntK; COG3265 316407007912 ligand-binding site; other site 316407007913 sulfate adenylyltransferase subunit 1; Provisional; Region: cysN; PRK05124 316407007914 CysN_ATPS subfamily. CysN, together with protein CysD, form the ATP sulfurylase (ATPS) complex in some bacteria and lower eukaryotes. ATPS catalyzes the production of ATP sulfurylase (APS) and pyrophosphate (PPi) from ATP and sulfate. CysD, which...; Region: CysN_ATPS; cd04166 316407007915 CysD dimerization site; other site 316407007916 G1 box; other site 316407007917 putative GEF interaction site; other site 316407007918 GTP/Mg2+ binding site; other site 316407007919 Switch I region; other site 316407007920 G2 box; other site 316407007921 G3 box; other site 316407007922 Switch II region; other site 316407007923 G4 box; other site 316407007924 G5 box; other site 316407007925 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...; Region: CysN_NodQ_II; cd03695 316407007926 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...; Region: CysN_NoDQ_III; cd04095 316407007927 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 316407007928 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 316407007929 Active Sites; active site 316407007930 alkaline phosphatase isozyme conversion aminopeptidase; Provisional; Region: PRK10199 316407007931 Peptidase dimerization domain; Region: M20_dimer; cl09126 316407007932 CRISPR-associated protein (Cas_Cas2CT1978); Region: Cas_Cas2CT1978; cl08187 316407007933 CRISPR associated protein Cas1; Region: Cas_Cas1; cl00656 316407007934 CRISPR-associated endonuclease Cas1; Region: cas1; TIGR00287 316407007935 CRISPR associated protein; Region: CRISPR_assoc; cl08497 316407007936 CRISPR-associated protein Cas5, N-terminal domain; Region: CRISPR_cas5; cl12040 316407007937 CRISPR-associated protein (Cas_Cas5); Region: Cas_Cas5d; pfam09704 316407007938 CT1975-like protein; Region: Cas_CT1975; cl09608 316407007939 CRISPR-associated protein Cse2 (CRISPR_cse2); Region: CRISPR_Cse2; cl09719 316407007940 CRISPR-associated protein Cse1 (CRISPR_cse1); Region: CRISPR_Cse1; cl08044 316407007941 helicase Cas3; Provisional; Region: PRK09694 316407007942 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 316407007943 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 316407007944 ATP binding site; other site 316407007945 putative Mg++ binding site; other site 316407007946 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; cl12029 316407007947 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 316407007948 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 316407007949 Active Sites; active site 316407007950 sulfite reductase subunit beta; Provisional; Region: PRK13504 316407007951 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 316407007952 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 316407007953 sulfite reductase subunit alpha; Provisional; Region: cysJ; PRK10953 316407007954 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 316407007955 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 316407007956 FAD binding pocket; other site 316407007957 FAD binding motif; other site 316407007958 catalytic residues; other site 316407007959 NAD binding pocket; other site 316407007960 phosphate binding motif; other site 316407007961 beta-alpha-beta structure motif; other site 316407007962 6-pyruvoyl tetrahydropterin synthase (PTPS). 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 uptake by a...; Region: PTPS; cd00470 316407007963 homohexamer interface; other site 316407007964 putative substrate stabilizing pore; other site 316407007965 pterin binding site; other site 316407007966 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407007967 ferredoxin-like protein FixX; Provisional; Region: PRK15449 316407007968 Glycerol-3-phosphate responsive antiterminator; Region: G3P_antiterm; cl00852 316407007969 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 316407007970 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 316407007971 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 316407007972 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 316407007973 Ligand binding site; other site 316407007974 Protein of unknown function (DUF2950); Region: DUF2950; pfam11453 316407007975 benzoate transport; Region: 2A0115; TIGR00895 316407007976 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 316407007977 putative substrate translocation pore; other site 316407007978 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 316407007979 FAD binding domain; Region: FAD_binding_4; cl10516 316407007980 2-deoxy-D-gluconate 3-dehydrogenase; Provisional; Region: PRK06935 316407007981 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407007982 Major Facilitator Superfamily; Region: MFS_1; pfam07690 316407007983 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 316407007984 Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]; Region: XylB; COG1070 316407007985 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; pfam00370 316407007986 FGGY family of carbohydrate kinases, C-terminal domain; Region: FGGY_C; pfam02782 316407007987 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 316407007988 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; cl14056 316407007989 Domain of unknown function (DUF477); Region: DUF477; cl01535 316407007990 enolase; Provisional; Region: eno; PRK00077 316407007991 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 316407007992 dimer interface; other site 316407007993 metal-binding site 316407007994 substrate binding pocket; other site 316407007995 CTP synthetase; Validated; Region: pyrG; PRK05380 316407007996 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...; Region: CTGs; cd03113 316407007997 Catalytic site; other site 316407007998 active site 316407007999 UTP binding site; other site 316407008000 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 316407008001 active site 316407008002 putative oxyanion hole; other site 316407008003 catalytic triad; other site 316407008004 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 316407008005 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00737 316407008006 PemK-like protein; Region: PemK; cl00995 316407008007 SpoVT / AbrB like domain; Region: SpoVT_AbrB; cl00877 316407008008 (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional; Region: relA; PRK10872 316407008009 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 316407008010 synthetase active site; other site 316407008011 NTP binding site; other site 316407008012 metal-binding site 316407008013 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...; Region: TGS_RelA_SpoT; cd01668 316407008014 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 316407008015 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 316407008016 TRAM domain; Region: TRAM; cl01282 316407008017 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 316407008018 S-adenosylmethionine binding site; other site 316407008019 hybrid sensory histidine kinase BarA; Provisional; Region: PRK11107 316407008020 Uncharacterized signal transduction histidine kinase domain (DUF2222); Region: DUF2222; pfam09984 316407008021 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 connected by an extended linker. The...; Region: HAMP; cl01054 316407008022 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 trans-...; Region: HisKA; cd00082 316407008023 dimer interface; other site 316407008024 phosphorylation site 316407008025 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 316407008026 ATP binding site; other site 316407008027 Mg2+ binding site; other site 316407008028 G-X-G motif; other site 316407008029 Uncharacterized domain of BarA-like signal transduction histidine kinases [Signal transduction mechanisms]; Region: COG4999 316407008030 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 316407008031 active site 316407008032 phosphorylation site 316407008033 intermolecular recognition site; other site 316407008034 dimerization interface; other site 316407008035 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 316407008036 putative binding surface; other site 316407008037 active site 316407008038 glucarate dehydratase; Region: glucar-dehydr; TIGR03247 316407008039 D-Glucarate dehydratase (GlucD) catalyzes the dehydration of both D-glucarate and L-idarate to form 5-keto-4-deoxy-D-glucarate (5-KDG) , the initial reaction of the catabolic pathway for (D)-glucarate. GlucD belongs to the enolase superfamily of...; Region: D-glucarate_dehydratase; cd03323 316407008040 active site 316407008041 tetramer interface; other site 316407008042 glucarate dehydratase; Region: glucar-dehydr; TIGR03247 316407008043 D-Glucarate dehydratase (GlucD) catalyzes the dehydration of both D-glucarate and L-idarate to form 5-keto-4-deoxy-D-glucarate (5-KDG) , the initial reaction of the catabolic pathway for (D)-glucarate. GlucD belongs to the enolase superfamily of...; Region: D-glucarate_dehydratase; cd03323 316407008044 active site 316407008045 tetramer interface; other site 316407008046 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 316407008047 d-galactonate transporter; Region: 2A0114; TIGR00893 316407008048 putative substrate translocation pore; other site 316407008049 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 316407008050 tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not...; Region: PseudoU_synth_TruC; cd02563 316407008051 probable active site; other site 316407008052 Domain of unknown function, DUF446; Region: DUF446; cl01187 316407008053 Syd protein; Region: Syd; cl06405 316407008054 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 316407008055 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 316407008056 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 316407008057 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 316407008058 Domain of unknown function (DUF3412); Region: DUF3412; pfam11892 316407008059 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 316407008060 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407008061 L-serine deaminase; Provisional; Region: PRK15023 316407008062 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 316407008063 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 316407008064 flap endonuclease-like protein; Provisional; Region: PRK09482 316407008065 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and...; Region: 53EXOc; cd00008 316407008066 metal binding site I; metal-binding site 316407008067 putative ssDNA interaction site; other site 316407008068 metal binding site II; metal-binding site 316407008069 lactaldehyde reductase; Region: lactal_redase; TIGR02638 316407008070 Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria; Region: LPO; cd08176 316407008071 dimer interface; other site 316407008072 active site 316407008073 metal-binding site 316407008074 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; cd00398 316407008075 intersubunit interface; other site 316407008076 active site 316407008077 Zn2+ binding site; other site 316407008078 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 316407008079 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 316407008080 putative substrate translocation pore; other site 316407008081 L-fucose isomerase; Provisional; Region: fucI; PRK10991 316407008082 L-fucose isomerase (FucIase); FucIase converts L-fucose, an aldohexose, to its ketose form, which prepares it for aldol cleavage (similar to the isomerization of glucose during glycolysis). L-fucose (or 6-deoxy-L-galactose) is found in blood group...; Region: L-fucose_isomerase; cd03556 316407008083 hexamer (dimer of trimers) interface; other site 316407008084 trimer interface; other site 316407008085 substrate binding site; other site 316407008086 Mn binding site; other site 316407008087 L-fuculokinase; Provisional; Region: PRK10331 316407008088 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; pfam00370 316407008089 FGGY family of carbohydrate kinases, C-terminal domain; Region: FGGY_C; pfam02782 316407008090 RbsD / FucU transport protein family; Region: RbsD_FucU; cl00809 316407008091 DNA-binding transcriptional activator FucR; Provisional; Region: PRK10411 316407008092 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407008093 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 316407008094 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional; Region: PRK11760 316407008095 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; cl12011 316407008096 Protein of unknown function (DUF423); Region: DUF423; cl01008 316407008097 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 316407008098 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407008099 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 316407008100 dimerization interface; other site 316407008101 substrate binding pocket; other site 316407008102 Bacterial protein of unknown function (DUF903); Region: DUF903; pfam06004 316407008103 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 316407008104 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 316407008105 pyridoxal 5'-phosphate binding pocket; other site 316407008106 catalytic residue; other site 316407008107 Fe-S metabolism associated domain; Region: SufE; cl00951 316407008108 sulfur acceptor protein CsdL; Provisional; Region: PRK15116 316407008109 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-...; Region: YgdL_like; cd00755 316407008110 putative ATP binding site; other site 316407008111 putative substrate interface; other site 316407008112 murein transglycosylase A; Provisional; Region: mltA; PRK11162 316407008113 MltA specific insert domain; Region: MltA; pfam03562 316407008114 3D domain; Region: 3D; cl01439 316407008115 Localisation of periplasmic protein complexes; Region: AMIN; pfam11741 316407008116 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 316407008117 active site 316407008118 metal-binding site 316407008119 N-acetylglutamate synthase; Validated; Region: PRK05279 316407008120 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 N-...; Region: AAK_NAGS-ABP; cd04237 316407008121 putative feedback inhibition sensing region; other site 316407008122 putative nucleotide binding site; other site 316407008123 putative substrate binding site; other site 316407008124 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 316407008125 exonuclease V subunit alpha; Provisional; Region: recD; PRK10875 316407008126 Putative ATPase (DUF699); Region: DUF699; pfam05127 316407008127 UvrD/REP helicase; Region: UvrD-helicase; cl14126 316407008128 UvrD/REP helicase; Region: UvrD-helicase; cl14126 316407008129 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 316407008130 protease3; Provisional; Region: PRK15101 316407008131 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 316407008132 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 316407008133 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 316407008134 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 316407008135 exodeoxyribonuclease V, gamma subunit; Region: recC; TIGR01450 316407008136 Prepilin peptidase dependent protein C; Region: DUF3728; cl08108 316407008137 Protein of unknown function (DUF2509); Region: DUF2509; cl11672 316407008138 hypothetical protein; Provisional; Region: PRK10557 316407008139 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 316407008140 hypothetical protein; Provisional; Region: PRK10506 316407008141 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 316407008142 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 316407008143 dimerization interface; other site 316407008144 active site 316407008145 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 316407008146 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional; Region: PRK11061 316407008147 GAF domain; Region: GAF; cl00853 316407008148 PEP-utilising enzyme, N-terminal; Region: PEP-utilizers_N; pfam05524 316407008149 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 316407008150 Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their...; Region: malate_synt; cl09155 316407008151 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...; Region: Ap4A_hydrolase_plant_like; cd03671 316407008152 putative active site; other site 316407008153 Ap4A binding site; other site 316407008154 nudix motif; other site 316407008155 putative metal binding site; other site 316407008156 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; Region: MutH_Sau3AI; cd00583 316407008157 putative DNA-binding cleft; other site 316407008158 putative DNA clevage site; other site 316407008159 molecular lever; other site 316407008160 Integral membrane protein TerC family; Region: TerC; cl10468 316407008161 peptidylprolyl isomerase; Provisional; Region: prsA; PRK04405 316407008162 Bacterial protein of unknown function (DUF903); Region: DUF903; pfam06004 316407008163 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...; Region: Aldo_ket_red; cd06660 316407008164 active site 316407008165 catalytic tetrad; other site 316407008166 lysophospholipid transporter LplT; Provisional; Region: PRK11195 316407008167 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; cl11420 316407008168 bifunctional acyl-[acyl carrier protein] synthetase/2-acylglycerophosphoethanolamine acyltransferase; Validated; Region: PRK08043 316407008169 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 316407008170 putative acyl-acceptor binding pocket; other site 316407008171 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 316407008172 DNA-binding transcriptional regulator GalR; Provisional; Region: PRK10727 316407008173 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 316407008174 DNA binding site 316407008175 domain linker motif; other site 316407008176 Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism; Region: PBP1_GalS_like; cd06270 316407008177 dimerization interface (closed form); other site 316407008178 ligand binding site; other site 316407008179 diaminopimelate decarboxylase; Provisional; Region: PRK11165 316407008180 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 316407008181 active site 316407008182 pyridoxal 5'-phosphate (PLP) binding site; other site 316407008183 substrate binding site; other site 316407008184 catalytic residues; other site 316407008185 dimer interface; other site 316407008186 DNA-binding transcriptional regulator LysR; Provisional; Region: PRK11013 316407008187 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407008188 The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold; Region: PBP2_LysR; cd08456 316407008189 putative dimerization interface; other site 316407008190 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 316407008191 aspartate racemase; Region: asp_race; TIGR00035 316407008192 MFS transporter, sugar porter (SP) family; Region: SP; TIGR00879 316407008193 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 316407008194 putative substrate translocation pore; other site 316407008195 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 316407008196 2-deoxy-D-gluconate 3-dehydrogenase; Validated; Region: PRK08993 316407008197 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407008198 KduI/IolB family; Region: KduI; cl01508 316407008199 putative acyltransferase; Provisional; Region: PRK05790 316407008200 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 316407008201 dimer interface; other site 316407008202 active site 316407008203 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 316407008204 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407008205 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...; Region: LuxR_C_like; cl10457 316407008206 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...; Region: trans_reg_C; cl00209 316407008207 chaperone protein SicA; Provisional; Region: PRK15331 316407008208 Tetratricopeptide repeat; Region: TPR_3; pfam07720 316407008209 Tetratricopeptide repeat; Region: TPR_3; pfam07720 316407008210 transcriptional regulator; Provisional; Region: PRK11906 316407008211 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...; Region: trans_reg_C; cd00383 316407008212 DNA binding site 316407008213 ECK2852:JW5457:b2854; predicted peptidoglycan-binding enzyme 316407008214 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 316407008215 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...; Region: LuxR_C_like; cd06170 316407008216 DNA binding residues 316407008217 dimerization interface; other site 316407008218 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 316407008219 invasion protein OrgB; Provisional; Region: PRK15322 316407008220 ECK2856:JW5460:b2858; hypothetical protein 316407008221 Bacterial type III secretion apparatus protein (OrgA_MxiK); Region: OrgA_MxiK; cl09716 316407008222 IS2 transposase TnpB; Reviewed; Region: PRK09409 316407008223 Integrase core domain; Region: rve; cl01316 316407008224 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; cl01116 316407008225 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 316407008226 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 316407008227 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 316407008228 putative peptidoglycan binding site; other site 316407008229 Peptidase family M23; Region: Peptidase_M23; pfam01551 316407008230 xanthine dehydrogenase subunit XdhA; Provisional; Region: PRK09970 316407008231 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; pfam01315 316407008232 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 316407008233 xanthine dehydrogenase subunit XdhB; Provisional; Region: PRK09971 316407008234 FAD binding domain; Region: FAD_binding_4; cl10516 316407008235 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; pfam03450 316407008236 xanthine dehydrogenase subunit XdhC; Provisional; Region: PRK09908 316407008237 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 316407008238 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 316407008239 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 316407008240 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...; Region: AAA; cd00009 316407008241 Walker A motif; other site 316407008242 ATP binding site; other site 316407008243 Walker B motif; other site 316407008244 arginine finger; other site 316407008245 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 316407008246 aspartate/ornithine carbamoyltransferase family protein; Validated; Region: PRK07200 316407008247 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 316407008248 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 316407008249 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 316407008250 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)...; Region: Trp-synth-beta_II; cd00640 316407008251 catalytic residue; other site 316407008252 Peptidase dimerization domain; Region: M20_dimer; cl09126 316407008253 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 316407008254 D-hydantoinase; Region: D-hydantoinase; TIGR02033 316407008255 D-hydantoinases (D-HYD) also called dihydropyrimidases (DHPase) and related proteins; DHPases are a family of enzymes that catalyze the reversible hydrolytic ring opening of the amide bond in five- or six-membered cyclic diamides, like...; Region: D-HYD; cd01314 316407008256 tetramer interface; other site 316407008257 active site 316407008258 AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an...; Region: AAK_CK; cd04235 316407008259 carbamate kinase; Reviewed; Region: PRK12686 316407008260 putative substrate binding site; other site 316407008261 homodimer interface; other site 316407008262 nucleotide binding site; other site 316407008263 nucleotide binding site; other site 316407008264 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 316407008265 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 316407008266 The M14 family of metallocarboxypeptidases (MCPs) are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key...; Region: Peptidase_M14_like; cl11393 316407008267 probable selenium-dependent hydroxylase accessory protein YqeC; Region: TIGR03172 316407008268 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 316407008269 Ligand binding site; other site 316407008270 metal-binding site 316407008271 putative selenate reductase subunit YgfK; Provisional; Region: PRK09853 316407008272 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407008273 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407008274 putative selenium metabolism protein SsnA; Region: Se_ssnA; TIGR03314 316407008275 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 316407008276 active site 316407008277 putative substrate binding pocket; other site 316407008278 FAD binding domain; Region: FAD_binding_4; cl10516 316407008279 probable selenate reductase, FAD-binding subunit; Region: Se_sel_red_FAD; TIGR03312 316407008280 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; pfam03450 316407008281 putative hypoxanthine oxidase; Provisional; Region: PRK09800 316407008282 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 316407008283 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; pfam01315 316407008284 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 316407008285 Permease family; Region: Xan_ur_permease; cl00967 316407008286 guanine deaminase; Provisional; Region: PRK09228 316407008287 Guanine deaminase (GDEase). Guanine deaminase is an aminohydrolase responsible for the conversion of guanine to xanthine and ammonia, the first step to utilize guanine as a nitrogen source. This reaction also removes the guanine base from the pool and...; Region: GDEase; cd01303 316407008288 active site 316407008289 Permease family; Region: Xan_ur_permease; cl00967 316407008290 putative oxidoreductase Fe-S binding subunit; Reviewed; Region: PRK12769 316407008291 putative oxidoreductase Fe-S binding subunit; Reviewed; Region: PRK12809 316407008292 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407008293 Permease family; Region: Xan_ur_permease; cl00967 316407008294 Isopentenyldiphosphate isomerase [Lipid metabolism]; Region: Idi; COG1443 316407008295 Isopentenyl diphosphate (IPP) isomerase, a member of the Nudix hydrolase superfamily, is a key enzyme in the isoprenoid biosynthetic pathway. Isoprenoids comprise a large family of natural products including sterols, carotenoids, dolichols and...; Region: IPP_Isomerase; cd02885 316407008296 active site 316407008297 metal-binding site 316407008298 nudix motif; other site 316407008299 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 316407008300 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-...; Region: LysRS_N; cd04322 316407008301 dimer interface; other site 316407008302 putative anticodon binding site; other site 316407008303 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 316407008304 motif 1; other site 316407008305 active site 316407008306 motif 2; other site 316407008307 motif 3; other site 316407008308 peptide chain release factor 2; Validated; Region: prfB; PRK00578 316407008309 RF-1 domain; Region: RF-1; cl02875 316407008310 RF-1 domain; Region: RF-1; cl02875 316407008311 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 316407008312 DHH family; Region: DHH; pfam01368 316407008313 DHHA1 domain; Region: DHHA1; pfam02272 316407008314 protein disulfide isomerase II DsbC; Provisional; Region: PRK10877 316407008315 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...; Region: DsbA_DsbC_DsbG; cd03020 316407008316 dimerization domain; other site 316407008317 dimer interface; other site 316407008318 catalytic residues; other site 316407008319 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 316407008320 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 of chromosomal replication, and stable plasmid...; Region: INT_XerDC; cd00798 316407008321 Int/Topo IB signature motif; other site 316407008322 active site 316407008323 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 316407008324 Protein of unknown function (DUF1434); Region: DUF1434; pfam07254 316407008325 Protein of unknown function (DUF339); Region: Sdh5; cl01110 316407008326 putative global regulator; Reviewed; Region: PRK09559 316407008327 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 316407008328 Haemolysin-III related; Region: HlyIII; cl03831 316407008329 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...; Region: ASCH_yqfb_like; cd06552 316407008330 Glycosyl hydrolase family 1; Region: Glyco_hydro_1; cl01046 316407008331 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407008332 short chain dehydrogenase; Provisional; Region: PRK06123 316407008333 glycine dehydrogenase; Provisional; Region: PRK05367 316407008334 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...; Region: GDC-P; cd00613 316407008335 tetramer interface; other site 316407008336 pyridoxal 5'-phosphate binding site; other site 316407008337 catalytic residue; other site 316407008338 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...; Region: GDC-P; cd00613 316407008339 tetramer interface; other site 316407008340 pyridoxal 5'-phosphate binding site; other site 316407008341 catalytic residue; other site 316407008342 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 L-...; Region: GCS_H; cd06848 316407008343 lipoyl attachment site; other site 316407008344 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 316407008345 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 316407008346 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407008347 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 316407008348 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407008349 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 316407008350 proline aminopeptidase P II; Provisional; Region: PRK10879 316407008351 Aminopeptidase P, N-terminal domain; Region: AMP_N; pfam05195 316407008352 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...; Region: Prolidase; cd01087 316407008353 active site 316407008354 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 316407008355 Cell division protein ZapA; Region: ZapA; cl01146 316407008356 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 316407008357 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 316407008358 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407008359 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 316407008360 L-serine binding site; other site 316407008361 ACT domain interface; other site 316407008362 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 316407008363 tetramer (dimer of dimers) interface; other site 316407008364 active site 316407008365 dimer interface; other site 316407008366 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 316407008367 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 316407008368 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407008369 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 316407008370 putative dimerization interface; other site 316407008371 methylmalonyl-CoA mutase; Reviewed; Region: PRK09426 316407008372 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Alpha subunit-like subfamily; contains proteins similar to the alpha subunit of Propionbacterium shermanni MCM, as well as human and E. coli MCM. Members of this subfamily...; Region: MM_CoA_mutase_alpha_like; cd03679 316407008373 active site 316407008374 substrate binding site; other site 316407008375 coenzyme B12 binding site; other site 316407008376 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen...; Region: MM_CoA_mut_B12_BD; cd02071 316407008377 B12 binding site; other site 316407008378 cobalt ligand; other site 316407008379 membrane ATPase/protein kinase; Provisional; Region: PRK09435 316407008380 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 316407008381 Walker A; other site 316407008382 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 316407008383 G4 box; other site 316407008384 G5 box; other site 316407008385 enoyl-CoA hydratase; Provisional; Region: PRK06688 316407008386 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 316407008387 substrate binding site; other site 316407008388 oxyanion hole (OAH) forming residues; other site 316407008389 trimer interface; other site 316407008390 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 316407008391 succinate CoA transferases; Region: YgfH_subfam; TIGR03458 316407008392 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407008393 Transcriptional regulator [Transcription]; Region: LysR; COG0583 316407008394 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 316407008395 Protein of unknown function (DUF541); Region: SIMPL; cl01077 316407008396 LysE type translocator; Region: LysE; cl00565 316407008397 mechanosensitive channel MscS; Provisional; Region: PRK10334 316407008398 Mechanosensitive ion channel; Region: MS_channel; pfam00924 316407008399 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 316407008400 Class II Type A, Fructose-1,6-bisphosphate (FBP) aldolases. The enzyme catalyses the zinc-dependent, reversible aldol condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to form fructose-1,6-bisphosphate. FBP aldolase is...; Region: FBP_aldolase_IIA; cd00946 316407008401 active site 316407008402 intersubunit interface; other site 316407008403 zinc binding site; other site 316407008404 Na+ binding site; other site 316407008405 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 316407008406 substrate binding site; other site 316407008407 hinge regions; other site 316407008408 ADP binding site; other site 316407008409 catalytic site; other site 316407008410 erythrose 4-phosphate dehydrogenase; Provisional; Region: PRK13535 316407008411 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407008412 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 316407008413 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407008414 active site 316407008415 Mannitol repressor; Region: MtlR; cl11450 316407008416 Bacterial fructose-1,6-bisphosphatase, glpX-encoded. A dimeric enzyme dependent on Mg(2+). glpX-encoded FPBase (FBPase class II) differs from other members of the inositol-phosphatase superfamily by permutation of secondary structure elements. The core...; Region: FBPase_glpX; cd01516 316407008417 Fructose-1,6-bisphosphatase/sedoheptulose 1,7-bisphosphatase and related proteins [Carbohydrate transport and metabolism]; Region: GlpX; COG1494 316407008418 putative active site; other site 316407008419 L-sorbose-1-phosphate reductase; Region: sorbose_phosphate_red; cd08238 316407008420 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 316407008421 putative NAD(P) binding site; other site 316407008422 catalytic Zn binding site; other site 316407008423 Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]; Region: MtlA; COG2213 316407008424 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 316407008425 PTS_IIB_mannitol: subunit IIB of enzyme II (EII) of the mannitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is a mannitol-specific permease with two cytoplasmic domains (IIA and IIB) and a...; Region: PTS_IIB_mannitol; cd05567 316407008426 active site 316407008427 P-loop; other site 316407008428 phosphorylation site 316407008429 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 316407008430 active site 316407008431 phosphorylation site 316407008432 transketolase; Reviewed; Region: PRK12753 316407008433 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 316407008434 TPP-binding site; other site 316407008435 dimer interface; other site 316407008436 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 316407008437 PYR/PP interface; other site 316407008438 dimer interface; other site 316407008439 TPP binding site; other site 316407008440 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 316407008441 Peptidase family M48; Region: Peptidase_M48; cl12018 316407008442 Arginase family; Region: Arginase; cl00306 316407008443 arginine decarboxylase; Provisional; Region: PRK05354 316407008444 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 316407008445 dimer interface; other site 316407008446 active site 316407008447 pyridoxal 5'-phosphate (PLP) binding site; other site 316407008448 catalytic residues; other site 316407008449 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 316407008450 Virulence promoting factor; Region: YqgB; pfam11036 316407008451 Protein of unknown function (DUF2684); Region: DUF2684; pfam10885 316407008452 S-adenosylmethionine synthetase; Validated; Region: PRK05250 316407008453 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 316407008454 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 316407008455 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 316407008456 MFS transporter, sugar porter (SP) family; Region: SP; TIGR00879 316407008457 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 316407008458 putative substrate translocation pore; other site 316407008459 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 316407008460 SprT homologues; Region: SprT; cl01182 316407008461 SprT-like family; Region: SprT-like; pfam10263 316407008462 DNA-specific endonuclease I; Provisional; Region: PRK15137 316407008463 Endonuclease I; Region: Endonuclease_1; cl01003 316407008464 RNA methyltransferase; Region: Methyltrans_RNA; cl00611 316407008465 glutathione synthetase; Provisional; Region: PRK05246 316407008466 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 316407008467 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 316407008468 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 316407008469 Uncharacterized protein family (UPF0081); Region: UPF0081; cl00525 316407008470 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 316407008471 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 316407008472 Walker A motif; other site 316407008473 ATP binding site; other site 316407008474 Walker B motif; other site 316407008475 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 316407008476 pyridoxal 5'-phosphate (PLP) binding site; other site 316407008477 catalytic residue; other site 316407008478 YGGT family; Region: YGGT; cl00508 316407008479 YGGT family; Region: YGGT; cl00508 316407008480 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 316407008481 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 Ham1-...; Region: HAM1; cd00515 316407008482 active site 316407008483 dimerization interface; other site 316407008484 HemN family oxidoreductase; Provisional; Region: PRK05660 316407008485 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 316407008486 FeS/SAM binding site; other site 316407008487 HemN C-terminal region; Region: HemN_C; pfam06969 316407008488 Protein of unknown function (DUF1202); Region: DUF1202; pfam06717 316407008489 Asparaginase (amidohydrolase): Asparaginases are tetrameric enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases, one highly specific for asparagine and localised to the...; Region: Asparaginase; cd00411 316407008490 tetramer interface; other site 316407008491 active site/substrate binding site 316407008492 Protein of unknown function (DUF2884); Region: DUF2884; cl08135 316407008493 Protein with unknown function (DUF469); Region: DUF469; cl01237 316407008494 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; cl12011 316407008495 adenine DNA glycosylase; Provisional; Region: PRK10880 316407008496 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 316407008497 minor groove reading motif; other site 316407008498 helix-hairpin-helix signature motif; other site 316407008499 substrate binding pocket; other site 316407008500 active site 316407008501 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 316407008502 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 316407008503 DNA binding and oxoG recognition site 316407008504 Bacterial Fe(2+) trafficking; Region: Iron_traffic; cl01104 316407008505 murein transglycosylase C; Provisional; Region: mltC; PRK11671 316407008506 Domain of unknown function (DUF3393); Region: DUF3393; pfam11873 316407008507 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 catalyze...; Region: LT_GEWL; cd00254 316407008508 N-acetyl-D-glucosamine binding site; other site 316407008509 catalytic residue; other site 316407008510 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128; cl11521 316407008511 Nucleoside H+ symporter; Region: Nuc_H_symport; pfam03825 316407008512 ornithine decarboxylase; Provisional; Region: PRK13578 316407008513 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; cl09944 316407008514 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...; Region: Orn_deC_like; cd00615 316407008515 homodimer interface; other site 316407008516 pyridoxal 5'-phosphate binding site; other site 316407008517 catalytic residue; other site 316407008518 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 316407008519 Protein of unknown function (DUF554); Region: DUF554; cl00784 316407008520 General secretion pathway, M protein; Region: GspM; cl01222 316407008521 ECK2964:JW5924:b2969; predicted secretion pathway protein, L-type protein 316407008522 putative type II secretion protein GspC; Provisional; Region: PRK09681 316407008523 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 C-...; Region: PDZ_serine_protease; cd00987 316407008524 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 316407008525 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 316407008526 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 316407008527 glycolate transporter; Provisional; Region: PRK09695 316407008528 L-lactate permease; Region: Lactate_perm; cl00701 316407008529 Malate synthase G (MSG), monomeric enzyme present in some bacteria. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate...; Region: malate_synt_G; cd00728 316407008530 active site 316407008531 Domain of unknown function (DUF336); Region: DUF336; cl01249 316407008532 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 316407008533 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 alpha-; Region: HCP_like; cl14655 316407008534 Cysteine-rich domain; Region: CCG; pfam02754 316407008535 Cysteine-rich domain; Region: CCG; pfam02754 316407008536 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 316407008537 FAD binding domain; Region: FAD_binding_4; cl10516 316407008538 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 316407008539 FAD binding domain; Region: FAD_binding_4; cl10516 316407008540 DNA-binding transcriptional regulator GlcC; Provisional; Region: PRK09990 316407008541 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407008542 DNA binding site 316407008543 FCD domain; Region: FCD; cl11656 316407008544 Transposase domain (DUF772); Region: DUF772; cl12084 316407008545 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 316407008546 Polysaccharide biosynthesis protein; Region: Polysacc_synt; cl10513 316407008547 Thymidylate kinase [Nucleotide transport and metabolism]; Region: Tmk; COG0125 316407008548 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407008549 active site 316407008550 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...; Region: TMPK; cd01672 316407008551 TMP-binding site; other site 316407008552 ATP-binding site; other site 316407008553 Thymidylate kinase [Nucleotide transport and metabolism]; Region: Tmk; COG0125 316407008554 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...; Region: TMPK; cd01672 316407008555 TMP-binding site; other site 316407008556 ATP-binding site; other site 316407008557 Phosphate transporter family; Region: PHO4; cl00396 316407008558 Phosphate transporter family; Region: PHO4; cl00396 316407008559 bifunctional glutathionylspermidine amidase/glutathionylspermidine synthetase; Provisional; Region: PRK10507 316407008560 NlpC/P60 family; Region: NLPC_P60; cl11438 316407008561 Glutathionylspermidine synthase; Region: GSP_synth; cl00503 316407008562 putative S-transferase; Provisional; Region: PRK11752 316407008563 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...; Region: GST_N_Ure2p_like; cd03048 316407008564 C-terminal domain interface; other site 316407008565 GSH binding site (G-site); other site 316407008566 dimer interface; other site 316407008567 GST_C 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...; Region: GST_C_Ure2p_like; cd03178 316407008568 dimer interface; other site 316407008569 N-terminal domain interface; other site 316407008570 putative substrate binding pocket (H-site); other site 316407008571 HupF/HypC family; Region: HupF_HypC; cl00394 316407008572 Hydrogenase expression/synthesis hypA family; Region: HypA; cl00418 316407008573 Protein of unknown function (DUF3457); Region: DUF3457; cl08122 316407008574 coenzyme F420-reducing hydrogenase delta subunit (putative coenzyme F420 hydrogenase processing subunit); Region: frhD; TIGR00130 316407008575 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...; Region: H2MP_MemB-H2up; cd06062 316407008576 putative substrate-binding site; other site 316407008577 nickel binding site; other site 316407008578 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; cl00417 316407008579 Polysulphide reductase [Energy production and conversion]; Region: COG5557; cl01295 316407008580 Polysulphide reductase, NrfD; Region: NrfD; pfam03916 316407008581 hydrogenase 2 protein HybA; Provisional; Region: PRK10882 316407008582 hydrogenase 2 small subunit; Provisional; Region: PRK10468 316407008583 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 316407008584 Protein of unknown function (DUF2623); Region: DUF2623; pfam11115 316407008585 ECK2993:JW5926:b2999; predicted hydrolase 316407008586 ECK2994:JW5496:b3000; predicted dienlactone hydrolase 316407008587 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...; Region: Aldo_ket_red; cd06660 316407008588 active site 316407008589 catalytic tetrad; other site 316407008590 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 316407008591 oxidoreductase; Provisional; Region: PRK07985 316407008592 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407008593 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 316407008594 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 316407008595 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 316407008596 cystathionine beta-lyase; Provisional; Region: PRK08114 316407008597 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 316407008598 homodimer interface; other site 316407008599 substrate-cofactor binding pocket; other site 316407008600 pyridoxal 5'-phosphate binding site; other site 316407008601 catalytic residue; other site 316407008602 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 316407008603 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 316407008604 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407008605 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 316407008606 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407008607 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 316407008608 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 316407008609 dimer interface; other site 316407008610 active site 316407008611 metal-binding site 316407008612 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...; Region: Aldo_ket_red; cd06660 316407008613 active site 316407008614 catalytic tetrad; other site 316407008615 Murein lipoprotein [Cell envelope biogenesis, outer membrane]; Region: COG4238; cl11539 316407008616 hypothetical protein; Provisional; Region: PRK01254 316407008617 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase...; Region: B12-binding_like; cl00293 316407008618 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; cl14056 316407008619 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 316407008620 FtsI repressor; Provisional; Region: PRK10883 316407008621 Multicopper oxidase; Region: Cu-oxidase; cl14658 316407008622 Multicopper oxidase; Region: Cu-oxidase; cl14658 316407008623 1-acyl-sn-glycerol-3-phosphate acyltransferase; Provisional; Region: PRK15018 316407008624 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 316407008625 putative acyl-acceptor binding pocket; other site 316407008626 DNA topoisomerase IV, A subunit, proteobacterial; Region: parC_Gneg; TIGR01062 316407008627 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 in...; Region: TOP4c; cd00187 316407008628 CAP-like domain; other site 316407008629 active site 316407008630 primary dimer interface; other site 316407008631 oligopeptide ABC transporter substrate-binding protein OppA; Provisional; Region: PRK15104 316407008632 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 316407008633 peptide binding site; other site 316407008634 putative zinc finger/helix-turn-helix protein, YgiT family; Region: CxxCG_CxxCG_HTH; TIGR03830 316407008635 YgiT-type zinc finger domain; Region: YgiT_finger; TIGR03831 316407008636 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl09100 316407008637 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; cl01368 316407008638 Bacterial OB fold (BOF) protein; Region: BOF; cl01196 316407008639 DNA-binding transcriptional regulator QseB; Provisional; Region: PRK10336 316407008640 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 316407008641 active site 316407008642 phosphorylation site 316407008643 intermolecular recognition site; other site 316407008644 dimerization interface; other site 316407008645 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...; Region: trans_reg_C; cd00383 316407008646 DNA binding site 316407008647 sensor protein QseC; Provisional; Region: PRK10337 316407008648 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 trans-...; Region: HisKA; cd00082 316407008649 dimer interface; other site 316407008650 phosphorylation site 316407008651 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 316407008652 ATP binding site; other site 316407008653 Mg2+ binding site; other site 316407008654 G-X-G motif; other site 316407008655 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 316407008656 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 316407008657 DNA topoisomerase IV, B subunit, proteobacterial; Region: parE_Gneg; TIGR01055 316407008658 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 316407008659 ATP binding site; other site 316407008660 Mg2+ binding site; other site 316407008661 G-X-G motif; other site 316407008662 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 316407008663 anchoring element; other site 316407008664 dimer interface; other site 316407008665 ATP binding site; other site 316407008666 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 316407008667 active site 316407008668 metal-binding site 316407008669 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 316407008670 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; cl12031 316407008671 Esterase/lipase [General function prediction only]; Region: COG1647 316407008672 cyclic 3',5'-adenosine monophosphate phosphodiesterase; Provisional; Region: PRK11148 316407008673 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 316407008674 active site 316407008675 metal-binding site 316407008676 hexamer interface; other site 316407008677 Protein of unknown function (DUF1249); Region: DUF1249; cl01223 316407008678 ADP-ribose pyrophosphatase NudF; Provisional; Region: nudF; PRK10729 316407008679 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...; Region: ADPRase_NUDT5; cd03424 316407008680 dimer interface; other site 316407008681 ADP-ribose binding site; other site 316407008682 active site 316407008683 nudix motif; other site 316407008684 metal-binding site 316407008685 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 316407008686 Outer membrane efflux protein; Region: OEP; pfam02321 316407008687 Outer membrane efflux protein; Region: OEP; pfam02321 316407008688 Protein of unknown function (DUF1190); Region: DUF1190; cl10031 316407008689 Glutathionylspermidine synthase; Region: GSP_synth; cl00503 316407008690 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 316407008691 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 316407008692 putative active site; other site 316407008693 metal-binding site 316407008694 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 316407008695 ZIP Zinc transporter; Region: Zip; pfam02535 316407008696 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 316407008697 Protein of unknown function (DUF526); Region: DUF526; cl01115 316407008698 Fimbrial protein; Region: Fimbrial; cl01416 316407008699 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; cl01116 316407008700 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 316407008701 IS2 transposase TnpB; Reviewed; Region: PRK09409 316407008702 Integrase core domain; Region: rve; cl01316 316407008703 pilin outer membrane usher protein SafC; Provisional; Region: PRK15223; cl14650 316407008704 Fimbrial Usher protein; Region: Usher; pfam00577 316407008705 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 316407008706 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 316407008707 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 316407008708 Glycogen synthesis protein; Region: GlgS; cl11663 316407008709 Protein of unknown function (DUF1449); Region: DUF1449; pfam07290 316407008710 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2268 316407008711 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...; Region: Band_7_flotillin; cd03399 316407008712 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional; Region: PRK11316 316407008713 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 316407008714 putative ribose interaction site; other site 316407008715 putative ADP binding site; other site 316407008716 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 316407008717 active site 316407008718 nucleotide binding site; other site 316407008719 HIGH motif; other site 316407008720 KMSKS motif; other site 316407008721 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 316407008722 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 316407008723 metal binding triad; other site 316407008724 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 316407008725 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 316407008726 metal binding triad; other site 316407008727 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 316407008728 Uncharacterized conserved protein [Function unknown]; Region: COG3025 316407008729 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 316407008730 putative active site; other site 316407008731 putative metal binding residues; other site 316407008732 signature motif; other site 316407008733 putative triphosphate binding site; other site 316407008734 CHAD domain; Region: CHAD; cl10506 316407008735 SH3 domain-containing protein; Provisional; Region: PRK10884 316407008736 Bacterial SH3 domain; Region: SH3_3; cl02551 316407008737 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 316407008738 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 316407008739 active site 316407008740 NTP binding site; other site 316407008741 metal binding triad; metal-binding site 316407008742 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 316407008743 Bacitracin resistance protein BacA; Region: BacA; cl00858 316407008744 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...; Region: DHNA_DHNTPE; cd00534 316407008745 homooctamer interface; other site 316407008746 active site 316407008747 Domain of unknown function (DUF205); Region: DUF205; cl00410 316407008748 transcriptional activator TtdR; Provisional; Region: PRK09801 316407008749 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407008750 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_9; cd08479 316407008751 putative effector binding pocket; other site 316407008752 putative dimerization interface; other site 316407008753 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 316407008754 Fumarase C-terminus; Region: Fumerase_C; cl00795 316407008755 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; cl09110 316407008756 transmembrane helices; other site 316407008757 UGMP family protein; Validated; Region: PRK09604 316407008758 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 316407008759 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 316407008760 DNA primase; Validated; Region: dnaG; PRK05667 316407008761 CHC2 zinc finger; Region: zf-CHC2; cl02597 316407008762 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 316407008763 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 316407008764 active site 316407008765 metal-binding site 316407008766 interdomain interaction site; other site 316407008767 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 316407008768 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; cl07879 316407008769 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 316407008770 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 316407008771 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 316407008772 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 316407008773 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 316407008774 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 316407008775 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...; Region: Sigma70_r4; cd06171 316407008776 DNA binding residues 316407008777 Uracil DNA glycosylase superfamily; Region: UDG; cl00483 316407008778 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 316407008779 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 316407008780 FAD binding pocket; other site 316407008781 FAD binding motif; other site 316407008782 phosphate binding motif; other site 316407008783 NAD binding pocket; other site 316407008784 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407008785 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 316407008786 PAS fold; Region: PAS_3; pfam08447 316407008787 putative active site; other site 316407008788 heme pocket; other site 316407008789 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 316407008790 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 316407008791 putrescine--2-oxoglutarate aminotransferase; Provisional; Region: PRK11522 316407008792 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 316407008793 inhibitor-cofactor binding pocket; inhibition site 316407008794 pyridoxal 5'-phosphate binding site; other site 316407008795 catalytic residue; other site 316407008796 tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain; Region: tRNA_bind_CsaA; cd02798 316407008797 dimer interface; other site 316407008798 putative tRNA-binding site; other site 316407008799 DNA-binding transcriptional repressor EbgR; Provisional; Region: PRK10339 316407008800 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 316407008801 DNA binding site 316407008802 domain linker motif; other site 316407008803 Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism; Region: PBP1_GalR; cd01544 316407008804 putative dimerization interface; other site 316407008805 putative ligand binding site; other site 316407008806 cryptic beta-D-galactosidase subunit alpha; Reviewed; Region: ebgA; PRK10340 316407008807 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 316407008808 domain; Region: Glyco_hydro_2; pfam00703 316407008809 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 316407008810 Beta galactosidase small chain; Region: Bgal_small_N; pfam02929 316407008811 Domain of unknown function (DUF386); Region: DUF386; cl01047 316407008812 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407008813 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 316407008814 alpha-glucosidase; Provisional; Region: PRK10137 316407008815 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; cl01801 316407008816 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 316407008817 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 316407008818 active site 316407008819 FMN binding site; other site 316407008820 2,4-decadienoyl-CoA binding site; other site 316407008821 catalytic residue; other site 316407008822 4Fe-4S cluster binding site; other site 316407008823 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 316407008824 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl09100 316407008825 Uncharacterized protein conserved in bacteria (DUF2136); Region: DUF2136; cl01912 316407008826 SAM-dependent 23S ribosomal RNA mG1835 methyltransferase; Provisional; Region: PRK15001 316407008827 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 316407008828 S-adenosylmethionine binding site; other site 316407008829 Protein of unknown function DUF45; Region: DUF45; cl00636 316407008830 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 316407008831 putative active site; other site 316407008832 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 316407008833 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407008834 Integral membrane protein TerC family; Region: TerC; cl10468 316407008835 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 316407008836 Bacterial inner membrane protein; Region: Imp-YgjV; pfam10688 316407008837 galactarate dehydratase; Region: galactar-dH20; TIGR03248 316407008838 SAF domain; Region: SAF; cl00555 316407008839 SAF domain; Region: SAF; cl00555 316407008840 Glucuronate isomerase; Region: UxaC; cl00829 316407008841 d-galactonate transporter; Region: 2A0114; TIGR00893 316407008842 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 316407008843 putative substrate translocation pore; other site 316407008844 DNA-binding transcriptional repressor ExuR; Provisional; Region: PRK11523 316407008845 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407008846 DNA binding site 316407008847 FCD domain; Region: FCD; cl11656 316407008848 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 316407008849 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 316407008850 EnvZ/OmpR regulon moderator; Provisional; Region: PRK10629 316407008851 Protein of unknown function (DUF1090); Region: DUF1090; pfam06476 316407008852 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 316407008853 Protein of unknown function (DUF1469); Region: DUF1469; cl12095 316407008854 DoxX; Region: DoxX; cl00976 316407008855 Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: ECM4; COG0435 316407008856 GST_C family, ECM4-like subfamily; composed of predominantly uncharacterized and taxonomically diverse proteins with similarity to the translation product of the Saccharomyces cerevisiae gene ECM4. ECM4, a gene of unknown function, is involved in cell...; Region: GST_C_ECM4_like; cd03190 316407008857 Protein of unknown function (DUF805); Region: DUF805; cl01224 316407008858 Protein of unknown function (DUF805); Region: DUF805; cl01224 316407008859 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407008860 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 316407008861 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 316407008862 dimerization interface; other site 316407008863 Cupin domain; Region: Cupin_2; cl09118 316407008864 L-cysteine desulfidase [Amino acid transport and metabolism]; Region: COG3681 316407008865 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 316407008866 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 316407008867 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 316407008868 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407008869 L-serine dehydratase TdcG; Provisional; Region: PRK15040 316407008870 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 316407008871 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 316407008872 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 316407008873 homotrimer interaction site; other site 316407008874 putative active site; other site 316407008875 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 316407008876 Pyruvate formate lyase 1; Region: PFL1; cd01678 316407008877 coenzyme A binding site; other site 316407008878 active site 316407008879 catalytic residues; other site 316407008880 glycine loop; other site 316407008881 Transposase domain (DUF772); Region: DUF772; cl12084 316407008882 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 316407008883 Acetokinase family; Region: Acetate_kinase; cl01029 316407008884 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407008885 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 316407008886 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 316407008887 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 316407008888 tetramer interface; other site 316407008889 pyridoxal 5'-phosphate binding site; other site 316407008890 catalytic residue; other site 316407008891 DNA-binding transcriptional activator TdcA; Provisional; Region: PRK10341 316407008892 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407008893 The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold; Region: PBP2_TdcA; cd08418 316407008894 putative substrate binding pocket; other site 316407008895 putative dimerization interface; other site 316407008896 DNA-binding transcriptional activator TdcR; Provisional; Region: PRK11424 316407008897 hypothetical protein; Provisional; Region: PRK09716 316407008898 Glycerate kinase family; Region: Gly_kinase; cl00841 316407008899 tartronate semialdehyde reductase; Provisional; Region: garR; PRK11559 316407008900 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407008901 Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their...; Region: malate_synt; cl09155 316407008902 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [Carbohydrate transport and metabolism]; Region: HpcH; COG3836 316407008903 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 316407008904 d-galactonate transporter; Region: 2A0114; TIGR00893 316407008905 putative substrate translocation pore; other site 316407008906 galactarate dehydratase; Region: galactar-dH20; TIGR03248 316407008907 SAF domain; Region: SAF; cl00555 316407008908 SAF domain; Region: SAF; cl00555 316407008909 SpoVT / AbrB like domain; Region: SpoVT_AbrB; cl00877 316407008910 Toxin with endonuclease activity YhaV; Region: Toxin_YhaV; pfam11663 316407008911 DNA-binding transcriptional regulator AgaR; Provisional; Region: PRK09802 316407008912 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407008913 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 316407008914 Tagatose 6 phosphate kinase; Region: Tagatose_6_P_K; cl09211 316407008915 Mannose/sorbose 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 is one of four...; Region: PTS_IIB_man; cd00001 316407008916 active site 316407008917 phosphorylation site 316407008918 ECK3122:JW3103:b3134; N-acetylgalactosamine-specific enzyme IIC component of PTS, fragment 316407008919 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...; Region: metallo-dependent_hydrolases; cl00281 316407008920 putative sugar isomerase, AgaS family; Region: agaS_fam; TIGR02815 316407008921 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 316407008922 dimer interface; other site 316407008923 active site 316407008924 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 316407008925 putative active site; other site 316407008926 Fructose/tagarose-bisphosphate aldolase class II. This family includes fructose-1,6-bisphosphate (FBP) and tagarose 1,6-bisphosphate (TBP) aldolases. FBP-aldolase is homodimeric and used in gluconeogenesis and glycolysis; the enzyme controls the...; Region: FTBP_aldolase_II; cd00453 316407008927 hypothetical protein; Provisional; Region: PRK08185 316407008928 active site 316407008929 intersubunit interface; other site 316407008930 zinc binding site; other site 316407008931 Na+ binding site; other site 316407008932 Mannose/sorbose 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 is one of four...; Region: PTS_IIB_man; cd00001 316407008933 active site 316407008934 phosphorylation site 316407008935 PTS system sorbose-specific iic component; Region: EII-Sor; cl01506 316407008936 PTS system mannose/fructose/sorbose family IID component; Region: EIID-AGA; cl01507 316407008937 GlcN6P_deaminase: Glucosamine-6-phosphate (GlcN6P) deaminase subfamily; GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium. The reaction is an aldo-keto isomerization coupled with an amination...; Region: GlcN6P_deaminase; cd01399 316407008938 active site 316407008939 trimer interface; other site 316407008940 allosteric site; other site 316407008941 active site lid 316407008942 Fimbrial protein; Region: Fimbrial; cl01416 316407008943 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 316407008944 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 316407008945 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 316407008946 pilin outer membrane usher protein SafC; Provisional; Region: PRK15223; cl14650 316407008947 Fimbrial Usher protein; Region: Usher; pfam00577 316407008948 Fimbrial protein; Region: Fimbrial; cl01416 316407008949 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 316407008950 Putative lipoprotein [General function prediction only]; Region: LppC; COG3107 316407008951 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 316407008952 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 316407008953 putative ligand binding site; other site 316407008954 Uncharacterized protein family UPF0102; Region: UPF0102; cl00516 316407008955 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 316407008956 dimer interface; other site 316407008957 active site 316407008958 outer membrane lipoprotein; Provisional; Region: PRK11023 316407008959 Putative phospholipid-binding domain; Region: BON; cl02771 316407008960 Putative phospholipid-binding domain; Region: BON; cl02771 316407008961 Predicted permease; Region: DUF318; cl00487 316407008962 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 316407008963 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407008964 A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_like; cd03134 316407008965 proposed catalytic triad; other site 316407008966 conserved cys residue; other site 316407008967 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 316407008968 GIY-YIG catalytic domain; Region: GIY-YIG; cl01061 316407008969 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 316407008970 SCP-2 sterol transfer family; Region: SCP2; cl01225 316407008971 Peptidase family U32; Region: Peptidase_U32; cl03113 316407008972 Peptidase family U32; Region: Peptidase_U32; cl03113 316407008973 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 316407008974 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 316407008975 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407008976 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 316407008977 ATP-dependent RNA helicase DeaD; Provisional; Region: PRK11634 316407008978 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 316407008979 ATP binding site; other site 316407008980 Mg++ binding site; other site 316407008981 motif III; other site 316407008982 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 316407008983 nucleotide binding region; other site 316407008984 ATP-binding site; other site 316407008985 DbpA RNA binding domain; Region: DbpA; pfam03880 316407008986 lipoprotein NlpI; Provisional; Region: PRK11189 316407008987 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 316407008988 binding surface 316407008989 TPR motif; other site 316407008990 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 316407008991 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 316407008992 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 316407008993 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 316407008994 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 316407008995 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 316407008996 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 316407008997 putative nucleic acid binding region; other site 316407008998 G-X-X-G motif; other site 316407008999 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 316407009000 RNA binding site; other site 316407009001 domain interface; other site 316407009002 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...; Region: Ribosomal_S15p_S13e; cd00353 316407009003 16S/18S rRNA binding site; other site 316407009004 S13e-L30e interaction site; other site 316407009005 25S rRNA binding site; other site 316407009006 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 316407009007 PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of...; Region: PseudoU_synth_EcTruB; cd02573 316407009008 RNA binding site; other site 316407009009 active site 316407009010 Ribosome-binding factor A; Region: RBFA; cl00542 316407009011 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 316407009012 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 316407009013 translation initiation factor IF-2; Region: IF-2; TIGR00487 316407009014 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 316407009015 IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily. IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases...; Region: IF2_eIF5B; cd01887 316407009016 G1 box; other site 316407009017 putative GEF interaction site; other site 316407009018 GTP/Mg2+ binding site; other site 316407009019 Switch I region; other site 316407009020 G2 box; other site 316407009021 G3 box; other site 316407009022 Switch II region; other site 316407009023 G4 box; other site 316407009024 G5 box; other site 316407009025 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...; Region: IF2_mtIF2_II; cd03702 316407009026 Translation-initiation factor 2; Region: IF-2; pfam11987 316407009027 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...; Region: mtIF2_IVc; cd03692 316407009028 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 316407009029 NusA N-terminal domain; Region: NusA_N; pfam08529 316407009030 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...; Region: S1_NusA; cd04455 316407009031 RNA binding site; other site 316407009032 homodimer interface; other site 316407009033 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 316407009034 G-X-X-G motif; other site 316407009035 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 316407009036 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 316407009037 ribosome maturation protein RimP; Reviewed; Region: PRK00092 316407009038 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members...; Region: Sm_like; cl00259 316407009039 YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix...; Region: YlxS_C; cd01734 316407009040 Sm1 motif; other site 316407009041 predicted subunit interaction site; other site 316407009042 RNA binding pocket; other site 316407009043 Sm2 motif; other site 316407009044 argininosuccinate synthase; Region: argG; TIGR00032 316407009045 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 316407009046 Ligand Binding Site; other site 316407009047 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 316407009048 Sulfatase; Region: Sulfatase; cl10460 316407009049 Preprotein translocase SecG subunit; Region: SecG; cl09123 316407009050 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 316407009051 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 UDP-N-...; Region: GlmM; cd05802 316407009052 active site 316407009053 substrate binding site; other site 316407009054 metal-binding site 316407009055 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 316407009056 substrate binding pocket; other site 316407009057 dimer interface; other site 316407009058 inhibitor binding site; inhibition site 316407009059 ATP-dependent metalloprotease; Reviewed; Region: hflB; PRK10733 316407009060 FtsH Extracellular; Region: FtsH_ext; pfam06480 316407009061 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...; Region: AAA; cd00009 316407009062 Walker A motif; other site 316407009063 ATP binding site; other site 316407009064 Walker B motif; other site 316407009065 arginine finger; other site 316407009066 Peptidase family M41; Region: Peptidase_M41; pfam01434 316407009067 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 316407009068 S-adenosylmethionine binding site; other site 316407009069 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 316407009070 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 316407009071 domain; Region: GreA_GreB_N; pfam03449 316407009072 C-term; Region: GreA_GreB; pfam01272 316407009073 Beta-lactamase; Region: Beta-lactamase; cl01009 316407009074 GTPase CgtA; Reviewed; Region: obgE; PRK12298 316407009075 GTP1/OBG; Region: GTP1_OBG; pfam01018 316407009076 Obg subfamily. The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins...; Region: Obg; cd01898 316407009077 G1 box; other site 316407009078 GTP/Mg2+ binding site; other site 316407009079 Switch I region; other site 316407009080 G2 box; other site 316407009081 G3 box; other site 316407009082 Switch II region; other site 316407009083 G4 box; other site 316407009084 G5 box; other site 316407009085 EamA-like transporter family; Region: EamA; cl01037 316407009086 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 316407009087 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 316407009088 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 316407009089 substrate binding pocket; other site 316407009090 chain length determination region; other site 316407009091 substrate-Mg2+ binding site; other site 316407009092 catalytic residues; other site 316407009093 aspartate-rich region 1; other site 316407009094 active site lid residues 316407009095 aspartate-rich region 2; other site 316407009096 Predicted transcriptional regulator [Transcription]; Region: Nlp; cl01357 316407009097 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Validated; Region: PRK09369 316407009098 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 316407009099 hinge; other site 316407009100 active site 316407009101 BolA-like protein; Region: BolA; cl00386 316407009102 Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; Region: STAS; cl00604 316407009103 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; cl01074 316407009104 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 316407009105 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 316407009106 mce related protein; Region: MCE; cl03606 316407009107 Domain of unknown function DUF140; Region: DUF140; cl00510 316407009108 putative ABC transporter ATP-binding protein YrbF; Provisional; Region: PRK11831 316407009109 ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex...; Region: ABC_Org_Solvent_Resistant; cd03261 316407009110 Walker A/P-loop; other site 316407009111 ATP binding site; other site 316407009112 Q-loop/lid; other site 316407009113 ABC transporter signature motif; other site 316407009114 Walker B; other site 316407009115 D-loop; other site 316407009116 H-loop/switch region; other site 316407009117 putative calcium/sodium:proton antiporter; Provisional; Region: PRK10734 316407009118 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 316407009119 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 316407009120 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 316407009121 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 5-...; Region: SIS_Kpsf; cd05014 316407009122 putative active site; other site 316407009123 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 316407009124 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; cl11391 316407009125 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 316407009126 Protein of unknown function (DUF1239); Region: DUF1239; pfam06835 316407009127 OstA-like protein; Region: OstA; cl00844 316407009128 lipopolysaccharide ABC transporter ATP-binding protein; Provisional; Region: PRK10895 316407009129 The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in...; Region: ABC_YhbG; cd03218 316407009130 Walker A/P-loop; other site 316407009131 ATP binding site; other site 316407009132 Q-loop/lid; other site 316407009133 ABC transporter signature motif; other site 316407009134 Walker B; other site 316407009135 D-loop; other site 316407009136 H-loop/switch region; other site 316407009137 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 316407009138 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 316407009139 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 316407009140 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 316407009141 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 A site...; Region: RaiA; cd00552 316407009142 30S subunit binding site; other site 316407009143 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 316407009144 active site 316407009145 phosphorylation site 316407009146 P-loop ATPase protein family; Region: ATP_bind_2; cl10035 316407009147 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 316407009148 dimerization domain swap beta strand; other site 316407009149 regulatory protein interface; other site 316407009150 active site 316407009151 regulatory phosphorylation site; other site 316407009152 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 316407009153 Transglycosylase; Region: Transgly; cl07896 316407009154 Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1; Region: GATase1_ES1; cd03133 316407009155 conserved cys residue; other site 316407009156 aerobic respiration control sensor protein ArcB; Provisional; Region: PRK11091 316407009157 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 316407009158 putative active site; other site 316407009159 heme pocket; other site 316407009160 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 trans-...; Region: HisKA; cd00082 316407009161 dimer interface; other site 316407009162 phosphorylation site 316407009163 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 316407009164 ATP binding site; other site 316407009165 Mg2+ binding site; other site 316407009166 G-X-G motif; other site 316407009167 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 316407009168 active site 316407009169 phosphorylation site 316407009170 intermolecular recognition site; other site 316407009171 dimerization interface; other site 316407009172 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 316407009173 putative binding surface; other site 316407009174 active site 316407009175 radical SAM protein, TIGR01212 family; Region: TIGR01212 316407009176 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; cl14056 316407009177 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 316407009178 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 N-...; Region: GltS; cd00713 316407009179 active site 316407009180 dimer interface; other site 316407009181 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 316407009182 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...; Region: GltS_FMN; cd02808 316407009183 active site 316407009184 FMN binding site; other site 316407009185 substrate binding site; other site 316407009186 3Fe-4S cluster binding site; other site 316407009187 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 316407009188 domain interface; other site 316407009189 glutamate synthase small subunit family protein, proteobacterial; Region: gltD_gamma_fam; TIGR01318 316407009190 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 alpha-; Region: HCP_like; cl14655 316407009191 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407009192 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407009193 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407009194 Protein of unknown function (DUF1120); Region: DUF1120; cl05856 316407009195 putative fimbrial chaperone protein; Provisional; Region: PRK09918 316407009196 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 316407009197 pilin outer membrane usher protein SafC; Provisional; Region: PRK15223; cl14650 316407009198 Fimbrial Usher protein; Region: Usher; pfam00577 316407009199 ECK3207:JW3184+JW3187:b4569; hypothetical protein 316407009200 ECK3207:JW3184:b3217; hypothetical protein, N-ter fragment 316407009201 ECK3207:JW3187:b4549; hypothetical protein, C-ter fragment 316407009202 Transposase domain (DUF772); Region: DUF772; cl12084 316407009203 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 316407009204 Protein of unknown function (DUF1120); Region: DUF1120; cl05856 316407009205 Protein of unknown function (DUF1016); Region: DUF1016; cl01979 316407009206 Domain of unknown function (DUF386); Region: DUF386; cl01047 316407009207 N-acetylmannosamine kinase; Provisional; Region: PRK05082 316407009208 ROK family; Region: ROK; cl09121 316407009209 ROK family; Region: ROK; cl09121 316407009210 N-acetylmannosamine-6-phosphate epimerase (NanE) converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate. This reaction is part of the pathway that allows the usage of sialic acid as a carbohydrate source. Sialic acids are a family...; Region: NanE; cd04729 316407009211 N-acetylmannosamine-6-phosphate 2-epimerase; Provisional; Region: PRK01130 316407009212 putative active site cavity; other site 316407009213 putative sialic acid transporter; Provisional; Region: PRK03893 316407009214 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 316407009215 putative substrate translocation pore; other site 316407009216 N-acetylneuraminate lyase; Region: nanA; TIGR00683 316407009217 N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL), which catalyses the reversible aldol reaction of N-acetyl-D-mannosamine and pyruvate to give N-acetyl-D-neuraminic acid (D-sialic acid). It has a widespread application as...; Region: NAL; cd00954 316407009218 inhibitor site; inhibition site 316407009219 active site 316407009220 dimer interface; other site 316407009221 catalytic residue; other site 316407009222 transcriptional regulator NanR; Provisional; Region: PRK03837 316407009223 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407009224 DNA binding site 316407009225 FCD domain; Region: FCD; cl11656 316407009226 C4-dicarboxylate transporter [Energy production and conversion]; Region: DcuC; cl14617 316407009227 C4-dicarboxylate anaerobic carrier; Region: DcuC; pfam03606 316407009228 Stringent starvation protein B; Region: SspB; cl01120 316407009229 stringent starvation protein A; Provisional; Region: sspA; PRK09481 316407009230 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 316407009231 C-terminal domain interface; other site 316407009232 putative GSH binding site (G-site); other site 316407009233 dimer interface; other site 316407009234 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_C_SspA; cd03186 316407009235 dimer interface; other site 316407009236 N-terminal domain interface; other site 316407009237 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 316407009238 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 316407009239 23S rRNA interface; other site 316407009240 L3 interface; other site 316407009241 AFG1-like ATPase; Region: AFG1_ATPase; pfam03969 316407009242 Protein of unknown function (DUF1043); Region: DUF1043; cl11473 316407009243 serine endoprotease; Provisional; Region: PRK10139 316407009244 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...; Region: Tryp_SPc; cl00149 316407009245 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 C-...; Region: PDZ_serine_protease; cd00987 316407009246 protein binding site; other site 316407009247 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 C-...; Region: PDZ_serine_protease; cd00987 316407009248 serine endoprotease; Provisional; Region: PRK10898 316407009249 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...; Region: Tryp_SPc; cl00149 316407009250 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 C-...; Region: PDZ_serine_protease; cd00987 316407009251 malate dehydrogenase; Provisional; Region: PRK05086 316407009252 Glyoxysomal and mitochondrial malate dehydrogenases; Region: MDH_glyoxysomal_mitochondrial; cd01337 316407009253 NAD binding site; other site 316407009254 dimerization interface; other site 316407009255 Substrate binding site; other site 316407009256 arginine repressor; Provisional; Region: PRK05066 316407009257 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 316407009258 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 316407009259 Protein of unknown function (DUF1471); Region: DUF1471; cl11507 316407009260 Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it thus inhibiting its potentially lethal RNase activity inside the...; Region: Barstar; cd05142 316407009261 RNAase interaction site; other site 316407009262 Bacterial protein of unknown function (DUF939); Region: DUF939; cl12136 316407009263 Fusaric acid resistance protein family; Region: FUSC; pfam04632 316407009264 p-hydroxybenzoic acid efflux subunit AaeA; Provisional; Region: PRK10559 316407009265 Protein of unknown function (DUF1656); Region: DUF1656; cl11658 316407009266 transcriptional regulator; Provisional; Region: PRK10632 316407009267 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407009268 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 316407009269 putative effector binding pocket; other site 316407009270 dimerization interface; other site 316407009271 Putative modulator of DNA gyrase; Region: PmbA_TldD; cl00398 316407009272 hypothetical protein; Provisional; Region: PRK10899 316407009273 ribonuclease G; Provisional; Region: PRK11712 316407009274 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 316407009275 homodimer interface; other site 316407009276 oligonucleotide binding site; other site 316407009277 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 316407009278 active site 316407009279 dimer interface; other site 316407009280 rod shape-determining protein MreD; Region: MreD; cl01087 316407009281 rod shape-determining protein MreC; Region: mreC; TIGR00219 316407009282 rod shape-determining protein MreC; Region: MreC; cl12287 316407009283 rod shape-determining protein MreB; Provisional; Region: PRK13927 316407009284 Actin; An ubiquitous protein involved in the formation of filaments that are a major component of the cytoskeleton. Interaction with myosin provides the basis of muscular contraction and many aspects of cell motility. Each actin protomer binds one...; Region: ACTIN; cl11528 316407009285 ATP binding site; other site 316407009286 profilin binding site; other site 316407009287 regulatory protein CsrD; Provisional; Region: PRK11059 316407009288 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316407009289 metal-binding site 316407009290 active site 316407009291 I-site; other site 316407009292 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 316407009293 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 316407009294 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 316407009295 NADP binding site; other site 316407009296 dimer interface; other site 316407009297 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 316407009298 carboxyltransferase (CT) interaction site; other site 316407009299 biotinylation site; other site 316407009300 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 316407009301 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 316407009302 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 316407009303 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 316407009304 Protein of unknown function (DUF997); Region: DUF997; cl01614 316407009305 Sodium:solute symporter family; Region: SSF; cl00456 316407009306 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; cl12011 316407009307 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 316407009308 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 316407009309 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...; Region: DUS_like_FMN; cd02801 316407009310 FMN binding site; other site 316407009311 active site 316407009312 catalytic residues; other site 316407009313 substrate binding site; other site 316407009314 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 316407009315 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; cl12011 316407009316 Protein of unknown function (DUF2556); Region: DUF2556; pfam10831 316407009317 DNA-binding transcriptional regulator EnvR; Provisional; Region: PRK09975 316407009318 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316407009319 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 316407009320 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 316407009321 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 316407009322 Protein export membrane protein; Region: SecD_SecF; cl14618 316407009323 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...; Region: PBPb; cd00134 316407009324 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 316407009325 substrate binding pocket; other site 316407009326 membrane-bound complex binding site; other site 316407009327 hinge residues; other site 316407009328 ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]; Region: BatB; COG4597 316407009329 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...; Region: TM_PBP2; cl00427 316407009330 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...; Region: TM_PBP2; cd06261 316407009331 dimer interface; other site 316407009332 conserved gate region; other site 316407009333 putative PBP binding loops; other site 316407009334 ABC-ATPase subunit interface; other site 316407009335 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 316407009336 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...; Region: TM_PBP2; cd06261 316407009337 dimer interface; other site 316407009338 conserved gate region; other site 316407009339 putative PBP binding loops; other site 316407009340 ABC-ATPase subunit interface; other site 316407009341 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 316407009342 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP; Region: ABC_HisP_GlnQ_permeases; cd03262 316407009343 Walker A/P-loop; other site 316407009344 ATP binding site; other site 316407009345 Q-loop/lid; other site 316407009346 ABC transporter signature motif; other site 316407009347 Walker B; other site 316407009348 D-loop; other site 316407009349 H-loop/switch region; other site 316407009350 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 316407009351 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 5-aminoimidazole-4-carboxamide-; Region: IMPCH; cd01421 316407009352 purine monophosphate binding site; other site 316407009353 dimer interface; other site 316407009354 putative catalytic residues; other site 316407009355 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 316407009356 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 316407009357 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 316407009358 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 316407009359 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 316407009360 transcriptional regulatory protein ZraR; Provisional; Region: PRK10365 316407009361 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 316407009362 active site 316407009363 phosphorylation site 316407009364 intermolecular recognition site; other site 316407009365 dimerization interface; other site 316407009366 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...; Region: AAA; cd00009 316407009367 Walker A motif; other site 316407009368 ATP binding site; other site 316407009369 Walker B motif; other site 316407009370 arginine finger; other site 316407009371 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 316407009372 sensor protein ZraS; Provisional; Region: PRK10364 316407009373 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 trans-...; Region: HisKA; cd00082 316407009374 dimer interface; other site 316407009375 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 316407009376 ATP binding site; other site 316407009377 Mg2+ binding site; other site 316407009378 G-X-G motif; other site 316407009379 P pilus assembly/Cpx signaling pathway, periplasmic inhibitor/zinc-resistance associated protein [Intracellular trafficking and secretion / Cell motility and secretio / Signal transduction mechanisms / Inorganic ion transport and metabolism]; Region: CpxP; cl01482 316407009380 Protein of unknown function (DUF1481); Region: DUF1481; pfam07356 316407009381 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 higher-...; Region: HU_IHF; cd00591 316407009382 IHF dimer interface; other site 316407009383 IHF - DNA interface; other site 316407009384 Protein of unknown function, DUF; Region: DUF416; cl01166 316407009385 Endonuclease_V, a DNA repair enzyme that initiates repair of nitrosative deaminated purine bases; Region: Endonuclease_V; cd06559 316407009386 active site 316407009387 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...; Region: URO-D; cd00717 316407009388 substrate binding site; other site 316407009389 active site 316407009390 NADH pyrophosphatase; Reviewed; Region: nudC; PRK00241 316407009391 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 316407009392 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 316407009393 NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for...; Region: NADH_pyrophosphatase; cd03429 316407009394 putative NADH binding site; other site 316407009395 putative active site; other site 316407009396 nudix motif; other site 316407009397 putative metal binding site; other site 316407009398 Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ; Region: Rsd_AlgQ; cl11478 316407009399 ThiC family; Region: ThiC; cl08031 316407009400 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- (beta-...; Region: TMP_TenI; cd00564 316407009401 thiamine phosphate binding site; other site 316407009402 active site 316407009403 pyrophosphate binding site; other site 316407009404 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...; Region: ThiF_MoeB_HesA_family; cd00757 316407009405 thiazole biosynthesis adenylyltransferase ThiF, E. coli subfamily; Region: adenyl_thiF; TIGR02356 316407009406 ATP binding site; other site 316407009407 substrate interface; other site 316407009408 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 316407009409 thiS-thiF/thiG interaction site; other site 316407009410 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 316407009411 ThiS interaction site; other site 316407009412 putative active site; other site 316407009413 tetramer interface; other site 316407009414 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09240 316407009415 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 316407009416 FeS/SAM binding site; other site 316407009417 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 316407009418 stationary phase growth adaptation protein; Provisional; Region: PRK09717 316407009419 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 316407009420 DNA-directed RNA polymerase, gamma subunit; Region: rpoC1_cyan; TIGR02387 316407009421 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 316407009422 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 316407009423 DNA-directed RNA polymerase subunit beta'; Provisional; Region: rpoC2; PRK02597 316407009424 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 316407009425 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 316407009426 Rpb1 - Rpb6 interaction site; other site 316407009427 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 316407009428 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 316407009429 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 316407009430 DNA binding site 316407009431 Rpb1 (beta') - Rpb2 (beta) interaction site; other site 316407009432 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; cl04593 316407009433 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 316407009434 RNA polymerase beta subunit; Region: RNA_pol_Rpb2_1; cl04591 316407009435 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 316407009436 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; cl04593 316407009437 RPB11 interaction site; other site 316407009438 RPB12 interaction site; other site 316407009439 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 316407009440 RPB3 interaction site; other site 316407009441 RPB1 interaction site; other site 316407009442 RPB11 interaction site; other site 316407009443 RPB10 interaction site; other site 316407009444 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 316407009445 core dimer interface; other site 316407009446 peripheral dimer interface; other site 316407009447 L10 interface; other site 316407009448 L11 interface; other site 316407009449 putative EF-Tu interaction site; other site 316407009450 putative EF-G interaction site; other site 316407009451 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...; Region: Ribosomal_L10; cd05797 316407009452 23S rRNA interface; other site 316407009453 Interface with L7/L12 ribosomal proteins; other site 316407009454 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...; Region: Ribosomal_L1; cd00403 316407009455 mRNA/rRNA interface; other site 316407009456 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 316407009457 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 316407009458 23S rRNA interface; other site 316407009459 L7/L12 interface; other site 316407009460 putative thiostrepton binding site; other site 316407009461 L25 interface; other site 316407009462 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 316407009463 Transcription termination factor nusG; Region: NusG; cl02766 316407009464 KOW (Kyprides, Ouzounis, Woese) motif; Region: KOW; smart00739 316407009465 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 316407009466 elongation factor Tu; Reviewed; Region: PRK00049 316407009467 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 316407009468 G1 box; other site 316407009469 GEF interaction site; other site 316407009470 GTP/Mg2+ binding site; other site 316407009471 Switch I region; other site 316407009472 G2 box; other site 316407009473 G3 box; other site 316407009474 Switch II region; other site 316407009475 G4 box; other site 316407009476 G5 box; other site 316407009477 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 316407009478 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 316407009479 Antibiotic Binding Site; other site 316407009480 pantothenate kinase; Provisional; Region: PRK05439 316407009481 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 in...; Region: PanK; cd02025 316407009482 ATP-binding site; other site 316407009483 CoA-binding site; other site 316407009484 Mg2+-binding site; other site 316407009485 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407009486 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 316407009487 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 316407009488 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 316407009489 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 316407009490 FAD binding domain; Region: FAD_binding_4; cl10516 316407009491 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 316407009492 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 316407009493 vitamin B12/cobalamin outer membrane transporter; Provisional; Region: btuB; PRK10641 316407009494 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 316407009495 N-terminal plug; other site 316407009496 ligand-binding site; other site 316407009497 tRNA (uracil-5-)-methyltransferase; Validated; Region: PRK05031 316407009498 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; cl12011 316407009499 Protein of unknown function (DUF1422); Region: DUF1422; cl11649 316407009500 DNA-binding transcriptional repressor FabR; Provisional; Region: PRK11202 316407009501 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316407009502 soluble pyridine nucleotide transhydrogenase; Provisional; Region: PRK05249 316407009503 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407009504 Pyridine nucleotide-disulphide oxidoreductase, dimerization domain; Region: Pyr_redox_dim; pfam02852 316407009505 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 316407009506 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407009507 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 316407009508 dimerization interface; other site 316407009509 argininosuccinate lyase; Provisional; Region: PRK04833 316407009510 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 316407009511 active sites 316407009512 tetramer interface; other site 316407009513 AAK_NAGK-NC: N-Acetyl-L-glutamate kinase - noncyclic (NAGK-NC) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of microbial arginine biosynthesis using the acetylated, noncyclic route of...; Region: AAK_NAGK-NC; cd04249 316407009514 nucleotide binding site; other site 316407009515 N-acetyl-L-glutamate binding site; other site 316407009516 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 316407009517 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407009518 Semialdehyde dehydrogenase, dimerization domain; Region: Semialdhyde_dhC; pfam02774 316407009519 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 316407009520 Peptidase dimerization domain; Region: M20_dimer; cl09126 316407009521 Phosphoenolpyruvate carboxylase [Carbohydrate transport and metabolism; Energy production and conversion]; Region: COG1892; cl14656 316407009522 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 316407009523 hypothetical protein; Provisional; Region: PRK10649 316407009524 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 316407009525 Sulfatase; Region: Sulfatase; cl10460 316407009526 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]; Region: COG4753 316407009527 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407009528 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA...; Region: PTS_IIB_fructose; cd05569 316407009529 P-loop; other site 316407009530 active site 316407009531 phosphorylation site 316407009532 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; cl14056 316407009533 pyruvate formate lyase II activase; Provisional; Region: PRK10076 316407009534 putative formate acetyltransferase 2; Provisional; Region: pflD; PRK09983 316407009535 Pyruvate formate lyase 2 and related enzymes; Region: PFL2_DhaB_BssA; cd01677 316407009536 dimer interface; other site 316407009537 active site 316407009538 glycine loop; other site 316407009539 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA...; Region: PTS_IIB_fructose; cd05569 316407009540 P-loop; other site 316407009541 active site 316407009542 phosphorylation site 316407009543 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 316407009544 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 316407009545 dimerization domain swap beta strand; other site 316407009546 regulatory protein interface; other site 316407009547 active site 316407009548 regulatory phosphorylation site; other site 316407009549 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 316407009550 PEP-utilising enzyme, N-terminal; Region: PEP-utilizers_N; pfam05524 316407009551 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 316407009552 Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their...; Region: malate_synt; cl09155 316407009553 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 316407009554 active site 316407009555 phosphorylation site 316407009556 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea, which are member of the MipB/TalC subfamily of class I aldolases. FSA catalyze an aldol cleavage of fructose 6-phosphate and do not utilize fructose, fructose 1-...; Region: Transaldolase_FSA; cd00956 316407009557 active site 316407009558 intersubunit interactions; other site 316407009559 catalytic residue; other site 316407009560 Glycerol dehydrogenases (GlyDH) catalyzes oxidation of glycerol to dihydroxyacetone in glycerol dissmilation; Region: GlyDH; cd08170 316407009561 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 316407009562 dimer interface; other site 316407009563 active site 316407009564 metal-binding site 316407009565 Domain of unknown function (DUF1287); Region: DUF1287; cl01519 316407009566 EamA-like transporter family; Region: EamA; cl01037 316407009567 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 316407009568 EamA-like transporter family; Region: EamA; cl01037 316407009569 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 316407009570 Heme-dependent peroxidases similar to plant peroxidases; Region: plant_peroxidase_like; cl00196 316407009571 heme binding site; other site 316407009572 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 316407009573 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...; Region: MTHFR; cd00537 316407009574 FAD binding site; other site 316407009575 bifunctional aspartate kinase II/homoserine dehydrogenase II; Provisional; Region: metL; PRK09466 316407009576 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 AKI-...; Region: AAK_AK-HSDH; cd04257 316407009577 putative catalytic residues; other site 316407009578 putative nucleotide binding site; other site 316407009579 putative aspartate binding site; other site 316407009580 ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase); Region: ACT_AK-like_2; cd04892 316407009581 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407009582 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 316407009583 cystathionine gamma-synthase; Provisional; Region: PRK08045 316407009584 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 316407009585 homodimer interface; other site 316407009586 substrate-cofactor binding pocket; other site 316407009587 pyridoxal 5'-phosphate binding site; other site 316407009588 catalytic residue; other site 316407009589 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' sequence; Region: Met_repressor_MetJ; cd00490 316407009590 dimerization interface; other site 316407009591 DNA binding site 316407009592 corepressor binding sites; other site 316407009593 Orthopoxvirus protein of unknown function (DUF830); Region: DUF830; cl13998 316407009594 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 316407009595 primosome assembly protein PriA; Validated; Region: PRK05580 316407009596 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 316407009597 ATP binding site; other site 316407009598 putative Mg++ binding site; other site 316407009599 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; cl12029 316407009600 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 316407009601 DNA binding site 316407009602 DNA-binding transcriptional regulator CytR; Provisional; Region: PRK11041 316407009603 domain linker motif; other site 316407009604 Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria; Region: PBP1_LacI_like_6; cd06284 316407009605 dimerization interface; other site 316407009606 ligand binding site; other site 316407009607 Sporulation related domain; Region: SPOR; cl10051 316407009608 cell division protein FtsN; Provisional; Region: PRK12757 316407009609 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 316407009610 active site 316407009611 HslU subunit interaction site; other site 316407009612 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 316407009613 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...; Region: AAA; cd00009 316407009614 Walker A motif; other site 316407009615 ATP binding site; other site 316407009616 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407009617 UbiA prenyltransferase family; Region: UbiA; cl00337 316407009618 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 316407009619 Protein of unknown function (DUF904); Region: DUF904; cl11531 316407009620 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-...; Region: MIP; cd00333 316407009621 amphipathic channel; other site 316407009622 Asn-Pro-Ala signature motifs; other site 316407009623 glycerol kinase; Provisional; Region: glpK; PRK00047 316407009624 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; pfam00370 316407009625 FGGY family of carbohydrate kinases, C-terminal domain; Region: FGGY_C; pfam02782 316407009626 Fructose-1,6-bisphosphatase/sedoheptulose 1,7-bisphosphatase and related proteins [Carbohydrate transport and metabolism]; Region: GlpX; COG1494 316407009627 Bacterial fructose-1,6-bisphosphatase, glpX-encoded. A dimeric enzyme dependent on Mg(2+). glpX-encoded FPBase (FBPase class II) differs from other members of the inositol-phosphatase superfamily by permutation of secondary structure elements. The core...; Region: FBPase_glpX; cd01516 316407009628 putative active site; other site 316407009629 ferredoxin-NADP reductase; Provisional; Region: PRK10926 316407009630 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 316407009631 FAD binding pocket; other site 316407009632 FAD binding motif; other site 316407009633 phosphate binding motif; other site 316407009634 beta-alpha-beta structure motif; other site 316407009635 NAD binding pocket; other site 316407009636 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 316407009637 Ligand Binding Site; other site 316407009638 Protein of unknown function (DUF406); Region: DUF406; cl11449 316407009639 Protein of unknown function (DUF805); Region: DUF805; cl01224 316407009640 Protein of unknown function (DUF1454); Region: DUF1454; pfam07305 316407009641 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 316407009642 substrate binding site; other site 316407009643 dimer interface; other site 316407009644 catalytic triad; other site 316407009645 CDP-diacylglycerol pyrophosphatase; Region: CDH; cl00934 316407009646 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 316407009647 6-phosphofructokinase; Provisional; Region: PRK03202 316407009648 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to a subfamily of the PFKA family (cd00363) and include bacterial ATP-dependent...; Region: Bacterial_PFK; cd00763 316407009649 active site 316407009650 ADP/pyrophosphate binding site; other site 316407009651 dimerization interface; other site 316407009652 allosteric effector site; other site 316407009653 fructose-1,6-bisphosphate binding site; other site 316407009654 Cation efflux family; Region: Cation_efflux; cl00316 316407009655 P pilus assembly/Cpx signaling pathway, periplasmic inhibitor/zinc-resistance associated protein [Intracellular trafficking and secretion / Cell motility and secretio / Signal transduction mechanisms / Inorganic ion transport and metabolism]; Region: CpxP; cl01482 316407009656 DNA-binding transcriptional regulator CpxR; Provisional; Region: PRK10955 316407009657 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 316407009658 active site 316407009659 intermolecular recognition site; other site 316407009660 dimerization interface; other site 316407009661 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...; Region: trans_reg_C; cd00383 316407009662 DNA binding site 316407009663 two-component sensor protein; Provisional; Region: cpxA; PRK09470 316407009664 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 connected by an extended linker. The...; Region: HAMP; cl01054 316407009665 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 trans-...; Region: HisKA; cd00082 316407009666 dimer interface; other site 316407009667 phosphorylation site 316407009668 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 316407009669 ATP binding site; other site 316407009670 Mg2+ binding site; other site 316407009671 G-X-G motif; other site 316407009672 6-N-hydroxylaminopurine resistance protein; Provisional; Region: PRK11536 316407009673 MOSC domain; Region: MOSC; pfam03473 316407009674 3-alpha domain; Region: 3-alpha; pfam03475 316407009675 2-keto-3-deoxygluconate permease; Region: KdgT; cl14653 316407009676 superoxide dismutase; Provisional; Region: PRK10925 316407009677 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 316407009678 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 316407009679 L-rhamnose-proton symport protein (RhaT); Region: RhaT; cl05728 316407009680 RhaT L-rhamnose-proton symporter family protein; Region: RhaT; TIGR00776 316407009681 transcriptional activator RhaR; Provisional; Region: PRK13500 316407009682 Cupin domain; Region: Cupin_2; cl09118 316407009683 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407009684 transcriptional activator RhaS; Provisional; Region: PRK13503 316407009685 Cupin domain; Region: Cupin_2; cl09118 316407009686 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407009687 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407009688 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; pfam00370 316407009689 rhamnulokinase; Provisional; Region: rhaB; PRK10640 316407009690 FGGY family of carbohydrate kinases, C-terminal domain; Region: FGGY_C; pfam02782 316407009691 L-rhamnose isomerase (RhaA); Region: RhaA; cl09945 316407009692 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; cd00398 316407009693 intersubunit interface; other site 316407009694 active site 316407009695 Zn2+ binding site; other site 316407009696 Domain of unknown function (DUF718); Region: DUF718; cl01281 316407009697 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 316407009698 active site 316407009699 phosphorylation site 316407009700 putative PTS system transporter subunits IIBC; Provisional; Region: PRK11404 316407009701 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA...; Region: PTS_IIB_fructose; cd05569 316407009702 P-loop; other site 316407009703 active site 316407009704 phosphorylation site 316407009705 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 316407009706 Peptidase dimerization domain; Region: M20_dimer; cl09126 316407009707 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 316407009708 putative frv operon regulatory protein; Provisional; Region: PRK09863 316407009709 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407009710 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 316407009711 active site 316407009712 phosphorylation site 316407009713 FdhD/NarQ family; Region: FdhD-NarQ; cl00659 316407009714 formate dehydrogenase, alpha subunit, proteobacterial-type; Region: formate-DH-alph; TIGR01553 316407009715 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 316407009716 [4Fe-4S] binding site; other site 316407009717 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 tungsten-...; Region: Molybdopterin-Binding; cl09928 316407009718 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 316407009719 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 316407009720 molybdopterin cofactor binding site; other site 316407009721 Fe-S containing; Region: FDH-beta; TIGR01582 316407009722 Formate dehydrogenase N, transmembrane; Region: Form-deh_trans; pfam09163 316407009723 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 316407009724 formate dehydrogenase accessory protein FdhE; Provisional; Region: PRK03564; cl11689 316407009725 Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]; Region: FdhE; COG3058 316407009726 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 316407009727 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 316407009728 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 316407009729 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...; Region: Dtyr_deacylase; cd00563 316407009730 putative active site; other site 316407009731 dimerization interface; other site 316407009732 putative tRNAtyr binding site; other site 316407009733 Ribonuclease BN-like family; Region: Ribonuclease_BN; cl07918 316407009734 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 316407009735 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 316407009736 motif II; other site 316407009737 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 316407009738 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407009739 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 316407009740 Ribokinase-like subgroup B. Found in bacteria and plants, this subgroup is part of the ribokinase/pfkB superfamily. Its oligomerization state is unknown at this time; Region: ribokinase_group_B; cd01945 316407009741 substrate binding site; other site 316407009742 ATP binding site; other site 316407009743 NADH-dependent gamma-hydroxybutyrate dehydrogenase; Provisional; Region: PRK15461 316407009744 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407009745 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; cl09108 316407009746 N-acyl-D-glucosamine 2-epimerase [Carbohydrate transport and metabolism]; Region: COG2942 316407009747 AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is...; Region: AGE; cd00249 316407009748 dimerization interface; other site 316407009749 putative active cleft; other site 316407009750 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 316407009751 Aldose 1-epimerase, similar to Escherichia coli YihR; Region: Aldose_epim_Ec_YihR; cd09022 316407009752 active site 316407009753 catalytic residues; other site 316407009754 alpha-glucosidase; Provisional; Region: PRK10426 316407009755 YihQ is a bacterial alpha-glucosidase with a conserved glycosyl hydrolase family 31 (GH31) domain that catalyzes the release of an alpha-glucosyl residue from the non-reducing end of alpha-glucoside substrates such as alpha-glucosyl fluoride. Orthologs...; Region: GH31_glucosidase_YihQ; cd06594 316407009756 putative active site; other site 316407009757 putative catalytic site; other site 316407009758 putative transporter; Provisional; Region: PRK11462 316407009759 sugar (Glycoside-Pentoside-Hexuronide) transporter; Region: gph; TIGR00792 316407009760 putative transporter; Provisional; Region: PRK11462 316407009761 sugar (Glycoside-Pentoside-Hexuronide) transporter; Region: gph; TIGR00792 316407009762 Oligogalacturonate-specific porin protein (KdgM); Region: KdgM; cl11629 316407009763 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 316407009764 putative substrate translocation pore; other site 316407009765 phosphoglycerate transporter family protein; Region: 2A0104; TIGR00881 316407009766 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 316407009767 transcriptional regulator protein; Region: phnR; TIGR03337 316407009768 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407009769 DNA binding site 316407009770 UTRA domain; Region: UTRA; cl06649 316407009771 GTP-binding protein; Provisional; Region: PRK10218 316407009772 TypA (tyrosine phosphorylated protein A)/BipA subfamily. BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants. BipA was originally described as a protein that is induced in Salmonella...; Region: TypA_BipA; cd01891 316407009773 G1 box; other site 316407009774 putative GEF interaction site; other site 316407009775 GTP/Mg2+ binding site; other site 316407009776 Switch I region; other site 316407009777 G2 box; other site 316407009778 G3 box; other site 316407009779 Switch II region; other site 316407009780 G4 box; other site 316407009781 G5 box; other site 316407009782 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 316407009783 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...; Region: BipA_TypA_C; cd03710 316407009784 glutamine synthetase; Provisional; Region: glnA; PRK09469 316407009785 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 316407009786 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 316407009787 nitrogen regulation protein NR(II); Provisional; Region: glnL; PRK11073 316407009788 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 trans-...; Region: HisKA; cd00082 316407009789 dimer interface; other site 316407009790 phosphorylation site 316407009791 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 316407009792 ATP binding site; other site 316407009793 Mg2+ binding site; other site 316407009794 G-X-G motif; other site 316407009795 nitrogen regulation protein NR(I); Provisional; Region: glnG; PRK10923 316407009796 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 316407009797 active site 316407009798 phosphorylation site 316407009799 intermolecular recognition site; other site 316407009800 dimerization interface; other site 316407009801 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...; Region: AAA; cd00009 316407009802 Walker A motif; other site 316407009803 ATP binding site; other site 316407009804 Walker B motif; other site 316407009805 arginine finger; other site 316407009806 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 316407009807 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 316407009808 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 316407009809 FeS/SAM binding site; other site 316407009810 HemN C-terminal region; Region: HemN_C; pfam06969 316407009811 Protein of unknown function, DUF414; Region: DUF414; cl01172 316407009812 The YihA (EngB) subfamily. This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and...; Region: YihA_EngB; cd01876 316407009813 G1 box; other site 316407009814 GTP/Mg2+ binding site; other site 316407009815 Switch I region; other site 316407009816 G2 box; other site 316407009817 G3 box; other site 316407009818 Switch II region; other site 316407009819 G4 box; other site 316407009820 G5 box; other site 316407009821 DNA polymerase I; Provisional; Region: PRK05755 316407009822 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and...; Region: 53EXOc; cd00008 316407009823 metal binding site I; metal-binding site 316407009824 putative ssDNA interaction site; other site 316407009825 metal binding site II; metal-binding site 316407009826 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 316407009827 active site 316407009828 catalytic site; other site 316407009829 substrate binding site; other site 316407009830 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 316407009831 active site 316407009832 DNA binding site 316407009833 catalytic site; other site 316407009834 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 316407009835 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 316407009836 putative acyl-acceptor binding pocket; other site 316407009837 hypothetical protein; Provisional; Region: PRK11367 316407009838 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5339 316407009839 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 316407009840 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 316407009841 catalytic residues; other site 316407009842 hinge region; other site 316407009843 alpha helical domain; other site 316407009844 Phosphotransferase enzyme family; Region: APH; pfam01636 316407009845 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 316407009846 ATP binding site; other site 316407009847 active site 316407009848 Protein of unknown function (DUF1040); Region: DUF1040; cl01176 316407009849 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 316407009850 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 316407009851 GTP binding site; other site 316407009852 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 316407009853 Walker A motif; other site 316407009854 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 316407009855 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 316407009856 Cation transport protein; Region: TrkH; cl10514 316407009857 hypothetical protein; Provisional; Region: PRK11568 316407009858 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 316407009859 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 316407009860 proline dipeptidase; Provisional; Region: PRK13607 316407009861 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...; Region: Prolidase; cd01087 316407009862 active site 316407009863 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadB; PRK11730 316407009864 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 316407009865 substrate binding site; other site 316407009866 oxyanion hole (OAH) forming residues; other site 316407009867 trimer interface; other site 316407009868 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407009869 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 316407009870 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 316407009871 3-ketoacyl-CoA thiolase; Reviewed; Region: fadA; PRK08947 316407009872 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 316407009873 dimer interface; other site 316407009874 active site 316407009875 FMN reductase; Validated; Region: fre; PRK08051 316407009876 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...; Region: flavin_oxioreductase; cd06189 316407009877 FAD binding pocket; other site 316407009878 FAD binding motif; other site 316407009879 phosphate binding motif; other site 316407009880 beta-alpha-beta structure motif; other site 316407009881 NAD binding pocket; other site 316407009882 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 316407009883 transcriptional activator RfaH; Provisional; Region: rfaH; PRK09014 316407009884 Transcription termination factor nusG; Region: NusG; cl02766 316407009885 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 316407009886 active site 316407009887 putative deoxyribonuclease YjjV; Provisional; Region: PRK11449 316407009888 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 316407009889 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 316407009890 sec-independent translocase; Provisional; Region: tatB; PRK00404 316407009891 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 316407009892 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 316407009893 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 316407009894 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 316407009895 SCP-2 sterol transfer family; Region: SCP2; cl01225 316407009896 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 316407009897 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 316407009898 S-adenosylmethionine binding site; other site 316407009899 DNA recombination protein RmuC; Provisional; Region: PRK10361 316407009900 RmuC family; Region: RmuC; pfam02646 316407009901 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 316407009902 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 316407009903 Dienelactone hydrolase family; Region: DLH; pfam01738 316407009904 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; cl12031 316407009905 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 316407009906 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 catalyses the last step in the production of methionine by...; Region: CIMS_N_terminal_like; cd03312 316407009907 THF binding site; other site 316407009908 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 catalyses the last step in the production of methionine by...; Region: CIMS_C_terminal_like; cd03311 316407009909 substrate binding site; other site 316407009910 THF binding site; other site 316407009911 zinc-binding site; other site 316407009912 DNA-binding transcriptional regulator MetR; Provisional; Region: PRK15421 316407009913 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407009914 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 316407009915 putative dimerization interface; other site 316407009916 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 316407009917 EamA-like transporter family; Region: EamA; cl01037 316407009918 putative hydrolase; Provisional; Region: PRK10976 316407009919 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 316407009920 active site 316407009921 motif I; other site 316407009922 motif II; other site 316407009923 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; cl11391 316407009924 lysophospholipase L2; Provisional; Region: PRK10749 316407009925 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; cl12031 316407009926 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; cl12031 316407009927 LysE type translocator; Region: LysE; cl00565 316407009928 LysE type translocator; Region: LysE; cl00565 316407009929 ATP-dependent DNA helicase RecQ; Provisional; Region: PRK11057 316407009930 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 316407009931 ATP binding site; other site 316407009932 putative Mg++ binding site; other site 316407009933 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 316407009934 nucleotide binding region; other site 316407009935 ATP-binding site; other site 316407009936 RQC domain; Region: RQC; pfam09382 316407009937 HRDC domain; Region: HRDC; cl02578 316407009938 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 Gram-...; Region: OMPLA; cd00541 316407009939 dimerization interface; other site 316407009940 substrate binding site; other site 316407009941 active site 316407009942 calcium binding site; other site 316407009943 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 316407009944 CoenzymeA binding site; other site 316407009945 subunit interaction site; other site 316407009946 PHB binding site; other site 316407009947 putative chloramphenical resistance permease RarD; Provisional; Region: PRK15430 316407009948 EamA-like transporter family; Region: EamA; cl01037 316407009949 hypothetical protein; Provisional; Region: PRK11371 316407009950 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 316407009951 CorA-like Mg2+ transporter protein; Region: CorA; cl00459 316407009952 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 316407009953 Predicted periplasmic protein (DUF2233); Region: DUF2233; cl10481 316407009954 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 316407009955 UvrD/REP helicase; Region: UvrD-helicase; cl14126 316407009956 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 316407009957 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 316407009958 motif II; other site 316407009959 Site-specific recombinase XerC [DNA replication, recombination, and repair]; Region: XerC; COG4973 316407009960 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 of chromosomal replication, and stable plasmid...; Region: INT_XerDC; cd00798 316407009961 Int/Topo IB signature motif; other site 316407009962 active site 316407009963 Protein of unknown function, DUF484; Region: DUF484; cl01228 316407009964 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 316407009965 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 316407009966 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 316407009967 Predicted small periplasmic lipoprotein [Cell motility and secretion]; Region: COG5567 316407009968 hypothetical protein; Provisional; Region: PRK09807 316407009969 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 in...; Region: Frataxin; cd00503 316407009970 putative iron binding site; other site 316407009971 Adenylate cyclase, class-I; Region: Adenylate_cycl; cl01168 316407009972 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 316407009973 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 316407009974 domain interfaces; other site 316407009975 active site 316407009976 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 316407009977 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...; Region: HemD; cd06578 316407009978 active site 316407009979 HemX; Region: HemX; cl14667 316407009980 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemX; COG2959 316407009981 putative protoheme IX biogenesis protein; Provisional; Region: PRK10747 316407009982 HemY protein N-terminus; Region: HemY_N; pfam07219 316407009983 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 316407009984 Sulfatase; Region: Sulfatase; cl10460 316407009985 Arylsulfatase regulator (Fe-S oxidoreductase) [General function prediction only]; Region: AslB; COG0641 316407009986 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 316407009987 FeS/SAM binding site; other site 316407009988 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407009989 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 316407009990 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 316407009991 WzyE protein; Region: WzyE; cl11643 316407009992 4-alpha-L-fucosyltransferase (Fuc4NAc transferase); Region: Fuc4NAc_transf; cl07929 316407009993 Polysaccharide biosynthesis protein; Region: Polysacc_synt; cl10513 316407009994 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 316407009995 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 316407009996 inhibitor-cofactor binding pocket; inhibition site 316407009997 pyridoxal 5'-phosphate binding site; other site 316407009998 catalytic residue; other site 316407009999 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 316407010000 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 316407010001 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 316407010002 substrate binding site; other site 316407010003 tetramer interface; other site 316407010004 dTDP-glucose 4,6-dehydratase; Provisional; Region: PRK10217 316407010005 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407010006 UDP-N-acetyl-D-mannosamine dehydrogenase; Provisional; Region: wecC; PRK11064 316407010007 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407010008 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 316407010009 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 316407010010 UDP-N-acetylglucosamine 2-epimerase; Region: wecB; TIGR00236 316407010011 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues...; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 316407010012 active site 316407010013 homodimer interface; other site 316407010014 Chain length determinant protein; Region: Wzz; cl01623 316407010015 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 316407010016 This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins. WecA is an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate (Und-P) GlcNAc-1-phosphate transferase that catalyzes the formation of a phosphodiester bond...; Region: GT_WecA_like; cd06853 316407010017 Mg++ binding site; other site 316407010018 putative catalytic motif; other site 316407010019 substrate binding site; other site 316407010020 transcription termination factor Rho; Provisional; Region: rho; PRK09376 316407010021 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 316407010022 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...; Region: Rho_CSD; cd04459 316407010023 RNA binding site; other site 316407010024 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...; Region: rho_factor; cd01128 316407010025 multimer interface; other site 316407010026 Walker A motif; other site 316407010027 ATP binding site; other site 316407010028 Walker B motif; other site 316407010029 putative rho operon leader peptide; Provisional; Region: PRK09979 316407010030 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 316407010031 catalytic residues; other site 316407010032 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 316407010033 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 316407010034 ATP binding site; other site 316407010035 Mg++ binding site; other site 316407010036 motif III; other site 316407010037 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 316407010038 nucleotide binding region; other site 316407010039 ATP-binding site; other site 316407010040 guanosine pentaphosphate phosphohydrolase; Provisional; Region: PRK11031 316407010041 exopolyphosphatase; Region: exo_poly_only; TIGR03706 316407010042 ATP-dependent DNA helicase Rep; Provisional; Region: PRK10919 316407010043 UvrD/REP helicase; Region: UvrD-helicase; cl14126 316407010044 UvrD/REP helicase; Region: UvrD-helicase; cl14126 316407010045 ECK3769:JW3750:b3777; conserved hypothetical protein 316407010046 PemK-like protein; Region: PemK; cl00995 316407010047 PPIC-type PPIASE domain; Region: Rotamase; cl08278 316407010048 ketol-acid reductoisomerase; Validated; Region: PRK05225 316407010049 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407010050 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 316407010051 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 316407010052 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407010053 DNA-binding transcriptional regulator IlvY; Provisional; Region: PRK11716 316407010054 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 316407010055 putative dimerization interface; other site 316407010056 threonine dehydratase; Reviewed; Region: PRK09224 316407010057 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 316407010058 tetramer interface; other site 316407010059 pyridoxal 5'-phosphate binding site; other site 316407010060 catalytic residue; other site 316407010061 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 316407010062 putative Ile/Val binding site; other site 316407010063 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 316407010064 putative Ile/Val binding site; other site 316407010065 Dehydratase family; Region: ILVD_EDD; cl00340 316407010066 dihydroxy-acid dehydratase; Region: ilvD; TIGR00110 316407010067 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 alpha-...; Region: BCAT_beta_family; cd01557 316407010068 homodimer interface; other site 316407010069 substrate-cofactor binding pocket; other site 316407010070 Aminotransferase class IV; Region: Aminotran_4; pfam01063 316407010071 catalytic residue; other site 316407010072 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 316407010073 ECK3760:JW3740+JW3741:b4488; large subunit of acetolactate synthase II 316407010074 ECK3760:JW3740:b3767; acetolactate synthase II, large subunit, N-ter fragment 316407010075 ECK3760:JW3741:b3768; acetolactate synthase II, large subunit, C-ter fragment 316407010076 putative ATP-dependent protease; Provisional; Region: PRK09862 316407010077 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407010078 Protein of unknown function, DUF; Region: DUF413; cl10479 316407010079 transcriptional regulator HdfR; Provisional; Region: PRK03601 316407010080 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407010081 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 316407010082 Transcriptional regulators [Transcription]; Region: FadR; COG2186 316407010083 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407010084 DNA binding site 316407010085 FCD domain; Region: FCD; cl11656 316407010086 putative transporter; Provisional; Region: PRK10504 316407010087 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 316407010088 putative substrate translocation pore; other site 316407010089 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 316407010090 transcriptional repressor RbsR; Provisional; Region: PRK10423 316407010091 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 316407010092 DNA binding site 316407010093 domain linker motif; other site 316407010094 Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli; Region: PBP1_PurR; cd06275 316407010095 dimerization interface; other site 316407010096 ligand binding site; other site 316407010097 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...; Region: ribokinase; cd01174 316407010098 substrate binding site; other site 316407010099 dimer interface; other site 316407010100 ATP binding site; other site 316407010101 D-ribose transporter subunit RbsB; Provisional; Region: PRK10653 316407010102 Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs; Region: PBP1_ribose_binding; cd06323 316407010103 ligand binding site; other site 316407010104 dimerization interface; other site 316407010105 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 316407010106 TM-ABC transporter signature motif; other site 316407010107 D-ribose transporter ATP binding protein; Provisional; Region: PRK10762 316407010108 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and...; Region: ABC_Carb_Monos_I; cd03216 316407010109 Walker A/P-loop; other site 316407010110 ATP binding site; other site 316407010111 Q-loop/lid; other site 316407010112 ABC transporter signature motif; other site 316407010113 Walker B; other site 316407010114 D-loop; other site 316407010115 H-loop/switch region; other site 316407010116 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (; Region: ABC_Carb_Monos_II; cd03215 316407010117 RbsD / FucU transport protein family; Region: RbsD_FucU; cl00809 316407010118 K+ potassium transporter; Region: K_trans; cl01227 316407010119 potassium uptake protein; Region: kup; TIGR00794 316407010120 regulatory ATPase RavA; Provisional; Region: PRK13531 316407010121 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...; Region: AAA; cd00009 316407010122 Walker A motif; other site 316407010123 ATP binding site; other site 316407010124 Walker B motif; other site 316407010125 arginine finger; other site 316407010126 Protein of unknown function (DUF3763); Region: DUF3763; pfam12592 316407010127 hypothetical protein; Provisional; Region: yieM; PRK10997 316407010128 VWA YIEM 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 para-...; Region: VWA_YIEM_type; cd01462 316407010129 metal ion-dependent adhesion site (MIDAS); other site 316407010130 Asparagine synthetase (aspartate-ammonia ligase) (AsnA) catalyses the conversion of L-aspartate to L-asparagine in the presence of ATP and ammonia. AsnA is a homodimeric enzyme which is structurally similiar to the catalytic core domain of class II...; Region: AsnA; cd00645 316407010131 dimer interface; other site 316407010132 active site 316407010133 DNA-binding transcriptional regulator AsnC; Provisional; Region: PRK11179 316407010134 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407010135 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 316407010136 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; cl11520 316407010137 glucose-inhibited division protein A; Region: gidA; TIGR00136 316407010138 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 316407010139 S-adenosylmethionine binding site; other site 316407010140 ATP synthase I chain; Region: ATP_synt_I; cl09170 316407010141 ATP synthase A chain; Region: ATP-synt_A; cl00413 316407010142 ATP synthase subunit C; Region: ATP-synt_C; cl00466 316407010143 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 316407010144 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 316407010145 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 316407010146 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 316407010147 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 316407010148 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 316407010149 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 316407010150 beta subunit interaction interface; other site 316407010151 Walker A motif; other site 316407010152 ATP binding site; other site 316407010153 Walker B motif; other site 316407010154 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 316407010155 ATP synthase; Region: ATP-synt; cl00365 316407010156 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 316407010157 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 316407010158 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 316407010159 alpha subunit interaction interface; other site 316407010160 Walker A motif; other site 316407010161 ATP binding site; other site 316407010162 Walker B motif; other site 316407010163 inhibitor binding site; inhibition site 316407010164 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 316407010165 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 316407010166 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 316407010167 ATP synthase, Delta/Epsilon chain, long alpha-helix domain; Region: ATP-synt_DE; pfam00401 316407010168 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK09451 316407010169 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 316407010170 Substrate binding site; other site 316407010171 Mg++ binding site; other site 316407010172 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 316407010173 active site 316407010174 substrate binding site; other site 316407010175 CoA binding site; other site 316407010176 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 316407010177 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...; Region: GFAT; cd00714 316407010178 glutaminase active site; other site 316407010179 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 316407010180 dimer interface; other site 316407010181 active site 316407010182 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 316407010183 dimer interface; other site 316407010184 active site 316407010185 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...; Region: PBPb; cd00134 316407010186 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...; Region: TM_PBP2; cd06261 316407010187 dimer interface; other site 316407010188 conserved gate region; other site 316407010189 putative PBP binding loops; other site 316407010190 ABC-ATPase subunit interface; other site 316407010191 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...; Region: TM_PBP2; cd06261 316407010192 dimer interface; other site 316407010193 conserved gate region; other site 316407010194 putative PBP binding loops; other site 316407010195 ABC-ATPase subunit interface; other site 316407010196 phosphate transporter ATP-binding protein; Provisional; Region: pstB; PRK10744 316407010197 Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein...; Region: ABC_PstB_phosphate_transporter; cd03260 316407010198 Walker A/P-loop; other site 316407010199 ATP binding site; other site 316407010200 Q-loop/lid; other site 316407010201 ABC transporter signature motif; other site 316407010202 Walker B; other site 316407010203 D-loop; other site 316407010204 H-loop/switch region; other site 316407010205 transcriptional regulator PhoU; Provisional; Region: PRK11115 316407010206 PhoU domain; Region: PhoU; pfam01895 316407010207 PhoU domain; Region: PhoU; pfam01895 316407010208 transcriptional antiterminator BglG; Provisional; Region: PRK09772 316407010209 CAT RNA binding domain; Region: CAT_RBD; pfam03123 316407010210 PRD domain; Region: PRD; pfam00874 316407010211 PRD domain; Region: PRD; pfam00874 316407010212 PTS system beta-glucoside-specific transporter subunits IIABC; Provisional; Region: PRK09824 316407010213 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...; Region: PTS_IIB_glc; cd00212 316407010214 active site turn 316407010215 phosphorylation site 316407010216 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 316407010217 PTS_IIA, PTS system, glucose/sucrose 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_glc; cd00210 316407010218 HPr interaction site; other site 316407010219 glycerol kinase (GK) interaction site; other site 316407010220 active site 316407010221 phosphorylation site 316407010222 Glycosyl hydrolase family 1; Region: Glyco_hydro_1; cl01046 316407010223 Protein of unknown function (DUF3205); Region: DUF3205; pfam11471 316407010224 The Maltoporin-like channels (LamB porin) form a trimeric structure which facilitate the diffusion of maltodextrins and other sugars across the outer membrane of Gram-negative bacteria. The membrane channel is formed by an 18-strand antiparallel beta-...; Region: Maltoporin-like; cd01346 316407010225 trimer interface; other site 316407010226 sugar binding site; other site 316407010227 Esterase N-terminal domain. Esterases catalyze the hydrolysis of organic esters to release an alcohol or thiol and acid. The term can be applied to enzymes that hydrolyze carboxylate, phosphate and sulphate esters, but is more often restricted to the...; Region: Esterase_N_term; cd02858 316407010228 Enterochelin esterase and related enzymes [Inorganic ion transport and metabolism]; Region: Fes; COG2382 316407010229 GlcN6P_deaminase: Glucosamine-6-phosphate (GlcN6P) deaminase subfamily; GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium. The reaction is an aldo-keto isomerization coupled with an amination...; Region: GlcN6P_deaminase; cd01399 316407010230 active site 316407010231 trimer interface; other site 316407010232 allosteric site; other site 316407010233 active site lid 316407010234 Uncharacterized protein family (UPF0167); Region: UPF0167; cl01252 316407010235 putative inner membrane protein; Provisional; Region: PRK09823 316407010236 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 316407010237 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 316407010238 active site 316407010239 motif I; other site 316407010240 motif II; other site 316407010241 Permease family; Region: Xan_ur_permease; cl00967 316407010242 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 316407010243 Phosphopantetheinyl transferase [Coenzyme metabolism]; Region: Sfp; COG2091 316407010244 IS2 transposase TnpB; Reviewed; Region: PRK09409 316407010245 Integrase core domain; Region: rve; cl01316 316407010246 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; cl01116 316407010247 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 316407010248 DNA-binding transcriptional regulator YidZ; Provisional; Region: PRK10216 316407010249 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407010250 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 316407010251 substrate binding pocket; other site 316407010252 dimerization interface; other site 316407010253 multidrug efflux system protein MdtL; Provisional; Region: PRK10473 316407010254 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 316407010255 putative substrate translocation pore; other site 316407010256 ECK3702:JW5619+JW5622:b3709; IS is inserted, intact tnaB is found in strain MG1655 316407010257 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407010258 Transposase domain (DUF772); Region: DUF772; cl12084 316407010259 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 316407010260 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407010261 tryptophanase/L-cysteine desulfhydrase, PLP-dependent; Provisional; Region: tnaA; PRK13238 316407010262 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 316407010263 pyridoxal 5'-phosphate binding pocket; other site 316407010264 catalytic residue; other site 316407010265 Transposase domain (DUF772); Region: DUF772; cl12084 316407010266 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 316407010267 tryptophanase leader peptide; Provisional; Region: PRK09806 316407010268 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 316407010269 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 316407010270 TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase...; Region: trmE; cd04164 316407010271 G1 box; other site 316407010272 GTP/Mg2+ binding site; other site 316407010273 Switch I region; other site 316407010274 G2 box; other site 316407010275 Switch II region; other site 316407010276 G3 box; other site 316407010277 G4 box; other site 316407010278 G5 box; other site 316407010279 membrane protein insertase; Provisional; Region: PRK01318 316407010280 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 316407010281 Domain of unknown function DUF37; Region: DUF37; cl00506 316407010282 Ribonuclease P; Region: Ribonuclease_P; cl00457 316407010283 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 316407010284 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 316407010285 hypothetical protein; Validated; Region: PRK06672 316407010286 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...; Region: AAA; cd00009 316407010287 Walker A motif; other site 316407010288 ATP binding site; other site 316407010289 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407010290 Walker B motif; other site 316407010291 arginine finger; other site 316407010292 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 316407010293 DnaA box-binding interface; other site 316407010294 DNA polymerase III subunit beta; Validated; Region: PRK05643 316407010295 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...; Region: beta_clamp; cd00140 316407010296 putative DNA binding surface; other site 316407010297 dimer interface; other site 316407010298 beta-clamp/clamp loader binding surface; other site 316407010299 beta-clamp/translesion DNA polymerase binding surface; other site 316407010300 recombination protein F; Reviewed; Region: recF; PRK00064 316407010301 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407010302 Walker A/P-loop; other site 316407010303 ATP binding site; other site 316407010304 Q-loop/lid; other site 316407010305 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407010306 ABC transporter signature motif; other site 316407010307 Walker B; other site 316407010308 D-loop; other site 316407010309 H-loop/switch region; other site 316407010310 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 316407010311 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 316407010312 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 316407010313 anchoring element; other site 316407010314 dimer interface; other site 316407010315 ATP binding site; other site 316407010316 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...; Region: TOPRIM_TopoIIA_GyrB; cd03366 316407010317 active site 316407010318 putative metal-binding site; other site 316407010319 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 316407010320 Bacterial protein of unknown function (DUF937); Region: DUF937; cl01528 316407010321 sugar phosphate phosphatase; Provisional; Region: PRK10513 316407010322 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 316407010323 active site 316407010324 motif I; other site 316407010325 motif II; other site 316407010326 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 316407010327 hypothetical protein; Provisional; Region: PRK10215 316407010328 Transcriptional regulators [Transcription]; Region: FadR; COG2186 316407010329 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407010330 DNA binding site 316407010331 FCD domain; Region: FCD; cl11656 316407010332 2-keto-3-deoxy-galactonokinase; Region: DGOK; cl01517 316407010333 Entner-Doudoroff aldolase; Region: eda; TIGR01182 316407010334 KDPG and KHG aldolase. This family belongs to the class I adolases whose reaction mechanism involves Schiff base formation between a substrate carbonyl and lysine residue in the active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, is best...; Region: KDPG_aldolase; cd00452 316407010335 active site 316407010336 intersubunit interface; other site 316407010337 catalytic residue; other site 316407010338 galactonate dehydratase; Provisional; Region: PRK14017 316407010339 D-galactonate dehydratase catalyses the dehydration of galactonate to 2-keto-3-deoxygalactnate (KDGal), as part of the D-galactonate nonphosphorolytic catabolic Entner-Doudoroff pathway. D-galactonate dehydratase belongs to the enolase superfamily of...; Region: D-galactonate_dehydratase; cd03325 316407010340 putative active site pocket; other site 316407010341 putative metal binding site; other site 316407010342 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 316407010343 d-galactonate transporter; Region: 2A0114; TIGR00893 316407010344 putative substrate translocation pore; other site 316407010345 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407010346 geranylgeranyl reductase family; Region: GG-red-SF; TIGR02032 316407010347 Protein of unknown function (DUF3748); Region: DUF3748; pfam12566 316407010348 tol-pal system beta propeller repeat protein TolB; Region: propeller_TolB; TIGR02800 316407010349 Protein of unknown function (DUF1375); Region: DUF1375; cl11456 316407010350 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 316407010351 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...; Region: ACD_IbpA-B_like; cd06470 316407010352 putative dimer interface; other site 316407010353 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 316407010354 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...; Region: ACD_IbpA-B_like; cd06470 316407010355 putative dimer interface; other site 316407010356 putative transporter; Validated; Region: PRK03818 316407010357 Predicted Permease Membrane Region; Region: Asp-Al_Ex; cl06061 316407010358 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; cl09110 316407010359 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; cl09110 316407010360 Predicted Permease Membrane Region; Region: Asp-Al_Ex; cl06061 316407010361 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 316407010362 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407010363 DNA binding site 316407010364 UTRA domain; Region: UTRA; cl06649 316407010365 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 316407010366 PTS system arbutin-specific transporter subunit IIB; Provisional; Region: PRK09702 316407010367 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 316407010368 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...; Region: PTS_IIB_glc; cd00212 316407010369 active site turn 316407010370 phosphorylation site 316407010371 ECK3673:JW3658:b3681; predicted 6-phospho-beta-glucosidase 316407010372 ECK3672:JW5937:b4556; hypothetical protein 316407010373 Cupin domain; Region: Cupin_2; cl09118 316407010374 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407010375 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 316407010376 Sodium:solute symporter family; Region: SSF; cl00456 316407010377 putative transporter; Provisional; Region: PRK10484 316407010378 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 316407010379 Sulfatase; Region: Sulfatase; cl10460 316407010380 Domain of unknown function DUF; Region: DUF202; cl09954 316407010381 Arylsulfatase regulator (Fe-S oxidoreductase) [General function prediction only]; Region: AslB; COG0641 316407010382 multidrug resistance protein D; Provisional; Region: emrD; PRK11652 316407010383 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 316407010384 putative substrate translocation pore; other site 316407010385 acetolactate synthase catalytic subunit; Validated; Region: PRK08155 316407010386 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 316407010387 PYR/PP interface; other site 316407010388 dimer interface; other site 316407010389 TPP binding site; other site 316407010390 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 316407010391 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 316407010392 TPP-binding site; other site 316407010393 dimer interface; other site 316407010394 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 316407010395 putative valine binding site; other site 316407010396 dimer interface; other site 316407010397 DNA-binding transcriptional activator UhpA; Provisional; Region: PRK10360 316407010398 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 316407010399 active site 316407010400 phosphorylation site 316407010401 intermolecular recognition site; other site 316407010402 dimerization interface; other site 316407010403 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...; Region: LuxR_C_like; cd06170 316407010404 DNA binding residues 316407010405 dimerization interface; other site 316407010406 sensory histidine kinase UhpB; Provisional; Region: PRK11644 316407010407 MASE1; Region: MASE1; cl01367 316407010408 Histidine kinase; Region: HisKA_3; pfam07730 316407010409 regulatory protein UhpC; Provisional; Region: PRK11663 316407010410 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 316407010411 putative substrate translocation pore; other site 316407010412 sugar phosphate antiporter; Reviewed; Region: uhpT; PRK09556 316407010413 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 316407010414 putative substrate translocation pore; other site 316407010415 cryptic adenine deaminase; Provisional; Region: PRK10027 316407010416 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...; Region: metallo-dependent_hydrolases; cl00281 316407010417 Adenine deaminase (AdeC) directly deaminates adenine to form hypoxanthine. This reaction is part of one of the adenine salvage pathways, as well as the degradation pathway. It is important for adenine utilization as a purine, as well as a nitrogen...; Region: AdeC; cd01295 316407010418 active site 316407010419 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...; Region: metallo-dependent_hydrolases; cl00281 316407010420 Permease family; Region: Xan_ur_permease; cl00967 316407010421 Protein of unknown function (DUF1198); Region: DUF1198; pfam06711 316407010422 ribonucleoside transporter; Reviewed; Region: nepI; PRK10213 316407010423 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 316407010424 putative substrate translocation pore; other site 316407010425 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 316407010426 EamA-like transporter family; Region: EamA; cl01037 316407010427 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 316407010428 EamA-like transporter family; Region: EamA; cl01037 316407010429 sugar efflux transporter; Region: 2A0120; TIGR00899 316407010430 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 316407010431 putative substrate translocation pore; other site 316407010432 putative transporter; Provisional; Region: PRK11462 316407010433 sugar (Glycoside-Pentoside-Hexuronide) transporter; Region: gph; TIGR00792 316407010434 Alpha-glucosidases, family 31 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: COG1501 316407010435 YicI alpha-xylosidase is a glycosyl hydrolase family 31 (GH31) enzyme that catalyzes the release of an alpha-xylosyl residue from the non-reducing end of alpha-xyloside substrates such as alpha-xylosyl fluoride and isoprimeverose. YicI forms a...; Region: GH31_xylosidase_YicI; cd06593 316407010436 active site 316407010437 homotrimer interface; other site 316407010438 catalytic site; other site 316407010439 homohexamer (dimer of homotrimers) interface; other site 316407010440 AsmA family; Region: AsmA; pfam05170 316407010441 Permease family; Region: Xan_ur_permease; cl00967 316407010442 Na+/glutamate symporter [Amino acid transport and metabolism]; Region: GltS; cl12073 316407010443 Sodium/glutamate symporter; Region: Glt_symporter; pfam03616 316407010444 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 316407010445 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 four-...; Region: RecG_wedge_OBF; cd04488 316407010446 generic binding surface II; other site 316407010447 ssDNA binding site; other site 316407010448 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 316407010449 ATP binding site; other site 316407010450 putative Mg++ binding site; other site 316407010451 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 316407010452 nucleotide binding region; other site 316407010453 ATP-binding site; other site 316407010454 tRNA guanosine-2'-O-methyltransferase; Provisional; Region: PRK11081 316407010455 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 316407010456 C-terminal; Region: SpoU_methylas_C; pfam12105 316407010457 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional; Region: PRK11092 316407010458 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 316407010459 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 316407010460 synthetase active site; other site 316407010461 NTP binding site; other site 316407010462 metal-binding site 316407010463 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...; Region: TGS_RelA_SpoT; cd01668 316407010464 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 316407010465 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 316407010466 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...; Region: GMPK; cd00071 316407010467 catalytic site; other site 316407010468 G-X2-G-X-G-K; other site 316407010469 NAD-dependent DNA ligase LigB; Reviewed; Region: ligB; PRK08097 316407010470 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 316407010471 nucleotide binding pocket; other site 316407010472 K-X-D-G motif; other site 316407010473 catalytic site; other site 316407010474 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 316407010475 Predicted membrane protein [Function unknown]; Region: COG2860 316407010476 UPF0126 domain; Region: UPF0126; pfam03458 316407010477 UPF0126 domain; Region: UPF0126; pfam03458 316407010478 DNA-damage-inducible protein D; Provisional; Region: dinD; PRK11525 316407010479 hypothetical protein; Provisional; Region: PRK11820 316407010480 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 316407010481 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 316407010482 ECK3633:JW3618:b3643; ribonuclease PH 316407010483 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 316407010484 division inhibitor protein; Provisional; Region: slmA; PRK09480 316407010485 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316407010486 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 316407010487 trimer interface; other site 316407010488 active site 316407010489 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 316407010490 Flavoprotein; Region: Flavoprotein; cl08021 316407010491 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 316407010492 hypothetical protein; Reviewed; Region: PRK00024 316407010493 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 316407010494 MPN+ (JAMM) motif; other site 316407010495 Zinc-binding site; other site 316407010496 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 316407010497 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 316407010498 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 316407010499 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 316407010500 DNA binding site 316407010501 catalytic residue; other site 316407010502 H2TH interface; other site 316407010503 putative catalytic residues; other site 316407010504 turnover-facilitating residue; other site 316407010505 intercalation triad; other site 316407010506 8OG recognition residue; other site 316407010507 putative reading head residues; other site 316407010508 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 316407010509 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 316407010510 Nicotinic acid mononucleotide adenylyltransferase [Coenzyme metabolism]; Region: NadD; COG1057 316407010511 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 316407010512 active site 316407010513 (T/H)XGH motif; other site 316407010514 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 316407010515 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 316407010516 Glycosyl transferases group 1; Region: Glycos_transf_1; cl12012 316407010517 lipopolysaccharide core biosynthesis protein; Provisional; Region: PRK10422 316407010518 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 316407010519 putative active site; other site 316407010520 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 316407010521 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 316407010522 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 316407010523 UDP-D-galactose:(glucosyl)lipopolysaccharide-1, 6-D-galactosyltransferase; Provisional; Region: PRK09922 316407010524 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 316407010525 putative ADP-binding pocket; other site 316407010526 lipopolysaccharide 1,3-galactosyltransferase; Provisional; Region: PRK15171 316407010527 A4GalT_like proteins catalyze the addition of galactose or glucose residues to the lipooligosaccharide (LOS) or lipopolysaccharide (LPS) of the bacterial cell surface; Region: GT8_A4GalT_like; cd04194 316407010528 Ligand binding site; other site 316407010529 metal-binding site 316407010530 Glycosyl transferase family 8 C-terminal; Region: Glyco_transf_8N; pfam08437 316407010531 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 316407010532 A4GalT_like proteins catalyze the addition of galactose or glucose residues to the lipooligosaccharide (LOS) or lipopolysaccharide (LPS) of the bacterial cell surface; Region: GT8_A4GalT_like; cd04194 316407010533 Ligand binding site; other site 316407010534 metal-binding site 316407010535 Glycosyl transferase family 8 C-terminal; Region: Glyco_transf_8N; pfam08437 316407010536 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 316407010537 lipopolysaccharide core biosynthesis protein; Provisional; Region: PRK09822 316407010538 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 316407010539 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 316407010540 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 316407010541 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 316407010542 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 316407010543 Glycosyltransferase family 9 (heptosyltransferase); Region: Glyco_transf_9; pfam01075 316407010544 putative active site; other site 316407010545 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 316407010546 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 316407010547 putative active site; other site 316407010548 ADP-L-glycero-D-mannoheptose-6-epimerase; Provisional; Region: rfaD; PRK11150 316407010549 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407010550 Bacterial protein of unknown function (HtrL_YibB); Region: HtrL_YibB; cl08171 316407010551 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 316407010552 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), 8-amino-7-...; Region: KBL_like; cd06454 316407010553 substrate-cofactor binding pocket; other site 316407010554 pyridoxal 5'-phosphate binding site; other site 316407010555 catalytic residue; other site 316407010556 L-threonine 3-dehydrogenase; Validated; Region: tdh; PRK05396 316407010557 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl14614 316407010558 NAD(P) binding site; other site 316407010559 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 316407010560 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 316407010561 active site 316407010562 Divergent polysaccharide deacetylase; Region: Polysacc_deac_2; cl04721 316407010563 AmiB activator; Provisional; Region: PRK11637 316407010564 HemX; Region: HemX; cl14667 316407010565 Peptidase family M23; Region: Peptidase_M23; pfam01551 316407010566 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 316407010567 Sulfatase; Region: Sulfatase; cl10460 316407010568 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 316407010569 active site residue 316407010570 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 316407010571 GSH binding site; other site 316407010572 catalytic residues; other site 316407010573 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 316407010574 SecA binding site; other site 316407010575 Preprotein binding site; other site 316407010576 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 316407010577 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407010578 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 316407010579 serine acetyltransferase; Provisional; Region: cysE; PRK11132 316407010580 Serine acetyltransferase, N-terminal; Region: SATase_N; pfam06426 316407010581 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 L-...; Region: LbH_SAT; cd03354 316407010582 trimer interface; other site 316407010583 active site 316407010584 substrate binding site; other site 316407010585 CoA binding site; other site 316407010586 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 316407010587 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 316407010588 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; cl09108 316407010589 phosphate binding site; other site 316407010590 DNA-binding transcriptional repressor LldR; Provisional; Region: PRK10421 316407010591 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407010592 DNA binding site 316407010593 FCD domain; Region: FCD; cl11656 316407010594 L-lactate permease; Region: Lactate_perm; cl00701 316407010595 glycolate transporter; Provisional; Region: PRK09695 316407010596 Protein of unknown function (DUF2810); Region: DUF2810; cl08159 316407010597 Mannitol repressor; Region: MtlR; cl11450 316407010598 mannitol-1-phosphate 5-dehydrogenase; Provisional; Region: PRK02318 316407010599 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 316407010600 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 316407010601 PTS system mannitol-specific transporter subunit IICBA; Provisional; Region: PRK15083 316407010602 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 316407010603 PTS_IIB_mannitol: subunit IIB of enzyme II (EII) of the mannitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is a mannitol-specific permease with two cytoplasmic domains (IIA and IIB) and a...; Region: PTS_IIB_mannitol; cd05567 316407010604 active site 316407010605 P-loop; other site 316407010606 phosphorylation site 316407010607 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 316407010608 active site 316407010609 phosphorylation site 316407010610 Protein of unknown function (DUF3302); Region: DUF3302; pfam11742 316407010611 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 316407010612 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 316407010613 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 316407010614 RHS protein; Region: RHS; pfam03527 316407010615 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 316407010616 putative lyase; Provisional; Region: PRK09687 316407010617 RHS Repeat; Region: RHS_repeat; cl11982 316407010618 RHS Repeat; Region: RHS_repeat; cl11982 316407010619 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 316407010620 RHS Repeat; Region: RHS_repeat; cl11982 316407010621 RHS Repeat; Region: RHS_repeat; cl11982 316407010622 RHS protein; Region: RHS; pfam03527 316407010623 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 316407010624 putative glutathione S-transferase; Provisional; Region: PRK10357 316407010625 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 316407010626 putative C-terminal domain interface; other site 316407010627 putative GSH binding site (G-site); other site 316407010628 putative dimer interface; other site 316407010629 GST_C family, unknown subfamily 6; 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_C_6; cd03205 316407010630 putative N-terminal domain interface; other site 316407010631 putative dimer interface; other site 316407010632 putative substrate binding pocket (H-site); other site 316407010633 selenocysteine synthase; Provisional; Region: PRK04311 316407010634 Selenocysteine synthase N terminal; Region: Se-cys_synth_N; pfam12390 316407010635 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 316407010636 selenocysteinyl-tRNA-specific translation factor; Provisional; Region: PRK10512 316407010637 SelB subfamily. SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of...; Region: SelB; cd04171 316407010638 G1 box; other site 316407010639 putative GEF interaction site; other site 316407010640 GTP/Mg2+ binding site; other site 316407010641 Switch I region; other site 316407010642 G2 box; other site 316407010643 G3 box; other site 316407010644 Switch II region; other site 316407010645 G4 box; other site 316407010646 G5 box; other site 316407010647 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...; Region: selB_II; cd03696 316407010648 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 316407010649 Elongation factor SelB, winged helix; Region: SelB-wing_2; pfam09106 316407010650 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 316407010651 Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria; Region: LPO; cd08176 316407010652 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 316407010653 dimer interface; other site 316407010654 active site 316407010655 metal-binding site 316407010656 delta-1-pyrroline-5-carboxylate dehydrogenase, group 2, putative; Region: D1pyr5carbox2; TIGR01237 316407010657 Ralstonia eutrophus NAD+-dependent acetaldehyde dehydrogenase II-like; Region: ALDH_ACDHII-AcoD; cd07116 316407010658 NAD(P) binding site; other site 316407010659 catalytic residues; other site 316407010660 Protein of unknown function (DUF3302); Region: DUF3302; pfam11742 316407010661 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 316407010662 Transcriptional regulator [Transcription]; Region: LysR; COG0583 316407010663 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407010664 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 316407010665 MltA-interacting protein MipA; Region: MipA; cl01504 316407010666 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; cd00398 316407010667 intersubunit interface; other site 316407010668 active site 316407010669 Zn2+ binding site; other site 316407010670 putative L-xylulose 5-phosphate 3-epimerase; Reviewed; Region: PRK13210 316407010671 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of D-arabino-6-...; Region: AP2Ec; cd00019 316407010672 AP (apurinic/apyrimidinic) site pocket; other site 316407010673 DNA interaction; other site 316407010674 Metal-binding active site; metal-binding site 316407010675 3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and D-arabino-3-hexulose-6-phosphate synthase (HPS). KGPDC catalyzes the formation of L-xylulose 5-phosphate and carbon dioxide from 3-keto-L-gulonate 6-phosphate as part of the anaerobic pathway for...; Region: KGPDC_HPS; cd04726 316407010676 active site 316407010677 dimer interface; other site 316407010678 magnesium binding site; other site 316407010679 Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]; Region: XylB; COG1070 316407010680 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; pfam00370 316407010681 FGGY family of carbohydrate kinases, C-terminal domain; Region: FGGY_C; pfam02782 316407010682 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 316407010683 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 316407010684 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; cl09110 316407010685 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 316407010686 Domain of unknown function (DUF386); Region: DUF386; cl01047 316407010687 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 316407010688 Transcriptional regulator [Transcription]; Region: IclR; COG1414 316407010689 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407010690 Bacterial transcriptional regulator; Region: IclR; pfam01614 316407010691 formate dehydrogenase-H ferredoxin subunit; Provisional; Region: PRK10330 316407010692 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 316407010693 pyridoxal 5'-phosphate binding site; other site 316407010694 homodimer interface; other site 316407010695 catalytic residue; other site 316407010696 alpha-amylase; Reviewed; Region: malS; PRK09505 316407010697 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 316407010698 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; cl00743 316407010699 Uncharacterized FlgJ-related protein [General function prediction only]; Region: Bax; COG2992 316407010700 Ligand-binding domain of DNA transcription repressor specific for xylose (XylR); Region: PBP1_XylR; cd01543 316407010701 putative dimerization interface; other site 316407010702 putative ligand binding site; other site 316407010703 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407010704 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 316407010705 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407010706 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 316407010707 TM-ABC transporter signature motif; other site 316407010708 xylose transporter ATP-binding subunit; Provisional; Region: PRK13549 316407010709 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and...; Region: ABC_Carb_Monos_I; cd03216 316407010710 Walker A/P-loop; other site 316407010711 ATP binding site; other site 316407010712 Q-loop/lid; other site 316407010713 ABC transporter signature motif; other site 316407010714 Walker B; other site 316407010715 D-loop; other site 316407010716 H-loop/switch region; other site 316407010717 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (; Region: ABC_Carb_Monos_II; cd03215 316407010718 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 316407010719 Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_xylose_binding; cd01538 316407010720 putative ligand binding site; other site 316407010721 L-rhamnose isomerase (RhaA); Region: RhaA; cl09945 316407010722 xylose isomerase; Region: PLN02923 316407010723 xylulokinase; Provisional; Region: PRK15027 316407010724 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; pfam00370 316407010725 FGGY family of carbohydrate kinases, C-terminal domain; Region: FGGY_C; pfam02782 316407010726 hypothetical protein; Provisional; Region: PRK11403 316407010727 yiaA/B two helix domain; Region: YiaAB; cl01759 316407010728 hypothetical protein; Provisional; Region: PRK11383 316407010729 yiaA/B two helix domain; Region: YiaAB; cl01759 316407010730 yiaA/B two helix domain; Region: YiaAB; cl01759 316407010731 Predicted acyltransferases [Lipid metabolism]; Region: COG1835; cl00792 316407010732 Acyltransferase family; Region: Acyl_transf_3; pfam01757 316407010733 glycyl-tRNA synthetase, tetrameric type, alpha subunit; Region: glyQ; TIGR00388 316407010734 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 316407010735 dimer interface; other site 316407010736 motif 1; other site 316407010737 active site 316407010738 motif 2; other site 316407010739 motif 3; other site 316407010740 glycyl-tRNA synthetase, tetrameric type, beta subunit; Region: glyS; TIGR00211 316407010741 Glycyl-tRNA synthetase beta subunit; Region: tRNA_synt_2f; pfam02092 316407010742 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 316407010743 putative transposase OrfB; Reviewed; Region: PHA02517 316407010744 Integrase core domain; Region: rve; cl01316 316407010745 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 316407010746 Hok/gef family; Region: HOK_GEF; cl11494 316407010747 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 protein...; Region: CSP_CDS; cd04458 316407010748 DNA binding site 316407010749 RNA-binding motif; other site 316407010750 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl09100 316407010751 Protein of unknown function (DUF3053); Region: DUF3053; pfam11254 316407010752 bifunctional glyoxylate/hydroxypyruvate reductase B; Provisional; Region: PRK15409 316407010753 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407010754 putative outer membrane lipoprotein; Provisional; Region: PRK10510 316407010755 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 316407010756 ligand binding site; other site 316407010757 molybdopterin guanine dinucleotide-containing S/N-oxide reductases; Region: bisC_fam; TIGR00509 316407010758 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 316407010759 molybdopterin cofactor binding site; other site 316407010760 substrate binding site; other site 316407010761 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 316407010762 molybdopterin cofactor binding site; other site 316407010763 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 316407010764 Coenzyme A binding pocket; other site 316407010765 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 316407010766 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 316407010767 Autotransporter beta-domain; Region: Autotransporter; cl02365 316407010768 Oxalate/Formate Antiporter; Region: 2A0111; TIGR00890 316407010769 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 316407010770 putative substrate translocation pore; other site 316407010771 phosphoethanolamine transferase; Provisional; Region: PRK11560 316407010772 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 316407010773 Sulfatase; Region: Sulfatase; cl10460 316407010774 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 316407010775 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 316407010776 peptide binding site; other site 316407010777 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...; Region: TM_PBP2; cd06261 316407010778 dimer interface; other site 316407010779 conserved gate region; other site 316407010780 putative PBP binding loops; other site 316407010781 ABC-ATPase subunit interface; other site 316407010782 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...; Region: TM_PBP2; cd06261 316407010783 dimer interface; other site 316407010784 conserved gate region; other site 316407010785 putative PBP binding loops; other site 316407010786 ABC-ATPase subunit interface; other site 316407010787 dipeptide transporter ATP-binding subunit; Provisional; Region: dppD; PRK11022 316407010788 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 316407010789 Walker A/P-loop; other site 316407010790 ATP binding site; other site 316407010791 Q-loop/lid; other site 316407010792 ABC transporter signature motif; other site 316407010793 Walker B; other site 316407010794 D-loop; other site 316407010795 H-loop/switch region; other site 316407010796 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 316407010797 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 316407010798 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 316407010799 Walker A/P-loop; other site 316407010800 ATP binding site; other site 316407010801 Q-loop/lid; other site 316407010802 ABC transporter signature motif; other site 316407010803 Walker B; other site 316407010804 D-loop; other site 316407010805 H-loop/switch region; other site 316407010806 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 316407010807 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 316407010808 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407010809 Protein of unknown function (DUF3260); Region: DUF3260; cl11881 316407010810 Protein of unknown function (DUF2636); Region: DUF2636; cl11897 316407010811 Protein of unknown function (DUF2819); Region: DUF2819; cl11882 316407010812 Protein of unknown function (DUF2629); Region: DUF2629; pfam10945 316407010813 ECK3519:JW5941:b3534; cell division protein; chromosome partitioning ATPase 316407010814 cellulose synthase catalytic subunit; Provisional; Region: bcsA; PRK11498 316407010815 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 316407010816 CESA_CelA_like are involved in the elongation of the glucan chain of cellulose; Region: CESA_CelA_like; cd06421 316407010817 DXD motif; other site 316407010818 PilZ domain; Region: PilZ; cl01260 316407010819 cellulose synthase regulator protein; Provisional; Region: PRK11114 316407010820 Bacterial cellulose synthase subunit; Region: BcsB; pfam03170 316407010821 Glycosyl hydrolases family 8; Region: Glyco_hydro_8; cl01351 316407010822 cellulose synthase subunit BcsC; Provisional; Region: PRK11447 316407010823 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 316407010824 binding surface 316407010825 TPR motif; other site 316407010826 Cellulose synthase operon protein C C-terminus (BCSC_C); Region: BCSC_C; pfam05420 316407010827 putative diguanylate cyclase; Provisional; Region: PRK13561 316407010828 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 316407010829 metal-binding site 316407010830 active site 316407010831 I-site; other site 316407010832 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 316407010833 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 316407010834 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 316407010835 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 316407010836 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 316407010837 substrate binding site; other site 316407010838 ATP binding site; other site 316407010839 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 316407010840 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 316407010841 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 316407010842 metabolite-proton symporter; Region: 2A0106; TIGR00883 316407010843 putative substrate translocation pore; other site 316407010844 Ribonuclease BN-like family; Region: Ribonuclease_BN; cl07918 316407010845 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407010846 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 316407010847 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 316407010848 putative effector binding pocket; other site 316407010849 putative dimerization interface; other site 316407010850 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 316407010851 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...; Region: LuxR_C_like; cd06170 316407010852 DNA binding residues 316407010853 dimerization interface; other site 316407010854 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; cl01801 316407010855 Neutral trehalase [Carbohydrate transport and metabolism]; Region: TreA; COG1626 316407010856 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 316407010857 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 316407010858 Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism]; Region: GadB; COG0076 316407010859 DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to DOPA/tyrosine decarboxylase (DDC), histidine decarboxylase (HDC), and...; Region: DOPA_deC_like; cd06450 316407010860 pyridoxal 5'-phosphate binding site; other site 316407010861 catalytic residue; other site 316407010862 DNA-binding transcriptional regulator GadX; Provisional; Region: PRK09978 316407010863 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407010864 transcriptional regulator YdeO; Provisional; Region: PRK09940 316407010865 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407010866 multidrug efflux system protein AcrB; Provisional; Region: PRK15127 316407010867 Protein export membrane protein; Region: SecD_SecF; cl14618 316407010868 multidrug efflux system protein MdtE; Provisional; Region: PRK09859 316407010869 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 316407010870 pyruvate kinase; Provisional; Region: PRK05826 316407010871 Uncharacterized conserved protein [Function unknown]; Region: HdeD; cl01277 316407010872 hns-dependent expression protein A (HdeA); Region: HdeA; cl05752 316407010873 acid-resistance protein; Provisional; Region: hdeB; PRK11566 316407010874 putative Mg(2+) transport ATPase; Provisional; Region: PRK09977 316407010875 MgtC family; Region: MgtC; cl12207 316407010876 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 316407010877 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...; Region: LuxR_C_like; cd06170 316407010878 DNA binding residues 316407010879 dimerization interface; other site 316407010880 Outer membrane lipoprotein Slp family; Region: Slp; cl01164 316407010881 Transposase domain (DUF772); Region: DUF772; cl12084 316407010882 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 316407010883 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 316407010884 catalytic residues; other site 316407010885 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 316407010886 transmembrane helices; other site 316407010887 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 316407010888 dimerization interface; other site 316407010889 putative DNA binding site; other site 316407010890 putative Zn2+ binding site; other site 316407010891 glutathione reductase; Validated; Region: PRK06116 316407010892 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407010893 Pyridine nucleotide-disulphide oxidoreductase, dimerization domain; Region: Pyr_redox_dim; pfam02852 316407010894 Protein of unknown function (DUF519); Region: DUF519; cl04492 316407010895 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 316407010896 Peptidase family M3 dipeptidyl carboxypeptidase (DCP; Dcp II; peptidyl dipeptidase; EC 3.4.15.5). This metal-binding M3A family also includes oligopeptidase A (OpdA; EC 3.4.24.70) enzyme. DCP cleaves dipeptides off the C-termini of various peptides and...; Region: M3A_DCP_Oligopeptidase_A; cd06456 316407010897 active site 316407010898 zinc binding site; other site 316407010899 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; cl12011 316407010900 dipeptide/tripeptide permease B; Provisional; Region: PRK10207 316407010901 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; cl11420 316407010902 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 316407010903 Ligand Binding Site; other site 316407010904 Universal stress protein B (UspB); Region: UspB; cl11669 316407010905 Phosphate transporter family; Region: PHO4; cl00396 316407010906 Phosphate transporter family; Region: PHO4; cl00396 316407010907 Predicted flavoproteins [General function prediction only]; Region: COG2081 316407010908 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407010909 Protein of unknown function (DUF2776); Region: DUF2776; pfam10951 316407010910 ECK3474:JW5674:b3489; hypothetical protein 316407010911 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 316407010912 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407010913 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 316407010914 Walker A/P-loop; other site 316407010915 ATP binding site; other site 316407010916 Q-loop/lid; other site 316407010917 ABC transporter signature motif; other site 316407010918 Walker B; other site 316407010919 D-loop; other site 316407010920 H-loop/switch region; other site 316407010921 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407010922 Walker A/P-loop; other site 316407010923 ATP binding site; other site 316407010924 Q-loop/lid; other site 316407010925 ABC transporter signature motif; other site 316407010926 Walker B; other site 316407010927 D-loop; other site 316407010928 H-loop/switch region; other site 316407010929 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 316407010930 ABC-2 type transporter; Region: ABC2_membrane; cl11417 316407010931 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 316407010932 ABC-2 type transporter; Region: ABC2_membrane; cl11417 316407010933 Transposase [DNA replication, recombination, and repair]; Region: COG5433 316407010934 Transposase [DNA replication, recombination, and repair]; Region: COG5433 316407010935 Transposase [DNA replication, recombination, and repair]; Region: COG5433 316407010936 ECK3468:JW5678:b4552; hypothetical protein fragment 316407010937 RHS Repeat; Region: RHS_repeat; cl11982 316407010938 RHS Repeat; Region: RHS_repeat; cl11982 316407010939 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 316407010940 RHS Repeat; Region: RHS_repeat; cl11982 316407010941 RHS Repeat; Region: RHS_repeat; cl11982 316407010942 RHS protein; Region: RHS; pfam03527 316407010943 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 316407010944 nickel responsive regulator; Provisional; Region: PRK02967 316407010945 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 316407010946 nickel transporter ATP-binding protein NikE; Provisional; Region: nikE; PRK10419 316407010947 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 316407010948 Walker A/P-loop; other site 316407010949 ATP binding site; other site 316407010950 Q-loop/lid; other site 316407010951 ABC transporter signature motif; other site 316407010952 Walker B; other site 316407010953 D-loop; other site 316407010954 H-loop/switch region; other site 316407010955 nickel transporter ATP-binding protein NikD; Provisional; Region: nikD; PRK10418 316407010956 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 316407010957 Walker A/P-loop; other site 316407010958 ATP binding site; other site 316407010959 Q-loop/lid; other site 316407010960 ABC transporter signature motif; other site 316407010961 Walker B; other site 316407010962 D-loop; other site 316407010963 H-loop/switch region; other site 316407010964 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...; Region: TM_PBP2; cd06261 316407010965 dimer interface; other site 316407010966 conserved gate region; other site 316407010967 putative PBP binding loops; other site 316407010968 ABC-ATPase subunit interface; other site 316407010969 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...; Region: TM_PBP2; cd06261 316407010970 dimer interface; other site 316407010971 conserved gate region; other site 316407010972 putative PBP binding loops; other site 316407010973 ABC-ATPase subunit interface; other site 316407010974 The substrate-binding component of an ABC-type nickel import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA; cd08489 316407010975 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 316407010976 substrate binding site; other site 316407010977 holo-(acyl carrier protein) synthase 2; Provisional; Region: PRK10351 316407010978 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 316407010979 Domain of unknown function DUF20; Region: UPF0118; cl00465 316407010980 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 316407010981 major facilitator superfamily transporter; Provisional; Region: PRK05122 316407010982 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 316407010983 putative substrate translocation pore; other site 316407010984 hypothetical protein; Provisional; Region: PRK11615 316407010985 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 316407010986 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 316407010987 CPxP motif; other site 316407010988 zinc/cadmium/mercury/lead-transporting ATPase; Provisional; Region: zntA; PRK11033 316407010989 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 316407010990 metal-binding site 316407010991 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 316407010992 YhhN-like protein; Region: YhhN; cl01505 316407010993 Protein of unknown function (DUF2500); Region: DUF2500; pfam10694 316407010994 Protein of unknown function (DUF1145); Region: DUF1145; cl11481 316407010995 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 316407010996 S-adenosylmethionine binding site; other site 316407010997 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 316407010998 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 316407010999 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 316407011000 P loop; other site 316407011001 GTP binding site; other site 316407011002 cell division protein FtsE; Provisional; Region: PRK10908 316407011003 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407011004 Walker A/P-loop; other site 316407011005 ATP binding site; other site 316407011006 Q-loop/lid; other site 316407011007 ABC transporter signature motif; other site 316407011008 Walker B; other site 316407011009 D-loop; other site 316407011010 H-loop/switch region; other site 316407011011 Predicted permease; Region: FtsX; cl11418 316407011012 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 316407011013 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 316407011014 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...; Region: Sigma70_r4; cd06171 316407011015 DNA binding residues 316407011016 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 316407011017 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 316407011018 dimerization interface; other site 316407011019 ligand binding site; other site 316407011020 Acetyltransferase, GNAT family; Region: DUF3749; pfam12568 316407011021 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 316407011022 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 316407011023 dimerization interface; other site 316407011024 ligand binding site; other site 316407011025 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 316407011026 TM-ABC transporter signature motif; other site 316407011027 leucine/isoleucine/valine transporter permease subunit; Provisional; Region: livM; PRK11301 316407011028 Domain of unknown function (DUF3382); Region: DUF3382; pfam11862 316407011029 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 316407011030 TM-ABC transporter signature motif; other site 316407011031 leucine/isoleucine/valine transporter ATP-binding subunit; Provisional; Region: livG; PRK11300 316407011032 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 316407011033 Walker A/P-loop; other site 316407011034 ATP binding site; other site 316407011035 Q-loop/lid; other site 316407011036 ABC transporter signature motif; other site 316407011037 Walker B; other site 316407011038 D-loop; other site 316407011039 H-loop/switch region; other site 316407011040 leucine/isoleucine/valine transporter ATP-binding subunit; Provisional; Region: livF; PRK11614 316407011041 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 316407011042 Walker A/P-loop; other site 316407011043 ATP binding site; other site 316407011044 Q-loop/lid; other site 316407011045 ABC transporter signature motif; other site 316407011046 Walker B; other site 316407011047 D-loop; other site 316407011048 H-loop/switch region; other site 316407011049 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 316407011050 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 316407011051 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 316407011052 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...; Region: TM_PBP2; cd06261 316407011053 dimer interface; other site 316407011054 conserved gate region; other site 316407011055 putative PBP binding loops; other site 316407011056 ABC-ATPase subunit interface; other site 316407011057 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...; Region: TM_PBP2; cd06261 316407011058 dimer interface; other site 316407011059 conserved gate region; other site 316407011060 putative PBP binding loops; other site 316407011061 ABC-ATPase subunit interface; other site 316407011062 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 316407011063 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 316407011064 Walker A/P-loop; other site 316407011065 ATP binding site; other site 316407011066 Q-loop/lid; other site 316407011067 ABC transporter signature motif; other site 316407011068 Walker B; other site 316407011069 D-loop; other site 316407011070 H-loop/switch region; other site 316407011071 TOBE domain; Region: TOBE_2; cl01440 316407011072 Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins; Region: GDPD_EcUgpQ_like; cd08562 316407011073 Glycerophosphoryl diester phosphodiesterase family; Region: GDPD; pfam03009 316407011074 putative active site; other site 316407011075 catalytic site; other site 316407011076 putative metal binding site; other site 316407011077 Protein of unknown function (DUF2756); Region: DUF2756; cl08110 316407011078 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 316407011079 gamma-glutamyltranspeptidase; Region: g_glut_trans; TIGR00066 316407011080 IS1 transposase; Region: Transposase_27; cl00721 316407011081 Insertion element protein; Region: Ins_element1; pfam03811 316407011082 Protein of unknown function (DUF796); Region: DUF796; cl01226 316407011083 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...; Region: HNHc; cl00083 316407011084 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 316407011085 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 316407011086 putative oxidoreductase; Provisional; Region: PRK10206 316407011087 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407011088 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 316407011089 Cupin domain; Region: Cupin_2; cl09118 316407011090 gluconate operon transcriptional regulator; Provisional; Region: PRK14987 316407011091 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 316407011092 DNA binding site 316407011093 domain linker motif; other site 316407011094 Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_GntR; cd01575 316407011095 putative ligand binding site; other site 316407011096 putative dimerization interface; other site 316407011097 Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits; Region: GntK; cd02021 316407011098 ATP-binding site; other site 316407011099 Gluconate-6-phosphate binding site; other site 316407011100 Gluconate kinase [Carbohydrate transport and metabolism]; Region: GntK; COG3265 316407011101 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; cl09110 316407011102 gluconate transporter; Region: gntP; TIGR00791 316407011103 MarC family integral membrane protein; Region: MarC; cl00919 316407011104 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 316407011105 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407011106 Semialdehyde dehydrogenase, dimerization domain; Region: Semialdhyde_dhC; pfam02774 316407011107 glycogen branching enzyme; Provisional; Region: PRK05402 316407011108 Glycogen branching enzyme N-terminus domain. Glycogen branching enzyme (AKA 1,4 alpha glucan branching enzyme) catalyzes the formation of alpha-1,6 branch points in either glycogen or starch by cleavage of the alpha-1,4 glucosidic linkage yielding a...; Region: Glycogen_branching_enzyme_N_term; cd02855 316407011109 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 316407011110 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; cl02706 316407011111 glycogen debranching enzyme; Provisional; Region: PRK03705 316407011112 Glycogen_debranching_enzyme N-terminal domain. Glycogen debranching enzymes have both 4-alpha-glucanotransferase and amylo-1,6-glucosidase activities. As a transferase it transfers a segment of a 1,4-alpha-D-glucan to a new 4-position in an acceptor...; Region: Glycogen_debranching_enzyme_N_term; cd02856 316407011113 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 316407011114 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 316407011115 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 316407011116 ligand binding site; other site 316407011117 oligomer interface; other site 316407011118 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 rate-...; Region: LbH_G1P_AT_C; cd04651 316407011119 sulfate 1 binding site; other site 316407011120 glycogen synthase; Provisional; Region: glgA; PRK00654 316407011121 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 316407011122 ADP-binding pocket; other site 316407011123 homodimer interface; other site 316407011124 glycogen phosphorylase; Provisional; Region: PRK14986 316407011125 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 316407011126 homodimer interface; other site 316407011127 active site pocket 316407011128 glycerol-3-phosphate dehydrogenase; Reviewed; Region: glpD; PRK12266 316407011129 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 316407011130 active site residue 316407011131 intramembrane serine protease GlpG; Provisional; Region: PRK10907 316407011132 Protein of unknown function (DUF3582); Region: DUF3582; pfam12122 316407011133 Rhomboid family; Region: Rhomboid; cl11446 316407011134 DNA-binding transcriptional repressor GlpR; Provisional; Region: PRK10906 316407011135 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407011136 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 316407011137 Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: RtcR; COG4650 316407011138 Regulator of RNA terminal phosphate cyclase; Region: RtcR; pfam06956 316407011139 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...; Region: AAA; cd00009 316407011140 Walker A motif; other site 316407011141 ATP binding site; other site 316407011142 Walker B motif; other site 316407011143 arginine finger; other site 316407011144 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a...; Region: Hint; cl12032 316407011145 hypothetical protein; Reviewed; Region: PRK09588 316407011146 RNA 3'-terminal-phosphate cyclase; Provisional; Region: PRK04204 316407011147 RNA 3' phosphate cyclase domain - RNA phosphate cyclases are enzymes that catalyze the ATP-dependent conversion of 3'-phosphate at the end of RNA into 2', 3'-cyclic phosphodiester bond. The enzymes are conserved in eucaryotes, bacteria and archaea...; Region: RNA_Cyclase; cd00295 316407011148 putative active site; other site 316407011149 adenylation catalytic residue; other site 316407011150 transcriptional regulator MalT; Provisional; Region: PRK04841 316407011151 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...; Region: LuxR_C_like; cd06170 316407011152 DNA binding residues 316407011153 dimerization interface; other site 316407011154 maltodextrin phosphorylase; Provisional; Region: PRK14985 316407011155 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 316407011156 homodimer interface; other site 316407011157 active site pocket 316407011158 4-alpha-glucanotransferase; Provisional; Region: malQ; PRK11052 316407011159 4-alpha-glucanotransferase; Region: Glyco_hydro_77; cl00711 316407011160 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; cl09110 316407011161 gluconate transporter; Region: gntP; TIGR00791 316407011162 Fe/S biogenesis protein NfuA; Provisional; Region: PRK11190 316407011163 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 316407011164 NifU-like domain; Region: NifU; cl00484 316407011165 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 316407011166 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 316407011167 carboxylesterase BioH; Provisional; Region: PRK10349 316407011168 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; cl12031 316407011169 putative transposase; Provisional; Region: PRK09857 316407011170 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 316407011171 FeoC like transcriptional regulator; Region: FeoC; cl07573 316407011172 ferrous iron transport protein B; Reviewed; Region: feoB; PRK09554 316407011173 Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this...; Region: FeoB; cd01879 316407011174 G1 box; other site 316407011175 GTP/Mg2+ binding site; other site 316407011176 Switch I region; other site 316407011177 G2 box; other site 316407011178 G3 box; other site 316407011179 Switch II region; other site 316407011180 G4 box; other site 316407011181 G5 box; other site 316407011182 Nucleoside recognition; Region: Gate; cl00486 316407011183 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 316407011184 Nucleoside recognition; Region: Gate; cl00486 316407011185 FeoA domain; Region: FeoA; cl00838 316407011186 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 316407011187 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 316407011188 Uncharacterized protein family (UPF0081); Region: UPF0081; cl00525 316407011189 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl11430 316407011190 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...; Region: S1_Tex; cd05685 316407011191 RNA binding site; other site 316407011192 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 316407011193 domain; Region: GreA_GreB_N; pfam03449 316407011194 C-term; Region: GreA_GreB; pfam01272 316407011195 osmolarity response regulator; Provisional; Region: ompR; PRK09468 316407011196 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 316407011197 active site 316407011198 phosphorylation site 316407011199 intermolecular recognition site; other site 316407011200 dimerization interface; other site 316407011201 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...; Region: trans_reg_C; cd00383 316407011202 DNA binding site 316407011203 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 316407011204 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 connected by an extended linker. The...; Region: HAMP; cl01054 316407011205 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 trans-...; Region: HisKA; cd00082 316407011206 dimer interface; other site 316407011207 phosphorylation site 316407011208 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 316407011209 ATP binding site; other site 316407011210 G-X-G motif; other site 316407011211 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 316407011212 active site 316407011213 substrate-binding site; other site 316407011214 metal-binding site 316407011215 ATP binding site; other site 316407011216 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 316407011217 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 316407011218 dimerization interface; other site 316407011219 domain crossover interface; other site 316407011220 redox-dependent activation switch; other site 316407011221 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 316407011222 RNA binding surface; other site 316407011223 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 316407011224 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 316407011225 motif II; other site 316407011226 Intracellular growth attenuator protein IgaA; Region: IgaA; pfam07095 316407011227 adenosine nucleotide hydrolase NudE; Provisional; Region: nudE; PRK11762 316407011228 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...; Region: ADPRase_NUDT5; cd03424 316407011229 dimer interface; other site 316407011230 ADP-ribose binding site; other site 316407011231 active site 316407011232 nudix motif; other site 316407011233 metal-binding site 316407011234 penicillin-binding protein 1a; Provisional; Region: mrcA; PRK11636 316407011235 Transglycosylase; Region: Transgly; cl07896 316407011236 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 316407011237 Tfp pilus assembly protein, ATPase PilM [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilM; COG4972 316407011238 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 316407011239 Protein of unknown function (DUF2531); Region: DUF2531; pfam10748 316407011240 outer membrane porin HofQ; Provisional; Region: hofQ; PRK10560 316407011241 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 316407011242 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 316407011243 shikimate kinase; Reviewed; Region: aroK; PRK00131 316407011244 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...; Region: SK; cd00464 316407011245 ADP binding site; other site 316407011246 magnesium binding site; other site 316407011247 putative shikimate binding site; other site 316407011248 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 316407011249 active site 316407011250 dimer interface; other site 316407011251 metal-binding site 316407011252 cell division protein DamX; Validated; Region: PRK10905 316407011253 Sporulation related domain; Region: SPOR; cl10051 316407011254 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl00408 316407011255 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...; Region: RPE; cd00429 316407011256 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 316407011257 substrate binding site; other site 316407011258 hexamer interface; other site 316407011259 metal-binding site 316407011260 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 316407011261 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 316407011262 motif II; other site 316407011263 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 316407011264 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 316407011265 active site 316407011266 HIGH motif; other site 316407011267 dimer interface; other site 316407011268 KMSKS motif; other site 316407011269 PRD domain protein EF_0829/AHA_3910; Region: EF_0829; TIGR03582 316407011270 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme yhfX; Region: PLPDE_III_yhfX_like; cd06811 316407011271 dimer interface; other site 316407011272 Predicted amino acid racemase [Amino acid transport and metabolism]; Region: COG3457 316407011273 active site 316407011274 pyridoxal 5'-phosphate (PLP) binding site; other site 316407011275 substrate binding site; other site 316407011276 catalytic residue; other site 316407011277 putative mutase; Provisional; Region: PRK12383 316407011278 Sulfatase; Region: Sulfatase; cl10460 316407011279 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: Php; COG1735 316407011280 Phosphotriesterase (PTE) catalyzes the hydrolysis of organophosphate nerve agents, including the chemical warfare agents VX, soman, and sarin as well as the insecticide paraoxon. PTE exists as a homodimer with one active site per monomer. The active...; Region: PTE; cd00530 316407011281 active site 316407011282 substrate binding pocket; other site 316407011283 homodimer interaction site; other site 316407011284 Protein of unknown function DUF2620; Region: DUF2620; pfam10941 316407011285 Protein of unknown function; Region: YhfT; pfam10797 316407011286 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 316407011287 DNA topoisomerase III, bacteria and conjugative plasmid; Region: topB; TIGR01056 316407011288 DNA-binding transcriptional regulator FrlR; Provisional; Region: PRK11402 316407011289 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407011290 DNA binding site 316407011291 UTRA domain; Region: UTRA; cl06649 316407011292 Fructoselysine kinase-like. Fructoselysine is a fructoseamine formed by glycation, a non-enzymatic reaction of glucose with a primary amine followed by an Amadori rearrangement, resulting in a protein that is modified at the amino terminus and at the...; Region: Fructoselysine_kinase_like; cd01940 316407011293 substrate binding site; other site 316407011294 ATP binding site; other site 316407011295 fructoselysine 3-epimerase; Provisional; Region: PRK09856 316407011296 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of D-arabino-6-...; Region: AP2Ec; cl12060 316407011297 AP (apurinic/apyrimidinic) site pocket; other site 316407011298 DNA interaction; other site 316407011299 Metal-binding active site; metal-binding site 316407011300 fructoselysine-6-P-deglycase; Provisional; Region: frlB; PRK11382 316407011301 SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars; Region: SIS; cl00389 316407011302 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 316407011303 dimer interface; other site 316407011304 active site 316407011305 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407011306 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 316407011307 siroheme synthase; Provisional; Region: cysG; PRK10637 316407011308 precorrin-2 dehydrogenase; Validated; Region: PRK06719 316407011309 Sirohaem synthase dimerization region; Region: CysG_dimerizer; pfam10414 316407011310 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 316407011311 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 316407011312 Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain...; Region: Rieske_NirD; cd03529 316407011313 nitrite reductase subunit NirD; Provisional; Region: PRK14989 316407011314 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407011315 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 316407011316 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 316407011317 putative transporter; Provisional; Region: PRK03699 316407011318 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 316407011319 putative substrate translocation pore; other site 316407011320 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 316407011321 substrate binding site; other site 316407011322 Protein of unknown function (DUF2559); Region: DUF2559; cl08097 316407011323 Fic/DOC family; Region: Fic; cl00960 316407011324 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 316407011325 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 316407011326 glutamine binding; other site 316407011327 catalytic triad; other site 316407011328 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein; Reviewed; Region: argD; PRK05093 316407011329 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 316407011330 inhibitor-cofactor binding pocket; inhibition site 316407011331 pyridoxal 5'-phosphate binding site; other site 316407011332 catalytic residue; other site 316407011333 integral membrane protein, YccS/YhfK family; Region: YCCS_YHJK; TIGR01667 316407011334 hypothetical membrane protein, TIGR01666; Region: YCCS 316407011335 DNA-binding transcriptional dual regulator Crp; Provisional; Region: PRK11753 316407011336 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 316407011337 ligand binding site; other site 316407011338 flexible hinge region; other site 316407011339 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 316407011340 putative switch regulator; other site 316407011341 non-specific DNA interactions; other site 316407011342 DNA binding site 316407011343 sequence specific DNA binding site; other site 316407011344 putative cAMP binding site; other site 316407011345 OsmC-like protein; Region: OsmC; cl00767 316407011346 Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. PRK catalyzes the phosphorylation of D-ribulose 5-phosphate...; Region: PRK_like; cd02029 316407011347 active site 316407011348 Uncharacterized protein family (UPF0270); Region: UPF0270; cl01180 316407011349 putative hydrolase; Provisional; Region: PRK10985 316407011350 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; cl12031 316407011351 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 316407011352 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407011353 Walker A/P-loop; other site 316407011354 ATP binding site; other site 316407011355 Q-loop/lid; other site 316407011356 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 316407011357 ABC transporter signature motif; other site 316407011358 Walker B; other site 316407011359 D-loop; other site 316407011360 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 316407011361 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 316407011362 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 316407011363 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 316407011364 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407011365 Probable metal-binding protein (DUF2387); Region: DUF2387; cl01410 316407011366 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 316407011367 SlyX; Region: SlyX; cl01090 316407011368 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK10902 316407011369 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 316407011370 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 316407011371 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 316407011372 YheO-like PAS domain; Region: PAS_6; pfam08348 316407011373 DsrE/DsrF-like family; Region: DrsE; cl00672 316407011374 DsrE/DsrF-like family; Region: DrsE; cl00672 316407011375 DsrH like protein; Region: DsrH; cl00953 316407011376 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 316407011377 S17 interaction site; other site 316407011378 S8 interaction site; other site 316407011379 16S rRNA interaction site; other site 316407011380 streptomycin interaction site; other site 316407011381 23S rRNA interaction site; other site 316407011382 aminoacyl-tRNA interaction site (A-site); other site 316407011383 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 316407011384 elongation factor G; Reviewed; Region: PRK00007 316407011385 Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved...; Region: EF-G; cd01886 316407011386 G1 box; other site 316407011387 putative GEF interaction site; other site 316407011388 GTP/Mg2+ binding site; other site 316407011389 Switch I region; other site 316407011390 G2 box; other site 316407011391 G3 box; other site 316407011392 Switch II region; other site 316407011393 G4 box; other site 316407011394 G5 box; other site 316407011395 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...; Region: EFG_mtEFG_II; cd04088 316407011396 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...; Region: EFG_mtEFG1_IV; cd01434 316407011397 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...; Region: EFG_mtEFG_C; cd03713 316407011398 elongation factor Tu; Reviewed; Region: PRK00049 316407011399 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 316407011400 G1 box; other site 316407011401 GEF interaction site; other site 316407011402 GTP/Mg2+ binding site; other site 316407011403 Switch I region; other site 316407011404 G2 box; other site 316407011405 G3 box; other site 316407011406 Switch II region; other site 316407011407 G4 box; other site 316407011408 G5 box; other site 316407011409 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 316407011410 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 316407011411 Antibiotic Binding Site; other site 316407011412 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cl00046 316407011413 PF-ChiA is an uncharacterized chitinase found in the hyperthermophilic archaeon Pyrococcus furiosus with a glycosyl hydrolase family 18 (GH18) catalytic domain as well as a cellulose-binding domain. Members of this domain family are found not only in...; Region: GH18_PF-ChiA-like; cd06543 316407011414 active site 316407011415 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 316407011416 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 316407011417 Ferritin-like domain; Region: Ferritin; pfam00210 316407011418 heme binding site; other site 316407011419 ferroxidase pore; other site 316407011420 ferroxidase diiron center; other site 316407011421 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 316407011422 General secretion pathway, M protein; Region: GspM; cl01222 316407011423 General secretion pathway protein L (GspL); Region: GspL; cl11448 316407011424 Type II secretory pathway, component PulK [Intracellular trafficking and secretion]; Region: PulK; COG3156 316407011425 Type II secretory pathway, component PulJ [Intracellular trafficking and secretion]; Region: PulJ; COG4795 316407011426 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 316407011427 Pseudopilin GspJ; Region: GspJ; pfam11612 316407011428 general secretion pathway protein I; Region: gspI; TIGR01707 316407011429 Bacterial type II secretion system protein I/J; Region: GSPII_IJ; pfam02501 316407011430 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 316407011431 general secretion pathway protein G; Region: typeII_sec_gspG; TIGR01710 316407011432 Bacterial type II secretion system protein G; Region: GSPII_G; pfam08334 316407011433 general secretion pathway protein F; Region: GspF; TIGR02120 316407011434 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 316407011435 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 316407011436 general secretory pathway protein E; Region: type_II_gspE; TIGR02533 316407011437 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 316407011438 Walker A motif; other site 316407011439 ATP binding site; other site 316407011440 Walker B motif; other site 316407011441 general secretion pathway protein D; Region: type_II_gspD; TIGR02517 316407011442 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 316407011443 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 316407011444 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 316407011445 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 316407011446 Type II secretory pathway, component PulC [Intracellular trafficking and secretion]; Region: PulC; COG3031 316407011447 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 316407011448 protein secretion protein GspB; Provisional; Region: PRK09697 316407011449 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 316407011450 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 316407011451 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 316407011452 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 316407011453 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 316407011454 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 316407011455 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 316407011456 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 316407011457 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 316407011458 protein-rRNA interface; other site 316407011459 putative translocon binding site; other site 316407011460 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 316407011461 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...; Region: 30S_S3_KH; cd02412 316407011462 G-X-X-G motif; other site 316407011463 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 316407011464 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 316407011465 23S rRNA interface; other site 316407011466 5S rRNA interface; other site 316407011467 putative antibiotic binding site; other site 316407011468 L25 interface; other site 316407011469 L27 interface; other site 316407011470 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...; Region: Ribosomal_L29_HIP; cd00427 316407011471 23S rRNA interface; other site 316407011472 putative translocon interaction site; other site 316407011473 signal recognition particle (SRP54) interaction site; other site 316407011474 L23 interface; other site 316407011475 trigger factor interaction site; other site 316407011476 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 316407011477 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 316407011478 KOW motif; Region: KOW; cl00354 316407011479 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 316407011480 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 316407011481 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 316407011482 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 316407011483 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 316407011484 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 316407011485 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 316407011486 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 316407011487 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 316407011488 23S rRNA interface; other site 316407011489 5S rRNA interface; other site 316407011490 L27 interface; other site 316407011491 L5 interface; other site 316407011492 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 316407011493 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 316407011494 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 316407011495 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...; Region: Ribosomal_L30; cd01658 316407011496 23S rRNA binding site; other site 316407011497 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 316407011498 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 316407011499 eubacterial secY protein; Region: SecY; pfam00344 316407011500 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 316407011501 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 316407011502 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 316407011503 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 316407011504 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 316407011505 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 316407011506 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 316407011507 RNA binding surface; other site 316407011508 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 316407011509 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 316407011510 alphaNTD homodimer interface; other site 316407011511 alphaNTD - beta interaction site; other site 316407011512 alphaNTD - beta' interaction site; other site 316407011513 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 316407011514 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 316407011515 Domain of unknown function (DUF1992); Region: DUF1992; cl08096 316407011516 zinc-responsive transcriptional regulator; Provisional; Region: zntR; PRK09514 316407011517 Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; Region: HTH_HMRTR; cd04770 316407011518 DNA binding residues 316407011519 dimer interface; other site 316407011520 metal-binding site 316407011521 Domain of unknown function; Region: DUF331; cl01149 316407011522 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 316407011523 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 316407011524 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407011525 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; cl09110 316407011526 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407011527 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; cl09110 316407011528 N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine transferase Sun, also known as RrmB or Fmu shares the RNA-binding non-catalytic domain with the transcription termination factor NusB. The precise biological...; Region: Methyltransferase_Sun; cd00620 316407011529 putative RNA binding site; other site 316407011530 16S rRNA methyltransferase B; Provisional; Region: PRK10901 316407011531 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 316407011532 S-adenosylmethionine binding site; other site 316407011533 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 316407011534 Formyl transferase; Region: Formyl_trans_N; cl00395 316407011535 Formyl transferase, C-terminal domain; Region: Formyl_trans_C; pfam02911 316407011536 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(...; Region: Pep_deformylase; cd00487 316407011537 active site 316407011538 catalytic residues; other site 316407011539 metal-binding site 316407011540 hypothetical protein; Provisional; Region: PRK10736 316407011541 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 316407011542 Protein of unknown function (DUF494); Region: DUF494; cl01103 316407011543 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 316407011544 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 316407011545 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 316407011546 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 316407011547 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 316407011548 shikimate 5-dehydrogenase; Region: aroE; TIGR00507 316407011549 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 316407011550 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 316407011551 shikimate binding site; other site 316407011552 NAD(P) binding site; other site 316407011553 Protein of unknown function (DUF1488); Region: DUF1488; pfam07369 316407011554 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 316407011555 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 316407011556 trimer interface; other site 316407011557 putative metal binding site; other site 316407011558 hypothetical protein; Provisional; Region: PRK10039 316407011559 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 316407011560 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 316407011561 proposed active site lysine; other site 316407011562 conserved cys residue; other site 316407011563 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 316407011564 malate synthase A; Region: malate_syn_A; TIGR01344 316407011565 active site 316407011566 isocitrate lyase; Provisional; Region: PRK06498 316407011567 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 316407011568 tetramer interface; other site 316407011569 active site 316407011570 Mg2+/Mn2+ binding site; other site 316407011571 Isocitrate dehydrogenase kinase/phosphatase (AceK); Region: AceK; cl01891 316407011572 ShET2 enterotoxin, N-terminal region; Region: Toxin_15; pfam07906 316407011573 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 316407011574 transcriptional repressor IclR; Provisional; Region: PRK11569 316407011575 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407011576 Bacterial transcriptional regulator; Region: IclR; pfam01614 316407011577 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 316407011578 Homocysteine/selenocysteine methylase (S-methylmethionine-dependent) [Amino acid transport and metabolism]; Region: MHT1; cl14105 316407011579 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 316407011580 substrate binding pocket; other site 316407011581 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 316407011582 B12 binding site; other site 316407011583 cobalt ligand; other site 316407011584 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 316407011585 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 316407011586 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 316407011587 Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E; Region: GAT1_Peptidase_E; cd03146 316407011588 active site pocket 316407011589 oxyanion hole; other site 316407011590 catalytic triad; other site 316407011591 active site nucleophile 316407011592 23S rRNA pseudouridine synthase F; Provisional; Region: PRK10475 316407011593 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 316407011594 RNA binding surface; other site 316407011595 PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like. This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_RluF; cd02554 316407011596 probable active site; other site 316407011597 Competence regulator Spx (YjbD); Region: ComReg_Spx; cl08125 316407011598 aspartate kinase III; Validated; Region: PRK09084 316407011599 AAK_AKiii-LysC-EC: Amino Acid Kinase Superfamily (AAK), AKiii-LysC-EC: this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKIII. AKIII is a monofunctional class enzyme (LysC) found in...; Region: AAK_AKiii-LysC-EC; cd04258 316407011600 nucleotide binding site; other site 316407011601 putative catalytic residues; other site 316407011602 aspartate binding site; other site 316407011603 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC_1; cd04932 316407011604 lysine allosteric regulatory site; other site 316407011605 dimer interface; other site 316407011606 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC_2; cd04917 316407011607 dimer interface; other site 316407011608 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 316407011609 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 316407011610 active site 316407011611 dimer interface; other site 316407011612 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 316407011613 dimer interface; other site 316407011614 active site 316407011615 Protein of unknown function (DUF2886); Region: DUF2886; pfam11102 316407011616 Protein of unknown function (DUF2886); Region: DUF2886; pfam11102 316407011617 SLBB-domain like (DUF1017); Region: DUF1017; pfam06251 316407011618 Bacterial putative lipoprotein (DUF940); Region: DUF940; pfam06082 316407011619 Phosphate-starvation-inducible E; Region: PsiE; cl01264 316407011620 D-xylose transporter XylE; Provisional; Region: xylE; PRK10077 316407011621 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 316407011622 putative substrate translocation pore; other site 316407011623 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 316407011624 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...; Region: TM_PBP2; cd06261 316407011625 dimer interface; other site 316407011626 conserved gate region; other site 316407011627 putative PBP binding loops; other site 316407011628 ABC-ATPase subunit interface; other site 316407011629 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...; Region: TM_PBP2; cd06261 316407011630 dimer interface; other site 316407011631 conserved gate region; other site 316407011632 putative PBP binding loops; other site 316407011633 ABC-ATPase subunit interface; other site 316407011634 Maltose-binding periplasmic proteins/domains [Carbohydrate transport and metabolism]; Region: MalE; COG2182 316407011635 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 316407011636 maltose/maltodextrin transporter ATP-binding protein; Provisional; Region: PRK11000 316407011637 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 316407011638 Walker A/P-loop; other site 316407011639 ATP binding site; other site 316407011640 Q-loop/lid; other site 316407011641 ABC transporter signature motif; other site 316407011642 Walker B; other site 316407011643 D-loop; other site 316407011644 H-loop/switch region; other site 316407011645 TOBE domain; Region: TOBE_2; cl01440 316407011646 The Maltoporin-like channels (LamB porin) form a trimeric structure which facilitate the diffusion of maltodextrins and other sugars across the outer membrane of Gram-negative bacteria. The membrane channel is formed by an 18-strand antiparallel beta-...; Region: Maltoporin-like; cd01346 316407011647 trimer interface; other site 316407011648 sugar binding site; other site 316407011649 Maltose operon periplasmic protein precursor (MalM); Region: MalM; cl11647 316407011650 hypothetical protein; Validated; Region: PRK09718 316407011651 Chorismate lyase; Region: Chor_lyase; cl01230 316407011652 UbiA prenyltransferase family; Region: UbiA; cl00337 316407011653 Glycerol-3-phosphate O-acyltransferase [Lipid metabolism]; Region: PlsB; COG2937 316407011654 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like; Region: LPLAT_DHAPAT-like; cd07993 316407011655 putative acyl-acceptor binding pocket; other site 316407011656 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 316407011657 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407011658 LexA repressor; Validated; Region: PRK00215 316407011659 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 (...; Region: S24_LexA-like; cd06529 316407011660 Catalytic site; other site 316407011661 DNA-damage-inducible SOS response protein; Provisional; Region: PRK10367 316407011662 MatE; Region: MatE; pfam01554 316407011663 MatE; Region: MatE; pfam01554 316407011664 CsbD-like; Region: CsbD; cl01272 316407011665 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 316407011666 metal binding site 2; metal-binding site 316407011667 putative DNA binding helix; other site 316407011668 metal binding site 1; metal-binding site 316407011669 dimer interface; other site 316407011670 structural Zn2+ binding site; other site 316407011671 Protein of unknown function (DUF2713); Region: DUF2713; pfam10897 316407011672 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...; Region: DUS_like_FMN; cd02801 316407011673 Dihydrouridine synthase (Dus); Region: Dus; pfam01207 316407011674 FMN binding site; other site 316407011675 active site 316407011676 catalytic residues; other site 316407011677 substrate binding site; other site 316407011678 Phage shock protein G (Phageshock_PspG); Region: Phageshock_PspG; cl11511 316407011679 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 316407011680 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 316407011681 NADP binding site; other site 316407011682 dimer interface; other site 316407011683 replicative DNA helicase; Provisional; Region: PRK08006 316407011684 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 316407011685 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 316407011686 Walker A motif; other site 316407011687 ATP binding site; other site 316407011688 Walker B motif; other site 316407011689 DNA binding loops 316407011690 alanine racemase; Reviewed; Region: alr; PRK00053 316407011691 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 316407011692 active site 316407011693 pyridoxal 5'-phosphate (PLP) binding site; other site 316407011694 substrate binding site; other site 316407011695 catalytic residues; other site 316407011696 dimer interface; other site 316407011697 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 316407011698 pyridoxal 5'-phosphate binding site; other site 316407011699 homodimer interface; other site 316407011700 catalytic residue; other site 316407011701 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 316407011702 active site 316407011703 motif I; other site 316407011704 motif II; other site 316407011705 Uncharacterized protein family UPF0047; Region: UPF0047; cl00439 316407011706 Protein of unknown function (DUF419); Region: DUF419; cl09948 316407011707 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 316407011708 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 316407011709 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 316407011710 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 316407011711 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 316407011712 dimer interface; other site 316407011713 ssDNA binding site; other site 316407011714 tetramer (dimer of dimers) interface; other site 316407011715 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 316407011716 Predicted signal transduction protein containing sensor and EAL domains [Signal transduction mechanisms]; Region: COG4943 316407011717 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 316407011718 DNA-binding transcriptional regulator SoxS; Provisional; Region: PRK10219 316407011719 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407011720 redox-sensitivie transcriptional activator SoxR; Provisional; Region: PRK15002 316407011721 Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Region: HTH_SoxR; cd01110 316407011722 DNA binding residues 316407011723 dimer interface; other site 316407011724 [2Fe-2S] cluster binding site; other site 316407011725 Permease family; Region: Xan_ur_permease; cl00967 316407011726 Na+/H+ antiporter, bacterial form; Region: a_cpa1; TIGR00831 316407011727 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 316407011728 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 316407011729 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 316407011730 Sodium:solute symporter family; Region: SSF; cl00456 316407011731 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 316407011732 Protein of unknown function, DUF485; Region: DUF485; cl01231 316407011733 acetyl-CoA synthetase; Provisional; Region: PRK00174 316407011734 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 316407011735 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 316407011736 Formate-dependent nitrite reductase, periplasmic cytochrome c552 subunit [Inorganic ion transport and metabolism]; Region: NrfA; COG3303 316407011737 cytochrome c nitrite reductase subunit c552; Provisional; Region: nrfA; cl10556 316407011738 cytochrome c nitrite reductase pentaheme subunit; Provisional; Region: PRK11659 316407011739 cytochrome c nitrite reductase subunit c552; Provisional; Region: nrfA; cl10556 316407011740 cytochrome c nitrite reductase, Fe-S protein; Region: cyt_nit_nrfC; TIGR03149 316407011741 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 alpha-; Region: HCP_like; cl14655 316407011742 Polysulphide reductase, NrfD; Region: NrfD; pfam03916 316407011743 Polysulphide reductase [Energy production and conversion]; Region: COG5557; cl01295 316407011744 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 316407011745 Cytochrome C biogenesis protein; Region: CcmH; cl01179 316407011746 formate-dependent nitrite reductase complex subunit NrfG; Provisional; Region: PRK10370 316407011747 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 316407011748 binding surface 316407011749 TPR motif; other site 316407011750 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 316407011751 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 316407011752 Sel1 repeat; Region: Sel1; cl02723 316407011753 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 316407011754 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)...; Region: MopB_Formate-Dh-H; cd02753 316407011755 [4Fe-4S] binding site; other site 316407011756 molybdopterin cofactor binding site; other site 316407011757 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)...; Region: MopB_CT_Formate-Dh_H; cd02790 316407011758 molybdopterin cofactor binding site; other site 316407011759 putative outer membrane efflux protein MdtP; Provisional; Region: PRK09915 316407011760 Outer membrane efflux protein; Region: OEP; pfam02321 316407011761 Bacterial protein of unknown function (DUF939); Region: DUF939; cl12136 316407011762 Predicted membrane protein [Function unknown]; Region: COG1289 316407011763 multidrug resistance protein MdtN; Provisional; Region: PRK10476 316407011764 Alkyl sulfatase and related hydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2015 316407011765 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 316407011766 Transposase domain (DUF772); Region: DUF772; cl12084 316407011767 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 316407011768 D-allose kinase; Provisional; Region: PRK09698 316407011769 ROK family; Region: ROK; cl09121 316407011770 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 316407011771 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...; Region: RPE; cd00429 316407011772 substrate binding site; other site 316407011773 hexamer interface; other site 316407011774 metal-binding site 316407011775 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 316407011776 TM-ABC transporter signature motif; other site 316407011777 D-allose transporter ATP-binding protein; Provisional; Region: PRK09700 316407011778 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 316407011779 Walker A/P-loop; other site 316407011780 ATP binding site; other site 316407011781 Q-loop/lid; other site 316407011782 ABC transporter signature motif; other site 316407011783 Walker B; other site 316407011784 D-loop; other site 316407011785 H-loop/switch region; other site 316407011786 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (; Region: ABC_Carb_Monos_II; cd03215 316407011787 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 316407011788 Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis; Region: PBP1_allose_binding; cd06320 316407011789 ligand binding site; other site 316407011790 dimerization interface; other site 316407011791 zinc binding site; other site 316407011792 DNA-binding transcriptional repressor RpiR; Provisional; Region: PRK11337 316407011793 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...; Region: SIS_RpiR; cd05013 316407011794 putative active site; other site 316407011795 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 316407011796 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 316407011797 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 316407011798 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 316407011799 Coenzyme A binding pocket; other site 316407011800 Guanylate kinase; Region: Guanylate_kin; cl12021 316407011801 phosphonate metabolism protein PhnM; Provisional; Region: PRK15446 316407011802 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...; Region: metallo-dependent_hydrolases; cl00281 316407011803 PhnM is believed to be a subunit of the membrane associated C-P lyase complex. C-P lyase is thought to catalyze the direct cleavage of inactivated C-P bonds to yield inorganic phosphate and the corresponding hydrocarbons. It is responsible for cleavage...; Region: PhnM; cd01306 316407011804 active site 316407011805 phosphonate C-P lyase system protein PhnL; Region: CP_lyasePhnL; TIGR02324 316407011806 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 316407011807 Walker A/P-loop; other site 316407011808 ATP binding site; other site 316407011809 Q-loop/lid; other site 316407011810 ABC transporter signature motif; other site 316407011811 Walker B; other site 316407011812 D-loop; other site 316407011813 H-loop/switch region; other site 316407011814 phosphonate C-P lyase system protein PhnK; Provisional; Region: phnK; PRK11701 316407011815 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 316407011816 Walker A/P-loop; other site 316407011817 ATP binding site; other site 316407011818 Q-loop/lid; other site 316407011819 ABC transporter signature motif; other site 316407011820 Walker B; other site 316407011821 D-loop; other site 316407011822 H-loop/switch region; other site 316407011823 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 316407011824 Phosphonate metabolism protein PhnJ; Region: PhnJ; cl01457 316407011825 Bacterial phosphonate metabolism protein (PhnI); Region: PhnI; cl01456 316407011826 Bacterial phosphonate metabolism protein (PhnH); Region: PhnH; cl01455 316407011827 Phosphonate metabolism protein PhnG; Region: PhnG; cl01454 316407011828 phosphonate metabolism transcriptional regulator PhnF; Provisional; Region: PRK10079 316407011829 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407011830 DNA binding site 316407011831 UTRA domain; Region: UTRA; cl06649 316407011832 ECK4096:JW4064:b4103; phosphonate/organophosphate ester transporter 316407011833 phosphonate ABC transporter, periplasmic phosphonate binding protein; Region: PhnD; TIGR03431 316407011834 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 316407011835 phosphonate/organophosphate ester transporter subunit; Provisional; Region: PRK09984 316407011836 ABC-type phosphate/phosphonate transport system. Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all...; Region: ABC_PhnC_transporter; cd03256 316407011837 Walker A/P-loop; other site 316407011838 ATP binding site; other site 316407011839 Q-loop/lid; other site 316407011840 ABC transporter signature motif; other site 316407011841 Walker B; other site 316407011842 D-loop; other site 316407011843 H-loop/switch region; other site 316407011844 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 316407011845 dimer interface; other site 316407011846 hypothetical protein; Provisional; Region: PRK10220 316407011847 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 316407011848 PhnA protein; Region: PhnA; pfam03831 316407011849 hypothetical protein; Provisional; Region: PRK09866 316407011850 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 316407011851 Era (E. coli Ras-like protein)-like. This family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngG), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs)...; Region: Era_like; cd00880 316407011852 Switch II region; other site 316407011853 G3 box; other site 316407011854 G4 box; other site 316407011855 G5 box; other site 316407011856 proline/glycine betaine transporter; Provisional; Region: PRK10642 316407011857 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 316407011858 putative substrate translocation pore; other site 316407011859 Osmosensory transporter coiled coil; Region: Osmo_CC; pfam08946 316407011860 sensor protein BasS/PmrB; Provisional; Region: PRK10755 316407011861 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 connected by an extended linker. The...; Region: HAMP; cl01054 316407011862 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 trans-...; Region: HisKA; cd00082 316407011863 dimer interface; other site 316407011864 phosphorylation site 316407011865 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 316407011866 ATP binding site; other site 316407011867 Mg2+ binding site; other site 316407011868 G-X-G motif; other site 316407011869 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 316407011870 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 316407011871 active site 316407011872 phosphorylation site 316407011873 intermolecular recognition site; other site 316407011874 dimerization interface; other site 316407011875 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...; Region: trans_reg_C; cd00383 316407011876 DNA binding site 316407011877 putative metal dependent hydrolase; Provisional; Region: PRK11598 316407011878 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 316407011879 Sulfatase; Region: Sulfatase; cl10460 316407011880 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407011881 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 316407011882 DNA-binding transcriptional regulator GadX; Provisional; Region: PRK09978 316407011883 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407011884 arginine decarboxylase; Provisional; Region: PRK15029 316407011885 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; cl09944 316407011886 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...; Region: Orn_deC_like; cd00615 316407011887 homodimer interface; other site 316407011888 pyridoxal 5'-phosphate binding site; other site 316407011889 catalytic residue; other site 316407011890 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 316407011891 DNA-binding transcriptional regulator MelR; Provisional; Region: PRK10371 316407011892 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407011893 alpha-galactosidase; Provisional; Region: PRK15076 316407011894 Glycoside Hydrolases Family 4; Alpha-glucosidases and alpha-galactosidases; Region: GH4_alpha_glucosidase_galactosidase; cd05297 316407011895 NAD binding site; other site 316407011896 sugar binding site; other site 316407011897 divalent metal binding site; other site 316407011898 putative tetramer (dimer of dimers) interface; other site 316407011899 dimer interface; other site 316407011900 melibiose:sodium symporter; Provisional; Region: PRK10429 316407011901 putative transporter; Provisional; Region: PRK11462 316407011902 Predicted membrane protein (DUF2238); Region: DUF2238; cl01464 316407011903 fumarate hydratase; Provisional; Region: PRK15389 316407011904 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 316407011905 Fumarase C-terminus; Region: Fumerase_C; cl00795 316407011906 Anaerobic c4-dicarboxylate membrane transporter; Region: DcuA_DcuB; cl01040 316407011907 DNA-binding transcriptional activator DcuR; Provisional; Region: PRK10430 316407011908 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 316407011909 active site 316407011910 phosphorylation site 316407011911 intermolecular recognition site; other site 316407011912 dimerization interface; other site 316407011913 sensory histidine kinase DcuS; Provisional; Region: PRK11086 316407011914 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 316407011915 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 316407011916 ATP binding site; other site 316407011917 Mg2+ binding site; other site 316407011918 G-X-G motif; other site 316407011919 Protein of unknown function (DUF1271); Region: DUF1271; cl01443 316407011920 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 316407011921 Protein of unknown function (DUF2566); Region: DUF2566; pfam10753 316407011922 lysyl-tRNA synthetase; Reviewed; Region: PRK12445 316407011923 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-...; Region: LysRS_N; cd04322 316407011924 dimer interface; other site 316407011925 putative anticodon binding site; other site 316407011926 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 316407011927 motif 1; other site 316407011928 active site 316407011929 motif 2; other site 316407011930 motif 3; other site 316407011931 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 316407011932 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 316407011933 putative substrate translocation pore; other site 316407011934 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; cl11420 316407011935 lysine decarboxylase CadA; Provisional; Region: PRK15400 316407011936 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; cl09944 316407011937 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...; Region: Orn_deC_like; cd00615 316407011938 homodimer interface; other site 316407011939 pyridoxal 5'-phosphate binding site; other site 316407011940 catalytic residue; other site 316407011941 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 316407011942 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407011943 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 316407011944 DNA-binding transcriptional activator CadC; Provisional; Region: PRK10153 316407011945 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...; Region: trans_reg_C; cd00383 316407011946 DNA binding site 316407011947 putative transcriptional regulator; Provisional; Region: PRK11640 316407011948 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 316407011949 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 316407011950 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl00515 316407011951 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 316407011952 DsbD alpha interface; other site 316407011953 catalytic residues; other site 316407011954 CutA1 divalent ion tolerance protein; Region: CutA1; cl00584 316407011955 Anaerobic c4-dicarboxylate membrane transporter; Region: DcuA_DcuB; cl01040 316407011956 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 316407011957 Aspartase; Region: Aspartase; cd01357 316407011958 active sites 316407011959 tetramer interface; other site 316407011960 FxsA cytoplasmic membrane protein; Region: FxsA; cl01148 316407011961 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407011962 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...; Region: cpn10; cd00320 316407011963 oligomerisation interface; other site 316407011964 mobile loop; other site 316407011965 roof hairpin; other site 316407011966 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 316407011967 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 316407011968 ring oligomerisation interface; other site 316407011969 ATP/Mg binding site; other site 316407011970 stacking interactions; other site 316407011971 hinge regions; other site 316407011972 Lysine 2,3-aminomutase [Amino acid transport and metabolism]; Region: KamA; COG1509 316407011973 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 316407011974 FeS/SAM binding site; other site 316407011975 elongation factor P; Validated; Region: PRK00529 316407011976 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 316407011977 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 N-formylmethionyl-...; Region: S1_EF-P_repeat_1; cd04470 316407011978 RNA binding site; other site 316407011979 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 N-formylmethionyl-...; Region: S1_EF-P_repeat_2; cd05794 316407011980 RNA binding site; other site 316407011981 entericidin A; Provisional; Region: PRK09810 316407011982 Entericidin EcnA/B family; Region: Entericidin; cl02322 316407011983 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 316407011984 Lipocalin / cytosolic fatty-acid binding protein family; Region: Lipocalin; cl01150 316407011985 Beta-lactamase; Region: Beta-lactamase; cl01009 316407011986 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 316407011987 Quinol:fumarate reductase (QFR) Type D subfamily, 13kD hydrophobic subunit D; 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:quinine...; Region: QFR_TypeD_subunitD; cd00547 316407011988 Iron-sulfur protein interface; other site 316407011989 proximal quinone binding site; other site 316407011990 C-subunit interface; other site 316407011991 distal quinone binding site; other site 316407011992 Quinol:fumarate reductase (QFR) Type D subfamily, 15kD hydrophobic subunit C; 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:quinine...; Region: QFR_TypeD_subunitC; cd00546 316407011993 D-subunit interface; other site 316407011994 Iron-sulfur protein interface; other site 316407011995 proximal quinone binding site; other site 316407011996 distal quinone binding site; other site 316407011997 fumarate reductase iron-sulfur subunit; Provisional; Region: PRK12385 316407011998 fumarate reductase flavoprotein subunit; Validated; Region: PRK09231 316407011999 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 316407012000 domain; Region: Succ_DH_flav_C; pfam02910 316407012001 poxB regulator PoxA; Provisional; Region: PRK09350 316407012002 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 316407012003 motif 1; other site 316407012004 dimer interface; other site 316407012005 active site 316407012006 motif 2; other site 316407012007 motif 3; other site 316407012008 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407012009 Protein of unknown function (DUF2645); Region: DUF2645; pfam10840 316407012010 putative mechanosensitive channel protein; Provisional; Region: PRK10929 316407012011 Mechanosensitive ion channel; Region: MS_channel; pfam00924 316407012012 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 316407012013 GTPase RsgA; Reviewed; Region: PRK12288 316407012014 YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence...; Region: YjeQ_engC; cd01854 316407012015 GTPase/OB domain interface; other site 316407012016 GTPase/Zn-binding domain interface; other site 316407012017 GTP/Mg2+ binding site; other site 316407012018 G4 box; other site 316407012019 G5 box; other site 316407012020 G1 box; other site 316407012021 Switch I region; other site 316407012022 G2 box; other site 316407012023 G3 box; other site 316407012024 Switch II region; other site 316407012025 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 316407012026 putative active site; other site 316407012027 putative substrate binding site; other site 316407012028 catalytic site; other site 316407012029 dimer interface; other site 316407012030 iron-sulfur cluster binding protein, putative; Region: TIGR00276 316407012031 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 316407012032 putative carbohydrate kinase; Provisional; Region: PRK10565 316407012033 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 316407012034 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 316407012035 putative substrate binding site; other site 316407012036 putative ATP binding site; other site 316407012037 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 316407012038 N-acetylmuramoyl-l-alanine amidase II; Provisional; Region: PRK10431 316407012039 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 316407012040 active site 316407012041 metal-binding site 316407012042 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 316407012043 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 316407012044 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 316407012045 ATP binding site; other site 316407012046 MutL C terminal dimerization domain; Region: MutL_C; cl07336 316407012047 IPP transferase; Region: IPPT; cl00403 316407012048 Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that...; Region: Hfq; cd01716 316407012049 Sm1 motif; other site 316407012050 intra - hexamer interaction site; other site 316407012051 inter - hexamer interaction site; other site 316407012052 nucleotide binding pocket; other site 316407012053 Sm2 motif; other site 316407012054 GTPase HflX; Provisional; Region: PRK11058 316407012055 HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual...; Region: HflX; cd01878 316407012056 G1 box; other site 316407012057 GTP/Mg2+ binding site; other site 316407012058 Switch I region; other site 316407012059 G2 box; other site 316407012060 G3 box; other site 316407012061 Switch II region; other site 316407012062 G4 box; other site 316407012063 G5 box; other site 316407012064 FtsH protease regulator HflK; Provisional; Region: PRK10930 316407012065 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 316407012066 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 316407012067 FtsH protease regulator HflC; Provisional; Region: PRK11029 316407012068 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 316407012069 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; cl01275 316407012070 adenylosuccinate synthetase; Provisional; Region: PRK01117 316407012071 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 r-...; Region: AdSS; cd03108 316407012072 GDP-binding site; other site 316407012073 ACT binding site; other site 316407012074 IMP binding site; other site 316407012075 Predicted transcriptional regulator [Transcription]; Region: COG1959 316407012076 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407012077 exoribonuclease R; Provisional; Region: PRK11642 316407012078 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 316407012079 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 316407012080 RNB domain; Region: RNB; pfam00773 316407012081 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 play an...; Region: S1_RNase_R; cd04471 316407012082 RNA binding site; other site 316407012083 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 316407012084 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 316407012085 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 316407012086 Uncharacterized protein conserved in bacteria (DUF2170); Region: DUF2170; cl01551 316407012087 PspA/IM30 family; Region: PspA_IM30; pfam04012 316407012088 Protein of unknown function (DUF2491); Region: DUF2491; pfam10679 316407012089 Predicted membrane protein [Function unknown]; Region: COG3766 316407012090 Domain of Unknown Function (DUF350); Region: DUF350; pfam03994 316407012091 Domain of Unknown Function (DUF350); Region: DUF350; pfam03994 316407012092 Protein of unknown function (DUF1190); Region: DUF1190; cl10031 316407012093 Glutathionylspermidine synthase; Region: GSP_synth; cl00503 316407012094 isovaleryl CoA dehydrogenase; Provisional; Region: PRK11561 316407012095 Proteins involved in DNA damage response, similar to the AidB gene product; Region: AidB; cd01154 316407012096 FAD binding site; other site 316407012097 substrate binding site; other site 316407012098 catalytic residues; other site 316407012099 Protein of unknown function (DUF1471); Region: DUF1471; cl11507 316407012100 Protein of unknown function (DUF1471); Region: DUF1471; cl11507 316407012101 esterase; Provisional; Region: PRK10566 316407012102 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; cl12031 316407012103 transcriptional repressor UlaR; Provisional; Region: PRK13509 316407012104 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407012105 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 316407012106 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 316407012107 PTS system sugar-specific permease component; Region: EIIC-GAT; cl04451 316407012108 PTS_IIB_ascorbate: subunit IIB of enzyme II (EII) of the L-ascorbate-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is an L-ascorbate-specific permease with two cytoplasmic subunits (IIA and IIB) and a...; Region: PTS_IIB_ascorbate; cd05563 316407012109 P-loop; other site 316407012110 active site 316407012111 phosphorylation site 316407012112 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 316407012113 active site 316407012114 phosphorylation site 316407012115 3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and D-arabino-3-hexulose-6-phosphate synthase (HPS). KGPDC catalyzes the formation of L-xylulose 5-phosphate and carbon dioxide from 3-keto-L-gulonate 6-phosphate as part of the anaerobic pathway for...; Region: KGPDC_HPS; cd04726 316407012116 active site 316407012117 dimer interface; other site 316407012118 magnesium binding site; other site 316407012119 L-xylulose 5-phosphate 3-epimerase; Reviewed; Region: PRK13209 316407012120 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of D-arabino-6-...; Region: AP2Ec; cd00019 316407012121 AP (apurinic/apyrimidinic) site pocket; other site 316407012122 DNA interaction; other site 316407012123 Metal-binding active site; metal-binding site 316407012124 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; cd00398 316407012125 intersubunit interface; other site 316407012126 active site 316407012127 Zn2+ binding site; other site 316407012128 Protein of unknown function (DUF1471); Region: DUF1471; cl11507 316407012129 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 316407012130 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 316407012131 dimer interface; other site 316407012132 ssDNA binding site; other site 316407012133 tetramer (dimer of dimers) interface; other site 316407012134 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 316407012135 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 316407012136 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 316407012137 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 316407012138 Protein of unknown function (DUF2686); Region: DUF2686; pfam10887 316407012139 Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]; Region: OapA; COG3061 316407012140 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 316407012141 peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK11570 316407012142 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 316407012143 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 316407012144 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 316407012145 Amino acid permease; Region: AA_permease; pfam00324 316407012146 iron-sulfur cluster repair di-iron protein; Provisional; Region: PRK10992 316407012147 Domain of Unknown function (DUF542); Region: ScdA_N; pfam04405 316407012148 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl11605 316407012149 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl11605 316407012150 EamA-like transporter family; Region: EamA; cl01037 316407012151 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 316407012152 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 316407012153 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407012154 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407012155 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407012156 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein; Reviewed; Region: cpdB; PRK09420 316407012157 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 316407012158 active site 316407012159 metal-binding site 316407012160 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 316407012161 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 cysteine...; Region: CysQ; cd01638 316407012162 active site 316407012163 Bacterial protein of unknown function (YtfJ_HI0045); Region: YtfJ_HI0045; cl01158 316407012164 Protein of unknown function (DUF1107); Region: DUF1107; pfam06526 316407012165 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 316407012166 Domain of unknown function DUF21; Region: DUF21; pfam01595 316407012167 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 316407012168 Transporter associated domain; Region: CorC_HlyC; pfam03471 316407012169 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 316407012170 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 316407012171 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 316407012172 Surface antigen; Region: Bac_surface_Ag; cl03097 316407012173 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 316407012174 Family of unknown function (DUF490); Region: DUF490; pfam04357 316407012175 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 316407012176 putative active site pocket; other site 316407012177 dimerization interface; other site 316407012178 putative catalytic residue; other site 316407012179 hypothetical protein; Provisional; Region: PRK09719 316407012180 SpoVT / AbrB like domain; Region: SpoVT_AbrB; cl00877 316407012181 PemK-like protein; Region: PemK; cl00995 316407012182 Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers; Region: pyrophosphatase; cd00412 316407012183 dimer interface; other site 316407012184 substrate binding site; other site 316407012185 metal binding sites; metal-binding site 316407012186 Periplasmic binding domain of ABC-type YtfQ-like transport systems; Region: PBP1_YtfQ_like; cd06309 316407012187 putative ligand binding site; other site 316407012188 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 316407012189 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and...; Region: ABC_Carb_Monos_I; cd03216 316407012190 Walker A/P-loop; other site 316407012191 ATP binding site; other site 316407012192 Q-loop/lid; other site 316407012193 ABC transporter signature motif; other site 316407012194 Walker B; other site 316407012195 D-loop; other site 316407012196 H-loop/switch region; other site 316407012197 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (; Region: ABC_Carb_Monos_II; cd03215 316407012198 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 316407012199 TM-ABC transporter signature motif; other site 316407012200 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 316407012201 TM-ABC transporter signature motif; other site 316407012202 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-1,7-...; Region: FBPase; cd00354 316407012203 AMP binding site; other site 316407012204 metal-binding site 316407012205 active site 316407012206 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 316407012207 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 316407012208 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 316407012209 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 316407012210 Protein of unknown function (DUF615); Region: DUF615; cl01147 316407012211 Putative modulator of DNA gyrase; Region: PmbA_TldD; cl00398 316407012212 ECK4231:JW4195:b4236; cytochrome b562, truncated 316407012213 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; cl14056 316407012214 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: NrdG; TIGR02491 316407012215 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK09263 316407012216 ATP cone domain; Region: ATP-cone; pfam03477 316407012217 Class III ribonucleotide reductase; Region: RNR_III; cd01675 316407012218 effector binding site; other site 316407012219 active site 316407012220 Zn binding site; other site 316407012221 glycine loop; other site 316407012222 trehalose-6-phosphate hydrolase; Provisional; Region: PRK10933 316407012223 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 316407012224 PTS system trehalose(maltose)-specific transporter subunits IIBC; Provisional; Region: PRK11007 316407012225 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...; Region: PTS_IIB_glc; cd00212 316407012226 active site turn 316407012227 phosphorylation site 316407012228 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 316407012229 trehalose repressor; Provisional; Region: treR; PRK09492 316407012230 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 316407012231 DNA binding site 316407012232 domain linker motif; other site 316407012233 Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_TreR_like; cd01542 316407012234 dimerization interface; other site 316407012235 ligand binding site; other site 316407012236 magnesium-transporting ATPase MgtA; Provisional; Region: PRK10517 316407012237 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 316407012238 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 316407012239 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; cl11391 316407012240 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 316407012241 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 316407012242 homotrimer interaction site; other site 316407012243 putative active site; other site 316407012244 aspartate carbamoyltransferase, regulatory subunit; Region: ATCase_reg; TIGR00240 316407012245 Aspartate carbamoyltransferase regulatory chain, allosteric domain; Region: PyrI; pfam01948 316407012246 Aspartate carbamoyltransferase regulatory chain, metal binding domain; Region: PyrI_C; pfam02748 316407012247 aspartate carbamoyltransferase; Region: asp_carb_tr; TIGR00670 316407012248 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 316407012249 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 316407012250 PyrBI operon leader peptide; Region: PyrBI_leader; cl11578 316407012251 YjgH belongs 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 similarity and no...; Region: YjgH_like; cd02198 316407012252 homotrimer interaction site; other site 316407012253 putative active site; other site 316407012254 oxidoreductase; Provisional; Region: PRK12742 316407012255 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407012256 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 316407012257 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 316407012258 Domain of unknown function (DUF386); Region: DUF386; cl01047 316407012259 ornithine carbamoyltransferase subunit I; Provisional; Region: PRK03515 316407012260 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 316407012261 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 316407012262 Protein of unknown function (DUF1260); Region: DUF1260; cl01170 316407012263 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 316407012264 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 316407012265 Bacterial protein of unknown function (DUF898); Region: DUF898; cl01738 316407012266 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 316407012267 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 316407012268 HIGH motif; other site 316407012269 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 316407012270 active site 316407012271 KMSKS motif; other site 316407012272 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 316407012273 tRNA binding surface; other site 316407012274 anticodon binding site; other site 316407012275 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 316407012276 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 316407012277 multifunctional aminopeptidase A; Provisional; Region: PRK00913 316407012278 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...; Region: Peptidase_M17; cd00433 316407012279 interface (dimer of trimers); other site 316407012280 Substrate-binding/catalytic site; other site 316407012281 Zn-binding sites; other site 316407012282 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; cl12074 316407012283 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; cl12074 316407012284 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 316407012285 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407012286 gluconate operon transcriptional regulator; Provisional; Region: PRK14987 316407012287 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 316407012288 DNA binding site 316407012289 domain linker motif; other site 316407012290 Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_GntR; cd01575 316407012291 putative dimerization interface; other site 316407012292 putative ligand binding site; other site 316407012293 gluconate transporter; Region: gntP; TIGR00791 316407012294 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; cl09110 316407012295 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407012296 2-deoxy-D-gluconate 3-dehydrogenase; Provisional; Region: PRK06935 316407012297 L-idonate 5-dehydrogenase; Provisional; Region: PRK09880 316407012298 L-idonate 5-dehydrogenase; Region: idonate-5-DH; cd08232 316407012299 putative NAD(P) binding site; other site 316407012300 catalytic Zn binding site; other site 316407012301 Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits; Region: GntK; cd02021 316407012302 Gluconate kinase [Carbohydrate transport and metabolism]; Region: GntK; COG3265 316407012303 ATP-binding site; other site 316407012304 Gluconate-6-phosphate binding site; other site 316407012305 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 316407012306 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 316407012307 putative NAD(P) binding site; other site 316407012308 putative substrate binding site; other site 316407012309 catalytic Zn binding site; other site 316407012310 structural Zn binding site; other site 316407012311 dimer interface; other site 316407012312 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 316407012313 Phage integrase family; Region: Phage_integrase; pfam00589 316407012314 Int/Topo IB signature motif; other site 316407012315 active site 316407012316 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; cl01116 316407012317 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 316407012318 IS2 transposase TnpB; Reviewed; Region: PRK09409 316407012319 Integrase core domain; Region: rve; cl01316 316407012320 ECK4266:JW4234:b4275; KpLE2 phage-like element; hypothetical protein, middle fragment 316407012321 ECK4266:JW5763:b4560; KpLE2 phage-like element; hypothetical protein, C-ter fragment 316407012322 ECK4266:JW5764+JW4234+JW5763:b4575; KpLE2 phage-like element; hypothetical protein 316407012323 ECK4266:JW5764:b4276; KpLE2 phage-like element; hypothetical protein, N-ter fragment 316407012324 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 316407012325 Transposase DDE domain; Region: Transposase_11; pfam01609 316407012326 putative sialic acid transporter; Provisional; Region: PRK12307 316407012327 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 316407012328 putative substrate translocation pore; other site 316407012329 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 316407012330 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 316407012331 ECK4271:JW5770:b4281; KpLE2 phage-like element; hypothetical protein 316407012332 ECK4272:JW4242:b4282; KpLE2 phage-like element; predicted membrane protein 316407012333 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; cl01116 316407012334 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 316407012335 Integrase core domain; Region: rve; cl01316 316407012336 ECK4273:JW5772:b4561; KpLE2 phage-like element; predicted transposase fragment 316407012337 ECK4274:JW4245:b4285; KpLE2 phage-like element; partial transposase 316407012338 ECK4275:JW5773:b4562; KpLE2 phage-like element; predicted transposase fragment 316407012339 Predicted dinucleotide-binding enzymes [General function prediction only]; Region: COG2085 316407012340 iron-dicitrate transporter ATP-binding subunit; Provisional; Region: fecE; PRK11231 316407012341 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 316407012342 Walker A/P-loop; other site 316407012343 ATP binding site; other site 316407012344 Q-loop/lid; other site 316407012345 ABC transporter signature motif; other site 316407012346 Walker B; other site 316407012347 D-loop; other site 316407012348 H-loop/switch region; other site 316407012349 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 316407012350 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...; Region: TM_ABC_iron-siderophores_like; cd06550 316407012351 ABC-ATPase subunit interface; other site 316407012352 dimer interface; other site 316407012353 putative PBP binding regions; other site 316407012354 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 316407012355 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...; Region: TM_ABC_iron-siderophores_like; cd06550 316407012356 dimer interface; other site 316407012357 ABC-ATPase subunit interface; other site 316407012358 putative PBP binding regions; other site 316407012359 iron-dicitrate transporter substrate-binding subunit; Provisional; Region: fecB; PRK11411 316407012360 Fe3+-siderophore binding domain FhuD. These proteins have been shown to function as initial receptors in ABC transport of Fe3+-siderophores in many eubacterial species. They belong to the TroA-like superfamily of helical backbone metal receptor...; Region: FhuD; cd01146 316407012361 siderophore binding site; other site 316407012362 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 316407012363 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 316407012364 N-terminal plug; other site 316407012365 ligand-binding site; other site 316407012366 fec operon regulator FecR; Reviewed; Region: PRK09774 316407012367 FecR protein; Region: FecR; pfam04773 316407012368 RNA polymerase sigma factor FecI; Provisional; Region: PRK09651 316407012369 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 316407012370 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...; Region: Sigma70_r4; cd06171 316407012371 DNA binding residues 316407012372 Insertion element protein; Region: Ins_element1; pfam03811 316407012373 ECK0022:JW4255+JW4256:b4576; IS1 transposase InsAB' 316407012374 ECK0022:JW4255:b4563; IS1 transposase InsAB', N-ter fragment 316407012375 ECK0022:JW4256:b4564; IS1 transposase InsAB', C-ter fragment 316407012376 Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]; Region: DeoR; COG2390 316407012377 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...; Region: Sigma70_r4; cd06171 316407012378 DNA binding residues 316407012379 Putative sugar-binding domain; Region: Sugar-bind; pfam04198 316407012380 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; cl09110 316407012381 Dehydratase family; Region: ILVD_EDD; cl00340 316407012382 probable dehydratase, YjhG/YagF family; Region: yjhG_yagF; TIGR03432 316407012383 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 316407012384 Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family...; Region: DHDPS-like; cd00408 316407012385 inhibitor site; inhibition site 316407012386 active site 316407012387 dimer interface; other site 316407012388 catalytic residue; other site 316407012389 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407012390 Transcriptional regulator [Transcription]; Region: IclR; COG1414 316407012391 Bacterial transcriptional regulator; Region: IclR; pfam01614 316407012392 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 316407012393 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407012394 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 316407012395 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 316407012396 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...; Region: RPE; cd00429 316407012397 substrate binding site; other site 316407012398 hexamer interface; other site 316407012399 metal-binding site 316407012400 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 316407012401 active site 316407012402 phosphorylation site 316407012403 BtpA family; Region: BtpA; cl00440 316407012404 PTS system sugar-specific permease component; Region: EIIC-GAT; cl04451 316407012405 PTS_IIB_galactitol: subunit IIB of enzyme II (EII) of the galactitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is a galactitol-specific permease with two cytoplasmic domains (IIA and IIB) and a...; Region: PTS_IIB_galactitol; cd05566 316407012406 P-loop; other site 316407012407 active site 316407012408 phosphorylation site 316407012409 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 316407012410 Peptidase dimerization domain; Region: M20_dimer; cl09126 316407012411 Peptidase dimerization domain; Region: M20_dimer; cl09126 316407012412 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 316407012413 S-adenosylmethionine binding site; other site 316407012414 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 316407012415 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 316407012416 Coenzyme A binding pocket; other site 316407012417 Uncharacterized protein conserved in bacteria (DUF2084); Region: DUF2084; cl01566 316407012418 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 316407012419 Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of...; Region: PLDc; cd00138 316407012420 active site 316407012421 signature motif; other site 316407012422 Domain of unknown function (DUF303); Region: DUF303; pfam03629 316407012423 N-acetylneuraminic acid mutarotase; Provisional; Region: PRK14131 316407012424 Kelch motif; Region: Kelch_1; cl02701 316407012425 Oligogalacturonate-specific porin protein (KdgM); Region: KdgM; cl11629 316407012426 FimB and FimE and related proteins, DNA breaking-rejoining enzymes, integrase/recombinases, catalytic domain. This CD includes those proteins similar to E.coli FimE and FimB regulatory proteins and Proteus mirabilis MrpI; Region: INT_FimBE_C; cd01197 316407012427 Phage integrase family; Region: Phage_integrase; pfam00589 316407012428 Int/Topo IB signature motif; other site 316407012429 FimB and FimE and related proteins, DNA breaking-rejoining enzymes, integrase/recombinases, catalytic domain. This CD includes those proteins similar to E.coli FimE and FimB regulatory proteins and Proteus mirabilis MrpI; Region: INT_FimBE_C; cd01197 316407012430 Phage integrase family; Region: Phage_integrase; pfam00589 316407012431 Int/Topo IB signature motif; other site 316407012432 Fimbrial protein; Region: Fimbrial; cl01416 316407012433 Fimbrial protein; Region: Fimbrial; cl01416 316407012434 fimbrial chaperone protein FimC; Provisional; Region: PRK15195 316407012435 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 316407012436 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 316407012437 pilin outer membrane usher protein SafC; Provisional; Region: PRK15223; cl14650 316407012438 Fimbrial Usher protein; Region: Usher; pfam00577 316407012439 Fimbrial protein; Region: Fimbrial; cl01416 316407012440 Fimbrial protein; Region: Fimbrial; cl01416 316407012441 FimH, mannose binding; Region: FimH_man-bind; pfam09160 316407012442 Fimbrial protein; Region: Fimbrial; cl01416 316407012443 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; cl09110 316407012444 gluconate transporter; Region: gntP; TIGR00791 316407012445 mannonate dehydratase; Region: uxuA; TIGR00695 316407012446 mannonate dehydratase; Provisional; Region: PRK03906 316407012447 D-mannonate oxidoreductase; Provisional; Region: PRK15037 316407012448 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 316407012449 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 316407012450 DNA-binding transcriptional repressor UxuR; Provisional; Region: PRK10225 316407012451 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407012452 DNA binding site 316407012453 FCD domain; Region: FCD; cl11656 316407012454 Protein of unknown function (DUF2686); Region: DUF2686; pfam10887 316407012455 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 316407012456 cell density-dependent motility repressor; Provisional; Region: PRK10082 316407012457 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 316407012458 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 316407012459 Isoaspartyl dipeptidase hydrolyzes the beta-L-isoaspartyl linkages in dipeptides, as part of the degradative pathway to eliminate proteins with beta-L-isoaspartyl peptide bonds, bonds whereby the beta-group of an aspartate forms the peptide link with...; Region: Isoaspartyl-dipeptidase; cd01308 316407012460 isoaspartyl dipeptidase IadA; Region: isoAsp_dipep; TIGR01975 316407012461 dimer interface; other site 316407012462 active site 316407012463 Nucleoside recognition; Region: Gate; cl00486 316407012464 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3314 316407012465 Nucleoside recognition; Region: Gate; cl00486 316407012466 RNA 2'-phosphotransferase, Tpt1 / KptA family; Region: PTS_2-RNA; cl00804 316407012467 Protein of unknown function (DUF1228); Region: DUF1228; pfam06779 316407012468 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3204 316407012469 SdiA-regulated; Region: SdiA-regulated; pfam06977 316407012470 ROK family; Region: ROK; cl09121 316407012471 Benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase subunit, BcrC/BadD/HgdB [Amino acid transport and metabolism]; Region: HgdB; COG1775 316407012472 N subunit; Region: benz_CoA_bzdN; cl11464 316407012473 Predicted membrane protein [Function unknown]; Region: COG2733 316407012474 multidrug efflux system protein MdtM; Provisional; Region: PRK15403 316407012475 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 316407012476 putative substrate translocation pore; other site 316407012477 ECK4329:JW5953:b4338; predicted transposase 316407012478 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 316407012479 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 316407012480 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407012481 DNA binding site 316407012482 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 316407012483 pyridoxal 5'-phosphate binding site; other site 316407012484 homodimer interface; other site 316407012485 catalytic residue; other site 316407012486 Domain of unknown function (DUF1127); Region: DUF1127; cl02276 316407012487 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 316407012488 ECK4334:JW5954:b4486; conserved hypothetical protein 316407012489 McrBC 5-methylcytosine restriction system component; Region: McrBC; cl01737 316407012490 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional; Region: PRK11331 316407012491 Domain of unknown function (DUF3578); Region: DUF3578; pfam12102 316407012492 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...; Region: AAA; cd00009 316407012493 Walker A motif; other site 316407012494 ATP binding site; other site 316407012495 Walker B motif; other site 316407012496 arginine finger; other site 316407012497 HSP20-like domain of unknown function (DUF1813); Region: DUF1813; cl07446 316407012498 EcoKI restriction-modification system protein HsdS; Provisional; Region: PRK09737 316407012499 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 316407012500 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 316407012501 HsdM N-terminal domain; Region: HsdM_N; pfam12161 316407012502 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 316407012503 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; cl12011 316407012504 type I restriction enzyme EcoKI subunit R; Provisional; Region: hsdR; PRK11448 316407012505 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 316407012506 ATP binding site; other site 316407012507 putative Mg++ binding site; other site 316407012508 Restriction endonuclease [Defense mechanisms]; Region: Mrr; COG1715 316407012509 Restriction endonuclease; Region: Mrr_cat; cl00747 316407012510 putative GTP-binding protein YjiA; Provisional; Region: PRK11537 316407012511 The function of this protein family is unkown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage...; Region: CobW_like; cd03112 316407012512 P-loop, Walker A motif; other site 316407012513 Base recognition motif; other site 316407012514 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 316407012515 Protein of unknown function (DUF466); Region: DUF466; cl01082 316407012516 Carbon starvation protein CstA; Region: CstA; cl00856 316407012517 methyl-accepting chemotaxis protein I; Provisional; Region: PRK15041 316407012518 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cd00181 316407012519 dimerization interface; other site 316407012520 ligand (aspartate) binding pocket; other site 316407012521 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 connected by an extended linker. The...; Region: HAMP; cd06225 316407012522 dimerization interface; other site 316407012523 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 316407012524 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 316407012525 d-galactonate transporter; Region: 2A0114; TIGR00893 316407012526 putative substrate translocation pore; other site 316407012527 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 316407012528 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 316407012529 DNA binding site 316407012530 Transcriptional regulators [Transcription]; Region: GntR; COG1802 316407012531 FCD domain; Region: FCD; cl11656 316407012532 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 316407012533 Alcohol dehydrogenases of the MDR family; Region: Zn_ADH7; cd08261 316407012534 putative NAD(P) binding site; other site 316407012535 catalytic Zn binding site; other site 316407012536 structural Zn binding site; other site 316407012537 Sulfatase; Region: Sulfatase; cl10460 316407012538 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 316407012539 Protein of unknown function (DUF2501); Region: DUF2501; cl08197 316407012540 DNA replication protein DnaC; Validated; Region: PRK07952 316407012541 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...; Region: AAA; cd00009 316407012542 Walker A motif; other site 316407012543 ATP binding site; other site 316407012544 Walker B motif; other site 316407012545 Phd_YefM; Region: PhdYeFM; cl09153 316407012546 Protein of unknown function (DUF1212); Region: DUF1212; cl01118 316407012547 Protein of unknown function (DUF1212); Region: DUF1212; cl01118 316407012548 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 316407012549 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...; Region: LuxR_C_like; cd06170 316407012550 DNA binding residues 316407012551 dimerization interface; other site 316407012552 DNA-binding transcriptional activator BglJ; Provisional; Region: PRK11475 316407012553 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...; Region: LuxR_C_like; cd06170 316407012554 DNA binding residues 316407012555 dimerization interface; other site 316407012556 ferric iron reductase involved in ferric hydroximate transport; Provisional; Region: PRK10647 316407012557 Ferric iron reductase FhuF-like transporter; Region: FhuF; pfam06276 316407012558 FhuF 2Fe-2S C-terminal domain; Region: FhuF_C; pfam11575 316407012559 Protein of unknown function (DUF1435); Region: DUF1435; pfam07256 316407012560 16S ribosomal RNA m2G1207 methyltransferase; Provisional; Region: rsmC; PRK09489 316407012561 Methyltransferase small domain N-terminal; Region: MTS_N; pfam08468 316407012562 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 316407012563 S-adenosylmethionine binding site; other site 316407012564 DNA polymerase III psi subunit; Region: DNA_III_psi; cl11436 316407012565 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 316407012566 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 316407012567 Coenzyme A binding pocket; other site 316407012568 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 316407012569 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 316407012570 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 316407012571 motif II; other site 316407012572 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 316407012573 RF3 subfamily. Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and...; Region: RF3; cd04169 316407012574 G1 box; other site 316407012575 putative GEF interaction site; other site 316407012576 GTP/Mg2+ binding site; other site 316407012577 Switch I region; other site 316407012578 G2 box; other site 316407012579 G3 box; other site 316407012580 Switch II region; other site 316407012581 G4 box; other site 316407012582 G5 box; other site 316407012583 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 316407012584 periplasmic protein; Provisional; Region: PRK10568 316407012585 Putative phospholipid-binding domain; Region: BON; cl02771 316407012586 Putative phospholipid-binding domain; Region: BON; cl02771 316407012587 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 316407012588 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 316407012589 active site 316407012590 nucleophile elbow; other site 316407012591 putative deoxyribonuclease YjjV; Provisional; Region: PRK11449 316407012592 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 316407012593 active site 316407012594 Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones]; Region: PflA; COG1180 316407012595 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 316407012596 FeS/SAM binding site; other site 316407012597 hypothetical protein; Provisional; Region: PRK10977 316407012598 Glycine radical; Region: Gly_radical; cl12026 316407012599 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family. DERA belongs to the class I aldolases and catalyzes a reversible aldol reaction between acetaldehyde and glyceraldehyde 3-phosphate to generate 2-deoxyribose 5-phosphate. DERA is unique in...; Region: DeoC; cd00959 316407012600 intersubunit interface; other site 316407012601 active site 316407012602 catalytic residue; other site 316407012603 thymidine phosphorylase; Reviewed; Region: deoA; PRK05820 316407012604 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 316407012605 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 316407012606 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; pfam07831 316407012607 Sulfatase; Region: Sulfatase; cl10460 316407012608 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 316407012609 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 316407012610 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 316407012611 putative DNA-binding transcriptional regulator; Provisional; Region: PRK09775 316407012612 HipA-like N-terminal domain; Region: HipA_N; pfam07805 316407012613 HipA-like C-terminal domain; Region: HipA_C; pfam07804 316407012614 lipoate-protein ligase A; Provisional; Region: lplA; PRK03822 316407012615 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 316407012616 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 316407012617 Bacterial lipoate protein ligase C-terminus; Region: Lip_prot_lig_C; pfam10437 316407012618 Bacterial virulence factor haemolysin; Region: SMP_2; cl11479 316407012619 phosphoserine phosphatase; Provisional; Region: serB; PRK11133 316407012620 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 316407012621 motif II; other site 316407012622 DNA repair protein RadA; Region: sms; TIGR00416 316407012623 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 316407012624 Walker A motif/ATP binding site; other site 316407012625 ATP binding site; other site 316407012626 Walker B motif; other site 316407012627 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 316407012628 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl09100 316407012629 bifunctional DNA-binding transcriptional repressor/ NMN adenylyltransferase; Provisional; Region: PRK08099 316407012630 Nicotinamide/nicotinate mononucleotide adenylyltransferase of bifunctional NadR-like proteins; Region: NMNAT_NadR; cd02167 316407012631 active site 316407012632 (T/H)XGH motif; other site 316407012633 Predicted ATPase/kinase involved in NAD metabolism [Coenzyme metabolism]; Region: NadR; cl01238 316407012634 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 316407012635 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 316407012636 Walker A/P-loop; other site 316407012637 ATP binding site; other site 316407012638 Q-loop/lid; other site 316407012639 ABC transporter signature motif; other site 316407012640 Walker B; other site 316407012641 D-loop; other site 316407012642 H-loop/switch region; other site 316407012643 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 316407012644 lytic murein transglycosylase; Provisional; Region: PRK11619 316407012645 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 catalyze...; Region: LT_GEWL; cd00254 316407012646 N-acetyl-D-glucosamine binding site; other site 316407012647 catalytic residue; other site 316407012648 Trp repressor protein; Region: Trp_repressor; cl01121 316407012649 Protein of unknown function DUF84; Region: NTPase_I-T; cl00866 316407012650 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 316407012651 catalytic core; other site 316407012652 right oriC-binding transcriptional activator; Provisional; Region: PRK15121 316407012653 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 316407012654 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; cl01368 316407012655 CreA protein; Region: CreA; cl01154 316407012656 DNA-binding response regulator CreB; Provisional; Region: PRK11083 316407012657 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 316407012658 active site 316407012659 phosphorylation site 316407012660 intermolecular recognition site; other site 316407012661 dimerization interface; other site 316407012662 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...; Region: trans_reg_C; cd00383 316407012663 DNA binding site 316407012664 sensory histidine kinase CreC; Provisional; Region: PRK11100 316407012665 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 connected by an extended linker. The...; Region: HAMP; cl01054 316407012666 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 trans-...; Region: HisKA; cd00082 316407012667 dimer interface; other site 316407012668 phosphorylation site 316407012669 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 316407012670 ATP binding site; other site 316407012671 Mg2+ binding site; other site 316407012672 G-X-G motif; other site 316407012673 Inner membrane protein CreD; Region: CreD; cl01844 316407012674 two-component response regulator; Provisional; Region: PRK11173 316407012675 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 316407012676 active site 316407012677 phosphorylation site 316407012678 intermolecular recognition site; other site 316407012679 dimerization interface; other site 316407012680 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...; Region: trans_reg_C; cd00383 316407012681 DNA binding site 316407012682 putative RNA methyltransferase; Provisional; Region: PRK10433 316407012683 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362