-- dump date 20140620_080733 -- class Genbank::misc_feature -- table misc_feature_note -- id note 391008000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 391008000002 DnaA N-terminal domain; Region: DnaA_N; pfam11638 391008000003 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008000004 ATP binding site [chemical binding]; other site 391008000005 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 391008000006 Walker B motif; other site 391008000007 arginine finger; other site 391008000008 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 391008000009 DnaA box-binding interface [nucleotide binding]; other site 391008000010 DNA polymerase III subunit beta; Validated; Region: PRK05643 391008000011 Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric...; Region: beta_clamp; cd00140 391008000012 putative DNA binding surface [nucleotide binding]; other site 391008000013 dimer interface [polypeptide binding]; other site 391008000014 beta-clamp/clamp loader binding surface; other site 391008000015 beta-clamp/translesion DNA polymerase binding surface; other site 391008000016 recombination protein F; Reviewed; Region: recF; PRK00064 391008000017 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 391008000018 Walker A/P-loop; other site 391008000019 ATP binding site [chemical binding]; other site 391008000020 Q-loop/lid; other site 391008000021 ABC transporter signature motif; other site 391008000022 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 391008000023 ABC transporter signature motif; other site 391008000024 Walker B; other site 391008000025 D-loop; other site 391008000026 H-loop/switch region; other site 391008000027 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 391008000028 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 391008000029 Mg2+ binding site [ion binding]; other site 391008000030 G-X-G motif; other site 391008000031 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 391008000032 anchoring element; other site 391008000033 dimer interface [polypeptide binding]; other site 391008000034 ATP binding site [chemical binding]; other site 391008000035 TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the...; Region: TOPRIM_TopoIIA_GyrB; cd03366 391008000036 active site 391008000037 putative metal-binding site [ion binding]; other site 391008000038 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 391008000039 CAAX protease self-immunity; Region: Abi; pfam02517 391008000040 Peptidase family M48; Region: Peptidase_M48; pfam01435 391008000041 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 391008000042 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 391008000043 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 391008000044 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 391008000045 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 391008000046 TolR protein; Region: tolR; TIGR02801 391008000047 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 391008000048 TolR protein; Region: tolR; TIGR02801 391008000049 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 391008000050 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 391008000051 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 391008000052 putative active site [active] 391008000053 catalytic site [active] 391008000054 catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_2; cd09112 391008000055 putative active site [active] 391008000056 catalytic site [active] 391008000057 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in...; Region: PNPsynthase; cd00003 391008000058 active site 391008000059 hydrophilic channel; other site 391008000060 dimerization interface [polypeptide binding]; other site 391008000061 catalytic residues [active] 391008000062 active site lid [active] 391008000063 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 391008000064 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 391008000065 FeS/SAM binding site; other site 391008000066 RHS Repeat; Region: RHS_repeat; cl11982 391008000067 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 391008000068 RHS Repeat; Region: RHS_repeat; cl11982 391008000069 RHS Repeat; Region: RHS_repeat; pfam05593 391008000070 RHS Repeat; Region: RHS_repeat; cl11982 391008000071 RHS Repeat; Region: RHS_repeat; pfam05593 391008000072 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 391008000073 Integral membrane protein TerC family; Region: TerC; cl10468 391008000074 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; cl17304 391008000075 fructose-1,6-bisphosphatase family protein; Region: PLN02628 391008000076 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1; Region: FBPase; cd00354 391008000077 AMP binding site [chemical binding]; other site 391008000078 metal binding site [ion binding]; metal-binding site 391008000079 active site 391008000080 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 391008000081 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 391008000082 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008000083 homodimer interface [polypeptide binding]; other site 391008000084 catalytic residue [active] 391008000085 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008000086 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 391008000087 N-terminal plug; other site 391008000088 ligand-binding site [chemical binding]; other site 391008000089 Ku protein, prokaryotic; Region: Ku_bact; TIGR02772 391008000090 Ku-core domain, Ku-like subfamily; composed of prokaryotic homologs of the eukaryotic DNA binding protein Ku. The alignment includes the core domain shared by the prokaryotic YkoV-like proteins and the eukaryotic Ku70 and Ku80. The prokaryotic Ku...; Region: KU_like; cd00789 391008000091 putative DNA binding site [nucleotide binding]; other site 391008000092 putative homodimer interface [polypeptide binding]; other site 391008000093 ATP-dependent DNA ligase; Reviewed; Region: ligD; PRK05972 391008000094 DNA ligase D, 3'-phosphoesterase domain; Region: LigD_PE_dom; TIGR02777 391008000095 Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_LigD_LigC; cd07906 391008000096 active site 391008000097 DNA binding site [nucleotide binding] 391008000098 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD is a DNA-binding module that is part of the catalytic core unit; Region: OBF_DNA_ligase_LigD; cd07971 391008000099 DNA binding site [nucleotide binding] 391008000100 PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for...; Region: PaeLigD_Pol_like; cd04862 391008000101 nucleotide binding site [chemical binding]; other site 391008000102 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 391008000103 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD3; cd08297 391008000104 NAD binding site [chemical binding]; other site 391008000105 substrate binding site [chemical binding]; other site 391008000106 catalytic Zn binding site [ion binding]; other site 391008000107 tetramer interface [polypeptide binding]; other site 391008000108 structural Zn binding site [ion binding]; other site 391008000109 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 391008000110 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 391008000111 active site 391008000112 intersubunit interface [polypeptide binding]; other site 391008000113 catalytic residue [active] 391008000114 Cysteine dioxygenase type I; Region: CDO_I; pfam05995 391008000115 Transcriptional regulators [Transcription]; Region: PurR; COG1609 391008000116 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 391008000117 DNA binding site [nucleotide binding] 391008000118 domain linker motif; other site 391008000119 Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_SalR; cd01545 391008000120 putative dimerization interface [polypeptide binding]; other site 391008000121 putative ligand binding site [chemical binding]; other site 391008000122 Prokaryotic phenylalanine-4-hydroxylase (pro_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes the eukaryotic proteins, phenylalanine-4-hydroxylase (eu_PheOH); Region: pro_PheOH; cd03348 391008000123 cofactor binding site; other site 391008000124 metal binding site [ion binding]; metal-binding site 391008000125 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 391008000126 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 391008000127 dimerization interface [polypeptide binding]; other site 391008000128 putative DNA binding site [nucleotide binding]; other site 391008000129 putative Zn2+ binding site [ion binding]; other site 391008000130 AsnC family; Region: AsnC_trans_reg; pfam01037 391008000131 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 391008000132 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 391008000133 nucleophile elbow; other site 391008000134 Domain of unknown function (DUF4339); Region: DUF4339; pfam14237 391008000135 Uncharacterized conserved protein [Function unknown]; Region: COG2013 391008000136 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008000137 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 391008000138 N-terminal plug; other site 391008000139 ligand-binding site [chemical binding]; other site 391008000140 PAP2, bacterial acid phosphatase or class A non-specific acid phosphatases. These enzymes catalyze phosphomonoester hydrolysis, with optimal activity in low pH conditions. They are secreted into the periplasmic space, and their physiological role remains...; Region: PAP2_acid_phosphatase; cd03397 391008000141 active site 391008000142 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 391008000143 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 391008000144 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 391008000145 Walker A/P-loop; other site 391008000146 ATP binding site [chemical binding]; other site 391008000147 Q-loop/lid; other site 391008000148 ABC transporter signature motif; other site 391008000149 Walker B; other site 391008000150 D-loop; other site 391008000151 H-loop/switch region; other site 391008000152 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 391008000153 Fatty acid desaturase; Region: FA_desaturase; pfam00487 391008000154 Di-iron ligands [ion binding]; other site 391008000155 EF-hand domain pair; Region: EF_hand_5; pfam13499 391008000156 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 391008000157 Ca2+ binding site [ion binding]; other site 391008000158 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 391008000159 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 391008000160 DNA binding site [nucleotide binding] 391008000161 catalytic residue [active] 391008000162 H2TH interface [polypeptide binding]; other site 391008000163 putative catalytic residues [active] 391008000164 turnover-facilitating residue; other site 391008000165 intercalation triad [nucleotide binding]; other site 391008000166 8OG recognition residue [nucleotide binding]; other site 391008000167 putative reading head residues; other site 391008000168 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 391008000169 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 391008000170 Periplasmic glucans biosynthesis protein [Inorganic ion transport and metabolism]; Region: MdoG; COG3131 391008000171 glucan biosynthesis protein D; Provisional; Region: mdoD; PRK13273 391008000172 thymidine kinase; Provisional; Region: PRK04296 391008000173 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 391008000174 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 391008000175 Part of AAA domain; Region: AAA_19; pfam13245 391008000176 Family description; Region: UvrD_C_2; pfam13538 391008000177 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 391008000178 Protein of unknown function, DUF480; Region: DUF480; pfam04337 391008000179 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 391008000180 active site 391008000181 motif I; other site 391008000182 motif II; other site 391008000183 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase...; Region: OMP_decarboxylase_like; cd04725 391008000184 active site 391008000185 dimer interface [polypeptide binding]; other site 391008000186 glycerol-3-phosphate O-acyltransferase; Region: plsB; TIGR03703 391008000187 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like; Region: LPLAT_DHAPAT-like; cd07993 391008000188 putative acyl-acceptor binding pocket; other site 391008000189 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 391008000190 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_II; cd01993 391008000191 Ligand Binding Site [chemical binding]; other site 391008000192 recombination associated protein; Reviewed; Region: rdgC; PRK00321 391008000193 Protein of unknown function DUF45; Region: DUF45; pfam01863 391008000194 MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate...; Region: MGS-like; cl00245 391008000195 substrate binding site [chemical binding]; other site 391008000196 MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate...; Region: MGS-like; cl00245 391008000197 substrate binding site [chemical binding]; other site 391008000198 PAS fold; Region: PAS_3; pfam08447 391008000199 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008000200 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008000201 dimer interface [polypeptide binding]; other site 391008000202 phosphorylation site [posttranslational modification] 391008000203 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 391008000204 ATP binding site [chemical binding]; other site 391008000205 Mg2+ binding site [ion binding]; other site 391008000206 G-X-G motif; other site 391008000207 Response regulator receiver domain; Region: Response_reg; pfam00072 391008000208 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 391008000209 active site 391008000210 phosphorylation site [posttranslational modification] 391008000211 intermolecular recognition site; other site 391008000212 dimerization interface [polypeptide binding]; other site 391008000213 glutamate synthase small subunit family protein, proteobacterial; Region: gltD_gamma_fam; TIGR01318 391008000214 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 391008000215 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 391008000216 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 391008000217 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 391008000218 Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The...; Region: GltS; cd00713 391008000219 active site 391008000220 dimer interface [polypeptide binding]; other site 391008000221 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 391008000222 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast...; Region: GltS_FMN; cd02808 391008000223 active site 391008000224 FMN binding site [chemical binding]; other site 391008000225 substrate binding site [chemical binding]; other site 391008000226 3Fe-4S cluster binding site [ion binding]; other site 391008000227 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 391008000228 domain interface; other site 391008000229 Peptidase inhibitor I78 family; Region: Inhibitor_I78; pfam11720 391008000230 Topoisomerase IB [DNA replication, recombination, and repair]; Region: COG3569 391008000231 DNA topoisomerase IB, C-terminal catalytic domain. Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes of...; Region: Topo_IB_C; cd00659 391008000232 active site 391008000233 DNA binding site [nucleotide binding] 391008000234 Int/Topo IB signature motif; other site 391008000235 catalytic residues [active] 391008000236 short chain dehydrogenase; Provisional; Region: PRK06701 391008000237 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008000238 NAD(P) binding site [chemical binding]; other site 391008000239 active site 391008000240 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 391008000241 Beta-lactamase; Region: Beta-lactamase; pfam00144 391008000242 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 391008000243 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008000244 siderophore transporter, RhtX/FptX family; Region: sider_RhtX_FptX; TIGR02718 391008000245 muropeptide transporter; Validated; Region: ampG; cl17669 391008000246 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 391008000247 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 391008000248 N-terminal plug; other site 391008000249 ligand-binding site [chemical binding]; other site 391008000250 Penicillinase repressor; Region: Pencillinase_R; pfam03965 391008000251 BlaR1 peptidase M56; Region: Peptidase_M56; pfam05569 391008000252 Peptidase inhibitor I78 family; Region: Inhibitor_I78; pfam11720 391008000253 RNase_H superfamily; Region: RNase_H_2; pfam13482 391008000254 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]; Region: COG1205 391008000255 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 391008000256 ATP binding site [chemical binding]; other site 391008000257 putative Mg++ binding site [ion binding]; other site 391008000258 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 391008000259 nucleotide binding region [chemical binding]; other site 391008000260 ATP-binding site [chemical binding]; other site 391008000261 Domain of unknown function (DUF1998); Region: DUF1998; pfam09369 391008000262 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 391008000263 Protein of unknown function DUF58; Region: DUF58; pfam01882 391008000264 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008000265 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 391008000266 Walker A motif; other site 391008000267 ATP binding site [chemical binding]; other site 391008000268 Walker B motif; other site 391008000269 arginine finger; other site 391008000270 Domain of unknown function (DUF4159); Region: DUF4159; pfam13709 391008000271 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; COG0312 391008000272 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; COG0312 391008000273 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; COG0312 391008000274 Protein of unknown function (DUF938); Region: DUF938; pfam06080 391008000275 HipA N-terminal domain; Region: Couple_hipA; cl11853 391008000276 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 391008000277 HipA-like N-terminal domain; Region: HipA_N; pfam07805 391008000278 HipA-like C-terminal domain; Region: HipA_C; pfam07804 391008000279 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 391008000280 indolepyruvate ferredoxin oxidoreductase; Validated; Region: PRK09193 391008000281 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 391008000282 dimer interface [polypeptide binding]; other site 391008000283 PYR/PP interface [polypeptide binding]; other site 391008000284 TPP binding site [chemical binding]; other site 391008000285 substrate binding site [chemical binding]; other site 391008000286 Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as...; Region: TPP_IOR_alpha; cd02008 391008000287 TPP-binding site; other site 391008000288 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 391008000289 FOG: TPR repeat [General function prediction only]; Region: NrfG; COG0457 391008000290 Ycf46; Provisional; Region: ycf46; CHL00195 391008000291 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008000292 Walker A motif; other site 391008000293 ATP binding site [chemical binding]; other site 391008000294 Walker B motif; other site 391008000295 arginine finger; other site 391008000296 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 391008000297 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 391008000298 P-loop; other site 391008000299 Magnesium ion binding site [ion binding]; other site 391008000300 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 391008000301 catalytic core [active] 391008000302 YceI-like domain; Region: YceI; pfam04264 391008000303 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 391008000304 PLD-like domain; Region: PLDc_2; pfam13091 391008000305 putative active site [active] 391008000306 catalytic site [active] 391008000307 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 391008000308 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 391008000309 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 391008000310 putative active site [active] 391008000311 catalytic site [active] 391008000312 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 391008000313 CoenzymeA binding site [chemical binding]; other site 391008000314 subunit interaction site [polypeptide binding]; other site 391008000315 PHB binding site; other site 391008000316 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 391008000317 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 391008000318 putative acyl-acceptor binding pocket; other site 391008000319 putative hydrolase; Provisional; Region: PRK10985 391008000320 Tetratricopeptide repeat; Region: TPR_16; pfam13432 391008000321 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 391008000322 TPR motif; other site 391008000323 binding surface 391008000324 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 391008000325 binding surface 391008000326 TPR motif; other site 391008000327 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 391008000328 binding surface 391008000329 TPR motif; other site 391008000330 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 391008000331 substrate binding site [chemical binding]; other site 391008000332 META domain; Region: META; pfam03724 391008000333 Domain of unknown function (DUF4377); Region: DUF4377; pfam14302 391008000334 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 391008000335 glutamine synthetase; Provisional; Region: glnA; PRK09469 391008000336 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 391008000337 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 391008000338 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 391008000339 Nitrogen regulatory protein P-II; Region: P-II; smart00938 391008000340 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 391008000341 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 391008000342 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 391008000343 Haemolysin secretion/activation protein ShlB/FhaC/HecB; Region: ShlB; pfam03865 391008000344 Extended Signal Peptide of Type V secretion system; Region: ESPR; pfam13018 391008000345 haemagglutination activity domain; Region: Haemagg_act; pfam05860 391008000346 Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion]; Region: FhaB; COG3210 391008000347 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 391008000348 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 391008000349 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 391008000350 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 391008000351 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 391008000352 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 391008000353 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 391008000354 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 391008000355 amidase catalytic site [active] 391008000356 Zn binding residues [ion binding]; other site 391008000357 substrate binding site [chemical binding]; other site 391008000358 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 391008000359 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 391008000360 active site 391008000361 phosphorylation site [posttranslational modification] 391008000362 intermolecular recognition site; other site 391008000363 dimerization interface [polypeptide binding]; other site 391008000364 LytTr DNA-binding domain; Region: LytTR; smart00850 391008000365 Histidine kinase; Region: His_kinase; pfam06580 391008000366 Uncharacterized protein conserved in bacteria (DUF2064); Region: DUF2064; cl17492 391008000367 TAP-like protein; Region: Abhydrolase_4; pfam08386 391008000368 Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane]; Region: MltA; COG2821 391008000369 MltA specific insert domain; Region: MltA; smart00925 391008000370 3D domain; Region: 3D; pfam06725 391008000371 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008000372 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 391008000373 N-terminal plug; other site 391008000374 ligand-binding site [chemical binding]; other site 391008000375 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 391008000376 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 391008000377 ATP binding site [chemical binding]; other site 391008000378 Mg2+ binding site [ion binding]; other site 391008000379 G-X-G motif; other site 391008000380 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 391008000381 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 391008000382 active site 391008000383 phosphorylation site [posttranslational modification] 391008000384 intermolecular recognition site; other site 391008000385 dimerization interface [polypeptide binding]; other site 391008000386 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008000387 Walker A motif; other site 391008000388 ATP binding site [chemical binding]; other site 391008000389 Walker B motif; other site 391008000390 arginine finger; other site 391008000391 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 391008000392 active site 391008000393 Cu2+ binding site [ion binding]; other site 391008000394 E-class dimer interface [polypeptide binding]; other site 391008000395 Zn2+ binding site [ion binding]; other site 391008000396 P-class dimer interface [polypeptide binding]; other site 391008000397 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 391008000398 E-class dimer interface [polypeptide binding]; other site 391008000399 P-class dimer interface [polypeptide binding]; other site 391008000400 active site 391008000401 Cu2+ binding site [ion binding]; other site 391008000402 Zn2+ binding site [ion binding]; other site 391008000403 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 391008000404 Gram-negative bacterial tonB protein; Region: TonB; cl10048 391008000405 acetyl-CoA acetyltransferase; Provisional; Region: PRK09268 391008000406 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 391008000407 dimer interface [polypeptide binding]; other site 391008000408 active site 391008000409 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemY; COG3071 391008000410 HemY protein N-terminus; Region: HemY_N; pfam07219 391008000411 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemX; COG2959 391008000412 Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in...; Region: HemD; cd06578 391008000413 Uroporphyrinogen-III synthase [Coenzyme metabolism]; Region: HemD; COG1587 391008000414 active site 391008000415 Putative thioesterase (yiiD_Cterm); Region: YiiD_Cterm; pfam09500 391008000416 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 391008000417 active site residue [active] 391008000418 preprotein translocase subunit SecB; Validated; Region: PRK05751 391008000419 SecA binding site; other site 391008000420 Preprotein binding site; other site 391008000421 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 391008000422 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 391008000423 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 391008000424 Ketosteroid isomerase homolog [Function unknown]; Region: COG4319 391008000425 Inhibitor of vertebrate lysozyme (Ivy); Region: Ivy; cl07428 391008000426 HipA N-terminal domain; Region: Couple_hipA; pfam13657 391008000427 HipA-like N-terminal domain; Region: HipA_N; pfam07805 391008000428 HipA-like C-terminal domain; Region: HipA_C; pfam07804 391008000429 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 391008000430 non-specific DNA binding site [nucleotide binding]; other site 391008000431 salt bridge; other site 391008000432 sequence-specific DNA binding site [nucleotide binding]; other site 391008000433 Predicted Zn-dependent protease (DUF2268); Region: DUF2268; cl02316 391008000434 sulfation-dependent quorum factor, Ax21 family; Region: Y_sulf_Ax21; TIGR04273 391008000435 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 391008000436 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 391008000437 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 391008000438 Dyp-type peroxidase family; Region: Dyp_perox; cl01067 391008000439 Nicotinamide mononucleotide transporter; Region: NMN_transporter; pfam04973 391008000440 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 391008000441 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 391008000442 N-terminal plug; other site 391008000443 ligand-binding site [chemical binding]; other site 391008000444 Phosphotransferase enzyme family; Region: APH; pfam01636 391008000445 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cl17270 391008000446 active site 391008000447 ATP binding site [chemical binding]; other site 391008000448 substrate binding site [chemical binding]; other site 391008000449 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 391008000450 N-acetyl-D-glucosamine binding site [chemical binding]; other site 391008000451 catalytic residue [active] 391008000452 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 391008000453 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 391008000454 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 391008000455 active site 391008000456 phosphorylation site [posttranslational modification] 391008000457 intermolecular recognition site; other site 391008000458 dimerization interface [polypeptide binding]; other site 391008000459 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 391008000460 DNA binding residues [nucleotide binding] 391008000461 dimerization interface [polypeptide binding]; other site 391008000462 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 391008000463 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 391008000464 substrate binding pocket [chemical binding]; other site 391008000465 membrane-bound complex binding site; other site 391008000466 hinge residues; other site 391008000467 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 391008000468 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 391008000469 substrate binding pocket [chemical binding]; other site 391008000470 membrane-bound complex binding site; other site 391008000471 hinge residues; other site 391008000472 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008000473 dimer interface [polypeptide binding]; other site 391008000474 phosphorylation site [posttranslational modification] 391008000475 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 391008000476 ATP binding site [chemical binding]; other site 391008000477 Mg2+ binding site [ion binding]; other site 391008000478 G-X-G motif; other site 391008000479 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 391008000480 active site 391008000481 phosphorylation site [posttranslational modification] 391008000482 intermolecular recognition site; other site 391008000483 dimerization interface [polypeptide binding]; other site 391008000484 Cytochrome c; Region: Cytochrom_C; cl11414 391008000485 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 391008000486 hydroxyglutarate oxidase; Provisional; Region: PRK11728 391008000487 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 391008000488 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 391008000489 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 391008000490 active site 391008000491 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008000492 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008000493 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 391008000494 dimerization interface [polypeptide binding]; other site 391008000495 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 391008000496 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 391008000497 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 391008000498 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 391008000499 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 391008000500 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 391008000501 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 391008000502 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 391008000503 Domain of unknown function (DUF4156); Region: DUF4156; pfam13698 391008000504 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09258 391008000505 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 391008000506 dimer interface [polypeptide binding]; other site 391008000507 active site 391008000508 CoA binding pocket [chemical binding]; other site 391008000509 haloalkane dehalogenase; Provisional; Region: PRK00870 391008000510 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 391008000511 peptide synthase; Provisional; Region: PRK09274 391008000512 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_1; cd05910 391008000513 acyl-activating enzyme (AAE) consensus motif; other site 391008000514 putative AMP binding site [chemical binding]; other site 391008000515 putative active site [active] 391008000516 putative CoA binding site [chemical binding]; other site 391008000517 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 391008000518 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008000519 NAD(P) binding site [chemical binding]; other site 391008000520 active site 391008000521 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 391008000522 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 391008000523 D-ala D-ala ligase C-terminus; Region: Dala_Dala_lig_C; pfam07478 391008000524 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 391008000525 SCP-2 sterol transfer family; Region: SCP2; pfam02036 391008000526 putative ubiquinone biosynthesis protein UbiB; Reviewed; Region: ubiB; PRK04750 391008000527 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 391008000528 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 391008000529 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 391008000530 S-adenosylmethionine binding site [chemical binding]; other site 391008000531 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 391008000532 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 391008000533 active site 391008000534 Uncharacterized protein conserved in bacteria (DUF2059); Region: DUF2059; cl01243 391008000535 hypothetical protein; Provisional; Region: PRK09256 391008000536 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 391008000537 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 391008000538 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ABO13168; Region: LPLAT_ABO13168-like; cd07988 391008000539 putative acyl-acceptor binding pocket; other site 391008000540 dipeptidyl carboxypeptidase II; Provisional; Region: PRK10280 391008000541 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 391008000542 active site 391008000543 Zn binding site [ion binding]; other site 391008000544 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 391008000545 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 391008000546 Catalytic site [active] 391008000547 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 391008000548 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 391008000549 putative substrate translocation pore; other site 391008000550 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 391008000551 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 391008000552 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008000553 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 391008000554 dimerization interface [polypeptide binding]; other site 391008000555 substrate binding pocket [chemical binding]; other site 391008000556 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008000557 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008000558 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 391008000559 dimerization interface [polypeptide binding]; other site 391008000560 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 391008000561 malate synthase A; Region: malate_syn_A; TIGR01344 391008000562 active site 391008000563 isocitrate lyase; Provisional; Region: PRK15063 391008000564 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 391008000565 tetramer interface [polypeptide binding]; other site 391008000566 active site 391008000567 Mg2+/Mn2+ binding site [ion binding]; other site 391008000568 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 391008000569 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 391008000570 ligand binding site [chemical binding]; other site 391008000571 flexible hinge region; other site 391008000572 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008000573 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008000574 metal binding site [ion binding]; metal-binding site 391008000575 active site 391008000576 I-site; other site 391008000577 cyclase homology domain; Region: CHD; cd07302 391008000578 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 391008000579 dimer interface [polypeptide binding]; other site 391008000580 nucleotidyl binding site; other site 391008000581 metal binding site [ion binding]; metal-binding site 391008000582 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 391008000583 putative FMN binding site [chemical binding]; other site 391008000584 NADPH bind site [chemical binding]; other site 391008000585 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 391008000586 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 391008000587 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 391008000588 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; pfam02785 391008000589 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 391008000590 carboxyltransferase (CT) interaction site; other site 391008000591 biotinylation site [posttranslational modification]; other site 391008000592 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 391008000593 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 391008000594 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 391008000595 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 391008000596 active site 391008000597 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 391008000598 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008000599 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 391008000600 Mycoplasma pulmonis MnuA nuclease-like; Region: MnuA_DNase1-like; cd10283 391008000601 putative active site [active] 391008000602 putative catalytic site [active] 391008000603 putative Mg binding site IVb [ion binding]; other site 391008000604 putative phosphate binding site [ion binding]; other site 391008000605 putative DNA binding site [nucleotide binding]; other site 391008000606 putative Mg binding site IVa [ion binding]; other site 391008000607 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 391008000608 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 391008000609 Predicted ATPase [General function prediction only]; Region: COG1485 391008000610 Protein of unknown function (DUF2884); Region: DUF2884; pfam11101 391008000611 ribonucleoside--diphosphate reductase large subunit; Region: PLN02437 391008000612 ATP cone domain; Region: ATP-cone; pfam03477 391008000613 Class I ribonucleotide reductase; Region: RNR_I; cd01679 391008000614 active site 391008000615 dimer interface [polypeptide binding]; other site 391008000616 catalytic residues [active] 391008000617 effector binding site; other site 391008000618 R2 peptide binding site; other site 391008000619 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 391008000620 dimer interface [polypeptide binding]; other site 391008000621 putative radical transfer pathway; other site 391008000622 diiron center [ion binding]; other site 391008000623 tyrosyl radical; other site 391008000624 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 391008000625 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 391008000626 NAD-dependent deacetylase; Provisional; Region: PRK05333 391008000627 SIRT4: Eukaryotic and prokaryotic group (class2) which includes human sirtuin SIRT4 and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein...; Region: SIRT4; cd01409 391008000628 NAD+ binding site [chemical binding]; other site 391008000629 substrate binding site [chemical binding]; other site 391008000630 Zn binding site [ion binding]; other site 391008000631 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 391008000632 Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing...; Region: OYE_YqiM_FMN; cd02932 391008000633 active site 391008000634 FMN binding site [chemical binding]; other site 391008000635 substrate binding site [chemical binding]; other site 391008000636 homotetramer interface [polypeptide binding]; other site 391008000637 catalytic residue [active] 391008000638 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008000639 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008000640 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 391008000641 putative effector binding pocket; other site 391008000642 dimerization interface [polypeptide binding]; other site 391008000643 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 391008000644 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 391008000645 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 391008000646 putative active site [active] 391008000647 putative substrate binding site [chemical binding]; other site 391008000648 putative cosubstrate binding site; other site 391008000649 catalytic site [active] 391008000650 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 391008000651 catalytic triad [active] 391008000652 metal binding site [ion binding]; metal-binding site 391008000653 conserved cis-peptide bond; other site 391008000654 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 391008000655 Family of unknown function (DUF1028); Region: DUF1028; pfam06267 391008000656 Predicted transcriptional regulator [General function prediction only]; Region: COG3800 391008000657 Domain of unknown function (DUF955); Region: DUF955; pfam06114 391008000658 Predicted transcriptional regulator (DUF2083); Region: DUF2083; pfam09856 391008000659 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 391008000660 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 391008000661 tetrameric interface [polypeptide binding]; other site 391008000662 NAD binding site [chemical binding]; other site 391008000663 catalytic residues [active] 391008000664 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 391008000665 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 391008000666 active site 391008000667 enoyl-CoA hydratase; Provisional; Region: PRK09076 391008000668 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 391008000669 substrate binding site [chemical binding]; other site 391008000670 oxyanion hole (OAH) forming residues; other site 391008000671 trimer interface [polypeptide binding]; other site 391008000672 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 391008000673 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 391008000674 substrate binding site [chemical binding]; other site 391008000675 oxyanion hole (OAH) forming residues; other site 391008000676 trimer interface [polypeptide binding]; other site 391008000677 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 391008000678 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 391008000679 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 391008000680 peroxiredoxin, Ohr subfamily; Region: organ_hyd_perox; TIGR03561 391008000681 Cation efflux family; Region: Cation_efflux; cl00316 391008000682 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 391008000683 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 391008000684 Sulfate transporter family; Region: Sulfate_transp; pfam00916 391008000685 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 391008000686 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 391008000687 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 391008000688 FMN binding site [chemical binding]; other site 391008000689 active site 391008000690 catalytic residues [active] 391008000691 substrate binding site [chemical binding]; other site 391008000692 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391008000693 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 391008000694 active site 391008000695 phosphorylation site [posttranslational modification] 391008000696 intermolecular recognition site; other site 391008000697 dimerization interface [polypeptide binding]; other site 391008000698 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008000699 DNA binding site [nucleotide binding] 391008000700 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 391008000701 dimer interface [polypeptide binding]; other site 391008000702 phosphorylation site [posttranslational modification] 391008000703 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 391008000704 ATP binding site [chemical binding]; other site 391008000705 Mg2+ binding site [ion binding]; other site 391008000706 G-X-G motif; other site 391008000707 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; pfam06167 391008000708 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 391008000709 Biotin operon repressor [Transcription]; Region: BirA; COG1654 391008000710 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 391008000711 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 391008000712 pantothenate kinase; Reviewed; Region: PRK13327 391008000713 Sporulation related domain; Region: SPOR; pfam05036 391008000714 putative addiction module killer protein; Region: upstrm_HI1419; TIGR02683 391008000715 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 391008000716 non-specific DNA binding site [nucleotide binding]; other site 391008000717 salt bridge; other site 391008000718 sequence-specific DNA binding site [nucleotide binding]; other site 391008000719 Arginase family; Region: Arginase; cd09989 391008000720 agmatinase; Region: agmatinase; TIGR01230 391008000721 active site 391008000722 Mn binding site [ion binding]; other site 391008000723 oligomer interface [polypeptide binding]; other site 391008000724 Predicted small secreted protein [Function unknown]; Region: COG5510 391008000725 CsbD-like; Region: CsbD; cl17424 391008000726 tryptophanyl-tRNA synthetase; Reviewed; Region: PRK12284 391008000727 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 391008000728 active site 391008000729 HIGH motif; other site 391008000730 dimer interface [polypeptide binding]; other site 391008000731 KMSKS motif; other site 391008000732 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 391008000733 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 391008000734 PA_M28_1_2: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 2. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic...; Region: PA_M28_1_2; cd04821 391008000735 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 391008000736 PA/protease or protease-like domain interface [polypeptide binding]; other site 391008000737 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA_1; cd05660 391008000738 metal binding site [ion binding]; metal-binding site 391008000739 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 391008000740 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 391008000741 putative substrate translocation pore; other site 391008000742 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 391008000743 EamA-like transporter family; Region: EamA; pfam00892 391008000744 EamA-like transporter family; Region: EamA; pfam00892 391008000745 Predicted permeases [General function prediction only]; Region: RarD; COG2962 391008000746 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 391008000747 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008000748 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008000749 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008000750 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 391008000751 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 391008000752 FtsX-like permease family; Region: FtsX; pfam02687 391008000753 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 391008000754 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 391008000755 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 391008000756 Walker A/P-loop; other site 391008000757 ATP binding site [chemical binding]; other site 391008000758 Q-loop/lid; other site 391008000759 ABC transporter signature motif; other site 391008000760 Walker B; other site 391008000761 D-loop; other site 391008000762 H-loop/switch region; other site 391008000763 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 391008000764 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008000765 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008000766 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 391008000767 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 391008000768 Walker A/P-loop; other site 391008000769 ATP binding site [chemical binding]; other site 391008000770 Q-loop/lid; other site 391008000771 ABC transporter signature motif; other site 391008000772 Walker B; other site 391008000773 D-loop; other site 391008000774 H-loop/switch region; other site 391008000775 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 391008000776 Histidine kinase; Region: HisKA_3; pfam07730 391008000777 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 391008000778 ATP binding site [chemical binding]; other site 391008000779 Mg2+ binding site [ion binding]; other site 391008000780 G-X-G motif; other site 391008000781 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 391008000782 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 391008000783 active site 391008000784 phosphorylation site [posttranslational modification] 391008000785 intermolecular recognition site; other site 391008000786 dimerization interface [polypeptide binding]; other site 391008000787 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 391008000788 DNA binding residues [nucleotide binding] 391008000789 dimerization interface [polypeptide binding]; other site 391008000790 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 391008000791 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 391008000792 putative heme binding pocket [chemical binding]; other site 391008000793 Leucyl aminopeptidase [Amino acid transport and metabolism]; Region: PepB; COG0260 391008000794 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 391008000795 interface (dimer of trimers) [polypeptide binding]; other site 391008000796 Substrate-binding/catalytic site; other site 391008000797 Zn-binding sites [ion binding]; other site 391008000798 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 391008000799 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 391008000800 motif II; other site 391008000801 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 391008000802 Domain of unknown function DUF20; Region: UPF0118; pfam01594 391008000803 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 391008000804 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 391008000805 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 391008000806 protein binding site [polypeptide binding]; other site 391008000807 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 391008000808 protein binding site [polypeptide binding]; other site 391008000809 Protein of unknown function (DUF1428); Region: DUF1428; pfam07237 391008000810 sulfation-dependent quorum factor, Ax21 family; Region: Y_sulf_Ax21; TIGR04273 391008000811 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 391008000812 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 391008000813 active site 391008000814 dimerization interface [polypeptide binding]; other site 391008000815 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 391008000816 DNA binding residues [nucleotide binding] 391008000817 dimerization interface [polypeptide binding]; other site 391008000818 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 391008000819 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 391008000820 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 391008000821 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008000822 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008000823 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_3; cd08436 391008000824 putative dimerization interface [polypeptide binding]; other site 391008000825 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4807 391008000826 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 391008000827 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 391008000828 classical (c) SDR, subgroup 5; Region: SDR_c5; cd05346 391008000829 malonic semialdehyde reductase; Provisional; Region: PRK10538 391008000830 putative NAD(P) binding site [chemical binding]; other site 391008000831 homotetramer interface [polypeptide binding]; other site 391008000832 homodimer interface [polypeptide binding]; other site 391008000833 active site 391008000834 Sporulation related domain; Region: SPOR; pfam05036 391008000835 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 391008000836 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 391008000837 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 391008000838 active site 391008000839 HIGH motif; other site 391008000840 KMSK motif region; other site 391008000841 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 391008000842 tRNA binding surface [nucleotide binding]; other site 391008000843 anticodon binding site; other site 391008000844 hypothetical protein; Reviewed; Region: PRK00024 391008000845 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 391008000846 MPN+ (JAMM) motif; other site 391008000847 Zinc-binding site [ion binding]; other site 391008000848 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 391008000849 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 391008000850 active site 391008000851 phosphorylation site [posttranslational modification] 391008000852 intermolecular recognition site; other site 391008000853 dimerization interface [polypeptide binding]; other site 391008000854 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 391008000855 DNA binding residues [nucleotide binding] 391008000856 dimerization interface [polypeptide binding]; other site 391008000857 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 391008000858 Flavoprotein; Region: Flavoprotein; pfam02441 391008000859 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 391008000860 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 391008000861 trimer interface [polypeptide binding]; other site 391008000862 active site 391008000863 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 391008000864 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 391008000865 active site 391008000866 substrate binding site [chemical binding]; other site 391008000867 metal binding site [ion binding]; metal-binding site 391008000868 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391008000869 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 391008000870 active site 391008000871 phosphorylation site [posttranslational modification] 391008000872 intermolecular recognition site; other site 391008000873 dimerization interface [polypeptide binding]; other site 391008000874 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008000875 DNA binding site [nucleotide binding] 391008000876 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 391008000877 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 391008000878 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 391008000879 Ligand Binding Site [chemical binding]; other site 391008000880 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008000881 dimer interface [polypeptide binding]; other site 391008000882 phosphorylation site [posttranslational modification] 391008000883 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 391008000884 ATP binding site [chemical binding]; other site 391008000885 Mg2+ binding site [ion binding]; other site 391008000886 G-X-G motif; other site 391008000887 K+-transporting ATPase, c chain; Region: KdpC; cl00944 391008000888 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 391008000889 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 391008000890 Soluble P-type ATPase [General function prediction only]; Region: COG4087 391008000891 potassium-transporting ATPase subunit A; Provisional; Region: PRK05482 391008000892 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 391008000893 active site 391008000894 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 391008000895 putative active site [active] 391008000896 putative catalytic site [active] 391008000897 putative DNA binding site [nucleotide binding]; other site 391008000898 putative phosphate binding site [ion binding]; other site 391008000899 metal binding site A [ion binding]; metal-binding site 391008000900 putative AP binding site [nucleotide binding]; other site 391008000901 putative metal binding site B [ion binding]; other site 391008000902 muropeptide transporter; Validated; Region: ampG; cl17669 391008000903 muropeptide transporter; Reviewed; Region: ampG; PRK11902 391008000904 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 391008000905 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 391008000906 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 391008000907 Peptidase family M23; Region: Peptidase_M23; pfam01551 391008000908 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 391008000909 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 391008000910 active site 391008000911 HIGH motif; other site 391008000912 dimer interface [polypeptide binding]; other site 391008000913 KMSKS motif; other site 391008000914 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 391008000915 RNA binding surface [nucleotide binding]; other site 391008000916 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 391008000917 PA_M28_1_2: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 2. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic...; Region: PA_M28_1_2; cd04821 391008000918 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 391008000919 PA/protease or protease-like domain interface [polypeptide binding]; other site 391008000920 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA_1; cd05660 391008000921 metal binding site [ion binding]; metal-binding site 391008000922 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 391008000923 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 391008000924 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 391008000925 Peptidase family M23; Region: Peptidase_M23; pfam01551 391008000926 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 391008000927 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 391008000928 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 391008000929 protein binding site [polypeptide binding]; other site 391008000930 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 391008000931 Catalytic dyad [active] 391008000932 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 391008000933 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; pfam03349 391008000934 Nicotinamide mononucleotide transporter; Region: NMN_transporter; pfam04973 391008000935 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 391008000936 Proline dehydrogenase; Region: Pro_dh; pfam01619 391008000937 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 391008000938 Glutamate binding site [chemical binding]; other site 391008000939 NAD binding site [chemical binding]; other site 391008000940 catalytic residues [active] 391008000941 Integral membrane protein (DUF2244); Region: DUF2244; pfam10003 391008000942 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 391008000943 cytochrome c oxidase, subunit II; Region: CoxB; TIGR02866 391008000944 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 391008000945 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 391008000946 Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_I; cd01663 391008000947 Subunit I/III interface [polypeptide binding]; other site 391008000948 D-pathway; other site 391008000949 Subunit I/VIIc interface [polypeptide binding]; other site 391008000950 Subunit I/IV interface [polypeptide binding]; other site 391008000951 Subunit I/II interface [polypeptide binding]; other site 391008000952 Low-spin heme (heme a) binding site [chemical binding]; other site 391008000953 Subunit I/VIIa interface [polypeptide binding]; other site 391008000954 Subunit I/VIa interface [polypeptide binding]; other site 391008000955 Dimer interface; other site 391008000956 Putative water exit pathway; other site 391008000957 Binuclear center (heme a3/CuB) [ion binding]; other site 391008000958 K-pathway; other site 391008000959 Subunit I/Vb interface [polypeptide binding]; other site 391008000960 Putative proton exit pathway; other site 391008000961 Subunit I/VIb interface; other site 391008000962 Subunit I/VIc interface [polypeptide binding]; other site 391008000963 Electron transfer pathway; other site 391008000964 Subunit I/VIIIb interface [polypeptide binding]; other site 391008000965 Subunit I/VIIb interface [polypeptide binding]; other site 391008000966 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 391008000967 Cytochrome c oxidase subunit III. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_III; cd01665 391008000968 Subunit III/VIIa interface [polypeptide binding]; other site 391008000969 Phospholipid binding site [chemical binding]; other site 391008000970 Subunit I/III interface [polypeptide binding]; other site 391008000971 Subunit III/VIb interface [polypeptide binding]; other site 391008000972 Subunit III/VIa interface; other site 391008000973 Subunit III/Vb interface [polypeptide binding]; other site 391008000974 Protein of unknown function (DUF2909); Region: DUF2909; pfam11137 391008000975 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cd06662 391008000976 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 391008000977 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 391008000978 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 391008000979 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 391008000980 UbiA prenyltransferase family; Region: UbiA; pfam01040 391008000981 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 391008000982 SBF-like CPA transporter family (DUF4137); Region: DUF4137; pfam13593 391008000983 Putative phosphatase (DUF442); Region: DUF442; cl17385 391008000984 DNA primase; Validated; Region: dnaG; PRK05667 391008000985 CHC2 zinc finger; Region: zf-CHC2; pfam01807 391008000986 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 391008000987 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 391008000988 active site 391008000989 metal binding site [ion binding]; metal-binding site 391008000990 interdomain interaction site; other site 391008000991 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 391008000992 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; pfam08278 391008000993 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 391008000994 Yqey-like protein; Region: YqeY; pfam09424 391008000995 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 391008000996 UGMP family protein; Validated; Region: PRK09604 391008000997 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 391008000998 Abi-like protein; Region: Abi_2; pfam07751 391008000999 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 391008001000 homooctamer interface [polypeptide binding]; other site 391008001001 active site 391008001002 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 391008001003 Mechanosensitive ion channel; Region: MS_channel; pfam00924 391008001004 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 391008001005 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 391008001006 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 391008001007 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 391008001008 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 391008001009 Predicted membrane protein [Function unknown]; Region: COG4682 391008001010 yiaA/B two helix domain; Region: YiaAB; pfam05360 391008001011 amino acid transporter; Region: 2A0306; TIGR00909 391008001012 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3786 391008001013 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 391008001014 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 391008001015 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 391008001016 putative active site [active] 391008001017 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 391008001018 L-Ala-D/L-Glu epimerase catalyzes the epimerization of L-Ala-D/L-Glu and other dipeptides. The genomic context and the substrate specificity of characterized members of this family from E.coli and B.subtilis indicates a possible role in the metabolism of...; Region: L-Ala-DL-Glu_epimerase; cd03319 391008001019 active site 391008001020 SH3 domain of the SH3b1 type; Region: SH3_6; pfam12913 391008001021 SH3 domain of SH3b2 type; Region: SH3_7; pfam12914 391008001022 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 391008001023 NlpC/P60 family; Region: NLPC_P60; cl17555 391008001024 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 391008001025 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 391008001026 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 391008001027 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008001028 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008001029 Beta-lactamase; Region: Beta-lactamase; pfam00144 391008001030 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 391008001031 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 391008001032 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cd00051 391008001033 EF-hand domain pair; Region: EF_hand_5; pfam13499 391008001034 Ca2+ binding site [ion binding]; other site 391008001035 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 391008001036 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cl17915 391008001037 motif II; other site 391008001038 Domain of unknown function (DUF1338); Region: DUF1338; pfam07063 391008001039 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5383 391008001040 succinate CoA transferase; Region: YgfH_subfam; TIGR03458 391008001041 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 391008001042 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 391008001043 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 391008001044 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 391008001045 metal binding triad; other site 391008001046 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 391008001047 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 391008001048 metal binding triad; other site 391008001049 Uncharacterized member of the PurR regulon [General function prediction only]; Region: yhhQ; COG1738 391008001050 Uncharacterized protein conserved in bacteria (DUF2145); Region: DUF2145; pfam09916 391008001051 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 391008001052 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 391008001053 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 391008001054 putative FMN binding site [chemical binding]; other site 391008001055 Uncharacterized conserved protein [Function unknown]; Region: COG2353 391008001056 leucine-zipper of insertion element IS481; Region: LZ_Tnp_IS481; pfam13011 391008001057 Winged helix-turn helix; Region: HTH_29; pfam13551 391008001058 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 391008001059 Integrase core domain; Region: rve; pfam00665 391008001060 Integrase core domain; Region: rve_3; pfam13683 391008001061 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 391008001062 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 391008001063 FAD binding pocket [chemical binding]; other site 391008001064 FAD binding motif [chemical binding]; other site 391008001065 phosphate binding motif [ion binding]; other site 391008001066 NAD binding pocket [chemical binding]; other site 391008001067 Predicted transcriptional regulators [Transcription]; Region: COG1695 391008001068 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 391008001069 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 391008001070 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 391008001071 dimer interface [polypeptide binding]; other site 391008001072 TPP-binding site [chemical binding]; other site 391008001073 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 391008001074 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 391008001075 ATP binding site [chemical binding]; other site 391008001076 putative Mg++ binding site [ion binding]; other site 391008001077 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 391008001078 WYL domain; Region: WYL; pfam13280 391008001079 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 391008001080 G1 box; other site 391008001081 GTP/Mg2+ binding site [chemical binding]; other site 391008001082 G2 box; other site 391008001083 Switch I region; other site 391008001084 G3 box; other site 391008001085 Switch II region; other site 391008001086 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 391008001087 G1 box; other site 391008001088 GTP/Mg2+ binding site [chemical binding]; other site 391008001089 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 391008001090 G3 box; other site 391008001091 Switch II region; other site 391008001092 G4 box; other site 391008001093 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 391008001094 GTP/Mg2+ binding site [chemical binding]; other site 391008001095 Dynamin family; Region: Dynamin_N; pfam00350 391008001096 G2 box; other site 391008001097 Switch I region; other site 391008001098 G3 box; other site 391008001099 Switch II region; other site 391008001100 G4 box; other site 391008001101 G5 box; other site 391008001102 Putative catalytic domain of uncharacterized hypothetical proteins with one or two copies of the HKD motif; Region: PLDc_unchar6; cd09176 391008001103 putative homodimer interface [polypeptide binding]; other site 391008001104 putative active site [active] 391008001105 catalytic site [active] 391008001106 Helicase conserved C-terminal domain; Region: Helicase_C; pfam00271 391008001107 ATP-binding site [chemical binding]; other site 391008001108 Uncharacterized conserved protein [Function unknown]; Region: COG3391 391008001109 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 391008001110 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 391008001111 TAP-like protein; Region: Abhydrolase_4; pfam08386 391008001112 Catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases; Region: CE4_NodB_like_1; cd10960 391008001113 NodB motif; other site 391008001114 putative active site [active] 391008001115 putative catalytic site [active] 391008001116 putative Zn binding site [ion binding]; other site 391008001117 Predicted archaeal methyltransferase [General function prediction only]; Region: COG2521 391008001118 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 391008001119 S-adenosylmethionine binding site [chemical binding]; other site 391008001120 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 391008001121 Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156; Region: RcnR-FrmR-like_DUF156; cd10153 391008001122 putative metal binding site [ion binding]; other site 391008001123 putative homodimer interface [polypeptide binding]; other site 391008001124 putative homotetramer interface [polypeptide binding]; other site 391008001125 putative homodimer-homodimer interface [polypeptide binding]; other site 391008001126 putative allosteric switch controlling residues; other site 391008001127 MerC mercury resistance protein; Region: MerC; pfam03203 391008001128 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 391008001129 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 391008001130 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; smart00833 391008001131 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; smart00833 391008001132 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 391008001133 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 391008001134 Walker A/P-loop; other site 391008001135 ATP binding site [chemical binding]; other site 391008001136 ABC transporter signature motif; other site 391008001137 Walker B; other site 391008001138 D-loop; other site 391008001139 H-loop/switch region; other site 391008001140 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 391008001141 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008001142 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008001143 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_7; cd08476 391008001144 putative effector binding pocket; other site 391008001145 putative dimerization interface [polypeptide binding]; other site 391008001146 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 391008001147 Beta-lactamase; Region: Beta-lactamase; pfam00144 391008001148 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 391008001149 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 391008001150 putative substrate translocation pore; other site 391008001151 Predicted signal transduction protein containing sensor and EAL domains [Signal transduction mechanisms]; Region: COG4943 391008001152 CSS motif domain associated with EAL; Region: CSS-motif; pfam12792 391008001153 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 391008001154 D-alanine/D-serine/glycine permease; Provisional; Region: PRK11049 391008001155 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 391008001156 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 391008001157 N-acetyl-D-glucosamine binding site [chemical binding]; other site 391008001158 catalytic residue [active] 391008001159 Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilF; COG3063 391008001160 NHL repeat; Region: NHL; pfam01436 391008001161 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 391008001162 NHL repeat; Region: NHL; pfam01436 391008001163 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3795 391008001164 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3795 391008001165 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 391008001166 dimer interface [polypeptide binding]; other site 391008001167 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_24; cd09012 391008001168 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 391008001169 Protein of unknown function (DUF1428); Region: DUF1428; pfam07237 391008001170 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]; Region: COG4941 391008001171 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391008001172 Curli production assembly/transport component CsgG; Region: CsgG; cl17434 391008001173 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 391008001174 PA_M28_1_2: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 2. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic...; Region: PA_M28_1_2; cd04821 391008001175 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 391008001176 PA/protease or protease-like domain interface [polypeptide binding]; other site 391008001177 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA_1; cd05660 391008001178 metal binding site [ion binding]; metal-binding site 391008001179 Histidine kinase; Region: His_kinase; pfam06580 391008001180 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 391008001181 Mg2+ binding site [ion binding]; other site 391008001182 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 391008001183 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 391008001184 active site 391008001185 phosphorylation site [posttranslational modification] 391008001186 intermolecular recognition site; other site 391008001187 dimerization interface [polypeptide binding]; other site 391008001188 LytTr DNA-binding domain; Region: LytTR; smart00850 391008001189 Uncharacterized protein conserved in bacteria (DUF2236); Region: DUF2236; pfam09995 391008001190 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 391008001191 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008001192 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 391008001193 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 391008001194 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 391008001195 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 391008001196 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 391008001197 active site 391008001198 Zn binding site [ion binding]; other site 391008001199 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 391008001200 PAS fold; Region: PAS_3; pfam08447 391008001201 putative active site [active] 391008001202 heme pocket [chemical binding]; other site 391008001203 PAS domain S-box; Region: sensory_box; TIGR00229 391008001204 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 391008001205 putative active site [active] 391008001206 heme pocket [chemical binding]; other site 391008001207 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008001208 metal binding site [ion binding]; metal-binding site 391008001209 active site 391008001210 I-site; other site 391008001211 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 391008001212 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008001213 LysR family transcriptional regulator; Provisional; Region: PRK14997 391008001214 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 391008001215 putative effector binding pocket; other site 391008001216 dimerization interface [polypeptide binding]; other site 391008001217 DoxX; Region: DoxX; pfam07681 391008001218 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 391008001219 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 391008001220 putative active site [active] 391008001221 metal binding site [ion binding]; metal-binding site 391008001222 Na+/H+ antiporter, bacterial form; Region: a_cpa1; TIGR00831 391008001223 Protein of unknown function (DUF3297); Region: DUF3297; pfam11730 391008001224 Protein of unknown function (DUF4031); Region: DUF4031; pfam13223 391008001225 flagellar motor protein MotB; Validated; Region: motB; PRK09041 391008001226 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 391008001227 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 391008001228 ligand binding site [chemical binding]; other site 391008001229 flagellar motor protein MotA; Validated; Region: PRK09110 391008001230 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 391008001231 methionine sulfoxide reductase B; Provisional; Region: PRK00222 391008001232 SelR domain; Region: SelR; pfam01641 391008001233 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 391008001234 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 391008001235 putative DNA binding site [nucleotide binding]; other site 391008001236 putative Zn2+ binding site [ion binding]; other site 391008001237 AsnC family; Region: AsnC_trans_reg; pfam01037 391008001238 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 391008001239 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 391008001240 hydroxyglutarate oxidase; Provisional; Region: PRK11728 391008001241 alanine racemase; Reviewed; Region: alr; PRK00053 391008001242 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 391008001243 active site 391008001244 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 391008001245 substrate binding site [chemical binding]; other site 391008001246 catalytic residues [active] 391008001247 dimer interface [polypeptide binding]; other site 391008001248 Protein of unknown function (DUF3016); Region: DUF3016; pfam11454 391008001249 PAS domain; Region: PAS_9; pfam13426 391008001250 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 391008001251 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 391008001252 putative active site [active] 391008001253 heme pocket [chemical binding]; other site 391008001254 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008001255 dimer interface [polypeptide binding]; other site 391008001256 phosphorylation site [posttranslational modification] 391008001257 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 391008001258 ATP binding site [chemical binding]; other site 391008001259 Mg2+ binding site [ion binding]; other site 391008001260 G-X-G motif; other site 391008001261 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 391008001262 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 391008001263 active site 391008001264 phosphorylation site [posttranslational modification] 391008001265 intermolecular recognition site; other site 391008001266 dimerization interface [polypeptide binding]; other site 391008001267 Protein of unknown function (DUF3247); Region: DUF3247; pfam11607 391008001268 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; Region: RsmC; COG2813 391008001269 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 391008001270 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 391008001271 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 391008001272 active site 391008001273 uracil binding [chemical binding]; other site 391008001274 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 391008001275 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 391008001276 motif II; other site 391008001277 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 391008001278 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 391008001279 dimer interface [polypeptide binding]; other site 391008001280 active site 391008001281 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 391008001282 dimer interface [polypeptide binding]; other site 391008001283 active site 1 [active] 391008001284 active site 2 [active] 391008001285 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 391008001286 active site 391008001287 DNA polymerase IV; Validated; Region: PRK02406 391008001288 DNA binding site [nucleotide binding] 391008001289 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 391008001290 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 391008001291 NADH(P)-binding; Region: NAD_binding_10; pfam13460 391008001292 NAD binding site [chemical binding]; other site 391008001293 substrate binding site [chemical binding]; other site 391008001294 putative active site [active] 391008001295 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008001296 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008001297 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 391008001298 putative effector binding pocket; other site 391008001299 dimerization interface [polypeptide binding]; other site 391008001300 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 391008001301 S-adenosylmethionine binding site [chemical binding]; other site 391008001302 phosphoglycolate phosphatase; Provisional; Region: PRK13222 391008001303 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 391008001304 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 391008001305 motif II; other site 391008001306 TonB-dependent vitamin B12 receptor; Region: TonB-B12; TIGR01779 391008001307 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 391008001308 N-terminal plug; other site 391008001309 ligand-binding site [chemical binding]; other site 391008001310 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; cl11399 391008001311 catalytic core [active] 391008001312 TfoX C-terminal domain; Region: TfoX_C; pfam04994 391008001313 GAF domain-containing protein [Signal transduction mechanisms]; Region: COG1956 391008001314 GAF domain; Region: GAF_2; pfam13185 391008001315 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 391008001316 AAA domain; Region: AAA_26; pfam13500 391008001317 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 391008001318 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 391008001319 DNA-binding site [nucleotide binding]; DNA binding site 391008001320 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 391008001321 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008001322 homodimer interface [polypeptide binding]; other site 391008001323 catalytic residue [active] 391008001324 methionine sulfoxide reductase A; Provisional; Region: PRK13014 391008001325 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 391008001326 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 391008001327 TlpA-like family, DipZ-like subfamily; composed uncharacterized proteins containing a TlpA-like TRX domain. Some members show domain architectures similar to that of E. coli DipZ protein (also known as DsbD). The only eukaryotic members of the TlpA...; Region: TlpA_like_DipZ_like; cd03012 391008001328 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 391008001329 catalytic residues [active] 391008001330 methionine sulfoxide reductase B; Provisional; Region: PRK00222 391008001331 SelR domain; Region: SelR; pfam01641 391008001332 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391008001333 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 391008001334 active site 391008001335 phosphorylation site [posttranslational modification] 391008001336 intermolecular recognition site; other site 391008001337 dimerization interface [polypeptide binding]; other site 391008001338 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008001339 DNA binding site [nucleotide binding] 391008001340 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008001341 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008001342 dimer interface [polypeptide binding]; other site 391008001343 phosphorylation site [posttranslational modification] 391008001344 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 391008001345 ATP binding site [chemical binding]; other site 391008001346 Mg2+ binding site [ion binding]; other site 391008001347 G-X-G motif; other site 391008001348 sensor protein RstB; Provisional; Region: PRK10604 391008001349 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 391008001350 dimerization interface [polypeptide binding]; other site 391008001351 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008001352 dimer interface [polypeptide binding]; other site 391008001353 phosphorylation site [posttranslational modification] 391008001354 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 391008001355 ATP binding site [chemical binding]; other site 391008001356 G-X-G motif; other site 391008001357 DNA-binding transcriptional regulator RstA; Provisional; Region: PRK10701 391008001358 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 391008001359 active site 391008001360 phosphorylation site [posttranslational modification] 391008001361 intermolecular recognition site; other site 391008001362 dimerization interface [polypeptide binding]; other site 391008001363 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008001364 DNA binding site [nucleotide binding] 391008001365 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 391008001366 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 391008001367 active site 391008001368 dimer interface [polypeptide binding]; other site 391008001369 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 391008001370 Ligand Binding Site [chemical binding]; other site 391008001371 Molecular Tunnel; other site 391008001372 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 391008001373 active site 391008001374 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008001375 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 391008001376 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008001377 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 391008001378 Peptidase M14-like domain; uncharacterized subgroup; Region: M14-like_1_1; cd06238 391008001379 putative active site [active] 391008001380 Zn binding site [ion binding]; other site 391008001381 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 391008001382 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 391008001383 Transposase; Region: DEDD_Tnp_IS110; pfam01548 391008001384 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 391008001385 dinuclear metal binding motif [ion binding]; other site 391008001386 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 391008001387 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 391008001388 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 391008001389 ATP binding site [chemical binding]; other site 391008001390 Mg++ binding site [ion binding]; other site 391008001391 motif III; other site 391008001392 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 391008001393 nucleotide binding region [chemical binding]; other site 391008001394 ATP-binding site [chemical binding]; other site 391008001395 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 391008001396 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 391008001397 maleylacetoacetate isomerase; Region: maiA; TIGR01262 391008001398 GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Zeta; cd03042 391008001399 C-terminal domain interface [polypeptide binding]; other site 391008001400 GSH binding site (G-site) [chemical binding]; other site 391008001401 putative dimer interface [polypeptide binding]; other site 391008001402 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 391008001403 dimer interface [polypeptide binding]; other site 391008001404 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 391008001405 N-terminal domain interface [polypeptide binding]; other site 391008001406 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 391008001407 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 391008001408 ATP binding site [chemical binding]; other site 391008001409 Walker B motif; other site 391008001410 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 391008001411 Protein of unknown function (DUF465); Region: DUF465; pfam04325 391008001412 cystathionine beta-synthase; Region: cysta_beta; TIGR01137 391008001413 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 391008001414 dimer interface [polypeptide binding]; other site 391008001415 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008001416 catalytic residue [active] 391008001417 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the pyridoxal-phosphate (PALP) dependent enzyme domain upstream. The vitamin B6 complex comprises pyridoxine, pyridoxal, and pyridoxamine, as well...; Region: CBS_pair_PALP_assoc2; cd04609 391008001418 Cys/Met metabolism PLP-dependent enzyme; Region: Cys_Met_Meta_PP; pfam01053 391008001419 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 391008001420 homodimer interface [polypeptide binding]; other site 391008001421 substrate-cofactor binding pocket; other site 391008001422 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008001423 catalytic residue [active] 391008001424 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 391008001425 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 391008001426 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 391008001427 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 391008001428 Walker A/P-loop; other site 391008001429 ATP binding site [chemical binding]; other site 391008001430 Q-loop/lid; other site 391008001431 ABC transporter signature motif; other site 391008001432 Walker B; other site 391008001433 D-loop; other site 391008001434 H-loop/switch region; other site 391008001435 Methyltransferase domain; Region: Methyltransf_31; pfam13847 391008001436 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 391008001437 S-adenosylmethionine binding site [chemical binding]; other site 391008001438 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 391008001439 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 391008001440 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 391008001441 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 391008001442 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 391008001443 active site 391008001444 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 391008001445 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 391008001446 active site 391008001447 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 391008001448 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 391008001449 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 391008001450 NAD binding site [chemical binding]; other site 391008001451 homodimer interface [polypeptide binding]; other site 391008001452 active site 391008001453 substrate binding site [chemical binding]; other site 391008001454 GtrA-like protein; Region: GtrA; pfam04138 391008001455 short chain dehydrogenase; Provisional; Region: PRK07102 391008001456 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 391008001457 NAD(P) binding site [chemical binding]; other site 391008001458 active site 391008001459 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 391008001460 FAD binding domain; Region: FAD_binding_4; pfam01565 391008001461 hypothetical protein; Validated; Region: PRK08238 391008001462 haloacid dehalogenase-like hydrolase; Region: HAD; pfam12710 391008001463 phosphoribose diphosphate:decaprenyl-phosphate phosphoribosyltransferase; Provisional; Region: PRK12324 391008001464 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 391008001465 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 391008001466 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 391008001467 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 391008001468 Ligand binding site [chemical binding]; other site 391008001469 Electron transfer flavoprotein domain; Region: ETF; pfam01012 391008001470 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 391008001471 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 391008001472 NAD binding site [chemical binding]; other site 391008001473 substrate binding site [chemical binding]; other site 391008001474 homodimer interface [polypeptide binding]; other site 391008001475 active site 391008001476 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 391008001477 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 391008001478 substrate binding site; other site 391008001479 tetramer interface; other site 391008001480 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; cl17405 391008001481 dTDP-4-dehydrorhamnose reductase; Region: rmlD; TIGR01214 391008001482 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 391008001483 NADP binding site [chemical binding]; other site 391008001484 active site 391008001485 putative substrate binding site [chemical binding]; other site 391008001486 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 391008001487 Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In...; Region: GFAT; cd00714 391008001488 glutaminase active site [active] 391008001489 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 391008001490 dimer interface [polypeptide binding]; other site 391008001491 active site 391008001492 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 391008001493 dimer interface [polypeptide binding]; other site 391008001494 active site 391008001495 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 391008001496 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 391008001497 Substrate binding site; other site 391008001498 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 391008001499 phosphomannomutase CpsG; Provisional; Region: PRK15414 391008001500 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 391008001501 active site 391008001502 substrate binding site [chemical binding]; other site 391008001503 metal binding site [ion binding]; metal-binding site 391008001504 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 391008001505 UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs; Region: UGD_SDR_e; cd05230 391008001506 NAD binding site [chemical binding]; other site 391008001507 putative substrate binding site 2 [chemical binding]; other site 391008001508 putative substrate binding site 1 [chemical binding]; other site 391008001509 active site 391008001510 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 391008001511 active site 391008001512 Predicted membrane protein [Function unknown]; Region: COG2246 391008001513 GtrA-like protein; Region: GtrA; pfam04138 391008001514 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 391008001515 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 391008001516 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 391008001517 ATP binding site [chemical binding]; other site 391008001518 putative Mg++ binding site [ion binding]; other site 391008001519 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 391008001520 nucleotide binding region [chemical binding]; other site 391008001521 ATP-binding site [chemical binding]; other site 391008001522 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 391008001523 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 391008001524 Glycosyl hydrolase family 99-like domain of WbsX-like glycosyltransferases; Region: Glyco_tran_WbsX; cd11579 391008001525 putative ligand binding site [chemical binding]; other site 391008001526 putative catalytic site [active] 391008001527 Lipopolysaccharide biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: RgpF; COG3754 391008001528 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_2; pfam13532 391008001529 Protein of unknown function (DUF330); Region: DUF330; cl01135 391008001530 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 391008001531 mce related protein; Region: MCE; pfam02470 391008001532 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 391008001533 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 391008001534 Walker A/P-loop; other site 391008001535 ATP binding site [chemical binding]; other site 391008001536 Q-loop/lid; other site 391008001537 ABC transporter signature motif; other site 391008001538 Walker B; other site 391008001539 D-loop; other site 391008001540 H-loop/switch region; other site 391008001541 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 391008001542 Permease; Region: Permease; pfam02405 391008001543 Uncharacterized conserved protein [Function unknown]; Region: COG2966 391008001544 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 391008001545 Protein of unknown function (DUF3815); Region: DUF3815; cl01118 391008001546 H-NS histone family; Region: Histone_HNS; pfam00816 391008001547 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 391008001548 prolyl-tRNA synthetase; Provisional; Region: PRK09194 391008001549 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_prok; cd00779 391008001550 dimer interface [polypeptide binding]; other site 391008001551 motif 1; other site 391008001552 active site 391008001553 motif 2; other site 391008001554 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and...; Region: ProRS-INS; cd04334 391008001555 putative deacylase active site [active] 391008001556 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 391008001557 active site 391008001558 motif 3; other site 391008001559 ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding; Region: ProRS_anticodon_short; cd00861 391008001560 anticodon binding site; other site 391008001561 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 391008001562 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 391008001563 CDP-diacylglycerol--serine O-phosphatidyltransferase; Region: pssA; TIGR00473 391008001564 DNA polymerase III psi subunit; Region: DNA_III_psi; cl11436 391008001565 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 391008001566 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391008001567 Coenzyme A binding pocket [chemical binding]; other site 391008001568 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 391008001569 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 391008001570 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 391008001571 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 391008001572 active site 391008001573 HIGH motif; other site 391008001574 nucleotide binding site [chemical binding]; other site 391008001575 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 391008001576 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 391008001577 active site 391008001578 KMSKS motif; other site 391008001579 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 391008001580 tRNA binding surface [nucleotide binding]; other site 391008001581 anticodon binding site; other site 391008001582 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 391008001583 DNA polymerase III subunit chi; Validated; Region: PRK05728 391008001584 multifunctional aminopeptidase A; Provisional; Region: PRK00913 391008001585 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 391008001586 interface (dimer of trimers) [polypeptide binding]; other site 391008001587 Substrate-binding/catalytic site; other site 391008001588 Zn-binding sites [ion binding]; other site 391008001589 Predicted permeases [General function prediction only]; Region: COG0795 391008001590 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 391008001591 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 391008001592 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 391008001593 RDD family; Region: RDD; pfam06271 391008001594 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 391008001595 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 391008001596 active site 391008001597 DNA binding site [nucleotide binding] 391008001598 Int/Topo IB signature motif; other site 391008001599 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 391008001600 dimerization domain [polypeptide binding]; other site 391008001601 dimer interface [polypeptide binding]; other site 391008001602 catalytic residues [active] 391008001603 chitin-binding domain of Chi A1-like proteins; Region: ChiA1_BD; cd12214 391008001604 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 391008001605 Interdomain contacts; other site 391008001606 Glyco_18 domain; Region: Glyco_18; smart00636 391008001607 The GH18 (glycosyl hydrolases, family 18) type II chitinases hydrolyze chitin, an abundant polymer of N-acetylglucosamine and have been identified in bacteria, fungi, insects, plants, viruses, and protozoan parasites. The structure of this domain is an...; Region: GH18_chitinase; cd06548 391008001608 active site 391008001609 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 391008001610 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 391008001611 dimerization interface [polypeptide binding]; other site 391008001612 ATP binding site [chemical binding]; other site 391008001613 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), second repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP; Region: PurL_repeat2; cd02204 391008001614 dimerization interface [polypeptide binding]; other site 391008001615 ATP binding site [chemical binding]; other site 391008001616 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 391008001617 putative active site [active] 391008001618 catalytic triad [active] 391008001619 Left-handed beta-roll, including virulence factors and various other proteins; Region: LbR-like; cl17507 391008001620 trimer interface [polypeptide binding]; other site 391008001621 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 391008001622 trimer interface [polypeptide binding]; other site 391008001623 Left-handed beta-roll, including virulence factors and various other proteins; Region: LbR-like; cl17507 391008001624 trimer interface [polypeptide binding]; other site 391008001625 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 391008001626 trimer interface [polypeptide binding]; other site 391008001627 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 391008001628 trimer interface [polypeptide binding]; other site 391008001629 Haemagglutinin; Region: HIM; pfam05662 391008001630 Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones]; Region: AprE; COG1404 391008001631 Peptidase S8 family domain, uncharacterized subfamily 13; Region: Peptidases_S8_13; cd07496 391008001632 active site 391008001633 catalytic triad [active] 391008001634 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 391008001635 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 391008001636 type II secretion system protein E; Region: type_II_gspE; TIGR02533 391008001637 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 391008001638 Walker A motif; other site 391008001639 ATP binding site [chemical binding]; other site 391008001640 Walker B motif; other site 391008001641 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 391008001642 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 391008001643 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 391008001644 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 391008001645 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 391008001646 general secretion pathway protein J; Validated; Region: PRK08808 391008001647 Type II secretory pathway, component PulK [Intracellular trafficking and secretion]; Region: PulK; COG3156 391008001648 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 391008001649 Type II secretion system (T2SS), protein M subtype b; Region: T2SM_b; pfam10741 391008001650 type II secretion system protein D; Region: type_II_gspD; TIGR02517 391008001651 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 391008001652 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 391008001653 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 391008001654 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 391008001655 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 391008001656 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 391008001657 Probable Catalytic site; other site 391008001658 metal-binding site 391008001659 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 391008001660 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 391008001661 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 391008001662 active site 391008001663 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 391008001664 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 391008001665 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 391008001666 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 391008001667 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 391008001668 PapC N-terminal domain; Region: PapC_N; pfam13954 391008001669 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 391008001670 PapC C-terminal domain; Region: PapC_C; pfam13953 391008001671 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 391008001672 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 391008001673 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 391008001674 active site 391008001675 homodimer interface [polypeptide binding]; other site 391008001676 Bacterial cellulose synthase subunit; Region: BcsB; cl15851 391008001677 bacteriophage N4 adsorption protein B; Provisional; Region: nfrB; PRK15489 391008001678 active site 391008001679 Glycosyl transferase family group 2; Region: Glyco_trans_2_3; pfam13632 391008001680 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 391008001681 Bacteriophage N adsorption protein A C-term; Region: NfrA_C; pfam13283 391008001682 hypothetical protein; Provisional; Region: PRK09936 391008001683 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 391008001684 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 391008001685 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 391008001686 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 391008001687 ABC transporter; Region: ABC_tran_2; pfam12848 391008001688 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 391008001689 Domain of unknown function (DUF3315); Region: DUF3315; pfam11776 391008001690 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 391008001691 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl...; Region: SHMT; cd00378 391008001692 dimer interface [polypeptide binding]; other site 391008001693 active site 391008001694 glycine-pyridoxal phosphate binding site [chemical binding]; other site 391008001695 folate binding site [chemical binding]; other site 391008001696 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 391008001697 ATP cone domain; Region: ATP-cone; pfam03477 391008001698 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 391008001699 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 391008001700 catalytic motif [active] 391008001701 Zn binding site [ion binding]; other site 391008001702 RibD C-terminal domain; Region: RibD_C; pfam01872 391008001703 sulfation-dependent quorum factor, Ax21 family; Region: Y_sulf_Ax21; TIGR04273 391008001704 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 391008001705 Lumazine binding domain; Region: Lum_binding; pfam00677 391008001706 Lumazine binding domain; Region: Lum_binding; pfam00677 391008001707 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 391008001708 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 391008001709 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 391008001710 dimerization interface [polypeptide binding]; other site 391008001711 active site 391008001712 lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-I; Region: Lumazine_synthase-I; cd09209 391008001713 homopentamer interface [polypeptide binding]; other site 391008001714 active site 391008001715 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 391008001716 putative RNA binding site [nucleotide binding]; other site 391008001717 thiamine monophosphate kinase; Provisional; Region: PRK05731 391008001718 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 391008001719 ATP binding site [chemical binding]; other site 391008001720 dimerization interface [polypeptide binding]; other site 391008001721 FAD binding domain; Region: FAD_binding_4; pfam01565 391008001722 glycolate oxidase, subunit GlcD; Region: glcD; TIGR00387 391008001723 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; pfam04307 391008001724 hypothetical protein; Reviewed; Region: PRK12497 391008001725 LppC putative lipoprotein; Region: LppC; pfam04348 391008001726 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 391008001727 putative ligand binding site [chemical binding]; other site 391008001728 Predicted methyltransferases [General function prediction only]; Region: COG0313 391008001729 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 391008001730 putative SAM binding site [chemical binding]; other site 391008001731 putative homodimer interface [polypeptide binding]; other site 391008001732 Electron transfer DM13; Region: DM13; pfam10517 391008001733 NRDE protein; Region: NRDE; pfam05742 391008001734 cell division protein MraZ; Reviewed; Region: PRK00326 391008001735 MraZ protein; Region: MraZ; pfam02381 391008001736 MraZ protein; Region: MraZ; pfam02381 391008001737 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 391008001738 MraW methylase family; Region: Methyltransf_5; cl17771 391008001739 Cell division protein FtsL; Region: FtsL; pfam04999 391008001740 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 391008001741 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 391008001742 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 391008001743 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 391008001744 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 391008001745 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 391008001746 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 391008001747 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 391008001748 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 391008001749 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 391008001750 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 391008001751 Phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) is an enzyme responsible for the formation of the first lipid intermediate in the synthesis of bacterial cell wall peptidoglycan. It catalyzes the formation of...; Region: GT_MraY; cd06852 391008001752 Mg++ binding site [ion binding]; other site 391008001753 putative catalytic motif [active] 391008001754 putative substrate binding site [chemical binding]; other site 391008001755 cell division protein FtsW; Region: ftsW; TIGR02614 391008001756 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 391008001757 MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide...; Region: GT1_MurG; cd03785 391008001758 active site 391008001759 homodimer interface [polypeptide binding]; other site 391008001760 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 391008001761 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 391008001762 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 391008001763 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 391008001764 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 391008001765 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 391008001766 ATP-grasp domain; Region: ATP-grasp_4; cl17255 391008001767 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 391008001768 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 391008001769 Cell division protein FtsQ; Region: FtsQ; pfam03799 391008001770 cell division protein FtsA; Region: ftsA; TIGR01174 391008001771 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 391008001772 nucleotide binding site [chemical binding]; other site 391008001773 SHS2 domain inserted in FTSA; Region: SHS2_FTSA; pfam02491 391008001774 Cell division protein FtsA; Region: FtsA; pfam14450 391008001775 cell division protein FtsZ; Validated; Region: PRK09330 391008001776 FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at...; Region: FtsZ_type1; cd02201 391008001777 nucleotide binding site [chemical binding]; other site 391008001778 SulA interaction site; other site 391008001779 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 391008001780 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 391008001781 Protein of unknown function (DUF721); Region: DUF721; cl02324 391008001782 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 391008001783 Peptidase family M23; Region: Peptidase_M23; pfam01551 391008001784 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 391008001785 DEAD/DEAH box helicase; Region: DEAD; pfam00270 391008001786 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 391008001787 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cl17351 391008001788 nucleotide binding region [chemical binding]; other site 391008001789 ATP-binding site [chemical binding]; other site 391008001790 SEC-C motif; Region: SEC-C; pfam02810 391008001791 hypothetical protein; Provisional; Region: PRK08999 391008001792 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 391008001793 active site 391008001794 8-oxo-dGMP binding site [chemical binding]; other site 391008001795 nudix motif; other site 391008001796 metal binding site [ion binding]; metal-binding site 391008001797 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 391008001798 thiamine phosphate binding site [chemical binding]; other site 391008001799 active site 391008001800 pyrophosphate binding site [ion binding]; other site 391008001801 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 391008001802 Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase...; Region: MTHFR; cd00537 391008001803 FAD binding site [chemical binding]; other site 391008001804 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 391008001805 Histidine kinase; Region: His_kinase; pfam06580 391008001806 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 391008001807 ATP binding site [chemical binding]; other site 391008001808 Mg2+ binding site [ion binding]; other site 391008001809 G-X-G motif; other site 391008001810 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 391008001811 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 391008001812 active site 391008001813 phosphorylation site [posttranslational modification] 391008001814 intermolecular recognition site; other site 391008001815 dimerization interface [polypeptide binding]; other site 391008001816 LytTr DNA-binding domain; Region: LytTR; smart00850 391008001817 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 391008001818 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 391008001819 Amidohydrolase; Region: Amidohydro_4; pfam13147 391008001820 active site 391008001821 HAMP domain; Region: HAMP; pfam00672 391008001822 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008001823 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008001824 dimer interface [polypeptide binding]; other site 391008001825 phosphorylation site [posttranslational modification] 391008001826 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 391008001827 ATP binding site [chemical binding]; other site 391008001828 Mg2+ binding site [ion binding]; other site 391008001829 G-X-G motif; other site 391008001830 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391008001831 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 391008001832 active site 391008001833 phosphorylation site [posttranslational modification] 391008001834 intermolecular recognition site; other site 391008001835 dimerization interface [polypeptide binding]; other site 391008001836 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008001837 DNA binding site [nucleotide binding] 391008001838 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein; Region: GATase1_Hsp31_like; cd03141 391008001839 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 391008001840 potential catalytic triad [active] 391008001841 conserved cys residue [active] 391008001842 Protein of unknown function (DUF3228); Region: DUF3228; pfam11539 391008001843 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 391008001844 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 391008001845 putative deacylase active site [active] 391008001846 Adenosylhomocysteinase; Provisional; Region: PTZ00075 391008001847 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 391008001848 homotetramer interface [polypeptide binding]; other site 391008001849 ligand binding site [chemical binding]; other site 391008001850 catalytic site [active] 391008001851 NAD binding site [chemical binding]; other site 391008001852 X-Pro dipeptidyl-peptidase (S15 family); Region: Peptidase_S15; pfam02129 391008001853 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 391008001854 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 391008001855 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 391008001856 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 391008001857 S-adenosylmethionine synthetase; Validated; Region: PRK05250 391008001858 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 391008001859 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 391008001860 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 391008001861 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 391008001862 putative acyl-acceptor binding pocket; other site 391008001863 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; pfam13444 391008001864 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 391008001865 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 391008001866 putative active site [active] 391008001867 putative metal binding site [ion binding]; other site 391008001868 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; pfam04307 391008001869 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 391008001870 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 391008001871 Ligand binding site; other site 391008001872 Putative Catalytic site; other site 391008001873 DXD motif; other site 391008001874 hypothetical protein; Provisional; Region: PRK08317 391008001875 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 391008001876 S-adenosylmethionine binding site [chemical binding]; other site 391008001877 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 391008001878 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 391008001879 FMN binding site [chemical binding]; other site 391008001880 active site 391008001881 catalytic residues [active] 391008001882 substrate binding site [chemical binding]; other site 391008001883 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008001884 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008001885 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_6; cd08475 391008001886 putative effector binding pocket; other site 391008001887 putative dimerization interface [polypeptide binding]; other site 391008001888 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 391008001889 Major Facilitator Superfamily; Region: MFS_1; pfam07690 391008001890 putative substrate translocation pore; other site 391008001891 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides...; Region: ribokinase; cd01174 391008001892 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 391008001893 substrate binding site [chemical binding]; other site 391008001894 dimer interface [polypeptide binding]; other site 391008001895 ATP binding site [chemical binding]; other site 391008001896 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 391008001897 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 391008001898 Nucleoside recognition; Region: Gate; pfam07670 391008001899 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 391008001900 voltage-dependent potassium channel beta subunit, animal; Region: Kv_beta; TIGR01293 391008001901 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 391008001902 active site 391008001903 catalytic tetrad [active] 391008001904 Hemin uptake protein hemP; Region: hemP; pfam10636 391008001905 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 391008001906 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 391008001907 N-terminal plug; other site 391008001908 ligand-binding site [chemical binding]; other site 391008001909 Putative heme degradation protein [Inorganic ion transport and metabolism]; Region: HemS; COG3720 391008001910 FtsX-like permease family; Region: FtsX; pfam02687 391008001911 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 391008001912 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 391008001913 Walker A/P-loop; other site 391008001914 ATP binding site [chemical binding]; other site 391008001915 Q-loop/lid; other site 391008001916 ABC transporter signature motif; other site 391008001917 Walker B; other site 391008001918 D-loop; other site 391008001919 H-loop/switch region; other site 391008001920 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 391008001921 active site 391008001922 catalytic triad [active] 391008001923 oxyanion hole [active] 391008001924 switch loop; other site 391008001925 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391008001926 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 391008001927 active site 391008001928 phosphorylation site [posttranslational modification] 391008001929 intermolecular recognition site; other site 391008001930 dimerization interface [polypeptide binding]; other site 391008001931 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008001932 DNA binding site [nucleotide binding] 391008001933 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008001934 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008001935 dimer interface [polypeptide binding]; other site 391008001936 phosphorylation site [posttranslational modification] 391008001937 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 391008001938 ATP binding site [chemical binding]; other site 391008001939 Mg2+ binding site [ion binding]; other site 391008001940 G-X-G motif; other site 391008001941 Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase_like_7; cd04502 391008001942 active site 391008001943 catalytic triad [active] 391008001944 oxyanion hole [active] 391008001945 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 391008001946 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 391008001947 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 391008001948 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 391008001949 putative substrate translocation pore; other site 391008001950 LemA family; Region: LemA; pfam04011 391008001951 Repair protein; Region: Repair_PSII; pfam04536 391008001952 Repair protein; Region: Repair_PSII; pfam04536 391008001953 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 391008001954 thymidylate synthase; Reviewed; Region: thyA; PRK01827 391008001955 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 391008001956 dimerization interface [polypeptide binding]; other site 391008001957 active site 391008001958 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 391008001959 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cd00209 391008001960 folate binding site [chemical binding]; other site 391008001961 NADP+ binding site [chemical binding]; other site 391008001962 Domain of unknown function (DUF1287); Region: DUF1287; pfam06940 391008001963 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 391008001964 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 391008001965 active site 391008001966 metal binding site [ion binding]; metal-binding site 391008001967 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 391008001968 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 391008001969 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 391008001970 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed; Region: pdxA; PRK00232 391008001971 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 391008001972 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 391008001973 SurA N-terminal domain; Region: SurA_N; pfam09312 391008001974 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 391008001975 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 391008001976 organic solvent tolerance protein; Provisional; Region: PRK04423 391008001977 Organic solvent tolerance protein; Region: OstA_C; pfam04453 391008001978 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 391008001979 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII_2; cd11599 391008001980 putative active site [active] 391008001981 Zn binding site [ion binding]; other site 391008001982 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 391008001983 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK05732 391008001984 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 391008001985 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Validated; Region: PRK08773 391008001986 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 391008001987 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 391008001988 EF-hand domain pair; Region: EF_hand_5; pfam13499 391008001989 pseudo EF-hand loop; other site 391008001990 peptide binding pocket; other site 391008001991 Ca2+ binding site [ion binding]; other site 391008001992 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional; Region: PRK11760 391008001993 FtsJ-like methyltransferase; Region: FtsJ; cl17430 391008001994 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 391008001995 nucleoside/Zn binding site; other site 391008001996 dimer interface [polypeptide binding]; other site 391008001997 catalytic motif [active] 391008001998 The Tellurite-resistance/Dicarboxylate Transporter (TDT) family; Region: TDT; cl04176 391008001999 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 391008002000 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 391008002001 active site 391008002002 HIGH motif; other site 391008002003 nucleotide binding site [chemical binding]; other site 391008002004 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 391008002005 active site 391008002006 KMSKS motif; other site 391008002007 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 391008002008 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 391008002009 methionine sulfoxide reductase A; Provisional; Region: PRK00058 391008002010 transaldolase-like protein; Provisional; Region: PTZ00411 391008002011 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 391008002012 active site 391008002013 dimer interface [polypeptide binding]; other site 391008002014 catalytic residue [active] 391008002015 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 391008002016 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 391008002017 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 391008002018 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008002019 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 391008002020 dimerization interface [polypeptide binding]; other site 391008002021 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 391008002022 Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the reduction...; Region: AhpF_NTD_N; cd02974 391008002023 catalytic residue [active] 391008002024 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 391008002025 catalytic residues [active] 391008002026 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 391008002027 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 391008002028 peroxiredoxin; Region: AhpC; TIGR03137 391008002029 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 391008002030 dimer interface [polypeptide binding]; other site 391008002031 decamer (pentamer of dimers) interface [polypeptide binding]; other site 391008002032 catalytic triad [active] 391008002033 peroxidatic and resolving cysteines [active] 391008002034 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 391008002035 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 391008002036 S-adenosylmethionine binding site [chemical binding]; other site 391008002037 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 391008002038 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008002039 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008002040 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 391008002041 putative effector binding pocket; other site 391008002042 dimerization interface [polypeptide binding]; other site 391008002043 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 391008002044 N-formylglutamate amidohydrolase; Region: FGase; cl01522 391008002045 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+; Region: ADPRase_NUDT5; cd03424 391008002046 ADP-ribose binding site [chemical binding]; other site 391008002047 dimer interface [polypeptide binding]; other site 391008002048 active site 391008002049 nudix motif; other site 391008002050 metal binding site [ion binding]; metal-binding site 391008002051 5'-3' exonuclease; Region: 53EXOc; smart00475 391008002052 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 391008002053 active site 391008002054 metal binding site 1 [ion binding]; metal-binding site 391008002055 putative 5' ssDNA interaction site; other site 391008002056 metal binding site 3; metal-binding site 391008002057 metal binding site 2 [ion binding]; metal-binding site 391008002058 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 391008002059 putative DNA binding site [nucleotide binding]; other site 391008002060 putative metal binding site [ion binding]; other site 391008002061 Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a...; Region: Arsenite_oxidase; cd02135 391008002062 putative FMN binding site [chemical binding]; other site 391008002063 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 391008002064 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 391008002065 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 391008002066 ligand binding site [chemical binding]; other site 391008002067 homodimer interface [polypeptide binding]; other site 391008002068 NAD(P) binding site [chemical binding]; other site 391008002069 trimer interface B [polypeptide binding]; other site 391008002070 trimer interface A [polypeptide binding]; other site 391008002071 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 391008002072 RNA polymerase factor sigma-70; Validated; Region: PRK09047 391008002073 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 391008002074 DNA binding residues [nucleotide binding] 391008002075 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 391008002076 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 391008002077 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 391008002078 probable FeS assembly SUF system protein SufT; Region: FeS_long_SufT; TIGR03406 391008002079 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 391008002080 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and...; Region: BCAT_beta_family; cd01557 391008002081 homodimer interface [polypeptide binding]; other site 391008002082 substrate-cofactor binding pocket; other site 391008002083 catalytic residue [active] 391008002084 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 391008002085 Winged helix DNA-binding domain; Region: HTH_34; pfam13601 391008002086 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 391008002087 Peptidase family M23; Region: Peptidase_M23; pfam01551 391008002088 Peptidase inhibitor I9; Region: Inhibitor_I9; pfam05922 391008002089 Peptidase S8 family domain, uncharacterized subfamily 13; Region: Peptidases_S8_13; cd07496 391008002090 active site 391008002091 catalytic triad [active] 391008002092 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 391008002093 Bacterial L-asparaginases and related enzymes; Region: L-asparaginase_like; cl00216 391008002094 active site 391008002095 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 391008002096 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 391008002097 ribonuclease BN/unknown domain fusion protein; Reviewed; Region: rbn; PRK04214 391008002098 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 391008002099 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 391008002100 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 391008002101 catalytic residues [active] 391008002102 polyphosphate kinase 2, PA0141 family; Region: PPK2_P_aer; TIGR03707 391008002103 leucine-zipper of insertion element IS481; Region: LZ_Tnp_IS481; pfam13011 391008002104 Winged helix-turn helix; Region: HTH_29; pfam13551 391008002105 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 391008002106 Integrase core domain; Region: rve; pfam00665 391008002107 Integrase core domain; Region: rve_3; pfam13683 391008002108 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 391008002109 binding surface 391008002110 Tetratricopeptide repeat; Region: TPR_16; pfam13432 391008002111 TPR motif; other site 391008002112 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 391008002113 peptide chain release factor 1; Validated; Region: prfA; PRK00591 391008002114 This domain is found in peptide chain release factors; Region: PCRF; smart00937 391008002115 RF-1 domain; Region: RF-1; pfam00472 391008002116 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 391008002117 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 391008002118 tRNA; other site 391008002119 putative tRNA binding site [nucleotide binding]; other site 391008002120 putative NADP binding site [chemical binding]; other site 391008002121 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 391008002122 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 391008002123 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 391008002124 TPR motif; other site 391008002125 binding surface 391008002126 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 391008002127 binding surface 391008002128 TPR motif; other site 391008002129 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 391008002130 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 391008002131 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 391008002132 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 391008002133 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK04923 391008002134 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 391008002135 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 391008002136 active site 391008002137 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 391008002138 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 391008002139 5S rRNA interface [nucleotide binding]; other site 391008002140 CTC domain interface [polypeptide binding]; other site 391008002141 L16 interface [polypeptide binding]; other site 391008002142 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 391008002143 putative active site [active] 391008002144 catalytic residue [active] 391008002145 GTP-binding protein YchF; Reviewed; Region: PRK09601 391008002146 YchF GTPase; Region: YchF; cd01900 391008002147 G1 box; other site 391008002148 GTP/Mg2+ binding site [chemical binding]; other site 391008002149 Switch I region; other site 391008002150 G2 box; other site 391008002151 Switch II region; other site 391008002152 G3 box; other site 391008002153 G4 box; other site 391008002154 G5 box; other site 391008002155 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 391008002156 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_19; cd07262 391008002157 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 391008002158 Autotransporter beta-domain; Region: Autotransporter; pfam03797 391008002159 transcriptional regulator RcsB; Provisional; Region: PRK10840 391008002160 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 391008002161 active site 391008002162 phosphorylation site [posttranslational modification] 391008002163 intermolecular recognition site; other site 391008002164 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 391008002165 DNA binding residues [nucleotide binding] 391008002166 dimerization interface [polypeptide binding]; other site 391008002167 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008002168 dimer interface [polypeptide binding]; other site 391008002169 phosphorylation site [posttranslational modification] 391008002170 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 391008002171 ATP binding site [chemical binding]; other site 391008002172 Mg2+ binding site [ion binding]; other site 391008002173 G-X-G motif; other site 391008002174 Response regulator receiver domain; Region: Response_reg; pfam00072 391008002175 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 391008002176 active site 391008002177 phosphorylation site [posttranslational modification] 391008002178 intermolecular recognition site; other site 391008002179 dimerization interface [polypeptide binding]; other site 391008002180 FOG: HPt domain [Signal transduction mechanisms]; Region: ArcB; COG2198 391008002181 putative binding surface; other site 391008002182 active site 391008002183 Response regulator receiver domain; Region: Response_reg; pfam00072 391008002184 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 391008002185 active site 391008002186 phosphorylation site [posttranslational modification] 391008002187 intermolecular recognition site; other site 391008002188 dimerization interface [polypeptide binding]; other site 391008002189 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 391008002190 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008002191 dimer interface [polypeptide binding]; other site 391008002192 phosphorylation site [posttranslational modification] 391008002193 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 391008002194 ATP binding site [chemical binding]; other site 391008002195 Mg2+ binding site [ion binding]; other site 391008002196 G-X-G motif; other site 391008002197 Response regulator receiver domain; Region: Response_reg; pfam00072 391008002198 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 391008002199 active site 391008002200 phosphorylation site [posttranslational modification] 391008002201 intermolecular recognition site; other site 391008002202 dimerization interface [polypeptide binding]; other site 391008002203 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008002204 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 391008002205 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008002206 Type 1 glutamine amidotransferase (GATase1)-like domain found in cyanophycinase; Region: GAT1_cyanophycinase; cd03145 391008002207 proposed catalytic triad [active] 391008002208 active site nucleophile [active] 391008002209 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 391008002210 catalytic nucleophile [active] 391008002211 elongation factor Tu; Reviewed; Region: PRK00049 391008002212 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 391008002213 G1 box; other site 391008002214 GEF interaction site [polypeptide binding]; other site 391008002215 GTP/Mg2+ binding site [chemical binding]; other site 391008002216 Switch I region; other site 391008002217 G2 box; other site 391008002218 G3 box; other site 391008002219 Switch II region; other site 391008002220 G4 box; other site 391008002221 G5 box; other site 391008002222 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 391008002223 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 391008002224 Antibiotic Binding Site [chemical binding]; other site 391008002225 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 391008002226 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 391008002227 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 391008002228 putative homodimer interface [polypeptide binding]; other site 391008002229 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 391008002230 heterodimer interface [polypeptide binding]; other site 391008002231 homodimer interface [polypeptide binding]; other site 391008002232 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 391008002233 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 391008002234 23S rRNA interface [nucleotide binding]; other site 391008002235 L7/L12 interface [polypeptide binding]; other site 391008002236 putative thiostrepton binding site; other site 391008002237 L25 interface [polypeptide binding]; other site 391008002238 Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds...; Region: Ribosomal_L1; cd00403 391008002239 mRNA/rRNA interface [nucleotide binding]; other site 391008002240 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein...; Region: Ribosomal_L10; cd05797 391008002241 23S rRNA interface [nucleotide binding]; other site 391008002242 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 391008002243 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 391008002244 core dimer interface [polypeptide binding]; other site 391008002245 peripheral dimer interface [polypeptide binding]; other site 391008002246 L10 interface [polypeptide binding]; other site 391008002247 L11 interface [polypeptide binding]; other site 391008002248 putative EF-Tu interaction site [polypeptide binding]; other site 391008002249 putative EF-G interaction site [polypeptide binding]; other site 391008002250 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 391008002251 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl17585 391008002252 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 391008002253 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 391008002254 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 391008002255 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 391008002256 RPB3 interaction site [polypeptide binding]; other site 391008002257 RPB1 interaction site [polypeptide binding]; other site 391008002258 RPB11 interaction site [polypeptide binding]; other site 391008002259 RPB10 interaction site [polypeptide binding]; other site 391008002260 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 391008002261 DNA-directed RNA polymerase, beta' subunit, predominant form; Region: rpoC_TIGR; TIGR02386 391008002262 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 391008002263 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 391008002264 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 391008002265 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 391008002266 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 391008002267 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 391008002268 DNA binding site [nucleotide binding] 391008002269 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 391008002270 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 391008002271 S17 interaction site [polypeptide binding]; other site 391008002272 S8 interaction site; other site 391008002273 16S rRNA interaction site [nucleotide binding]; other site 391008002274 streptomycin interaction site [chemical binding]; other site 391008002275 23S rRNA interaction site [nucleotide binding]; other site 391008002276 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 391008002277 30S ribosomal protein S7; Validated; Region: PRK05302 391008002278 elongation factor G; Reviewed; Region: PRK00007 391008002279 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 391008002280 G1 box; other site 391008002281 putative GEF interaction site [polypeptide binding]; other site 391008002282 GTP/Mg2+ binding site [chemical binding]; other site 391008002283 Switch I region; other site 391008002284 G2 box; other site 391008002285 G3 box; other site 391008002286 Switch II region; other site 391008002287 G4 box; other site 391008002288 G5 box; other site 391008002289 EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis...; Region: EFG_mtEFG_II; cd04088 391008002290 EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2...; Region: EFG_mtEFG1_IV; cd01434 391008002291 EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2...; Region: EFG_mtEFG_C; cd03713 391008002292 elongation factor Tu; Reviewed; Region: PRK00049 391008002293 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 391008002294 G1 box; other site 391008002295 GEF interaction site [polypeptide binding]; other site 391008002296 GTP/Mg2+ binding site [chemical binding]; other site 391008002297 Switch I region; other site 391008002298 G2 box; other site 391008002299 G3 box; other site 391008002300 Switch II region; other site 391008002301 G4 box; other site 391008002302 G5 box; other site 391008002303 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 391008002304 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 391008002305 Antibiotic Binding Site [chemical binding]; other site 391008002306 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 391008002307 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 391008002308 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 391008002309 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 391008002310 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 391008002311 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 391008002312 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 391008002313 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 391008002314 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 391008002315 putative translocon binding site; other site 391008002316 protein-rRNA interface [nucleotide binding]; other site 391008002317 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 391008002318 K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH...; Region: 30S_S3_KH; cd02412 391008002319 G-X-X-G motif; other site 391008002320 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 391008002321 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 391008002322 23S rRNA interface [nucleotide binding]; other site 391008002323 5S rRNA interface [nucleotide binding]; other site 391008002324 putative antibiotic binding site [chemical binding]; other site 391008002325 L25 interface [polypeptide binding]; other site 391008002326 L27 interface [polypeptide binding]; other site 391008002327 Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it...; Region: Ribosomal_L29_HIP; cd00427 391008002328 putative translocon interaction site; other site 391008002329 23S rRNA interface [nucleotide binding]; other site 391008002330 signal recognition particle (SRP54) interaction site; other site 391008002331 L23 interface [polypeptide binding]; other site 391008002332 trigger factor interaction site; other site 391008002333 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 391008002334 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 391008002335 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 391008002336 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 391008002337 RNA binding site [nucleotide binding]; other site 391008002338 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 391008002339 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 391008002340 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 391008002341 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 391008002342 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 391008002343 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 391008002344 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 391008002345 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 391008002346 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 391008002347 5S rRNA interface [nucleotide binding]; other site 391008002348 23S rRNA interface [nucleotide binding]; other site 391008002349 L5 interface [polypeptide binding]; other site 391008002350 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 391008002351 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 391008002352 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 391008002353 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that...; Region: Ribosomal_L30; cd01658 391008002354 23S rRNA binding site [nucleotide binding]; other site 391008002355 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 391008002356 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 391008002357 SecY translocase; Region: SecY; pfam00344 391008002358 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 391008002359 30S ribosomal protein S13; Region: bact_S13; TIGR03631 391008002360 30S ribosomal protein S11; Validated; Region: PRK05309 391008002361 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 391008002362 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 391008002363 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 391008002364 RNA binding surface [nucleotide binding]; other site 391008002365 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 391008002366 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 391008002367 alphaNTD homodimer interface [polypeptide binding]; other site 391008002368 alphaNTD - beta interaction site [polypeptide binding]; other site 391008002369 alphaNTD - beta' interaction site [polypeptide binding]; other site 391008002370 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 391008002371 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 391008002372 disulfide bond formation protein B; Provisional; Region: PRK04388 391008002373 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008002374 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008002375 Class-II DAHP synthetase family; Region: DAHP_synth_2; pfam01474 391008002376 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 391008002377 Mechanosensitive ion channel; Region: MS_channel; pfam00924 391008002378 amidase; Provisional; Region: PRK08137 391008002379 Amidase; Region: Amidase; cl11426 391008002380 Predicted membrane protein (DUF2127); Region: DUF2127; pfam09900 391008002381 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 391008002382 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 391008002383 G1 box; other site 391008002384 putative GEF interaction site [polypeptide binding]; other site 391008002385 GTP/Mg2+ binding site [chemical binding]; other site 391008002386 Switch I region; other site 391008002387 G2 box; other site 391008002388 G3 box; other site 391008002389 Switch II region; other site 391008002390 G4 box; other site 391008002391 G5 box; other site 391008002392 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 391008002393 BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly...; Region: BipA_TypA_C; cd03710 391008002394 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cd00317 391008002395 active site 391008002396 Phosphoribosylformylglycinamidine (FGAM) synthase; Region: PurS; cl00789 391008002397 malate dehydrogenase; Provisional; Region: PRK05442 391008002398 Chloroplast-like malate dehydrogenases; Region: MDH_choloroplast_like; cd01338 391008002399 NAD(P) binding site [chemical binding]; other site 391008002400 dimer interface [polypeptide binding]; other site 391008002401 malate binding site [chemical binding]; other site 391008002402 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 391008002403 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 391008002404 active site 391008002405 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 391008002406 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 391008002407 acyl-activating enzyme (AAE) consensus motif; other site 391008002408 AMP binding site [chemical binding]; other site 391008002409 active site 391008002410 CoA binding site [chemical binding]; other site 391008002411 Suppressor of fused protein (SUFU); Region: SUFU; pfam05076 391008002412 glutathionine S-transferase; Provisional; Region: PRK10542 391008002413 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 391008002414 C-terminal domain interface [polypeptide binding]; other site 391008002415 GSH binding site (G-site) [chemical binding]; other site 391008002416 dimer interface [polypeptide binding]; other site 391008002417 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 391008002418 dimer interface [polypeptide binding]; other site 391008002419 N-terminal domain interface [polypeptide binding]; other site 391008002420 substrate binding pocket (H-site) [chemical binding]; other site 391008002421 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 391008002422 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 391008002423 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 391008002424 active site 391008002425 FMN binding site [chemical binding]; other site 391008002426 2,4-decadienoyl-CoA binding site; other site 391008002427 catalytic residue [active] 391008002428 4Fe-4S cluster binding site [ion binding]; other site 391008002429 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 391008002430 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 391008002431 Predicted membrane protein [Function unknown]; Region: COG2364 391008002432 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 391008002433 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 391008002434 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 391008002435 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 391008002436 putative NAD(P) binding site [chemical binding]; other site 391008002437 dimer interface [polypeptide binding]; other site 391008002438 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 391008002439 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 391008002440 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 391008002441 ligand binding site [chemical binding]; other site 391008002442 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 391008002443 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 391008002444 RNA binding surface [nucleotide binding]; other site 391008002445 Pseudouridine synthases, RsuA subfamily; Region: PseudoU_synth_RsuA_like; cd02870 391008002446 active site 391008002447 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 391008002448 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS); Region: KBL_like; cd06454 391008002449 substrate-cofactor binding pocket; other site 391008002450 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008002451 catalytic residue [active] 391008002452 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 391008002453 L-threonine 3-dehydrogenase; Validated; Region: tdh; PRK05396 391008002454 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 391008002455 NAD(P) binding site [chemical binding]; other site 391008002456 Peptidase S46; Region: Peptidase_S46; pfam10459 391008002457 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 391008002458 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 391008002459 catalytic core [active] 391008002460 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 391008002461 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 391008002462 Sporulation related domain; Region: SPOR; pfam05036 391008002463 Sporulation related domain; Region: SPOR; pfam05036 391008002464 amidophosphoribosyltransferase; Provisional; Region: PRK09246 391008002465 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 391008002466 active site 391008002467 tetramer interface [polypeptide binding]; other site 391008002468 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 391008002469 active site 391008002470 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 391008002471 dinuclear metal binding motif [ion binding]; other site 391008002472 Uncharacterized conserved protein (DUF2235); Region: DUF2235; cl01480 391008002473 Metallo-peptidase family M12B Reprolysin-like; Region: Reprolysin_4; pfam13583 391008002474 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 391008002475 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 391008002476 putative active site [active] 391008002477 putative metal binding site [ion binding]; other site 391008002478 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 391008002479 active site 391008002480 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 391008002481 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 391008002482 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008002483 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008002484 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008002485 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008002486 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008002487 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 391008002488 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 391008002489 polyphosphate kinase; Provisional; Region: PRK05443 391008002490 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 391008002491 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 391008002492 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 391008002493 putative domain interface [polypeptide binding]; other site 391008002494 putative active site [active] 391008002495 catalytic site [active] 391008002496 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 391008002497 putative domain interface [polypeptide binding]; other site 391008002498 putative active site [active] 391008002499 catalytic site [active] 391008002500 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 391008002501 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 391008002502 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008002503 dimer interface [polypeptide binding]; other site 391008002504 phosphorylation site [posttranslational modification] 391008002505 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 391008002506 ATP binding site [chemical binding]; other site 391008002507 Mg2+ binding site [ion binding]; other site 391008002508 G-X-G motif; other site 391008002509 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 391008002510 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 391008002511 active site 391008002512 phosphorylation site [posttranslational modification] 391008002513 intermolecular recognition site; other site 391008002514 dimerization interface [polypeptide binding]; other site 391008002515 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008002516 DNA binding site [nucleotide binding] 391008002517 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 391008002518 Peptidase family M48; Region: Peptidase_M48; pfam01435 391008002519 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 391008002520 GSH binding site [chemical binding]; other site 391008002521 catalytic residues [active] 391008002522 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 391008002523 isocitrate dehydrogenase; Provisional; Region: PRK08997 391008002524 tartrate dehydrogenase; Region: TTC; TIGR02089 391008002525 Isochorismatase family; Region: Isochorismatase; pfam00857 391008002526 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 391008002527 catalytic triad [active] 391008002528 conserved cis-peptide bond; other site 391008002529 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008002530 LysR family transcriptional regulator; Provisional; Region: PRK14997 391008002531 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 391008002532 putative effector binding pocket; other site 391008002533 dimerization interface [polypeptide binding]; other site 391008002534 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 391008002535 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 391008002536 Bax inhibitor 1 like; Region: BaxI_1; cl17691 391008002537 trigger factor; Provisional; Region: tig; PRK01490 391008002538 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 391008002539 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 391008002540 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 391008002541 oligomer interface [polypeptide binding]; other site 391008002542 active site residues [active] 391008002543 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 391008002544 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 391008002545 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008002546 Walker A motif; other site 391008002547 ATP binding site [chemical binding]; other site 391008002548 Walker B motif; other site 391008002549 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 391008002550 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 391008002551 Found in ATP-dependent protease La (LON); Region: LON; smart00464 391008002552 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008002553 Walker A motif; other site 391008002554 ATP binding site [chemical binding]; other site 391008002555 Walker B motif; other site 391008002556 arginine finger; other site 391008002557 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 391008002558 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 391008002559 IHF dimer interface [polypeptide binding]; other site 391008002560 IHF - DNA interface [nucleotide binding]; other site 391008002561 periplasmic folding chaperone; Provisional; Region: PRK10788 391008002562 SurA N-terminal domain; Region: SurA_N_3; cl07813 391008002563 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 391008002564 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 391008002565 N-acetyl-D-glucosamine binding site [chemical binding]; other site 391008002566 catalytic residue [active] 391008002567 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 391008002568 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 391008002569 Methyltransferase domain; Region: Methyltransf_11; pfam08241 391008002570 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 391008002571 RNA/DNA hybrid binding site [nucleotide binding]; other site 391008002572 active site 391008002573 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 391008002574 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 391008002575 active site 391008002576 catalytic site [active] 391008002577 substrate binding site [chemical binding]; other site 391008002578 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 391008002579 Protein phosphatase 2C; Region: PP2C; pfam00481 391008002580 active site 391008002581 Predicted periplasmic protein [Function unknown]; Region: COG3904 391008002582 Autotransporter beta-domain; Region: Autotransporter; pfam03797 391008002583 Protein of unknown function (DUF4254); Region: DUF4254; pfam14063 391008002584 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 391008002585 Glycosyltransferase family 9 (heptosyltransferase); Region: Glyco_transf_9; pfam01075 391008002586 putative active site [active] 391008002587 3-deoxy-D-manno-octulosonic-acid kinase; Reviewed; Region: PRK01723 391008002588 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 391008002589 active site 391008002590 ATP binding site [chemical binding]; other site 391008002591 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 391008002592 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4994 391008002593 Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism]; Region: EmrE; COG2076 391008002594 Extended Signal Peptide of Type V secretion system; Region: ESPR; pfam13018 391008002595 Autotransporter-associated beta strand repeat; Region: Autotrns_rpt; pfam12951 391008002596 Autotransporter-associated beta strand repeat; Region: Autotrns_rpt; pfam12951 391008002597 Autotransporter-associated beta strand repeat; Region: Autotrns_rpt; pfam12951 391008002598 Autotransporter-associated beta strand repeat; Region: Autotrns_rpt; pfam12951 391008002599 Autotransporter beta-domain; Region: Autotransporter; pfam03797 391008002600 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 391008002601 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 391008002602 tetramer interface [polypeptide binding]; other site 391008002603 active site 391008002604 Mg2+/Mn2+ binding site [ion binding]; other site 391008002605 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 391008002606 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008002607 Walker A motif; other site 391008002608 ATP binding site [chemical binding]; other site 391008002609 Walker B motif; other site 391008002610 arginine finger; other site 391008002611 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 391008002612 hypothetical protein; Validated; Region: PRK00153 391008002613 recombination protein RecR; Reviewed; Region: recR; PRK00076 391008002614 RecR protein; Region: RecR; pfam02132 391008002615 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 391008002616 putative active site [active] 391008002617 putative metal-binding site [ion binding]; other site 391008002618 tetramer interface [polypeptide binding]; other site 391008002619 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 391008002620 nucleotide binding site/active site [active] 391008002621 HIT family signature motif; other site 391008002622 catalytic residue [active] 391008002623 Outer membrane lipoprotein Slp family; Region: Slp; pfam03843 391008002624 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 391008002625 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 391008002626 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 391008002627 Domain of unknown function (DUF4129); Region: DUF4129; pfam13559 391008002628 Protein of unknown function DUF58; Region: DUF58; pfam01882 391008002629 MoxR-like ATPases [General function prediction only]; Region: COG0714 391008002630 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008002631 Walker A motif; other site 391008002632 ATP binding site [chemical binding]; other site 391008002633 Walker B motif; other site 391008002634 arginine finger; other site 391008002635 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 391008002636 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 391008002637 Maf-like protein; Region: Maf; pfam02545 391008002638 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 391008002639 active site 391008002640 dimer interface [polypeptide binding]; other site 391008002641 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 391008002642 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 391008002643 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 391008002644 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 391008002645 dimer interface [polypeptide binding]; other site 391008002646 active site 391008002647 CoA binding pocket [chemical binding]; other site 391008002648 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 391008002649 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 391008002650 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 391008002651 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008002652 NAD(P) binding site [chemical binding]; other site 391008002653 active site 391008002654 acyl carrier protein; Provisional; Region: acpP; PRK00982 391008002655 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 391008002656 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 391008002657 dimer interface [polypeptide binding]; other site 391008002658 active site 391008002659 hypothetical protein; Validated; Region: PRK09070 391008002660 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 391008002661 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 391008002662 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 391008002663 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 391008002664 dimerization interface [polypeptide binding]; other site 391008002665 thymidylate kinase; Validated; Region: tmk; PRK00698 391008002666 Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step...; Region: TMPK; cd01672 391008002667 TMP-binding site; other site 391008002668 ATP-binding site [chemical binding]; other site 391008002669 DNA polymerase III subunit delta'; Validated; Region: PRK08769 391008002670 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_HprK; cl00270 391008002671 active site 391008002672 nucleotide-binding site [chemical binding]; other site 391008002673 DNA polymerase III subunit delta'; Validated; Region: PRK08485 391008002674 PilZ domain; Region: PilZ; cl01260 391008002675 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 391008002676 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 391008002677 dimer interface [polypeptide binding]; other site 391008002678 hexamer interface [polypeptide binding]; other site 391008002679 active site 2 [active] 391008002680 Phage protein D [General function prediction only]; Region: COG3500 391008002681 Phage Tail Protein X; Region: Phage_tail_X; cl02088 391008002682 Phage P2 GpU; Region: Phage_P2_GpU; pfam06995 391008002683 Phage-related minor tail protein; Region: PhageMin_Tail; pfam10145 391008002684 Mu-like prophage FluMu protein gp41; Region: FluMu_gp41; pfam10109 391008002685 Phage tail tube protein FII; Region: Phage_tube; pfam04985 391008002686 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 391008002687 Chaperone of endosialidase; Region: Peptidase_S74; pfam13884 391008002688 Phage tail protein (Tail_P2_I); Region: Tail_P2_I; cl01817 391008002689 Baseplate J-like protein; Region: Baseplate_J; cl01294 391008002690 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 391008002691 phage baseplate assembly protein V; Region: phage_P2_V; TIGR01644 391008002692 Phage P2 baseplate assembly protein gpV [General function prediction only]; Region: gpV; COG4540 391008002693 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 391008002694 catalytic residue [active] 391008002695 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 391008002696 DNA-binding interface [nucleotide binding]; DNA binding site 391008002697 deoxynucleoside monophosphate kinase; Provisional; Region: 1; PHA02575 391008002698 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 391008002699 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4643 391008002700 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 391008002701 active site 391008002702 metal binding site [ion binding]; metal-binding site 391008002703 interdomain interaction site; other site 391008002704 Virulence-associated protein E; Region: VirE; pfam05272 391008002705 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 391008002706 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 391008002707 N-terminal plug; other site 391008002708 ligand-binding site [chemical binding]; other site 391008002709 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 391008002710 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 391008002711 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 391008002712 putative substrate translocation pore; other site 391008002713 DNA-bindng transcriptional repressor SrlR; Provisional; Region: srlR; PRK10434 391008002714 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 391008002715 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 391008002716 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 391008002717 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 391008002718 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 391008002719 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 391008002720 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 391008002721 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 391008002722 DNA-binding site [nucleotide binding]; DNA binding site 391008002723 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 391008002724 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008002725 homodimer interface [polypeptide binding]; other site 391008002726 catalytic residue [active] 391008002727 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008002728 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008002729 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_7; cd08476 391008002730 putative effector binding pocket; other site 391008002731 putative dimerization interface [polypeptide binding]; other site 391008002732 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 391008002733 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 391008002734 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 391008002735 N-terminal plug; other site 391008002736 ligand-binding site [chemical binding]; other site 391008002737 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008002738 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 391008002739 dimerization interface [polypeptide binding]; other site 391008002740 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 391008002741 dimer interface [polypeptide binding]; other site 391008002742 phosphorylation site [posttranslational modification] 391008002743 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 391008002744 ATP binding site [chemical binding]; other site 391008002745 Mg2+ binding site [ion binding]; other site 391008002746 G-X-G motif; other site 391008002747 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391008002748 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 391008002749 active site 391008002750 phosphorylation site [posttranslational modification] 391008002751 intermolecular recognition site; other site 391008002752 dimerization interface [polypeptide binding]; other site 391008002753 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008002754 DNA binding site [nucleotide binding] 391008002755 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 391008002756 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008002757 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008002758 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 391008002759 Protein export membrane protein; Region: SecD_SecF; cl14618 391008002760 Uncharacterized conserved protein [Function unknown]; Region: COG3791 391008002761 Domain of unknown function (DUF4105); Region: DUF4105; pfam13387 391008002762 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 391008002763 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 391008002764 Major Facilitator Superfamily; Region: MFS_1; pfam07690 391008002765 Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Region: HTH_SoxR; cd01110 391008002766 redox-sensitive transcriptional activator SoxR; Region: SoxR; TIGR01950 391008002767 DNA binding residues [nucleotide binding] 391008002768 dimer interface [polypeptide binding]; other site 391008002769 [2Fe-2S] cluster binding site [ion binding]; other site 391008002770 Lin1944 and related proteins, classical (c) SDRs; Region: Lin1944_like_SDR_c; cd11731 391008002771 putative NAD(P) binding site [chemical binding]; other site 391008002772 homodimer interface [polypeptide binding]; other site 391008002773 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008002774 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008002775 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_8; cd08477 391008002776 putative effector binding pocket; other site 391008002777 putative dimerization interface [polypeptide binding]; other site 391008002778 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 391008002779 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 391008002780 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 391008002781 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 391008002782 catalytic residue [active] 391008002783 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 391008002784 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 391008002785 Walker A motif; other site 391008002786 ATP binding site [chemical binding]; other site 391008002787 Walker B motif; other site 391008002788 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 391008002789 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 391008002790 Walker A motif; other site 391008002791 ATP binding site [chemical binding]; other site 391008002792 Walker B motif; other site 391008002793 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 391008002794 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 391008002795 active site 391008002796 catalytic tetrad [active] 391008002797 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008002798 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008002799 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 391008002800 putative effector binding pocket; other site 391008002801 putative dimerization interface [polypeptide binding]; other site 391008002802 Domain of unknown function (DUF4287); Region: DUF4287; pfam14117 391008002803 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 391008002804 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391008002805 Coenzyme A binding pocket [chemical binding]; other site 391008002806 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 391008002807 Uncharacterized conserved protein [Function unknown]; Region: COG1284 391008002808 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 391008002809 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 391008002810 hypothetical protein; Validated; Region: PRK00228 391008002811 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 391008002812 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 391008002813 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 391008002814 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 391008002815 Transposase IS200 like; Region: Y1_Tnp; pfam01797 391008002816 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 391008002817 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 391008002818 MgtE intracellular N domain; Region: MgtE_N; smart00924 391008002819 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 391008002820 Divalent cation transporter; Region: MgtE; pfam01769 391008002821 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 391008002822 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 391008002823 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 391008002824 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 391008002825 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 391008002826 dimerization domain swap beta strand [polypeptide binding]; other site 391008002827 regulatory protein interface [polypeptide binding]; other site 391008002828 active site 391008002829 regulatory phosphorylation site [posttranslational modification]; other site 391008002830 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_man; cl00025 391008002831 active pocket/dimerization site; other site 391008002832 active site 391008002833 phosphorylation site [posttranslational modification] 391008002834 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 391008002835 HPr kinase/phosphorylase; Provisional; Region: PRK05428 391008002836 HPr Serine kinase N terminus; Region: Hpr_kinase_N; pfam02603 391008002837 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent...; Region: HprK_C; cd01918 391008002838 Hpr binding site; other site 391008002839 active site 391008002840 homohexamer subunit interaction site [polypeptide binding]; other site 391008002841 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 391008002842 active site 391008002843 phosphorylation site [posttranslational modification] 391008002844 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cd00552 391008002845 30S subunit binding site; other site 391008002846 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 391008002847 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 391008002848 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 391008002849 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 391008002850 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 391008002851 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 391008002852 Walker A/P-loop; other site 391008002853 ATP binding site [chemical binding]; other site 391008002854 Q-loop/lid; other site 391008002855 ABC transporter signature motif; other site 391008002856 Walker B; other site 391008002857 D-loop; other site 391008002858 H-loop/switch region; other site 391008002859 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 391008002860 OstA-like protein; Region: OstA; pfam03968 391008002861 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117 391008002862 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 391008002863 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 391008002864 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 391008002865 active site 391008002866 motif I; other site 391008002867 motif II; other site 391008002868 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 391008002869 KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose...; Region: SIS_Kpsf; cd05014 391008002870 putative active site [active] 391008002871 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 391008002872 Predicted transcriptional regulator, BolA superfamily [Transcription]; Region: COG5007 391008002873 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 391008002874 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 391008002875 hinge; other site 391008002876 active site 391008002877 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 391008002878 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 391008002879 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 391008002880 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 391008002881 active site 391008002882 substrate binding site [chemical binding]; other site 391008002883 cosubstrate binding site; other site 391008002884 catalytic site [active] 391008002885 Predicted membrane protein (DUF2238); Region: DUF2238; pfam09997 391008002886 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 391008002887 PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine biosynthesis; Region: PurM; cd02196 391008002888 dimerization interface [polypeptide binding]; other site 391008002889 putative ATP binding site [chemical binding]; other site 391008002890 Uncharacterized protein conserved in bacteria (DUF2066); Region: DUF2066; pfam09839 391008002891 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 391008002892 Domain of unknown function DUF20; Region: UPF0118; pfam01594 391008002893 hypothetical protein; Validated; Region: PRK08727 391008002894 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 391008002895 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 391008002896 Transposase; Region: HTH_Tnp_1; cl17663 391008002897 putative transposase OrfB; Reviewed; Region: PHA02517 391008002898 HTH-like domain; Region: HTH_21; pfam13276 391008002899 Integrase core domain; Region: rve; pfam00665 391008002900 Integrase core domain; Region: rve_2; pfam13333 391008002901 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 391008002902 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 391008002903 Substrate binding site; other site 391008002904 metal-binding site 391008002905 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 391008002906 Phosphotransferase enzyme family; Region: APH; pfam01636 391008002907 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 391008002908 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_5; cd05682 391008002909 hypothetical protein; Provisional; Region: PRK08201 391008002910 metal binding site [ion binding]; metal-binding site 391008002911 putative dimer interface [polypeptide binding]; other site 391008002912 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 391008002913 hypothetical protein; Provisional; Region: PRK06132 391008002914 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 391008002915 L,D-transpeptidase catalytic domain; Region: YkuD_2; pfam13645 391008002916 HutD; Region: HutD; pfam05962 391008002917 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 391008002918 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_like1; cd06200 391008002919 FAD binding pocket [chemical binding]; other site 391008002920 FAD binding motif [chemical binding]; other site 391008002921 catalytic residues [active] 391008002922 NAD binding pocket [chemical binding]; other site 391008002923 phosphate binding motif [ion binding]; other site 391008002924 beta-alpha-beta structure motif; other site 391008002925 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 391008002926 ApbE family; Region: ApbE; pfam02424 391008002927 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 391008002928 Predicted periplasmic protein (DUF2271); Region: DUF2271; cl17856 391008002929 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 391008002930 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 391008002931 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 391008002932 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 391008002933 N-terminal plug; other site 391008002934 ligand-binding site [chemical binding]; other site 391008002935 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 391008002936 Sel1-like repeats; Region: SEL1; smart00671 391008002937 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 391008002938 Sel1-like repeats; Region: SEL1; smart00671 391008002939 Sel1-like repeats; Region: SEL1; smart00671 391008002940 Sel1-like repeats; Region: SEL1; smart00671 391008002941 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 391008002942 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 391008002943 N-terminal plug; other site 391008002944 ligand-binding site [chemical binding]; other site 391008002945 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 a...; Region: Rieske_RO_ferredoxin; cd03528 391008002946 [2Fe-2S] cluster binding site [ion binding]; other site 391008002947 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 391008002948 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391008002949 Coenzyme A binding pocket [chemical binding]; other site 391008002950 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 391008002951 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 391008002952 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 391008002953 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 391008002954 catalytic residue [active] 391008002955 Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]; Region: SufB; COG0719 391008002956 FeS assembly protein SufD; Region: sufD; TIGR01981 391008002957 FeS assembly ATPase SufC; Region: sufC; TIGR01978 391008002958 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 391008002959 Walker A/P-loop; other site 391008002960 ATP binding site [chemical binding]; other site 391008002961 Q-loop/lid; other site 391008002962 ABC transporter signature motif; other site 391008002963 Walker B; other site 391008002964 D-loop; other site 391008002965 H-loop/switch region; other site 391008002966 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814 391008002967 putative ABC transporter; Region: ycf24; CHL00085 391008002968 FeS assembly SUF system regulator, gammaproteobacterial; Region: suf_reg_Xantho; TIGR02944 391008002969 Transcriptional regulator; Region: Rrf2; pfam02082 391008002970 Proteins containing SET domain [General function prediction only]; Region: COG2940 391008002971 SET domain; Region: SET; pfam00856 391008002972 Protein of unknown function (DUF1439); Region: DUF1439; cl06345 391008002973 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cl00257 391008002974 IHF dimer interface [polypeptide binding]; other site 391008002975 IHF - DNA interface [nucleotide binding]; other site 391008002976 peroxiredoxin, OsmC subfamily; Region: osmo_induc_OsmC; TIGR03562 391008002977 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 391008002978 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 391008002979 bifunctional aspartate kinase/diaminopimelate decarboxylase protein; Provisional; Region: PRK08961 391008002980 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 391008002981 nucleotide binding site [chemical binding]; other site 391008002982 substrate binding site [chemical binding]; other site 391008002983 ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein; Region: ACT_AKiii-DAPDC_1; cd04935 391008002984 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 391008002985 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 391008002986 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 391008002987 catalytic residue [active] 391008002988 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK04690 391008002989 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cd01983 391008002990 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 391008002991 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 391008002992 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 391008002993 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 391008002994 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 391008002995 substrate binding pocket [chemical binding]; other site 391008002996 chain length determination region; other site 391008002997 substrate-Mg2+ binding site; other site 391008002998 catalytic residues [active] 391008002999 aspartate-rich region 1; other site 391008003000 active site lid residues [active] 391008003001 aspartate-rich region 2; other site 391008003002 Alpha amylase catalytic domain found in oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase) and related proteins; Region: AmyAc_OligoGlu; cd11330 391008003003 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 391008003004 active site 391008003005 catalytic site [active] 391008003006 Domain of unknown function (DUF3459); Region: DUF3459; pfam11941 391008003007 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 391008003008 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008003009 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008003010 Glycoside hydrolase 97; Region: Glyco_hydro_97; pfam10566 391008003011 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 391008003012 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 391008003013 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 391008003014 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 391008003015 Alpha amylase catalytic domain found in bacterial cyclomaltodextrinases and related proteins; Region: AmyAc_bac_CMD_like_2; cd11339 391008003016 active site 391008003017 catalytic site [active] 391008003018 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 391008003019 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 391008003020 ABC-type transport system involved in multi-copper enzyme maturation, permease component [General function prediction only]; Region: NosY; COG1277 391008003021 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 391008003022 Zn binding site [ion binding]; other site 391008003023 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 391008003024 ABC-type multidrug transport system, ATPase component; Region: ABC_drug_resistance_like; cd03264 391008003025 Walker A/P-loop; other site 391008003026 ATP binding site [chemical binding]; other site 391008003027 Q-loop/lid; other site 391008003028 ABC transporter signature motif; other site 391008003029 Walker B; other site 391008003030 D-loop; other site 391008003031 H-loop/switch region; other site 391008003032 circadian clock protein KaiC; Reviewed; Region: PRK09302 391008003033 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 391008003034 Walker A motif; other site 391008003035 ATP binding site [chemical binding]; other site 391008003036 Walker B motif; other site 391008003037 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 391008003038 Walker A motif; other site 391008003039 ATP binding site [chemical binding]; other site 391008003040 Walker B motif; other site 391008003041 PAS fold; Region: PAS_4; pfam08448 391008003042 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 391008003043 putative active site [active] 391008003044 heme pocket [chemical binding]; other site 391008003045 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 391008003046 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008003047 dimer interface [polypeptide binding]; other site 391008003048 phosphorylation site [posttranslational modification] 391008003049 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 391008003050 ATP binding site [chemical binding]; other site 391008003051 Mg2+ binding site [ion binding]; other site 391008003052 G-X-G motif; other site 391008003053 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 391008003054 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 391008003055 active site 391008003056 phosphorylation site [posttranslational modification] 391008003057 intermolecular recognition site; other site 391008003058 dimerization interface [polypeptide binding]; other site 391008003059 Transcriptional regulators [Transcription]; Region: PurR; COG1609 391008003060 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 391008003061 DNA binding site [nucleotide binding] 391008003062 domain linker motif; other site 391008003063 Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators; Region: PBP1_CelR; cd06295 391008003064 putative dimerization interface [polypeptide binding]; other site 391008003065 putative ligand binding site [chemical binding]; other site 391008003066 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 391008003067 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 391008003068 dimer interface [polypeptide binding]; other site 391008003069 ssDNA binding site [nucleotide binding]; other site 391008003070 tetramer (dimer of dimers) interface [polypeptide binding]; other site 391008003071 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 391008003072 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 391008003073 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 391008003074 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 391008003075 ATP binding site [chemical binding]; other site 391008003076 putative Mg++ binding site [ion binding]; other site 391008003077 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 391008003078 nucleotide binding region [chemical binding]; other site 391008003079 ATP-binding site [chemical binding]; other site 391008003080 RmuC family; Region: RmuC; pfam02646 391008003081 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 391008003082 HsdM N-terminal domain; Region: HsdM_N; pfam12161 391008003083 Methyltransferase domain; Region: Methyltransf_26; pfam13659 391008003084 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 391008003085 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 391008003086 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 391008003087 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 391008003088 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 391008003089 NADP binding site [chemical binding]; other site 391008003090 active site 391008003091 steroid binding site; other site 391008003092 Cupin; Region: Cupin_6; pfam12852 391008003093 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 391008003094 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 391008003095 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 391008003096 putative FAD-binding dehydrogenase; Reviewed; Region: PRK12834 391008003097 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 391008003098 Gluconate 2-dehydrogenase subunit 3; Region: Gluconate_2-dh3; pfam13618 391008003099 Domain of Unknown Function (DUF1080); Region: DUF1080; pfam06439 391008003100 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 391008003101 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 391008003102 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 391008003103 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 391008003104 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 391008003105 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 391008003106 nucleoside transporter; Region: 2A0110; TIGR00889 391008003107 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 391008003108 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cl12060 391008003109 Metal-binding active site; metal-binding site 391008003110 AP endonuclease family 2 C terminus; Region: AP_endonuc_2_N; pfam07582 391008003111 Transcriptional regulators [Transcription]; Region: PurR; COG1609 391008003112 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 391008003113 DNA binding site [nucleotide binding] 391008003114 domain linker motif; other site 391008003115 Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria; Region: PBP1_LacI_like_6; cd06284 391008003116 dimerization interface [polypeptide binding]; other site 391008003117 ligand binding site [chemical binding]; other site 391008003118 MASE2 domain; Region: MASE2; pfam05230 391008003119 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008003120 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008003121 metal binding site [ion binding]; metal-binding site 391008003122 active site 391008003123 I-site; other site 391008003124 Transcriptional regulators [Transcription]; Region: MarR; COG1846 391008003125 MarR family; Region: MarR_2; pfam12802 391008003126 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391008003127 Coenzyme A binding pocket [chemical binding]; other site 391008003128 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008003129 The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold; Region: PBP2_BudR; cd08451 391008003130 putative dimerization interface [polypeptide binding]; other site 391008003131 putative substrate binding pocket [chemical binding]; other site 391008003132 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 391008003133 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 391008003134 tetramer interface [polypeptide binding]; other site 391008003135 active site 391008003136 Mg2+/Mn2+ binding site [ion binding]; other site 391008003137 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 391008003138 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008003139 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008003140 metal binding site [ion binding]; metal-binding site 391008003141 active site 391008003142 I-site; other site 391008003143 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 391008003144 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008003145 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008003146 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 391008003147 putative effector binding pocket; other site 391008003148 putative dimerization interface [polypeptide binding]; other site 391008003149 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 391008003150 Protein of unknown function (DUF2867); Region: DUF2867; pfam11066 391008003151 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 391008003152 dimerization interface [polypeptide binding]; other site 391008003153 putative DNA binding site [nucleotide binding]; other site 391008003154 putative Zn2+ binding site [ion binding]; other site 391008003155 Protein of unknown function (DUF2975); Region: DUF2975; pfam11188 391008003156 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 391008003157 non-specific DNA binding site [nucleotide binding]; other site 391008003158 salt bridge; other site 391008003159 sequence-specific DNA binding site [nucleotide binding]; other site 391008003160 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 391008003161 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 391008003162 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 391008003163 Transporter associated domain; Region: CorC_HlyC; pfam03471 391008003164 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 391008003165 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 391008003166 putative active site [active] 391008003167 putative metal binding site [ion binding]; other site 391008003168 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 391008003169 metabolite-proton symporter; Region: 2A0106; TIGR00883 391008003170 putative substrate translocation pore; other site 391008003171 NH_hydro_CaPnhB: A subgroup of nucleoside hydrolases similar to Corynebacterium ammoniagenes Purine/pyrimidine nucleoside hydrolase (pnhB). Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These...; Region: nuc_hydro_CaPnhB; cd02650 391008003172 active site 391008003173 Transcriptional regulators [Transcription]; Region: GntR; COG1802 391008003174 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 391008003175 DNA-binding site [nucleotide binding]; DNA binding site 391008003176 FCD domain; Region: FCD; pfam07729 391008003177 Dicarboxylate carrier protein MatC N-terminus; Region: MatC_N; pfam07158 391008003178 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 391008003179 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 391008003180 malonate decarboxylase, epsilon subunit; Region: malonate_mdcH; TIGR03131 391008003181 triphosphoribosyl-dephospho-CoA synthase MdcB; Region: malonate_mdcB; TIGR03132 391008003182 phosphoribosyl-dephospho-CoA transferase; Provisional; Region: PRK02098 391008003183 Phosphoribosyl-dephospho-CoA transferase MdcG; Region: MdcG; pfam10620 391008003184 malonate decarboxylase, gamma subunit; Region: malonate_gamma; TIGR03134 391008003185 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189 391008003186 malonate decarboxylase subunit delta; Provisional; Region: PRK02103 391008003187 malonate decarboxylase, alpha subunit; Region: mdcA; TIGR01110 391008003188 Coenzyme A transferase; Region: CoA_trans; cl17247 391008003189 ferric-rhodotorulic acid outer membrane transporter; Provisional; Region: PRK10003 391008003190 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 391008003191 N-terminal plug; other site 391008003192 ligand-binding site [chemical binding]; other site 391008003193 malate:quinone oxidoreductase; Validated; Region: PRK05257 391008003194 malate:quinone-oxidoreductase; Region: mal_quin_oxido; TIGR01320 391008003195 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 391008003196 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391008003197 Coenzyme A binding pocket [chemical binding]; other site 391008003198 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 391008003199 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008003200 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 391008003201 dimerization interface [polypeptide binding]; other site 391008003202 LysE type translocator; Region: LysE; cl00565 391008003203 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 391008003204 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 391008003205 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 391008003206 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 391008003207 POT family; Region: PTR2; cl17359 391008003208 Predicted membrane protein [Function unknown]; Region: COG3503 391008003209 Predicted membrane protein [Function unknown]; Region: COG1297 391008003210 putative oligopeptide transporter, OPT family; Region: TIGR00733 391008003211 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 391008003212 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 391008003213 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 391008003214 Protein of unknown function (DUF819); Region: DUF819; pfam05684 391008003215 cell division topological specificity factor MinE; Reviewed; Region: minE; PRK00296 391008003216 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 391008003217 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 391008003218 Switch I; other site 391008003219 Switch II; other site 391008003220 septum formation inhibitor; Reviewed; Region: minC; PRK04596 391008003221 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 391008003222 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 391008003223 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 391008003224 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 391008003225 Histidine kinase; Region: HisKA_3; pfam07730 391008003226 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 391008003227 ATP binding site [chemical binding]; other site 391008003228 Mg2+ binding site [ion binding]; other site 391008003229 G-X-G motif; other site 391008003230 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 391008003231 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 391008003232 active site 391008003233 phosphorylation site [posttranslational modification] 391008003234 intermolecular recognition site; other site 391008003235 dimerization interface [polypeptide binding]; other site 391008003236 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 391008003237 DNA binding residues [nucleotide binding] 391008003238 dimerization interface [polypeptide binding]; other site 391008003239 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_1; cd07818 391008003240 putative hydrophobic ligand binding site [chemical binding]; other site 391008003241 Protein of unknown function (DUF423); Region: DUF423; cl01008 391008003242 D-alanyl-D-alanine carboxypeptidase; Region: VanY; pfam02557 391008003243 Domain of unknown function (DUF4177); Region: DUF4177; pfam13783 391008003244 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4877 391008003245 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. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual...; Region: Band_7_2; cd03402 391008003246 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 391008003247 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 391008003248 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008003249 ATP-grasp domain; Region: ATP-grasp; pfam02222 391008003250 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 391008003251 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 391008003252 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 391008003253 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 391008003254 Ca2+ binding site [ion binding]; other site 391008003255 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 391008003256 EF-hand domain pair; Region: EF_hand_5; pfam13499 391008003257 Ca2+ binding site [ion binding]; other site 391008003258 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 391008003259 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391008003260 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 391008003261 DNA binding residues [nucleotide binding] 391008003262 Acyl-CoA thioesterase [Lipid metabolism]; Region: TesB; COG1946 391008003263 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 391008003264 active site 391008003265 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 391008003266 catalytic triad [active] 391008003267 dimer interface [polypeptide binding]; other site 391008003268 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 391008003269 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 391008003270 substrate binding site [chemical binding]; other site 391008003271 oxyanion hole (OAH) forming residues; other site 391008003272 trimer interface [polypeptide binding]; other site 391008003273 Protein of unknown function (DUF461); Region: DUF461; pfam04314 391008003274 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 391008003275 active site 391008003276 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 391008003277 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 391008003278 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 391008003279 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 391008003280 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 391008003281 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 391008003282 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 391008003283 GTPase CgtA; Reviewed; Region: obgE; PRK12299 391008003284 GTP1/OBG; Region: GTP1_OBG; pfam01018 391008003285 Obg GTPase; Region: Obg; cd01898 391008003286 G1 box; other site 391008003287 GTP/Mg2+ binding site [chemical binding]; other site 391008003288 Switch I region; other site 391008003289 G2 box; other site 391008003290 G3 box; other site 391008003291 Switch II region; other site 391008003292 G4 box; other site 391008003293 G5 box; other site 391008003294 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 391008003295 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 391008003296 MviN-like protein; Region: MVIN; pfam03023 391008003297 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 391008003298 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 391008003299 active site 391008003300 Riboflavin kinase; Region: Flavokinase; pfam01687 391008003301 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 391008003302 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 391008003303 active site 391008003304 HIGH motif; other site 391008003305 nucleotide binding site [chemical binding]; other site 391008003306 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 391008003307 active site 391008003308 KMSKS motif; other site 391008003309 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 391008003310 tRNA binding surface [nucleotide binding]; other site 391008003311 anticodon binding site; other site 391008003312 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 391008003313 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 391008003314 lipoprotein signal peptidase; Provisional; Region: PRK14787 391008003315 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 391008003316 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 391008003317 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 391008003318 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 391008003319 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 391008003320 YhhN-like protein; Region: YhhN; pfam07947 391008003321 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008003322 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 391008003323 N-terminal plug; other site 391008003324 ligand-binding site [chemical binding]; other site 391008003325 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 391008003326 FecR protein; Region: FecR; pfam04773 391008003327 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 391008003328 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391008003329 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 391008003330 DNA binding residues [nucleotide binding] 391008003331 Autotransporter beta-domain; Region: Autotransporter; pfam03797 391008003332 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 391008003333 D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains; Region: LDH_like_2; cd12183 391008003334 putative ligand binding site [chemical binding]; other site 391008003335 putative NAD binding site [chemical binding]; other site 391008003336 catalytic site [active] 391008003337 Protein of unknown function (DUF2846); Region: DUF2846; pfam11008 391008003338 GyrI-like small molecule binding domain; Region: GyrI-like; cl01368 391008003339 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 391008003340 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 391008003341 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 391008003342 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 391008003343 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 391008003344 D-pathway; other site 391008003345 Putative ubiquinol binding site [chemical binding]; other site 391008003346 Low-spin heme (heme b) binding site [chemical binding]; other site 391008003347 Putative water exit pathway; other site 391008003348 Binuclear center (heme o3/CuB) [ion binding]; other site 391008003349 K-pathway; other site 391008003350 Putative proton exit pathway; other site 391008003351 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 391008003352 Subunit I/III interface [polypeptide binding]; other site 391008003353 Subunit III/IV interface [polypeptide binding]; other site 391008003354 cytochrome o ubiquinol oxidase subunit IV; Region: CyoD; TIGR02847 391008003355 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 391008003356 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 391008003357 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 391008003358 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008003359 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008003360 metal binding site [ion binding]; metal-binding site 391008003361 active site 391008003362 I-site; other site 391008003363 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 391008003364 DNA repair protein RadA; Provisional; Region: PRK11823 391008003365 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 391008003366 Walker A motif/ATP binding site; other site 391008003367 ATP binding site [chemical binding]; other site 391008003368 Walker B motif; other site 391008003369 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 391008003370 Molecular chaperone, HSP90 family [Posttranslational modification, protein turnover, chaperones]; Region: HtpG; COG0326 391008003371 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 391008003372 ATP binding site [chemical binding]; other site 391008003373 Mg2+ binding site [ion binding]; other site 391008003374 G-X-G motif; other site 391008003375 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 391008003376 signal recognition particle protein; Provisional; Region: PRK10867 391008003377 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 391008003378 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 391008003379 P loop; other site 391008003380 GTP binding site [chemical binding]; other site 391008003381 Signal peptide binding domain; Region: SRP_SPB; pfam02978 391008003382 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 391008003383 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 391008003384 FMN binding site [chemical binding]; other site 391008003385 substrate binding site [chemical binding]; other site 391008003386 putative catalytic residue [active] 391008003387 hypothetical protein; Provisional; Region: PRK09266 391008003388 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 391008003389 homodimer interface [polypeptide binding]; other site 391008003390 substrate-cofactor binding pocket; other site 391008003391 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008003392 catalytic residue [active] 391008003393 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 391008003394 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 391008003395 RimM N-terminal domain; Region: RimM; pfam01782 391008003396 PRC-barrel domain; Region: PRC; pfam05239 391008003397 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 391008003398 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 391008003399 Uncharacterized conserved protein [Function unknown]; Region: COG5649 391008003400 Uncharacterized conserved protein [Function unknown]; Region: COG5649 391008003401 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 391008003402 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 391008003403 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 391008003404 RNA binding surface [nucleotide binding]; other site 391008003405 Cellulase (glycosyl hydrolase family 5); Region: Cellulase; pfam00150 391008003406 Bacterial protein of unknown function (DUF937); Region: DUF937; pfam06078 391008003407 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 391008003408 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 391008003409 tetramer interface [polypeptide binding]; other site 391008003410 heme binding pocket [chemical binding]; other site 391008003411 NADPH binding site [chemical binding]; other site 391008003412 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 391008003413 MutS domain I; Region: MutS_I; pfam01624 391008003414 MutS domain II; Region: MutS_II; pfam05188 391008003415 MutS domain III; Region: MutS_III; pfam05192 391008003416 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 391008003417 Walker A/P-loop; other site 391008003418 ATP binding site [chemical binding]; other site 391008003419 Q-loop/lid; other site 391008003420 ABC transporter signature motif; other site 391008003421 Walker B; other site 391008003422 D-loop; other site 391008003423 H-loop/switch region; other site 391008003424 Barstar_SaI14_like contains sequences that are similar to SaI14, an RNAase inhibitor, which are members of the Barstar family. Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds...; Region: Barstar_SaI14_like; cd05143 391008003425 putative RNAase interaction site [polypeptide binding]; other site 391008003426 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 391008003427 HAMP domain; Region: HAMP; pfam00672 391008003428 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 391008003429 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 391008003430 dimer interface [polypeptide binding]; other site 391008003431 putative CheW interface [polypeptide binding]; other site 391008003432 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 391008003433 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 391008003434 ABC-2 type transporter; Region: ABC2_membrane; cl17235 391008003435 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 391008003436 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 391008003437 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008003438 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008003439 Outer membrane efflux protein; Region: OEP; pfam02321 391008003440 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 391008003441 Switch II region; other site 391008003442 G3 box; other site 391008003443 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 391008003444 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008003445 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 391008003446 dimerization interface [polypeptide binding]; other site 391008003447 Lysine efflux permease [General function prediction only]; Region: COG1279 391008003448 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 391008003449 active site 391008003450 Protein of unknown function (DUF3423); Region: DUF3423; pfam11903 391008003451 Bleomycin binding protein (BLMA) and similar proteins; BLMA confers bleomycin (Bm) resistance by directly binding to Bm; Region: BLMA_like; cd08349 391008003452 dimer interface [polypeptide binding]; other site 391008003453 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 391008003454 ligand binding site [chemical binding]; other site 391008003455 Arginase-like and histone-like hydrolases; Region: Arginase_HDAC; cl17011 391008003456 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 391008003457 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 391008003458 4-aminobutyrate aminotransferase and related aminotransferases [Amino acid transport and metabolism]; Region: GabT; COG0160 391008003459 inhibitor-cofactor binding pocket; inhibition site 391008003460 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008003461 catalytic residue [active] 391008003462 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 391008003463 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 391008003464 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 391008003465 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 391008003466 catalytic residue [active] 391008003467 Esterase/lipase [General function prediction only]; Region: COG1647 391008003468 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 391008003469 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 391008003470 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008003471 dimer interface [polypeptide binding]; other site 391008003472 phosphorylation site [posttranslational modification] 391008003473 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 391008003474 ATP binding site [chemical binding]; other site 391008003475 Mg2+ binding site [ion binding]; other site 391008003476 G-X-G motif; other site 391008003477 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391008003478 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 391008003479 active site 391008003480 phosphorylation site [posttranslational modification] 391008003481 intermolecular recognition site; other site 391008003482 dimerization interface [polypeptide binding]; other site 391008003483 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008003484 DNA binding site [nucleotide binding] 391008003485 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 391008003486 Shewanella-like phosphatases, metallophosphatase domain; Region: MPP_Shelphs; cd07425 391008003487 active site 391008003488 metal binding site [ion binding]; metal-binding site 391008003489 Predicted transcriptional regulators [Transcription]; Region: COG1733 391008003490 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 391008003491 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 391008003492 heme-binding site [chemical binding]; other site 391008003493 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008003494 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008003495 metal binding site [ion binding]; metal-binding site 391008003496 active site 391008003497 I-site; other site 391008003498 outer membrane receptor FepA; Provisional; Region: PRK13524 391008003499 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 391008003500 N-terminal plug; other site 391008003501 ligand-binding site [chemical binding]; other site 391008003502 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 391008003503 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 391008003504 Endonuclease_V, a DNA repair enzyme that initiates repair of nitrosative deaminated purine bases; Region: Endonuclease_V; cd06559 391008003505 Active_site [active] 391008003506 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 391008003507 catalytic core [active] 391008003508 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 391008003509 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 391008003510 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 391008003511 active site 391008003512 Zn binding site [ion binding]; other site 391008003513 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 391008003514 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 391008003515 Zn2+ binding site [ion binding]; other site 391008003516 Mg2+ binding site [ion binding]; other site 391008003517 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 391008003518 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 391008003519 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 391008003520 ATP binding site [chemical binding]; other site 391008003521 putative Mg++ binding site [ion binding]; other site 391008003522 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 391008003523 nucleotide binding region [chemical binding]; other site 391008003524 ATP-binding site [chemical binding]; other site 391008003525 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 391008003526 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 391008003527 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 391008003528 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 391008003529 DNA-binding response regulator CreB; Provisional; Region: PRK11083 391008003530 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 391008003531 active site 391008003532 phosphorylation site [posttranslational modification] 391008003533 intermolecular recognition site; other site 391008003534 dimerization interface [polypeptide binding]; other site 391008003535 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008003536 DNA binding site [nucleotide binding] 391008003537 sensory histidine kinase CreC; Provisional; Region: PRK11100 391008003538 HAMP domain; Region: HAMP; pfam00672 391008003539 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008003540 dimer interface [polypeptide binding]; other site 391008003541 phosphorylation site [posttranslational modification] 391008003542 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 391008003543 ATP binding site [chemical binding]; other site 391008003544 Mg2+ binding site [ion binding]; other site 391008003545 G-X-G motif; other site 391008003546 inner membrane protein; Provisional; Region: PRK11715 391008003547 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 391008003548 M28 Zn-Peptidases; Region: M28_like_4; cd08015 391008003549 Peptidase family M28; Region: Peptidase_M28; pfam04389 391008003550 metal binding site [ion binding]; metal-binding site 391008003551 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 391008003552 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 391008003553 active site 391008003554 HIGH motif; other site 391008003555 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 391008003556 active site 391008003557 KMSKS motif; other site 391008003558 Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; Region: GH38-57_N_LamB_YdjC_SF; cl17191 391008003559 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 391008003560 metal binding site 2 [ion binding]; metal-binding site 391008003561 putative DNA binding helix; other site 391008003562 metal binding site 1 [ion binding]; metal-binding site 391008003563 dimer interface [polypeptide binding]; other site 391008003564 structural Zn2+ binding site [ion binding]; other site 391008003565 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 391008003566 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008003567 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008003568 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 391008003569 putative substrate translocation pore; other site 391008003570 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 391008003571 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008003572 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 391008003573 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 391008003574 N-terminal plug; other site 391008003575 ligand-binding site [chemical binding]; other site 391008003576 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008003577 MerC mercury resistance protein; Region: MerC; pfam03203 391008003578 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 391008003579 Sulfatase; Region: Sulfatase; cl17466 391008003580 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 391008003581 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 391008003582 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 391008003583 DNA binding site [nucleotide binding] 391008003584 active site 391008003585 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 391008003586 Helix-turn-helix domain; Region: HTH_18; pfam12833 391008003587 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008003588 AlkA N-terminal domain; Region: AlkA_N; pfam06029 391008003589 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]; Region: AlkA; COG0122 391008003590 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 391008003591 minor groove reading motif; other site 391008003592 helix-hairpin-helix signature motif; other site 391008003593 substrate binding pocket [chemical binding]; other site 391008003594 active site 391008003595 Predicted periplasmic protein [Function unknown]; Region: COG3904 391008003596 Protein of unknown function (DUF4019); Region: DUF4019; pfam13211 391008003597 MAPEG family; Region: MAPEG; cl09190 391008003598 hypothetical protein; Provisional; Region: PRK09126 391008003599 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 391008003600 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 391008003601 RNA binding surface [nucleotide binding]; other site 391008003602 helicase 45; Provisional; Region: PTZ00424 391008003603 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 391008003604 ATP binding site [chemical binding]; other site 391008003605 Mg++ binding site [ion binding]; other site 391008003606 motif III; other site 391008003607 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 391008003608 nucleotide binding region [chemical binding]; other site 391008003609 ATP-binding site [chemical binding]; other site 391008003610 RNA recognition motif in Escherichia coli cold-shock DEAD box protein A (CsdA) and similar proteins; Region: RRM_EcCsdA_like; cd12499 391008003611 putative RNA binding site [nucleotide binding]; other site 391008003612 PAS domain S-box; Region: sensory_box; TIGR00229 391008003613 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 391008003614 putative active site [active] 391008003615 heme pocket [chemical binding]; other site 391008003616 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008003617 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008003618 metal binding site [ion binding]; metal-binding site 391008003619 active site 391008003620 I-site; other site 391008003621 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 391008003622 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008003623 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008003624 metal binding site [ion binding]; metal-binding site 391008003625 active site 391008003626 I-site; other site 391008003627 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 391008003628 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 391008003629 RNA binding surface [nucleotide binding]; other site 391008003630 Pseudouridine synthase, Escherichia coli RluF like; Region: PseudoU_synth_RluF; cd02554 391008003631 probable active site [active] 391008003632 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 391008003633 GAF domain; Region: GAF; pfam01590 391008003634 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008003635 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008003636 metal binding site [ion binding]; metal-binding site 391008003637 active site 391008003638 I-site; other site 391008003639 Predicted ATPase [General function prediction only]; Region: COG4637 391008003640 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 391008003641 Walker A/P-loop; other site 391008003642 ATP binding site [chemical binding]; other site 391008003643 EamA-like transporter family; Region: EamA; pfam00892 391008003644 Protein of unknown function DUF72; Region: DUF72; pfam01904 391008003645 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_14; cd08355 391008003646 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 391008003647 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 391008003648 Beta-lactamase; Region: Beta-lactamase; pfam00144 391008003649 Domain of unknown function (DUF3471); Region: DUF3471; pfam11954 391008003650 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 391008003651 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 391008003652 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 391008003653 Walker A/P-loop; other site 391008003654 ATP binding site [chemical binding]; other site 391008003655 Q-loop/lid; other site 391008003656 ABC transporter signature motif; other site 391008003657 Walker B; other site 391008003658 D-loop; other site 391008003659 H-loop/switch region; other site 391008003660 glucose-1-phosphatase/inositol phosphatase; Provisional; Region: PRK10173 391008003661 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 391008003662 catalytic core [active] 391008003663 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 391008003664 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 391008003665 Uncharacterized conserved protein [Function unknown]; Region: COG3791 391008003666 Domain of unknown function (DUF4349); Region: DUF4349; pfam14257 391008003667 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 391008003668 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008003669 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 391008003670 dimerization interface [polypeptide binding]; other site 391008003671 substrate binding pocket [chemical binding]; other site 391008003672 EamA-like transporter family; Region: EamA; pfam00892 391008003673 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cd00317 391008003674 active site 391008003675 Predicted transcriptional regulators [Transcription]; Region: COG1695 391008003676 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 391008003677 Predicted membrane protein [Function unknown]; Region: COG4709 391008003678 Putative sensor; Region: Sensor; pfam13796 391008003679 polyhydroxyalkanoate depolymerase, intracellular; Region: PHB_depoly_PhaZ; TIGR01849 391008003680 PHB de-polymerase C-terminus; Region: PHB_depo_C; pfam06850 391008003681 Methyltransferase domain; Region: Methyltransf_23; pfam13489 391008003682 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 391008003683 S-adenosylmethionine binding site [chemical binding]; other site 391008003684 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 391008003685 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 391008003686 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 391008003687 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 391008003688 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 391008003689 putative active site [active] 391008003690 putative PHP Thumb interface [polypeptide binding]; other site 391008003691 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 391008003692 generic binding surface II; other site 391008003693 generic binding surface I; other site 391008003694 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 391008003695 RNA/DNA hybrid binding site [nucleotide binding]; other site 391008003696 active site 391008003697 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 391008003698 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 391008003699 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 391008003700 UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A biosynthetic...; Region: LbH_UDP-GlcNAc_AT; cd03351 391008003701 active site 391008003702 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 391008003703 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 391008003704 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 391008003705 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2; Region: LbH_LpxD; cd03352 391008003706 trimer interface [polypeptide binding]; other site 391008003707 active site 391008003708 UDP-GlcNAc binding site [chemical binding]; other site 391008003709 lipid binding site [chemical binding]; lipid-binding site 391008003710 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 391008003711 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 391008003712 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 391008003713 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 391008003714 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 391008003715 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 391008003716 Surface antigen; Region: Bac_surface_Ag; pfam01103 391008003717 zinc metallopeptidase RseP; Provisional; Region: PRK10779 391008003718 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 391008003719 active site 391008003720 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 391008003721 protein binding site [polypeptide binding]; other site 391008003722 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ...; Region: PDZ_metalloprotease; cd00989 391008003723 protein binding site [polypeptide binding]; other site 391008003724 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 391008003725 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 391008003726 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 391008003727 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 391008003728 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 391008003729 CDP-diglyceride synthase; Provisional; Region: cdsA; PRK11624 391008003730 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 391008003731 undecaprenyl pyrophosphate synthase; Provisional; Region: PRK14836 391008003732 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 391008003733 catalytic residue [active] 391008003734 putative FPP diphosphate binding site; other site 391008003735 putative FPP binding hydrophobic cleft; other site 391008003736 dimer interface [polypeptide binding]; other site 391008003737 putative IPP diphosphate binding site; other site 391008003738 ribosome recycling factor; Reviewed; Region: frr; PRK00083 391008003739 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another...; Region: RRF; cd00520 391008003740 hinge region; other site 391008003741 UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and...; Region: AAK_UMPK-PyrH-Ec; cd04254 391008003742 putative nucleotide binding site [chemical binding]; other site 391008003743 uridine monophosphate binding site [chemical binding]; other site 391008003744 homohexameric interface [polypeptide binding]; other site 391008003745 HDOD domain; Region: HDOD; pfam08668 391008003746 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008003747 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008003748 metal binding site [ion binding]; metal-binding site 391008003749 active site 391008003750 I-site; other site 391008003751 elongation factor Ts; Provisional; Region: tsf; PRK09377 391008003752 UBA/TS-N domain; Region: UBA; pfam00627 391008003753 Elongation factor TS; Region: EF_TS; pfam00889 391008003754 Elongation factor TS; Region: EF_TS; pfam00889 391008003755 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 391008003756 rRNA interaction site [nucleotide binding]; other site 391008003757 S8 interaction site; other site 391008003758 putative laminin-1 binding site; other site 391008003759 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 391008003760 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 391008003761 Spore Coat Protein U domain; Region: SCPU; pfam05229 391008003762 Spore Coat Protein U domain; Region: SCPU; pfam05229 391008003763 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 391008003764 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 391008003765 PapC C-terminal domain; Region: PapC_C; pfam13953 391008003766 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 391008003767 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 391008003768 Spore Coat Protein U domain; Region: SCPU; pfam05229 391008003769 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 391008003770 active site 391008003771 PII uridylyl-transferase; Provisional; Region: PRK04374 391008003772 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 391008003773 metal binding triad; other site 391008003774 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 391008003775 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 391008003776 Zn2+ binding site [ion binding]; other site 391008003777 Mg2+ binding site [ion binding]; other site 391008003778 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 391008003779 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 391008003780 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 391008003781 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 391008003782 trimer interface [polypeptide binding]; other site 391008003783 active site 391008003784 substrate binding site [chemical binding]; other site 391008003785 CoA binding site [chemical binding]; other site 391008003786 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 391008003787 ArsC family; Region: ArsC; pfam03960 391008003788 putative catalytic residues [active] 391008003789 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 391008003790 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 391008003791 metal binding site [ion binding]; metal-binding site 391008003792 dimer interface [polypeptide binding]; other site 391008003793 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 391008003794 asparagine synthetase B; Provisional; Region: asnB; PRK09431 391008003795 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 391008003796 active site 391008003797 dimer interface [polypeptide binding]; other site 391008003798 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 391008003799 Ligand Binding Site [chemical binding]; other site 391008003800 Molecular Tunnel; other site 391008003801 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 391008003802 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 391008003803 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 391008003804 Penicillin G acylase (PGA) belongs to a family of beta-lactam acylases that includes cephalosporin acylase (CA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and...; Region: Ntn_PGA_like; cd03747 391008003805 active site 391008003806 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 391008003807 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 391008003808 heme binding site [chemical binding]; other site 391008003809 ferroxidase pore; other site 391008003810 ferroxidase diiron center [ion binding]; other site 391008003811 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 391008003812 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 391008003813 CAP-like domain; other site 391008003814 active site 391008003815 primary dimer interface [polypeptide binding]; other site 391008003816 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 391008003817 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008003818 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 391008003819 MarR family; Region: MarR_2; pfam12802 391008003820 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 391008003821 multidrug efflux system protein EmrA; Provisional; Region: PRK15136 391008003822 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008003823 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008003824 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 391008003825 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 391008003826 putative substrate translocation pore; other site 391008003827 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 391008003828 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 391008003829 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008003830 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008003831 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 391008003832 putative dimerization interface [polypeptide binding]; other site 391008003833 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 391008003834 ribonuclease R; Region: RNase_R; TIGR02063 391008003835 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 391008003836 RNB domain; Region: RNB; pfam00773 391008003837 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase...; Region: S1_RNase_R; cd04471 391008003838 RNA binding site [nucleotide binding]; other site 391008003839 Uncharacterized conserved protein [Function unknown]; Region: COG3791 391008003840 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 391008003841 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 391008003842 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 391008003843 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 391008003844 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 391008003845 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 391008003846 Walker A/P-loop; other site 391008003847 ATP binding site [chemical binding]; other site 391008003848 Q-loop/lid; other site 391008003849 ABC transporter signature motif; other site 391008003850 Walker B; other site 391008003851 D-loop; other site 391008003852 H-loop/switch region; other site 391008003853 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 391008003854 FtsX-like permease family; Region: FtsX; pfam02687 391008003855 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 391008003856 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008003857 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008003858 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391008003859 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 391008003860 active site 391008003861 phosphorylation site [posttranslational modification] 391008003862 intermolecular recognition site; other site 391008003863 dimerization interface [polypeptide binding]; other site 391008003864 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008003865 DNA binding site [nucleotide binding] 391008003866 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 391008003867 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 391008003868 ATP binding site [chemical binding]; other site 391008003869 Mg2+ binding site [ion binding]; other site 391008003870 G-X-G motif; other site 391008003871 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 391008003872 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 391008003873 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008003874 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008003875 metal binding site [ion binding]; metal-binding site 391008003876 active site 391008003877 I-site; other site 391008003878 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 391008003879 DEDDh 3'-5' exonuclease domain of RNase T; Region: RNaseT; cd06134 391008003880 dimer interface [polypeptide binding]; other site 391008003881 catalytic site [active] 391008003882 putative active site [active] 391008003883 putative substrate binding site [chemical binding]; other site 391008003884 Predicted membrane protein [Function unknown]; Region: COG2259 391008003885 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 391008003886 hypothetical protein; Provisional; Region: PRK05409 391008003887 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 391008003888 PhoU domain; Region: PhoU; pfam01895 391008003889 PhoU domain; Region: PhoU; pfam01895 391008003890 phosphate transporter ATP-binding protein; Provisional; Region: pstB; PRK10744 391008003891 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 391008003892 Walker A/P-loop; other site 391008003893 ATP binding site [chemical binding]; other site 391008003894 Q-loop/lid; other site 391008003895 ABC transporter signature motif; other site 391008003896 Walker B; other site 391008003897 D-loop; other site 391008003898 H-loop/switch region; other site 391008003899 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 391008003900 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 391008003901 dimer interface [polypeptide binding]; other site 391008003902 conserved gate region; other site 391008003903 putative PBP binding loops; other site 391008003904 ABC-ATPase subunit interface; other site 391008003905 phosphate transporter permease subunit PstC; Provisional; Region: pstC; PRK11275 391008003906 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 391008003907 dimer interface [polypeptide binding]; other site 391008003908 conserved gate region; other site 391008003909 putative PBP binding loops; other site 391008003910 ABC-ATPase subunit interface; other site 391008003911 PBP superfamily domain; Region: PBP_like_2; cl17296 391008003912 PBP superfamily domain; Region: PBP_like_2; cl17296 391008003913 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 391008003914 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 391008003915 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 391008003916 minor groove reading motif; other site 391008003917 helix-hairpin-helix signature motif; other site 391008003918 substrate binding pocket [chemical binding]; other site 391008003919 active site 391008003920 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 391008003921 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 391008003922 3-hydroxybutyryl-CoA dehydratase; Validated; Region: PRK05809 391008003923 substrate binding site [chemical binding]; other site 391008003924 oxyanion hole (OAH) forming residues; other site 391008003925 trimer interface [polypeptide binding]; other site 391008003926 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 391008003927 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 391008003928 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 391008003929 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 391008003930 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 391008003931 putative active site [active] 391008003932 putative CoA binding site [chemical binding]; other site 391008003933 nudix motif; other site 391008003934 metal binding site [ion binding]; metal-binding site 391008003935 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it...; Region: TST_Repeat_1; cd01448 391008003936 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 391008003937 active site residue [active] 391008003938 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 391008003939 active site residue [active] 391008003940 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 391008003941 amidase catalytic site [active] 391008003942 Zn binding residues [ion binding]; other site 391008003943 substrate binding site [chemical binding]; other site 391008003944 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 391008003945 Serine hydrolase; Region: Ser_hydrolase; cl17834 391008003946 23S rRNA m(2)G2445 methyltransferase; Provisional; Region: rlmL; PRK11783 391008003947 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 391008003948 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 391008003949 Protein of unknown function (DUF3325); Region: DUF3325; pfam11804 391008003950 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 391008003951 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 391008003952 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 391008003953 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 391008003954 N-terminal plug; other site 391008003955 ligand-binding site [chemical binding]; other site 391008003956 Protein of unknown function (DUF445); Region: DUF445; pfam04286 391008003957 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 391008003958 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 391008003959 inhibitor-cofactor binding pocket; inhibition site 391008003960 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008003961 catalytic residue [active] 391008003962 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; Provisional; Region: PRK09847 391008003963 Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like; Region: ALDH_GABALDH-PuuC; cd07112 391008003964 NAD(P) binding site [chemical binding]; other site 391008003965 catalytic residues [active] 391008003966 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 391008003967 metabolite-proton symporter; Region: 2A0106; TIGR00883 391008003968 putative substrate translocation pore; other site 391008003969 Hemerythrin; Region: Hemerythrin; cd12107 391008003970 Fe binding site [ion binding]; other site 391008003971 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 391008003972 active site 391008003973 phosphorylation site [posttranslational modification] 391008003974 intermolecular recognition site; other site 391008003975 dimerization interface [polypeptide binding]; other site 391008003976 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 391008003977 Response regulator receiver domain; Region: Response_reg; pfam00072 391008003978 active site 391008003979 phosphorylation site [posttranslational modification] 391008003980 intermolecular recognition site; other site 391008003981 dimerization interface [polypeptide binding]; other site 391008003982 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008003983 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008003984 metal binding site [ion binding]; metal-binding site 391008003985 active site 391008003986 I-site; other site 391008003987 MASE1; Region: MASE1; cl17823 391008003988 MASE1; Region: MASE1; cl17823 391008003989 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 391008003990 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 391008003991 Peptidase C26; Region: Peptidase_C26; pfam07722 391008003992 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 391008003993 catalytic triad [active] 391008003994 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 391008003995 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 391008003996 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 391008003997 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 391008003998 Bacterial extracellular solute-binding protein; Region: SBP_bac_6; pfam13343 391008003999 flavin-dependent oxidoreductase, MSMEG_0569 family; Region: MSMEG_0569_nitr; TIGR04046 391008004000 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 391008004001 putrescine transporter ATP-binding subunit; Provisional; Region: potG; PRK11607 391008004002 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 391008004003 Walker A/P-loop; other site 391008004004 ATP binding site [chemical binding]; other site 391008004005 Q-loop/lid; other site 391008004006 ABC transporter signature motif; other site 391008004007 Walker B; other site 391008004008 D-loop; other site 391008004009 H-loop/switch region; other site 391008004010 TOBE domain; Region: TOBE_2; pfam08402 391008004011 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 391008004012 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 391008004013 dimer interface [polypeptide binding]; other site 391008004014 conserved gate region; other site 391008004015 putative PBP binding loops; other site 391008004016 ABC-ATPase subunit interface; other site 391008004017 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 391008004018 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 391008004019 dimer interface [polypeptide binding]; other site 391008004020 conserved gate region; other site 391008004021 putative PBP binding loops; other site 391008004022 ABC-ATPase subunit interface; other site 391008004023 putative succinate semialdehyde dehydrogenase; Provisional; Region: PRK13968 391008004024 Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 1-like; Region: ALDH_SSADH1_GabD1; cd07100 391008004025 NAD(P) binding site [chemical binding]; other site 391008004026 catalytic residues [active] 391008004027 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 391008004028 Mycobacterium tuberculosis CorA-like subfamily; Region: MtCorA-like; cd12830 391008004029 oligomer interface [polypeptide binding]; other site 391008004030 metal binding site [ion binding]; metal-binding site 391008004031 metal binding site [ion binding]; metal-binding site 391008004032 putative Cl binding site [ion binding]; other site 391008004033 basic sphincter; other site 391008004034 hydrophobic gate; other site 391008004035 periplasmic entrance; other site 391008004036 Domain of unknown function (DUF4105); Region: DUF4105; pfam13387 391008004037 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 391008004038 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 391008004039 Transporter associated domain; Region: CorC_HlyC; smart01091 391008004040 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG0319 391008004041 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 391008004042 PhoH-like protein; Region: PhoH; pfam02562 391008004043 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008004044 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008004045 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 391008004046 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 391008004047 Walker A/P-loop; other site 391008004048 ATP binding site [chemical binding]; other site 391008004049 Q-loop/lid; other site 391008004050 ABC transporter signature motif; other site 391008004051 Walker B; other site 391008004052 D-loop; other site 391008004053 H-loop/switch region; other site 391008004054 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 391008004055 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 391008004056 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 391008004057 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 391008004058 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 391008004059 FeS/SAM binding site; other site 391008004060 TRAM domain; Region: TRAM; pfam01938 391008004061 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 391008004062 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 391008004063 putative C-terminal domain interface [polypeptide binding]; other site 391008004064 putative GSH binding site (G-site) [chemical binding]; other site 391008004065 putative dimer interface [polypeptide binding]; other site 391008004066 C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases; Region: GST_C_8; cd03207 391008004067 dimer interface [polypeptide binding]; other site 391008004068 N-terminal domain interface [polypeptide binding]; other site 391008004069 putative substrate binding pocket (H-site) [chemical binding]; other site 391008004070 WYL domain; Region: WYL; pfam13280 391008004071 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 391008004072 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 391008004073 N-acetyl-D-glucosamine binding site [chemical binding]; other site 391008004074 catalytic residue [active] 391008004075 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 391008004076 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 391008004077 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including...; Region: Rieske_cytochrome_bc1; cd03470 391008004078 [2Fe-2S] cluster binding site [ion binding]; other site 391008004079 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 391008004080 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cd00284 391008004081 Qi binding site; other site 391008004082 intrachain domain interface; other site 391008004083 interchain domain interface [polypeptide binding]; other site 391008004084 heme bH binding site [chemical binding]; other site 391008004085 heme bL binding site [chemical binding]; other site 391008004086 Qo binding site; other site 391008004087 interchain domain interface [polypeptide binding]; other site 391008004088 intrachain domain interface; other site 391008004089 Qi binding site; other site 391008004090 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 391008004091 Qo binding site; other site 391008004092 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 391008004093 stringent starvation protein A; Provisional; Region: sspA; PRK09481 391008004094 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 391008004095 C-terminal domain interface [polypeptide binding]; other site 391008004096 putative GSH binding site (G-site) [chemical binding]; other site 391008004097 dimer interface [polypeptide binding]; other site 391008004098 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 391008004099 dimer interface [polypeptide binding]; other site 391008004100 N-terminal domain interface [polypeptide binding]; other site 391008004101 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 391008004102 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 391008004103 Uncharacterized protein conserved in bacteria (DUF2272); Region: DUF2272; pfam10030 391008004104 Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]; Region: NadC; COG0157 391008004105 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with...; Region: QPRTase; cd01572 391008004106 dimerization interface [polypeptide binding]; other site 391008004107 active site 391008004108 Trm112p-like protein; Region: Trm112p; cl01066 391008004109 Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]; Region: PurE; COG0041 391008004110 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 391008004111 ATP-grasp domain; Region: ATP-grasp; pfam02222 391008004112 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 391008004113 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 391008004114 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 391008004115 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 391008004116 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 391008004117 putative GSH binding site [chemical binding]; other site 391008004118 catalytic residues [active] 391008004119 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008004120 NAD(P) binding site [chemical binding]; other site 391008004121 active site 391008004122 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 391008004123 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008004124 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008004125 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 391008004126 Domain of unknown function (DUF3412); Region: DUF3412; pfam11892 391008004127 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 391008004128 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 391008004129 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 391008004130 Tfp pilus assembly protein PilV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilV; COG4967 391008004131 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 391008004132 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 391008004133 Tfp pilus assembly protein PilX [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilX; COG4726 391008004134 PilX N-terminal; Region: PilX_N; pfam14341 391008004135 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 391008004136 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 391008004137 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 391008004138 Type II transport protein GspH; Region: GspH; pfam12019 391008004139 excinuclease ABC subunit B; Provisional; Region: PRK05298 391008004140 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 391008004141 ATP binding site [chemical binding]; other site 391008004142 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 391008004143 nucleotide binding region [chemical binding]; other site 391008004144 ATP-binding site [chemical binding]; other site 391008004145 Ultra-violet resistance protein B; Region: UvrB; pfam12344 391008004146 UvrB/uvrC motif; Region: UVR; pfam02151 391008004147 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 391008004148 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 391008004149 catalytic residues [active] 391008004150 MltA-interacting protein MipA; Region: MipA; cl01504 391008004151 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391008004152 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 391008004153 active site 391008004154 phosphorylation site [posttranslational modification] 391008004155 intermolecular recognition site; other site 391008004156 dimerization interface [polypeptide binding]; other site 391008004157 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008004158 DNA binding site [nucleotide binding] 391008004159 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008004160 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008004161 dimer interface [polypeptide binding]; other site 391008004162 phosphorylation site [posttranslational modification] 391008004163 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 391008004164 ATP binding site [chemical binding]; other site 391008004165 Mg2+ binding site [ion binding]; other site 391008004166 G-X-G motif; other site 391008004167 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 391008004168 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 391008004169 Competence protein; Region: Competence; pfam03772 391008004170 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 391008004171 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 391008004172 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 391008004173 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 391008004174 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 391008004175 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 391008004176 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 391008004177 Walker A/P-loop; other site 391008004178 ATP binding site [chemical binding]; other site 391008004179 Q-loop/lid; other site 391008004180 ABC transporter signature motif; other site 391008004181 Walker B; other site 391008004182 D-loop; other site 391008004183 H-loop/switch region; other site 391008004184 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 391008004185 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 391008004186 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 391008004187 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 391008004188 Ligand binding site; other site 391008004189 oligomer interface; other site 391008004190 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 391008004191 Low molecular weight phosphatase family; Region: LMWPc; cd00115 391008004192 active site 391008004193 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 391008004194 NHL repeat; Region: NHL; pfam01436 391008004195 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 391008004196 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 391008004197 GIY-YIG motif/motif A; other site 391008004198 active site 391008004199 catalytic site [active] 391008004200 putative DNA binding site [nucleotide binding]; other site 391008004201 metal binding site [ion binding]; metal-binding site 391008004202 UvrB/uvrC motif; Region: UVR; pfam02151 391008004203 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 391008004204 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 391008004205 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 391008004206 geranylgeranyl reductase family; Region: GG-red-SF; TIGR02032 391008004207 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 391008004208 FtsX-like permease family; Region: FtsX; pfam02687 391008004209 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 391008004210 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 391008004211 Walker A/P-loop; other site 391008004212 ATP binding site [chemical binding]; other site 391008004213 Q-loop/lid; other site 391008004214 ABC transporter signature motif; other site 391008004215 Walker B; other site 391008004216 D-loop; other site 391008004217 H-loop/switch region; other site 391008004218 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008004219 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008004220 Domain of unknown function (DUF4344); Region: DUF4344; pfam14247 391008004221 Flavin Reductases; Region: FlaRed; cl00801 391008004222 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 391008004223 dimerization interface [polypeptide binding]; other site 391008004224 putative DNA binding site [nucleotide binding]; other site 391008004225 putative Zn2+ binding site [ion binding]; other site 391008004226 Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ProS; COG0442 391008004227 Thioesterase-like superfamily; Region: 4HBT_3; pfam13622 391008004228 AAA domain; Region: AAA_33; pfam13671 391008004229 AAA domain; Region: AAA_17; pfam13207 391008004230 Cupin; Region: Cupin_6; pfam12852 391008004231 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008004232 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 391008004233 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008004234 camphor resistance protein CrcB; Provisional; Region: PRK14198 391008004235 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 391008004236 sequence-specific DNA binding site [nucleotide binding]; other site 391008004237 salt bridge; other site 391008004238 4Fe-4S dicluster domain; Region: Fer4_18; pfam13746 391008004239 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 391008004240 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 391008004241 apolar tunnel; other site 391008004242 heme binding site [chemical binding]; other site 391008004243 dimerization interface [polypeptide binding]; other site 391008004244 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 391008004245 HemN C-terminal domain; Region: HemN_C; pfam06969 391008004246 Sensors of blue-light using FAD; Region: BLUF; pfam04940 391008004247 UDP-N-acetyl-D-mannosaminuronate dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: WecC; COG0677 391008004248 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 391008004249 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 391008004250 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 391008004251 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast...; Region: GltS_FMN; cd02808 391008004252 active site 391008004253 FMN binding site [chemical binding]; other site 391008004254 substrate binding site [chemical binding]; other site 391008004255 3Fe-4S cluster binding site [ion binding]; other site 391008004256 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 391008004257 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391008004258 Coenzyme A binding pocket [chemical binding]; other site 391008004259 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 391008004260 uncharacterized flavoprotein, PP_4765 family; Region: flavo_PP4765; TIGR03862 391008004261 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 391008004262 The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia. This group contains both alpha and beta subunits of component 1 of the three known genetically distinct types of nitrogenase systems: a molybdenum-dependent; Region: Oxidoreductase_nitrogenase; cl02775 391008004263 rhodanese superfamily protein; Provisional; Region: PRK05320 391008004264 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 391008004265 active site residue [active] 391008004266 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 391008004267 probable oxidoreductase, LLM family; Region: LLM_2I7G; TIGR03858 391008004268 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 391008004269 Exopolysaccharide synthesis, ExoD; Region: ExoD; pfam06055 391008004270 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 391008004271 Domain of unknown function DUF21; Region: DUF21; pfam01595 391008004272 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 391008004273 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cd02205 391008004274 Transporter associated domain; Region: CorC_HlyC; smart01091 391008004275 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 391008004276 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 391008004277 Carboxypeptidase C (cathepsin A) [Amino acid transport and metabolism]; Region: COG2939 391008004278 Serine carboxypeptidase; Region: Peptidase_S10; cl08270 391008004279 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 391008004280 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 391008004281 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 391008004282 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 391008004283 Mg2+ binding site [ion binding]; other site 391008004284 G-X-G motif; other site 391008004285 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 391008004286 anchoring element; other site 391008004287 dimer interface [polypeptide binding]; other site 391008004288 ATP binding site [chemical binding]; other site 391008004289 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 391008004290 active site 391008004291 metal binding site [ion binding]; metal-binding site 391008004292 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 391008004293 CTP synthetase; Validated; Region: pyrG; PRK05380 391008004294 CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer nascent...; Region: CTGs; cd03113 391008004295 Catalytic site [active] 391008004296 active site 391008004297 UTP binding site [chemical binding]; other site 391008004298 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 391008004299 active site 391008004300 putative oxyanion hole; other site 391008004301 catalytic triad [active] 391008004302 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 391008004303 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 391008004304 enolase; Provisional; Region: eno; PRK00077 391008004305 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 391008004306 dimer interface [polypeptide binding]; other site 391008004307 metal binding site [ion binding]; metal-binding site 391008004308 substrate binding pocket [chemical binding]; other site 391008004309 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 391008004310 cell division protein FtsB; Reviewed; Region: ftsB; PRK00888 391008004311 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 391008004312 substrate binding site; other site 391008004313 dimer interface; other site 391008004314 MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis; Region: MECDP_synthase; cd00554 391008004315 homotrimer interaction site [polypeptide binding]; other site 391008004316 zinc binding site [ion binding]; other site 391008004317 CDP-binding sites; other site 391008004318 tRNA pseudouridine synthase D; Reviewed; Region: truD; PRK00984 391008004319 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 391008004320 Permutation of conserved domain; other site 391008004321 active site 391008004322 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 391008004323 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 391008004324 Smr domain; Region: Smr; pfam01713 391008004325 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 391008004326 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 391008004327 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 391008004328 S-adenosylmethionine binding site [chemical binding]; other site 391008004329 Predicted membrane protein [Function unknown]; Region: COG1238 391008004330 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 391008004331 Peptidase family M23; Region: Peptidase_M23; pfam01551 391008004332 Transposase; Region: DEDD_Tnp_IS110; pfam01548 391008004333 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 391008004334 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 391008004335 putative lipoprotein; Provisional; Region: PRK10533 391008004336 Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome; Region: Xcc1710_like; cd05560 391008004337 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]; Region: COG1534 391008004338 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 391008004339 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 391008004340 S-adenosylmethionine binding site [chemical binding]; other site 391008004341 FtsH Extracellular; Region: FtsH_ext; pfam06480 391008004342 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 391008004343 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008004344 Walker A motif; other site 391008004345 ATP binding site [chemical binding]; other site 391008004346 Walker B motif; other site 391008004347 arginine finger; other site 391008004348 Peptidase family M41; Region: Peptidase_M41; pfam01434 391008004349 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 391008004350 dihydropteroate synthase; Region: DHPS; TIGR01496 391008004351 substrate binding pocket [chemical binding]; other site 391008004352 dimer interface [polypeptide binding]; other site 391008004353 inhibitor binding site; inhibition site 391008004354 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 391008004355 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 391008004356 bacterial Hfq-like; Region: Hfq; cd01716 391008004357 hexamer interface [polypeptide binding]; other site 391008004358 Sm1 motif; other site 391008004359 RNA binding site [nucleotide binding]; other site 391008004360 Sm2 motif; other site 391008004361 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 391008004362 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 391008004363 HflX GTPase family; Region: HflX; cd01878 391008004364 G1 box; other site 391008004365 GTP/Mg2+ binding site [chemical binding]; other site 391008004366 Switch I region; other site 391008004367 G2 box; other site 391008004368 G3 box; other site 391008004369 Switch II region; other site 391008004370 G4 box; other site 391008004371 G5 box; other site 391008004372 Competence-damaged protein; Region: CinA; cl00666 391008004373 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 391008004374 ABC1 family; Region: ABC1; cl17513 391008004375 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 391008004376 LexA repressor; Validated; Region: PRK00215 391008004377 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 391008004378 Catalytic site [active] 391008004379 recombinase A; Provisional; Region: recA; PRK09354 391008004380 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 391008004381 hexamer interface [polypeptide binding]; other site 391008004382 Walker A motif; other site 391008004383 ATP binding site [chemical binding]; other site 391008004384 Walker B motif; other site 391008004385 recombination regulator RecX; Reviewed; Region: recX; PRK00117 391008004386 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 391008004387 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: AlaRS_core; cd00673 391008004388 motif 1; other site 391008004389 active site 391008004390 motif 2; other site 391008004391 motif 3; other site 391008004392 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 391008004393 DHHA1 domain; Region: DHHA1; pfam02272 391008004394 carbon storage regulator; Provisional; Region: PRK01712 391008004395 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008004396 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 391008004397 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008004398 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 391008004399 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008004400 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 391008004401 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 391008004402 N-terminal plug; other site 391008004403 ligand-binding site [chemical binding]; other site 391008004404 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 391008004405 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008004406 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008004407 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 391008004408 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 391008004409 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 391008004410 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 391008004411 dimer interface [polypeptide binding]; other site 391008004412 TPP-binding site [chemical binding]; other site 391008004413 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 391008004414 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391008004415 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 391008004416 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 391008004417 FecR protein; Region: FecR; pfam04773 391008004418 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 391008004419 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008004420 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008004421 PhoD-like phosphatase; Region: PhoD; pfam09423 391008004422 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 391008004423 putative active site [active] 391008004424 putative metal binding site [ion binding]; other site 391008004425 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 391008004426 phospholipase C, phosphocholine-specific, Pseudomonas-type; Region: PC_PLC; TIGR03396 391008004427 Phosphoesterase family; Region: Phosphoesterase; pfam04185 391008004428 Domain of unknown function (DUF756); Region: DUF756; pfam05506 391008004429 Domain of unknown function (DUF756); Region: DUF756; pfam05506 391008004430 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008004431 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008004432 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008004433 Cytochrome c [Energy production and conversion]; Region: COG3258 391008004434 Cytochrome c; Region: Cytochrom_C; pfam00034 391008004435 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 391008004436 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 391008004437 Cytochrome c; Region: Cytochrom_C; pfam00034 391008004438 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 391008004439 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 391008004440 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 391008004441 Major Facilitator Superfamily; Region: MFS_1; pfam07690 391008004442 methyl indole-3-acetate methyltransferase; Region: PLN02211; cl17657 391008004443 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 391008004444 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 391008004445 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 391008004446 N-terminal plug; other site 391008004447 ligand-binding site [chemical binding]; other site 391008004448 Pirin-related protein [General function prediction only]; Region: COG1741 391008004449 Pirin; Region: Pirin; pfam02678 391008004450 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 391008004451 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008004452 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 391008004453 dimerization interface [polypeptide binding]; other site 391008004454 Predicted alpha/beta hydrolase [General function prediction only]; Region: COG4757 391008004455 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 391008004456 substrate binding site [chemical binding]; other site 391008004457 dimer interface [polypeptide binding]; other site 391008004458 ATP binding site [chemical binding]; other site 391008004459 Protein of unknown function (DUF1275); Region: DUF1275; pfam06912 391008004460 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 391008004461 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 391008004462 putative active site [active] 391008004463 PhoH-like protein; Region: PhoH; pfam02562 391008004464 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 391008004465 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 391008004466 catalytic triad [active] 391008004467 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 391008004468 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 391008004469 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; Region: ACT_GcvR_2; cd04869 391008004470 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 391008004471 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 391008004472 dimer interface [polypeptide binding]; other site 391008004473 active site 391008004474 catalytic residue [active] 391008004475 Ferredoxin [Energy production and conversion]; Region: COG1146 391008004476 4Fe-4S binding domain; Region: Fer4; cl02805 391008004477 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 391008004478 D-xylose transporter XylE; Provisional; Region: xylE; PRK10077 391008004479 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 391008004480 putative substrate translocation pore; other site 391008004481 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 391008004482 poly(A) polymerase; Region: pcnB; TIGR01942 391008004483 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 391008004484 active site 391008004485 NTP binding site [chemical binding]; other site 391008004486 metal binding triad [ion binding]; metal-binding site 391008004487 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 391008004488 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 391008004489 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 391008004490 catalytic center binding site [active] 391008004491 ATP binding site [chemical binding]; other site 391008004492 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 391008004493 oligomerization interface [polypeptide binding]; other site 391008004494 active site 391008004495 metal binding site [ion binding]; metal-binding site 391008004496 Pantoate-beta-alanine ligase; Region: PanC; cd00560 391008004497 pantoate--beta-alanine ligase; Region: panC; TIGR00018 391008004498 active site 391008004499 ATP-binding site [chemical binding]; other site 391008004500 pantoate-binding site; other site 391008004501 HXXH motif; other site 391008004502 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 391008004503 tetramerization interface [polypeptide binding]; other site 391008004504 active site 391008004505 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 391008004506 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 391008004507 active site 391008004508 dimer interface [polypeptide binding]; other site 391008004509 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 391008004510 dimer interface [polypeptide binding]; other site 391008004511 active site 391008004512 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 391008004513 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 391008004514 active site 391008004515 phosphorylation site [posttranslational modification] 391008004516 intermolecular recognition site; other site 391008004517 dimerization interface [polypeptide binding]; other site 391008004518 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 391008004519 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008004520 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 391008004521 dimer interface [polypeptide binding]; other site 391008004522 phosphorylation site [posttranslational modification] 391008004523 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 391008004524 ATP binding site [chemical binding]; other site 391008004525 Mg2+ binding site [ion binding]; other site 391008004526 G-X-G motif; other site 391008004527 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 391008004528 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 391008004529 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 391008004530 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 391008004531 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 391008004532 active site 391008004533 response regulator; Provisional; Region: PRK09483 391008004534 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 391008004535 active site 391008004536 phosphorylation site [posttranslational modification] 391008004537 intermolecular recognition site; other site 391008004538 dimerization interface [polypeptide binding]; other site 391008004539 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 391008004540 DNA binding residues [nucleotide binding] 391008004541 dimerization interface [polypeptide binding]; other site 391008004542 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 391008004543 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 391008004544 active site 391008004545 intersubunit interface [polypeptide binding]; other site 391008004546 catalytic residue [active] 391008004547 phosphogluconate dehydratase; Validated; Region: PRK09054 391008004548 6-phosphogluconate dehydratase; Region: edd; TIGR01196 391008004549 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 391008004550 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 391008004551 putative active site [active] 391008004552 glucokinase; Provisional; Region: glk; PRK00292 391008004553 glucokinase, proteobacterial type; Region: glk; TIGR00749 391008004554 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 391008004555 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 391008004556 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 391008004557 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 391008004558 The N-terminal ATPase domain of the maltose transporter, MalK; Region: ABC_MalK_N; cd03301 391008004559 Walker A/P-loop; other site 391008004560 ATP binding site [chemical binding]; other site 391008004561 Q-loop/lid; other site 391008004562 ABC transporter signature motif; other site 391008004563 Walker B; other site 391008004564 D-loop; other site 391008004565 H-loop/switch region; other site 391008004566 TOBE domain; Region: TOBE_2; pfam08402 391008004567 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 391008004568 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 391008004569 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 391008004570 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 391008004571 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 391008004572 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 391008004573 Iron-sulfur protein interface; other site 391008004574 proximal quinone binding site [chemical binding]; other site 391008004575 SdhD (CybS) interface [polypeptide binding]; other site 391008004576 proximal heme binding site [chemical binding]; other site 391008004577 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory...; Region: SQR_TypeC_SdhD_like; cd03495 391008004578 putative SdhC subunit interface [polypeptide binding]; other site 391008004579 putative proximal heme binding site [chemical binding]; other site 391008004580 putative Iron-sulfur protein interface [polypeptide binding]; other site 391008004581 putative proximal quinone binding site; other site 391008004582 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 391008004583 L-aspartate oxidase; Provisional; Region: PRK06175 391008004584 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 391008004585 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 391008004586 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 391008004587 catalytic loop [active] 391008004588 iron binding site [ion binding]; other site 391008004589 Uncharacterized conserved protein [Function unknown]; Region: COG2938 391008004590 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 391008004591 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 391008004592 FtsX-like permease family; Region: FtsX; pfam02687 391008004593 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 391008004594 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 391008004595 Walker A/P-loop; other site 391008004596 ATP binding site [chemical binding]; other site 391008004597 Q-loop/lid; other site 391008004598 ABC transporter signature motif; other site 391008004599 Walker B; other site 391008004600 D-loop; other site 391008004601 H-loop/switch region; other site 391008004602 oxidative damage protection protein; Provisional; Region: PRK05408 391008004603 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 391008004604 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 391008004605 minor groove reading motif; other site 391008004606 helix-hairpin-helix signature motif; other site 391008004607 substrate binding pocket [chemical binding]; other site 391008004608 active site 391008004609 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 391008004610 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 391008004611 DNA binding and oxoG recognition site [nucleotide binding] 391008004612 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 391008004613 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 391008004614 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 391008004615 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 391008004616 heat shock protein 90; Provisional; Region: PRK05218 391008004617 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 391008004618 ATP binding site [chemical binding]; other site 391008004619 Mg2+ binding site [ion binding]; other site 391008004620 G-X-G motif; other site 391008004621 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 391008004622 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 391008004623 S-adenosylmethionine binding site [chemical binding]; other site 391008004624 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 391008004625 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 391008004626 active site 391008004627 (T/H)XGH motif; other site 391008004628 ferredoxin; Validated; Region: PRK07118 391008004629 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 391008004630 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 391008004631 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 391008004632 psiF repeat; Region: PsiF_repeat; pfam07769 391008004633 psiF repeat; Region: PsiF_repeat; pfam07769 391008004634 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 391008004635 active site 391008004636 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 391008004637 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008004638 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 391008004639 NHL repeat; Region: NHL; pfam01436 391008004640 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 391008004641 active site 391008004642 metal binding site [ion binding]; metal-binding site 391008004643 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 391008004644 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 391008004645 dimer interface [polypeptide binding]; other site 391008004646 substrate binding site [chemical binding]; other site 391008004647 metal binding sites [ion binding]; metal-binding site 391008004648 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 391008004649 DNA photolyase; Region: DNA_photolyase; pfam00875 391008004650 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 391008004651 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 391008004652 ligand binding site [chemical binding]; other site 391008004653 LysR family transcriptional regulator; Provisional; Region: PRK14997 391008004654 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008004655 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 391008004656 putative effector binding pocket; other site 391008004657 dimerization interface [polypeptide binding]; other site 391008004658 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 391008004659 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008004660 NAD(P) binding site [chemical binding]; other site 391008004661 active site 391008004662 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 391008004663 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008004664 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008004665 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 391008004666 Porcine testicular carbonyl reductase (PTCR)-like, classical (c) SDRs; Region: carb_red_PTCR-like_SDR_c; cd05324 391008004667 C factor cell-cell signaling protein; Provisional; Region: PRK09009 391008004668 NADP binding site [chemical binding]; other site 391008004669 substrate binding site [chemical binding]; other site 391008004670 active site 391008004671 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 391008004672 Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; Region: EEP-1; cd09083 391008004673 putative catalytic site [active] 391008004674 putative metal binding site [ion binding]; other site 391008004675 putative phosphate binding site [ion binding]; other site 391008004676 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 391008004677 Cytochrome P450; Region: p450; cl12078 391008004678 LuxR family transcriptional regulatory, chaperone HchA-associated; Region: reg_near_HchA; TIGR03541 391008004679 Autoinducer binding domain; Region: Autoind_bind; pfam03472 391008004680 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 391008004681 DNA binding residues [nucleotide binding] 391008004682 dimerization interface [polypeptide binding]; other site 391008004683 chaperone protein HchA; Provisional; Region: PRK04155 391008004684 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 391008004685 conserved cys residue [active] 391008004686 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 391008004687 Putative serine esterase (DUF676); Region: DUF676; pfam05057 391008004688 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 391008004689 Peptidase S8 family domain, uncharacterized subfamily 13; Region: Peptidases_S8_13; cd07496 391008004690 active site 391008004691 catalytic triad [active] 391008004692 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 391008004693 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008004694 ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]; Region: SunT; COG2274 391008004695 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39C; cd02419 391008004696 putative active site [active] 391008004697 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 391008004698 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 391008004699 Walker A/P-loop; other site 391008004700 ATP binding site [chemical binding]; other site 391008004701 Q-loop/lid; other site 391008004702 ABC transporter signature motif; other site 391008004703 Walker B; other site 391008004704 D-loop; other site 391008004705 H-loop/switch region; other site 391008004706 CAAX protease self-immunity; Region: Abi; pfam02517 391008004707 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 391008004708 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391008004709 Coenzyme A binding pocket [chemical binding]; other site 391008004710 Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for releasing stalled ribosome from damaged messenger RNAs; Region: SmpB; cd09294 391008004711 SmpB-tmRNA interface; other site 391008004712 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 391008004713 putative coenzyme Q binding site [chemical binding]; other site 391008004714 hypothetical protein; Validated; Region: PRK01777 391008004715 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 391008004716 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 391008004717 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 391008004718 metal binding site 2 [ion binding]; metal-binding site 391008004719 putative DNA binding helix; other site 391008004720 metal binding site 1 [ion binding]; metal-binding site 391008004721 dimer interface [polypeptide binding]; other site 391008004722 structural Zn2+ binding site [ion binding]; other site 391008004723 SGNH_hydrolase subfamily, similar to the putative arylesterase/acylhydrolase from the rumen anaerobe Prevotella bryantii XynE. The P. bryantii XynE gene is located in a xylanase gene cluster. SGNH hydrolases are a diverse family of lipases and esterases; Region: XynE_like; cd01830 391008004724 active site 391008004725 catalytic triad [active] 391008004726 oxyanion hole [active] 391008004727 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008004728 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008004729 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 391008004730 dimerization interface [polypeptide binding]; other site 391008004731 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 391008004732 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 391008004733 Walker A/P-loop; other site 391008004734 ATP binding site [chemical binding]; other site 391008004735 Q-loop/lid; other site 391008004736 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 391008004737 ABC transporter signature motif; other site 391008004738 Walker B; other site 391008004739 D-loop; other site 391008004740 H-loop/switch region; other site 391008004741 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 391008004742 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 391008004743 GrpE; Region: GrpE; pfam01025 391008004744 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 391008004745 dimer interface [polypeptide binding]; other site 391008004746 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 391008004747 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 391008004748 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 391008004749 nucleotide binding site [chemical binding]; other site 391008004750 chaperone protein DnaJ; Provisional; Region: PRK10767 391008004751 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 391008004752 HSP70 interaction site [polypeptide binding]; other site 391008004753 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 391008004754 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 391008004755 dimer interface [polypeptide binding]; other site 391008004756 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 391008004757 Helix-turn-helix domain; Region: HTH_18; pfam12833 391008004758 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008004759 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 391008004760 Major Facilitator Superfamily; Region: MFS_1; pfam07690 391008004761 putative substrate translocation pore; other site 391008004762 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 391008004763 dimer interface [polypeptide binding]; other site 391008004764 pyridoxamine kinase; Validated; Region: PRK05756 391008004765 pyridoxal binding site [chemical binding]; other site 391008004766 ATP binding site [chemical binding]; other site 391008004767 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain; Region: 2-Hacid_dh_C; pfam02826 391008004768 prephenate dehydrogenase; Provisional; Region: PRK08818 391008004769 prephenate dehydrogenase; Validated; Region: PRK08507 391008004770 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 391008004771 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 391008004772 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 391008004773 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 391008004774 Walker A/P-loop; other site 391008004775 ATP binding site [chemical binding]; other site 391008004776 Q-loop/lid; other site 391008004777 ABC transporter signature motif; other site 391008004778 Walker B; other site 391008004779 D-loop; other site 391008004780 H-loop/switch region; other site 391008004781 Uncharacterized conserved protein [Function unknown]; Region: COG1739 391008004782 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 391008004783 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 391008004784 RNA polymerase sigma factor; Provisional; Region: PRK12513 391008004785 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391008004786 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 391008004787 DNA binding residues [nucleotide binding] 391008004788 GAF domain; Region: GAF; cl17456 391008004789 GAF domain; Region: GAF_2; pfam13185 391008004790 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 391008004791 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 391008004792 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008004793 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008004794 metal binding site [ion binding]; metal-binding site 391008004795 active site 391008004796 I-site; other site 391008004797 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 391008004798 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 391008004799 Ornithine/acetylornithine aminotransferase [Amino acid transport and metabolism]; Region: ArgD; COG4992 391008004800 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 391008004801 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 391008004802 catalytic residue [active] 391008004803 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 391008004804 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 391008004805 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 391008004806 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 391008004807 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 391008004808 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 391008004809 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 391008004810 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 391008004811 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 391008004812 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 391008004813 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 391008004814 Protein export membrane protein; Region: SecD_SecF; pfam02355 391008004815 trans-2-enoyl-CoA reductase; Provisional; Region: PRK13656 391008004816 NAD(P)H binding domain of trans-2-enoyl-CoA reductase; Region: Eno-Rase_NADH_b; pfam12242 391008004817 Trans-2-enoyl-CoA reductase catalytic region; Region: Enoyl_reductase; pfam12241 391008004818 Enoyl reductase FAD binding domain; Region: Eno-Rase_FAD_bd; pfam07055 391008004819 Response regulator receiver domain; Region: Response_reg; pfam00072 391008004820 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 391008004821 active site 391008004822 phosphorylation site [posttranslational modification] 391008004823 dimerization interface [polypeptide binding]; other site 391008004824 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 391008004825 putative active site [active] 391008004826 heme pocket [chemical binding]; other site 391008004827 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008004828 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008004829 metal binding site [ion binding]; metal-binding site 391008004830 active site 391008004831 I-site; other site 391008004832 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 391008004833 HI0933-like protein; Region: HI0933_like; pfam03486 391008004834 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 391008004835 Domain of unknown function (DUF1853); Region: DUF1853; cl01545 391008004836 YaeQ protein; Region: YaeQ; pfam07152 391008004837 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 391008004838 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 391008004839 active site 391008004840 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; pfam02639 391008004841 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 391008004842 DNA-binding site [nucleotide binding]; DNA binding site 391008004843 RNA-binding motif; other site 391008004844 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 391008004845 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 391008004846 putative C-terminal domain interface [polypeptide binding]; other site 391008004847 putative GSH binding site (G-site) [chemical binding]; other site 391008004848 putative dimer interface [polypeptide binding]; other site 391008004849 C-terminal, alpha helical domain of GTT1-like Glutathione S-transferases; Region: GST_C_GTT1_like; cd03189 391008004850 putative N-terminal domain interface [polypeptide binding]; other site 391008004851 putative dimer interface [polypeptide binding]; other site 391008004852 putative substrate binding pocket (H-site) [chemical binding]; other site 391008004853 hypothetical protein; Validated; Region: PRK00029 391008004854 Uncharacterized conserved protein [Function unknown]; Region: COG0397 391008004855 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 391008004856 active site 391008004857 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 391008004858 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 391008004859 ATP binding site [chemical binding]; other site 391008004860 Mg++ binding site [ion binding]; other site 391008004861 motif III; other site 391008004862 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 391008004863 nucleotide binding region [chemical binding]; other site 391008004864 ATP-binding site [chemical binding]; other site 391008004865 RNA recognition motif in Escherichia coli RNA helicase dbpA and similar proteins; Region: RRM_EcDbpA_like; cd12501 391008004866 putative RNA binding site [nucleotide binding]; other site 391008004867 Predicted membrane protein [Function unknown]; Region: COG2855 391008004868 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 391008004869 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008004870 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 391008004871 putative dimerization interface [polypeptide binding]; other site 391008004872 ABC transporter ATPase component; Reviewed; Region: PRK11147 391008004873 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 391008004874 Walker A/P-loop; other site 391008004875 ATP binding site [chemical binding]; other site 391008004876 Q-loop/lid; other site 391008004877 ABC transporter signature motif; other site 391008004878 Walker B; other site 391008004879 D-loop; other site 391008004880 H-loop/switch region; other site 391008004881 ABC transporter; Region: ABC_tran_2; pfam12848 391008004882 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 391008004883 Transposase; Region: DEDD_Tnp_IS110; pfam01548 391008004884 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 391008004885 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 391008004886 Cytochrome c553 [Energy production and conversion]; Region: COG2863 391008004887 Cytochrome c; Region: Cytochrom_C; cl11414 391008004888 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 391008004889 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008004890 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008004891 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 391008004892 Protein export membrane protein; Region: SecD_SecF; cl14618 391008004893 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 391008004894 Protein export membrane protein; Region: SecD_SecF; cl14618 391008004895 Uncharacterized homolog of PrgY (pheromone shutdown protein) [Function unknown]; Region: COG1916 391008004896 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 391008004897 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391008004898 Coenzyme A binding pocket [chemical binding]; other site 391008004899 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 391008004900 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 391008004901 putative active site; other site 391008004902 catalytic triad [active] 391008004903 putative dimer interface [polypeptide binding]; other site 391008004904 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957; cl01113 391008004905 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 391008004906 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 391008004907 cytidylate kinase; Provisional; Region: cmk; PRK00023 391008004908 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 391008004909 CMP-binding site; other site 391008004910 The sites determining sugar specificity; other site 391008004911 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 391008004912 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 391008004913 RNA binding site [nucleotide binding]; other site 391008004914 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 391008004915 RNA binding site [nucleotide binding]; other site 391008004916 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec3; cd05688 391008004917 RNA binding site [nucleotide binding]; other site 391008004918 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 391008004919 RNA binding site [nucleotide binding]; other site 391008004920 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 391008004921 RNA binding site [nucleotide binding]; other site 391008004922 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec6; cd05691 391008004923 RNA binding site [nucleotide binding]; other site 391008004924 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 391008004925 IHF dimer interface [polypeptide binding]; other site 391008004926 IHF - DNA interface [nucleotide binding]; other site 391008004927 tetratricopeptide repeat protein; Provisional; Region: PRK11788 391008004928 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 391008004929 binding surface 391008004930 TPR motif; other site 391008004931 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 391008004932 The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine precursor; Region: GT_WbpL_WbcO_like; cd06854 391008004933 Mg++ binding site [ion binding]; other site 391008004934 putative catalytic motif [active] 391008004935 putative substrate binding site [chemical binding]; other site 391008004936 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 391008004937 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 391008004938 NAD(P) binding site [chemical binding]; other site 391008004939 homodimer interface [polypeptide binding]; other site 391008004940 substrate binding site [chemical binding]; other site 391008004941 active site 391008004942 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 391008004943 active site 391008004944 tetramer interface; other site 391008004945 acetyl-CoA acetyltransferase; Provisional; Region: PRK09052 391008004946 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 391008004947 dimer interface [polypeptide binding]; other site 391008004948 active site 391008004949 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 391008004950 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 391008004951 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 391008004952 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 391008004953 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008004954 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 391008004955 active site 391008004956 multimer interface [polypeptide binding]; other site 391008004957 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 391008004958 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 391008004959 FeS/SAM binding site; other site 391008004960 Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilF; COG3063 391008004961 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 391008004962 binding surface 391008004963 TPR motif; other site 391008004964 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 391008004965 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 391008004966 non-specific DNA binding site [nucleotide binding]; other site 391008004967 salt bridge; other site 391008004968 sequence-specific DNA binding site [nucleotide binding]; other site 391008004969 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 391008004970 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 391008004971 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 391008004972 binding surface 391008004973 TPR motif; other site 391008004974 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 391008004975 Beta-barrel assembly machinery (Bam) complex component B and related proteins; Region: BamB_YfgL; cd10276 391008004976 Trp docking motif [polypeptide binding]; other site 391008004977 GTP-binding protein Der; Reviewed; Region: PRK00093 391008004978 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 391008004979 G1 box; other site 391008004980 GTP/Mg2+ binding site [chemical binding]; other site 391008004981 Switch I region; other site 391008004982 G2 box; other site 391008004983 Switch II region; other site 391008004984 G3 box; other site 391008004985 G4 box; other site 391008004986 G5 box; other site 391008004987 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 391008004988 G1 box; other site 391008004989 GTP/Mg2+ binding site [chemical binding]; other site 391008004990 Switch I region; other site 391008004991 G2 box; other site 391008004992 G3 box; other site 391008004993 Switch II region; other site 391008004994 G4 box; other site 391008004995 G5 box; other site 391008004996 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 391008004997 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 391008004998 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 391008004999 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008005000 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008005001 molybdopterin biosynthesis protein MoeB; Validated; Region: PRK08762 391008005002 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 391008005003 active site residue [active] 391008005004 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD...; Region: ThiF_MoeB_HesA_family; cd00757 391008005005 ATP binding site [chemical binding]; other site 391008005006 substrate interface [chemical binding]; other site 391008005007 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 391008005008 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 391008005009 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 391008005010 TrkA-N domain; Region: TrkA_N; pfam02254 391008005011 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 391008005012 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 391008005013 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 391008005014 homodimer interface [polypeptide binding]; other site 391008005015 NADP binding site [chemical binding]; other site 391008005016 substrate binding site [chemical binding]; other site 391008005017 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 391008005018 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 391008005019 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a...; Region: CBS_pair_IMPDH; cd04601 391008005020 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 391008005021 active site 391008005022 GMP synthase; Reviewed; Region: guaA; PRK00074 391008005023 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 391008005024 AMP/PPi binding site [chemical binding]; other site 391008005025 candidate oxyanion hole; other site 391008005026 catalytic triad [active] 391008005027 potential glutamine specificity residues [chemical binding]; other site 391008005028 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 391008005029 ATP Binding subdomain [chemical binding]; other site 391008005030 Ligand Binding sites [chemical binding]; other site 391008005031 Dimerization subdomain; other site 391008005032 KTSC domain; Region: KTSC; pfam13619 391008005033 Domain of unknown function DUF87; Region: DUF87; pfam01935 391008005034 HerA helicase [Replication, recombination, and repair]; Region: COG0433 391008005035 SIR2-like domain; Region: SIR2_2; pfam13289 391008005036 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4487 391008005037 Uncharacterized protein conserved in bacteria (DUF2130); Region: DUF2130; pfam09903 391008005038 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008005039 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008005040 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 391008005041 putative effector binding pocket; other site 391008005042 dimerization interface [polypeptide binding]; other site 391008005043 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein; Region: GATase1_Hsp31_like; cd03141 391008005044 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 391008005045 potential catalytic triad [active] 391008005046 conserved cys residue [active] 391008005047 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 391008005048 Zn binding site [ion binding]; other site 391008005049 3-hydroxybutyrate dehydrogenase; Provisional; Region: PRK12429 391008005050 d-3-hydroxybutyrate dehydrogenase (HBDH), classical (c) SDRs; Region: HBDH_SDR_c; cd08940 391008005051 NAD binding site [chemical binding]; other site 391008005052 homotetramer interface [polypeptide binding]; other site 391008005053 homodimer interface [polypeptide binding]; other site 391008005054 substrate binding site [chemical binding]; other site 391008005055 active site 391008005056 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; some contain an N-terminal GntR family winged HTH DNA-binding domain; Region: SRPBCC_CalC_Aha1-like_GntR-HTH; cd08893 391008005057 putative hydrophobic ligand binding site [chemical binding]; other site 391008005058 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 391008005059 dimerization interface [polypeptide binding]; other site 391008005060 putative DNA binding site [nucleotide binding]; other site 391008005061 putative Zn2+ binding site [ion binding]; other site 391008005062 Putative hydrophobic ligand-binding SRPBCC domain of Micromonospora echinospora CalC, human Aha1, and related proteins; Region: SRPBCC_CalC_Aha1-like; cd07814 391008005063 putative hydrophobic ligand binding site [chemical binding]; other site 391008005064 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391008005065 Coenzyme A binding pocket [chemical binding]; other site 391008005066 short chain dehydrogenase; Provisional; Region: PRK06180 391008005067 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 391008005068 NADP binding site [chemical binding]; other site 391008005069 active site 391008005070 steroid binding site; other site 391008005071 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 391008005072 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 391008005073 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008005074 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 391008005075 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008005076 transcriptional activator FtrA; Provisional; Region: ftrA; PRK09393 391008005077 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 391008005078 conserved cys residue [active] 391008005079 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008005080 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008005081 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 391008005082 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 391008005083 N-terminal plug; other site 391008005084 ligand-binding site [chemical binding]; other site 391008005085 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 391008005086 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 391008005087 Protein of unknown function (DUF3088); Region: DUF3088; pfam11287 391008005088 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 391008005089 probable oxidoreductase, LLM family; Region: LLM_2I7G; TIGR03858 391008005090 FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family; Region: FMN_nitrolo; TIGR03860 391008005091 nitrilotriacetate monoxygenase oxidizes nitrilotriacetate utilizing reduced flavin mononucleotide (FMNH2) and oxygen. The FMNH2 is provided by an NADH:flavin mononucleotide (FMN) oxidorductase that uses NADH to reduce FMN to FMNH2; Region: Nitrilotriacetate_monoxgenase; cd01095 391008005092 active site 391008005093 non-prolyl cis peptide bond; other site 391008005094 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 391008005095 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 391008005096 metal binding site [ion binding]; metal-binding site 391008005097 putative dimer interface [polypeptide binding]; other site 391008005098 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391008005099 Coenzyme A binding pocket [chemical binding]; other site 391008005100 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 391008005101 dimer interface [polypeptide binding]; other site 391008005102 conserved gate region; other site 391008005103 putative PBP binding loops; other site 391008005104 ABC-ATPase subunit interface; other site 391008005105 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 391008005106 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 391008005107 Walker A/P-loop; other site 391008005108 ATP binding site [chemical binding]; other site 391008005109 Q-loop/lid; other site 391008005110 ABC transporter signature motif; other site 391008005111 Walker B; other site 391008005112 D-loop; other site 391008005113 H-loop/switch region; other site 391008005114 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 391008005115 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 391008005116 substrate binding pocket [chemical binding]; other site 391008005117 membrane-bound complex binding site; other site 391008005118 hinge residues; other site 391008005119 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 391008005120 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 391008005121 short chain dehydrogenase; Provisional; Region: PRK07825 391008005122 NADP binding site [chemical binding]; other site 391008005123 active site 391008005124 steroid binding site; other site 391008005125 Protein of unknown function (DUF1097); Region: DUF1097; pfam06496 391008005126 tetrahydroxynaphthalene/trihydroxynaphthalene reductase-like, classical (c) SDRs; Region: THN_reductase-like_SDR_c; cd05362 391008005127 short chain dehydrogenase; Provisional; Region: PRK12937 391008005128 NADP binding site [chemical binding]; other site 391008005129 homodimer interface [polypeptide binding]; other site 391008005130 active site 391008005131 substrate binding site [chemical binding]; other site 391008005132 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 391008005133 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 391008005134 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 391008005135 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008005136 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 391008005137 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 391008005138 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008005139 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 391008005140 dimerization interface [polypeptide binding]; other site 391008005141 Major Facilitator Superfamily; Region: MFS_1; pfam07690 391008005142 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 391008005143 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 391008005144 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 391008005145 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008005146 NAD(P) binding site [chemical binding]; other site 391008005147 active site 391008005148 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 391008005149 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 391008005150 dimerization interface [polypeptide binding]; other site 391008005151 putative DNA binding site [nucleotide binding]; other site 391008005152 putative Zn2+ binding site [ion binding]; other site 391008005153 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 391008005154 active site residue [active] 391008005155 Protein of unknown function (DUF2938); Region: DUF2938; pfam11158 391008005156 Aminoglycoside 3'-phosphotransferase (APH). The APH subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin...; Region: APH; cd05150 391008005157 active site 391008005158 ATP binding site [chemical binding]; other site 391008005159 Phosphotransferase enzyme family; Region: APH; pfam01636 391008005160 antibiotic binding site [chemical binding]; other site 391008005161 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 391008005162 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008005163 Phosphotransferase enzyme family; Region: APH; pfam01636 391008005164 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 391008005165 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 391008005166 EamA-like transporter family; Region: EamA; cl17759 391008005167 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 391008005168 FAD binding domain; Region: FAD_binding_4; pfam01565 391008005169 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 391008005170 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 391008005171 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires...; Region: DHOD_2_like; cd04738 391008005172 quinone interaction residues [chemical binding]; other site 391008005173 active site 391008005174 catalytic residues [active] 391008005175 FMN binding site [chemical binding]; other site 391008005176 substrate binding site [chemical binding]; other site 391008005177 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 391008005178 S-adenosylmethionine binding site [chemical binding]; other site 391008005179 Domain of unknown function (DUF4190); Region: DUF4190; pfam13828 391008005180 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 391008005181 classical (c) SDRs; Region: SDR_c; cd05233 391008005182 NAD(P) binding site [chemical binding]; other site 391008005183 active site 391008005184 aldehyde dehydrogenase family 7 member; Region: PLN02315 391008005185 NAD+-dependent alpha-aminoadipic semialdehyde dehydrogenase, ALDH family members 7A1 and 7B; Region: ALDH_F7_AASADH; cd07130 391008005186 tetrameric interface [polypeptide binding]; other site 391008005187 NAD binding site [chemical binding]; other site 391008005188 catalytic residues [active] 391008005189 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 391008005190 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 391008005191 inhibitor site; inhibition site 391008005192 active site 391008005193 dimer interface [polypeptide binding]; other site 391008005194 catalytic residue [active] 391008005195 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 391008005196 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 391008005197 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 391008005198 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 391008005199 Helix-turn-helix domain; Region: HTH_18; pfam12833 391008005200 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008005201 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 391008005202 Ligand Binding Site [chemical binding]; other site 391008005203 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008005204 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 391008005205 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 391008005206 active site 391008005207 phosphorylation site [posttranslational modification] 391008005208 intermolecular recognition site; other site 391008005209 dimerization interface [polypeptide binding]; other site 391008005210 PAS domain S-box; Region: sensory_box; TIGR00229 391008005211 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 391008005212 putative active site [active] 391008005213 histidine kinase; Provisional; Region: PRK13557 391008005214 heme pocket [chemical binding]; other site 391008005215 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 391008005216 ATP binding site [chemical binding]; other site 391008005217 G-X-G motif; other site 391008005218 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 391008005219 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 391008005220 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008005221 dimer interface [polypeptide binding]; other site 391008005222 phosphorylation site [posttranslational modification] 391008005223 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 391008005224 ATP binding site [chemical binding]; other site 391008005225 Mg2+ binding site [ion binding]; other site 391008005226 G-X-G motif; other site 391008005227 Response regulator receiver domain; Region: Response_reg; pfam00072 391008005228 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 391008005229 active site 391008005230 phosphorylation site [posttranslational modification] 391008005231 intermolecular recognition site; other site 391008005232 dimerization interface [polypeptide binding]; other site 391008005233 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 391008005234 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 391008005235 active site 391008005236 phosphorylation site [posttranslational modification] 391008005237 intermolecular recognition site; other site 391008005238 dimerization interface [polypeptide binding]; other site 391008005239 Response regulator receiver domain; Region: Response_reg; pfam00072 391008005240 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 391008005241 active site 391008005242 phosphorylation site [posttranslational modification] 391008005243 intermolecular recognition site; other site 391008005244 dimerization interface [polypeptide binding]; other site 391008005245 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 391008005246 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 391008005247 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 391008005248 CheB methylesterase; Region: CheB_methylest; pfam01339 391008005249 Response regulator receiver domain; Region: Response_reg; pfam00072 391008005250 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 391008005251 active site 391008005252 phosphorylation site [posttranslational modification] 391008005253 intermolecular recognition site; other site 391008005254 dimerization interface [polypeptide binding]; other site 391008005255 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008005256 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008005257 dimer interface [polypeptide binding]; other site 391008005258 phosphorylation site [posttranslational modification] 391008005259 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 391008005260 ATP binding site [chemical binding]; other site 391008005261 Mg2+ binding site [ion binding]; other site 391008005262 G-X-G motif; other site 391008005263 Sensors of blue-light using FAD; Region: BLUF; pfam04940 391008005264 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 391008005265 dimerization interface [polypeptide binding]; other site 391008005266 putative DNA binding site [nucleotide binding]; other site 391008005267 putative Zn2+ binding site [ion binding]; other site 391008005268 Predicted transporter component [General function prediction only]; Region: COG2391 391008005269 Predicted transporter component [General function prediction only]; Region: COG2391 391008005270 Sulphur transport; Region: Sulf_transp; pfam04143 391008005271 Choloylglycine hydrolase (CGH) is a bile salt-modifying enzyme that hydrolyzes non-peptide carbon-nitrogen bonds in choloylglycine and choloyltaurine, both of which are present in bile. CGH is present in a number of probiotic microbial organisms that...; Region: Ntn_CGH; cd01902 391008005272 Linear amide C-N hydrolases, choloylglycine hydrolase family; Region: CBAH; pfam02275 391008005273 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008005274 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 391008005275 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008005276 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 391008005277 bifunctional aspartokinase I/homoserine dehydrogenase I; Provisional; Region: thrA; PRK09436 391008005278 AAK_AK-HSDH: Amino Acid Kinase Superfamily (AAK), AK-HSDH; this CD includes the N-terminal catalytic domain of aspartokinase (AK) of the bifunctional enzyme AK - homoserine dehydrogenase (HSDH). These aspartokinases are found in bacteria (E. coli...; Region: AAK_AK-HSDH; cd04257 391008005279 putative catalytic residues [active] 391008005280 putative nucleotide binding site [chemical binding]; other site 391008005281 putative aspartate binding site [chemical binding]; other site 391008005282 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA-like_1; cd04921 391008005283 dimer interface [polypeptide binding]; other site 391008005284 putative threonine allosteric regulatory site; other site 391008005285 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA_2; cd04922 391008005286 putative threonine allosteric regulatory site; other site 391008005287 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 391008005288 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 391008005289 homoserine kinase; Provisional; Region: PRK01212 391008005290 threonine synthase; Validated; Region: PRK09225 391008005291 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 391008005292 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 391008005293 catalytic residue [active] 391008005294 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 391008005295 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 391008005296 ligand binding site [chemical binding]; other site 391008005297 flexible hinge region; other site 391008005298 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 391008005299 putative switch regulator; other site 391008005300 non-specific DNA interactions [nucleotide binding]; other site 391008005301 DNA binding site [nucleotide binding] 391008005302 sequence specific DNA binding site [nucleotide binding]; other site 391008005303 putative cAMP binding site [chemical binding]; other site 391008005304 Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: HisS; COG0124 391008005305 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 391008005306 dimer interface [polypeptide binding]; other site 391008005307 motif 1; other site 391008005308 active site 391008005309 motif 2; other site 391008005310 motif 3; other site 391008005311 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 391008005312 anticodon binding site; other site 391008005313 Trp repressor protein; Region: Trp_repressor; cl17266 391008005314 ATP phosphoribosyltransferase; Reviewed; Region: hisG; PRK00489 391008005315 ATP phosphoribosyltransferase; Region: hisG; TIGR00070 391008005316 ATP phosphoribosyltransferase, C-terminal domain; Region: HisG_C-term; TIGR03455 391008005317 Histidinol dehydrogenase, HisD, E.C 1.1.1.23. Histidinol dehydrogenase catalyzes the last two steps in the L-histidine biosynthesis pathway, which is conserved in bacteria, archaea, fungi, and plants. These last two steps are (i) the NAD-dependent...; Region: Histidinol_dh; cd06572 391008005318 histidinol dehydrogenase; Region: hisD; TIGR00069 391008005319 NAD binding site [chemical binding]; other site 391008005320 dimerization interface [polypeptide binding]; other site 391008005321 product binding site; other site 391008005322 substrate binding site [chemical binding]; other site 391008005323 zinc binding site [ion binding]; other site 391008005324 catalytic residues [active] 391008005325 histidinol-phosphate aminotransferase; Provisional; Region: PRK04781 391008005326 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 391008005327 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008005328 homodimer interface [polypeptide binding]; other site 391008005329 catalytic residue [active] 391008005330 imidazole glycerol-phosphate dehydratase/histidinol phosphatase; Provisional; Region: PRK05446 391008005331 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 391008005332 active site 391008005333 motif I; other site 391008005334 motif II; other site 391008005335 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 391008005336 putative active site pocket [active] 391008005337 4-fold oligomerization interface [polypeptide binding]; other site 391008005338 metal binding residues [ion binding]; metal-binding site 391008005339 3-fold/trimer interface [polypeptide binding]; other site 391008005340 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13141 391008005341 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 391008005342 putative active site [active] 391008005343 oxyanion strand; other site 391008005344 catalytic triad [active] 391008005345 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 391008005346 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 391008005347 catalytic residues [active] 391008005348 The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)...; Region: HisF; cd04731 391008005349 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 391008005350 substrate binding site [chemical binding]; other site 391008005351 glutamase interaction surface [polypeptide binding]; other site 391008005352 Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]; Region: HisI; COG0139 391008005353 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 391008005354 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 391008005355 metal binding site [ion binding]; metal-binding site 391008005356 Cna protein B-type domain; Region: Cna_B_2; pfam13715 391008005357 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cd00838 391008005358 active site 391008005359 metal binding site [ion binding]; metal-binding site 391008005360 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 391008005361 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 391008005362 active site 391008005363 metal binding site [ion binding]; metal-binding site 391008005364 glucokinase; Provisional; Region: PRK12408 391008005365 glucokinase, proteobacterial type; Region: glk; TIGR00749 391008005366 Glycosylasparaginase catalyzes the hydrolysis of the glycosylamide bond of asparagine-linked glycoproteins. This enzyme is an amidase located inside lysosomes. Mutation of this gene in humans causes a genetic disorder known as aspartylglycosaminuria (AGU)...; Region: Glycosylasparaginase; cd04513 391008005367 active site 391008005368 dimer interface [polypeptide binding]; other site 391008005369 catalytic nucleophile [active] 391008005370 Uncharacterized protein involved in copper resistance [Inorganic ion transport and metabolism]; Region: CutC; COG3142 391008005371 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008005372 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008005373 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 391008005374 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 391008005375 metal-binding site [ion binding] 391008005376 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 391008005377 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 391008005378 metal-binding site [ion binding] 391008005379 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 391008005380 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 391008005381 motif II; other site 391008005382 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 391008005383 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 391008005384 DNA binding residues [nucleotide binding] 391008005385 dimer interface [polypeptide binding]; other site 391008005386 copper binding site [ion binding]; other site 391008005387 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 391008005388 metal-binding site [ion binding] 391008005389 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 391008005390 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008005391 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008005392 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 391008005393 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 391008005394 Transcriptional regulators [Transcription]; Region: PurR; COG1609 391008005395 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 391008005396 DNA binding site [nucleotide binding] 391008005397 domain linker motif; other site 391008005398 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 391008005399 putative ligand binding site [chemical binding]; other site 391008005400 putative dimerization interface [polypeptide binding]; other site 391008005401 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 391008005402 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 391008005403 putative substrate translocation pore; other site 391008005404 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 391008005405 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 391008005406 Fructokinases (FRKs) mainly from bacteria and plants are enzymes with high specificity for fructose, as are all FRKs, but they catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into...; Region: bac_FRK; cd01167 391008005407 putative substrate binding site [chemical binding]; other site 391008005408 putative ATP binding site [chemical binding]; other site 391008005409 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 391008005410 dimerization interface [polypeptide binding]; other site 391008005411 putative active cleft [active] 391008005412 Beta-galactosidase/beta-glucuronidase [Carbohydrate transport and metabolism]; Region: LacZ; COG3250 391008005413 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 391008005414 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 391008005415 Predicted enolase-phosphatase [Energy production and conversion]; Region: COG4229 391008005416 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cl17915 391008005417 motif I; other site 391008005418 motif II; other site 391008005419 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1791 391008005420 Cupin domain; Region: Cupin_2; cl17218 391008005421 methylthioribulose-1-phosphate dehydratase; Provisional; Region: PRK09220 391008005422 intersubunit interface [polypeptide binding]; other site 391008005423 active site 391008005424 Zn2+ binding site [ion binding]; other site 391008005425 amino acid transporter; Region: 2A0306; TIGR00909 391008005426 C-terminus of AA_permease; Region: AA_permease_C; pfam13906 391008005427 amino acid transporter; Region: 2A0306; TIGR00909 391008005428 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. They also contain a...; Region: Nudix_Hydrolase_1; cd03674 391008005429 nudix motif; other site 391008005430 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 391008005431 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_3; cd12176 391008005432 ligand binding site [chemical binding]; other site 391008005433 NAD binding site [chemical binding]; other site 391008005434 tetramer interface [polypeptide binding]; other site 391008005435 catalytic site [active] 391008005436 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 391008005437 L-serine binding site [chemical binding]; other site 391008005438 ACT domain interface; other site 391008005439 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 391008005440 FAD binding domain; Region: FAD_binding_4; pfam01565 391008005441 Protein of unknown function (DUF2388); Region: DUF2388; cl09731 391008005442 Domain of unknown function (DUF4105); Region: DUF4105; pfam13387 391008005443 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008005444 HAMP domain; Region: HAMP; pfam00672 391008005445 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008005446 dimer interface [polypeptide binding]; other site 391008005447 phosphorylation site [posttranslational modification] 391008005448 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 391008005449 ATP binding site [chemical binding]; other site 391008005450 Mg2+ binding site [ion binding]; other site 391008005451 G-X-G motif; other site 391008005452 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391008005453 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 391008005454 active site 391008005455 phosphorylation site [posttranslational modification] 391008005456 intermolecular recognition site; other site 391008005457 dimerization interface [polypeptide binding]; other site 391008005458 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008005459 DNA binding site [nucleotide binding] 391008005460 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 391008005461 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008005462 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 391008005463 Predicted periplasmic protein [General function prediction only]; Region: COG3895 391008005464 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; pfam09864 391008005465 elongation factor P; Provisional; Region: PRK04542 391008005466 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 391008005467 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_1; cd04470 391008005468 RNA binding site [nucleotide binding]; other site 391008005469 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_2; cd05794 391008005470 RNA binding site [nucleotide binding]; other site 391008005471 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08217 391008005472 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008005473 NAD(P) binding site [chemical binding]; other site 391008005474 active site 391008005475 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 391008005476 active site 391008005477 catalytic residues [active] 391008005478 metal binding site [ion binding]; metal-binding site 391008005479 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_19; cd07262 391008005480 enoyl-CoA hydratase; Provisional; Region: PRK05995 391008005481 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 391008005482 substrate binding site [chemical binding]; other site 391008005483 oxyanion hole (OAH) forming residues; other site 391008005484 trimer interface [polypeptide binding]; other site 391008005485 FeoA domain; Region: FeoA; pfam04023 391008005486 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 391008005487 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 391008005488 G1 box; other site 391008005489 GTP/Mg2+ binding site [chemical binding]; other site 391008005490 Switch I region; other site 391008005491 G2 box; other site 391008005492 G3 box; other site 391008005493 Switch II region; other site 391008005494 G4 box; other site 391008005495 G5 box; other site 391008005496 Nucleoside recognition; Region: Gate; pfam07670 391008005497 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 391008005498 Nucleoside recognition; Region: Gate; pfam07670 391008005499 Domain of unknown function (DUF4304); Region: DUF4304; pfam14137 391008005500 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 391008005501 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 391008005502 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 391008005503 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 391008005504 DNA binding residues [nucleotide binding] 391008005505 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08642 391008005506 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008005507 NAD(P) binding site [chemical binding]; other site 391008005508 active site 391008005509 dihydrodipicolinate reductase; Provisional; Region: PRK00048 391008005510 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 391008005511 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 391008005512 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 391008005513 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 391008005514 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 391008005515 catalytic site [active] 391008005516 subunit interface [polypeptide binding]; other site 391008005517 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 391008005518 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 391008005519 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 391008005520 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 391008005521 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 391008005522 ATP-grasp domain; Region: ATP-grasp_4; cl17255 391008005523 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 391008005524 IMP binding site; other site 391008005525 dimer interface [polypeptide binding]; other site 391008005526 interdomain contacts; other site 391008005527 partial ornithine binding site; other site 391008005528 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 391008005529 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 391008005530 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 391008005531 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4255 391008005532 Protein of unknown function (DUF1176); Region: DUF1176; pfam06674 391008005533 Protein of unknown function (DUF1176); Region: DUF1176; pfam06674 391008005534 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 391008005535 DHH family; Region: DHH; pfam01368 391008005536 DHHA1 domain; Region: DHHA1; pfam02272 391008005537 Protein of unknown function (DUF1176); Region: DUF1176; pfam06674 391008005538 Vault protein inter-alpha-trypsin domain; Region: VIT; cl02699 391008005539 Uncharacterized protein conserved in bacteria (DUF2135); Region: DUF2135; pfam09906 391008005540 Transposase; Region: DEDD_Tnp_IS110; pfam01548 391008005541 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 391008005542 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 391008005543 glucans biosynthesis protein; Provisional; Region: opgC; PRK03854 391008005544 glucans biosynthesis protein; Provisional; Region: opgC; PRK03854 391008005545 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 391008005546 LytTr DNA-binding domain; Region: LytTR; smart00850 391008005547 peptide chain release factor 2; Provisional; Region: PRK08787 391008005548 This domain is found in peptide chain release factors; Region: PCRF; smart00937 391008005549 RF-1 domain; Region: RF-1; pfam00472 391008005550 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 391008005551 salt bridge; other site 391008005552 non-specific DNA binding site [nucleotide binding]; other site 391008005553 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 391008005554 sequence-specific DNA binding site [nucleotide binding]; other site 391008005555 putative succinate semialdehyde dehydrogenase; Provisional; Region: PRK13968 391008005556 Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 1-like; Region: ALDH_SSADH1_GabD1; cd07100 391008005557 NAD(P) binding site [chemical binding]; other site 391008005558 catalytic residues [active] 391008005559 acetolactate synthase; Reviewed; Region: PRK08322 391008005560 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 391008005561 PYR/PP interface [polypeptide binding]; other site 391008005562 dimer interface [polypeptide binding]; other site 391008005563 TPP binding site [chemical binding]; other site 391008005564 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 391008005565 Thiamine pyrophosphate (TPP) family, Acetolactate synthase (ALS) subfamily, TPP-binding module; composed of proteins similar to Klebsiella pneumoniae ALS, a catabolic enzyme required for butanediol fermentation. ALS catalyzes the conversion of 2...; Region: TPP_ALS; cd02010 391008005566 TPP-binding site [chemical binding]; other site 391008005567 dimer interface [polypeptide binding]; other site 391008005568 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 391008005569 LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop; Region: LysRS_N; cd04322 391008005570 dimer interface [polypeptide binding]; other site 391008005571 putative anticodon binding site; other site 391008005572 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 391008005573 motif 1; other site 391008005574 active site 391008005575 motif 2; other site 391008005576 motif 3; other site 391008005577 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 391008005578 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 391008005579 active site 391008005580 phosphorylation site [posttranslational modification] 391008005581 intermolecular recognition site; other site 391008005582 dimerization interface [polypeptide binding]; other site 391008005583 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 391008005584 Zn2+ binding site [ion binding]; other site 391008005585 Mg2+ binding site [ion binding]; other site 391008005586 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008005587 dimer interface [polypeptide binding]; other site 391008005588 phosphorylation site [posttranslational modification] 391008005589 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 391008005590 ATP binding site [chemical binding]; other site 391008005591 Mg2+ binding site [ion binding]; other site 391008005592 G-X-G motif; other site 391008005593 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 391008005594 Response regulator receiver domain; Region: Response_reg; pfam00072 391008005595 active site 391008005596 phosphorylation site [posttranslational modification] 391008005597 intermolecular recognition site; other site 391008005598 dimerization interface [polypeptide binding]; other site 391008005599 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 391008005600 putative binding surface; other site 391008005601 active site 391008005602 enoyl-CoA hydratase; Validated; Region: PRK08788 391008005603 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 391008005604 substrate binding site [chemical binding]; other site 391008005605 oxyanion hole (OAH) forming residues; other site 391008005606 trimer interface [polypeptide binding]; other site 391008005607 putative long-chain fatty acyl CoA ligase; Provisional; Region: PRK08751 391008005608 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 391008005609 acyl-activating enzyme (AAE) consensus motif; other site 391008005610 putative AMP binding site [chemical binding]; other site 391008005611 putative active site [active] 391008005612 putative CoA binding site [chemical binding]; other site 391008005613 choline dehydrogenase; Validated; Region: PRK02106 391008005614 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 391008005615 betaine aldehyde dehydrogenase; Provisional; Region: PRK13252 391008005616 NAD+-dependent 4-trimethylaminobutyraldehyde dehydrogenase, ALDH family 9A1; Region: ALDH_F9_TMBADH; cd07090 391008005617 tetrameric interface [polypeptide binding]; other site 391008005618 NAD binding site [chemical binding]; other site 391008005619 catalytic residues [active] 391008005620 transcriptional regulator BetI; Validated; Region: PRK00767 391008005621 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008005622 Bacterial transcriptional repressor; Region: TetR_C_6; pfam13977 391008005623 BCCT family transporter; Region: BCCT; pfam02028 391008005624 aconitate hydratase; Validated; Region: PRK09277 391008005625 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 391008005626 substrate binding site [chemical binding]; other site 391008005627 ligand binding site [chemical binding]; other site 391008005628 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 391008005629 substrate binding site [chemical binding]; other site 391008005630 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 391008005631 SpoVT / AbrB like domain; Region: SpoVT_AbrB; smart00966 391008005632 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB-like; cd09875 391008005633 putative active site [active] 391008005634 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 391008005635 Protein of unknown function (DUF2848); Region: DUF2848; pfam11010 391008005636 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change in...; Region: AcnB_Swivel; cd01576 391008005637 substrate binding site [chemical binding]; other site 391008005638 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 391008005639 substrate binding site [chemical binding]; other site 391008005640 ligand binding site [chemical binding]; other site 391008005641 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 391008005642 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 391008005643 TonB family C-terminal domain; Region: tonB_Cterm; TIGR01352 391008005644 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 391008005645 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 391008005646 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 391008005647 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 391008005648 active site 391008005649 phosphorylation site [posttranslational modification] 391008005650 intermolecular recognition site; other site 391008005651 dimerization interface [polypeptide binding]; other site 391008005652 CheB methylesterase; Region: CheB_methylest; pfam01339 391008005653 chemoreceptor glutamine deamidase CheD; Provisional; Region: PRK13487 391008005654 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 391008005655 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 391008005656 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 391008005657 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 391008005658 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 391008005659 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 391008005660 dimerization interface [polypeptide binding]; other site 391008005661 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 391008005662 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 391008005663 dimer interface [polypeptide binding]; other site 391008005664 putative CheW interface [polypeptide binding]; other site 391008005665 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 391008005666 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 391008005667 dimerization interface [polypeptide binding]; other site 391008005668 PAS domain; Region: PAS_9; pfam13426 391008005669 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 391008005670 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 391008005671 dimer interface [polypeptide binding]; other site 391008005672 putative CheW interface [polypeptide binding]; other site 391008005673 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 391008005674 putative CheA interaction surface; other site 391008005675 Flagellar regulator YcgR; Region: YcgR; pfam07317 391008005676 PilZ domain; Region: PilZ; pfam07238 391008005677 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 391008005678 ligand binding domain of Tar- and Tsr-related chemoreceptors; Region: Tar_Tsr_LBD; cl00144 391008005679 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 391008005680 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 391008005681 dimer interface [polypeptide binding]; other site 391008005682 putative CheW interface [polypeptide binding]; other site 391008005683 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 391008005684 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 391008005685 putative binding surface; other site 391008005686 active site 391008005687 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 391008005688 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 391008005689 ATP binding site [chemical binding]; other site 391008005690 Mg2+ binding site [ion binding]; other site 391008005691 G-X-G motif; other site 391008005692 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 391008005693 Response regulator receiver domain; Region: Response_reg; pfam00072 391008005694 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 391008005695 active site 391008005696 phosphorylation site [posttranslational modification] 391008005697 intermolecular recognition site; other site 391008005698 dimerization interface [polypeptide binding]; other site 391008005699 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 391008005700 anti sigma factor interaction site; other site 391008005701 regulatory phosphorylation site [posttranslational modification]; other site 391008005702 CheW-like domain; Region: CheW; pfam01584 391008005703 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 391008005704 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 391008005705 P-loop; other site 391008005706 Magnesium ion binding site [ion binding]; other site 391008005707 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 391008005708 Magnesium ion binding site [ion binding]; other site 391008005709 flagellar motor protein MotD; Reviewed; Region: PRK09038 391008005710 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 391008005711 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 391008005712 ligand binding site [chemical binding]; other site 391008005713 flagellar motor protein; Reviewed; Region: motC; PRK09109 391008005714 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 391008005715 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 391008005716 putative binding surface; other site 391008005717 active site 391008005718 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 391008005719 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 391008005720 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 391008005721 ATP binding site [chemical binding]; other site 391008005722 Mg2+ binding site [ion binding]; other site 391008005723 G-X-G motif; other site 391008005724 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 391008005725 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 391008005726 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 391008005727 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 391008005728 active site 391008005729 phosphorylation site [posttranslational modification] 391008005730 intermolecular recognition site; other site 391008005731 dimerization interface [polypeptide binding]; other site 391008005732 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 391008005733 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391008005734 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 391008005735 DNA binding residues [nucleotide binding] 391008005736 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 391008005737 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 391008005738 P-loop; other site 391008005739 flagellar biosynthesis regulator FlhF; Provisional; Region: PRK12727 391008005740 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 391008005741 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 391008005742 FHIPEP family; Region: FHIPEP; pfam00771 391008005743 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 391008005744 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 391008005745 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 391008005746 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 391008005747 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 391008005748 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008005749 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008005750 metal binding site [ion binding]; metal-binding site 391008005751 active site 391008005752 I-site; other site 391008005753 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 391008005754 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 391008005755 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 391008005756 Flagellar biosynthesis protein, FliO; Region: FliO; pfam04347 391008005757 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 391008005758 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 391008005759 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 391008005760 Flagellar basal body-associated protein FliL; Region: FliL; pfam03748 391008005761 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 391008005762 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 391008005763 Flagellar FliJ protein; Region: FliJ; pfam02050 391008005764 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 391008005765 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 391008005766 Walker A motif/ATP binding site; other site 391008005767 Walker B motif; other site 391008005768 Flagellar assembly protein FliH; Region: FliH; pfam02108 391008005769 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 391008005770 FliG C-terminal domain; Region: FliG_C; pfam01706 391008005771 flagellar MS-ring protein; Reviewed; Region: fliF; PRK12800 391008005772 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 391008005773 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 391008005774 Flagellar hook-basal body complex protein FliE; Region: FliE; pfam02049 391008005775 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 391008005776 Flagellar regulatory protein FleQ; Region: FleQ; pfam06490 391008005777 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008005778 Walker A motif; other site 391008005779 ATP binding site [chemical binding]; other site 391008005780 Walker B motif; other site 391008005781 arginine finger; other site 391008005782 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 391008005783 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 391008005784 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 391008005785 active site 391008005786 phosphorylation site [posttranslational modification] 391008005787 intermolecular recognition site; other site 391008005788 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 391008005789 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 391008005790 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 391008005791 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 391008005792 leucine-zipper of insertion element IS481; Region: LZ_Tnp_IS481; pfam13011 391008005793 Winged helix-turn helix; Region: HTH_29; pfam13551 391008005794 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 391008005795 Integrase core domain; Region: rve; pfam00665 391008005796 Integrase core domain; Region: rve_3; pfam13683 391008005797 leucine-zipper of insertion element IS481; Region: LZ_Tnp_IS481; pfam13011 391008005798 Winged helix-turn helix; Region: HTH_29; pfam13551 391008005799 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 391008005800 Integrase core domain; Region: rve; pfam00665 391008005801 Integrase core domain; Region: rve_3; pfam13683 391008005802 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 391008005803 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 391008005804 active site 391008005805 phosphorylation site [posttranslational modification] 391008005806 intermolecular recognition site; other site 391008005807 dimerization interface [polypeptide binding]; other site 391008005808 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 391008005809 DNA binding residues [nucleotide binding] 391008005810 flagellar protein FliS; Validated; Region: fliS; PRK05685 391008005811 flagellar capping protein; Reviewed; Region: fliD; PRK08032 391008005812 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 391008005813 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 391008005814 flagellin; Reviewed; Region: PRK08869 391008005815 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 391008005816 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 391008005817 flagellin; Reviewed; Region: PRK08869 391008005818 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 391008005819 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 391008005820 flagellin; Reviewed; Region: PRK08869 391008005821 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 391008005822 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 391008005823 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 391008005824 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 391008005825 flagellar hook-associated protein FlgK; Provisional; Region: flgK; PRK12714 391008005826 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 391008005827 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 391008005828 flagellar rod assembly protein/muramidase FlgJ; Reviewed; Region: flgJ; PRK12711 391008005829 Rod binding protein; Region: Rod-binding; cl01626 391008005830 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 391008005831 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 391008005832 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 391008005833 Flagellar L-ring protein; Region: FlgH; pfam02107 391008005834 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 391008005835 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 391008005836 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 391008005837 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 391008005838 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 391008005839 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 391008005840 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 391008005841 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 391008005842 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 391008005843 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 391008005844 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK12634 391008005845 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 391008005846 flagellar basal body rod protein FlgC; Provisional; Region: flgC; PRK12629 391008005847 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 391008005848 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 391008005849 flagellar basal body rod protein FlgB; Provisional; Region: flgB; PRK12620 391008005850 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 391008005851 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 391008005852 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 391008005853 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 391008005854 active site 391008005855 phosphorylation site [posttranslational modification] 391008005856 intermolecular recognition site; other site 391008005857 dimerization interface [polypeptide binding]; other site 391008005858 SAF-like; Region: SAF_2; pfam13144 391008005859 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 391008005860 flagellar biosynthesis anti-sigma factor FlgM; Region: FlgM_jcvi; TIGR03824 391008005861 FlgN protein; Region: FlgN; pfam05130 391008005862 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 391008005863 dimer interface [polypeptide binding]; other site 391008005864 phosphorylation site [posttranslational modification] 391008005865 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 391008005866 ATP binding site [chemical binding]; other site 391008005867 Mg2+ binding site [ion binding]; other site 391008005868 G-X-G motif; other site 391008005869 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008005870 metal binding site [ion binding]; metal-binding site 391008005871 active site 391008005872 I-site; other site 391008005873 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 391008005874 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 391008005875 Response regulator receiver domain; Region: Response_reg; pfam00072 391008005876 active site 391008005877 phosphorylation site [posttranslational modification] 391008005878 intermolecular recognition site; other site 391008005879 dimerization interface [polypeptide binding]; other site 391008005880 PAS domain S-box; Region: sensory_box; TIGR00229 391008005881 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 391008005882 putative active site [active] 391008005883 heme pocket [chemical binding]; other site 391008005884 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 391008005885 PAS domain; Region: PAS_9; pfam13426 391008005886 putative active site [active] 391008005887 heme pocket [chemical binding]; other site 391008005888 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 391008005889 Histidine kinase; Region: HisKA_3; pfam07730 391008005890 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 391008005891 ATP binding site [chemical binding]; other site 391008005892 Mg2+ binding site [ion binding]; other site 391008005893 G-X-G motif; other site 391008005894 PAS fold; Region: PAS_3; pfam08447 391008005895 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 391008005896 heme pocket [chemical binding]; other site 391008005897 putative active site [active] 391008005898 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 391008005899 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 391008005900 putative active site [active] 391008005901 heme pocket [chemical binding]; other site 391008005902 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008005903 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008005904 metal binding site [ion binding]; metal-binding site 391008005905 active site 391008005906 I-site; other site 391008005907 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 391008005908 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 391008005909 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 391008005910 dimer interface [polypeptide binding]; other site 391008005911 putative CheW interface [polypeptide binding]; other site 391008005912 putative lysogenization regulator; Reviewed; Region: PRK00218 391008005913 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 391008005914 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 391008005915 Contains a crystal structure of the Nudix hydrolase from Nitrosomonas europaea, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes...; Region: Nudix_Hydrolase_2; cd03675 391008005916 nudix motif; other site 391008005917 Uncharacterized conserved protein [Function unknown]; Region: COG2127 391008005918 Aminoglycoside/hydroxyurea antibiotic resistance kinase; Region: APH_6_hur; cl17810 391008005919 ATP-dependent Clp protease ATP-binding subunit; Provisional; Region: clpA; PRK11034 391008005920 Clp amino terminal domain; Region: Clp_N; pfam02861 391008005921 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008005922 Walker A motif; other site 391008005923 ATP binding site [chemical binding]; other site 391008005924 Walker B motif; other site 391008005925 arginine finger; other site 391008005926 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008005927 Walker A motif; other site 391008005928 ATP binding site [chemical binding]; other site 391008005929 Walker B motif; other site 391008005930 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 391008005931 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 391008005932 rRNA binding site [nucleotide binding]; other site 391008005933 predicted 30S ribosome binding site; other site 391008005934 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 391008005935 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 391008005936 Protein of unknown function, DUF482; Region: DUF482; pfam04339 391008005937 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 391008005938 active site 391008005939 thioredoxin reductase; Provisional; Region: PRK10262 391008005940 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 391008005941 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 391008005942 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 391008005943 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 391008005944 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 391008005945 Domain of Unknown Function with PDB structure (DUF3857); Region: DUF3857; pfam12969 391008005946 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 391008005947 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 391008005948 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 391008005949 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 391008005950 recombination factor protein RarA; Reviewed; Region: PRK13342 391008005951 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008005952 Walker A motif; other site 391008005953 ATP binding site [chemical binding]; other site 391008005954 Walker B motif; other site 391008005955 arginine finger; other site 391008005956 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 391008005957 Protein of unknown function (DUF805); Region: DUF805; pfam05656 391008005958 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819 391008005959 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 391008005960 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 391008005961 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 391008005962 intersubunit interface [polypeptide binding]; other site 391008005963 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 391008005964 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 391008005965 ABC-ATPase subunit interface; other site 391008005966 dimer interface [polypeptide binding]; other site 391008005967 putative PBP binding regions; other site 391008005968 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 391008005969 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 391008005970 Walker A/P-loop; other site 391008005971 ATP binding site [chemical binding]; other site 391008005972 Q-loop/lid; other site 391008005973 ABC transporter signature motif; other site 391008005974 Walker B; other site 391008005975 D-loop; other site 391008005976 H-loop/switch region; other site 391008005977 elongation factor G; Reviewed; Region: PRK12739 391008005978 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 391008005979 G1 box; other site 391008005980 GTP/Mg2+ binding site [chemical binding]; other site 391008005981 G2 box; other site 391008005982 Switch I region; other site 391008005983 G3 box; other site 391008005984 Switch II region; other site 391008005985 G4 box; other site 391008005986 G5 box; other site 391008005987 EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis...; Region: EFG_mtEFG_II; cd04088 391008005988 Elongation Factor G-like domain IV. This family includes the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria), ribosomal protection proteins that mediate tetracycline resistance and, an evolutionarily...; Region: EFG_like_IV; cl02789 391008005989 EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2...; Region: EFG_mtEFG_C; cd03713 391008005990 SapC; Region: SapC; pfam07277 391008005991 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 391008005992 ATP binding site [chemical binding]; other site 391008005993 Mg2+ binding site [ion binding]; other site 391008005994 G-X-G motif; other site 391008005995 Response regulator receiver domain; Region: Response_reg; pfam00072 391008005996 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 391008005997 active site 391008005998 phosphorylation site [posttranslational modification] 391008005999 intermolecular recognition site; other site 391008006000 dimerization interface [polypeptide binding]; other site 391008006001 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 391008006002 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 391008006003 active site 391008006004 phosphorylation site [posttranslational modification] 391008006005 intermolecular recognition site; other site 391008006006 dimerization interface [polypeptide binding]; other site 391008006007 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 391008006008 DNA binding residues [nucleotide binding] 391008006009 dimerization interface [polypeptide binding]; other site 391008006010 Bacterial lipocalin [Cell envelope biogenesis, outer membrane]; Region: Blc; COG3040 391008006011 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 391008006012 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 391008006013 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 391008006014 S-adenosylmethionine binding site [chemical binding]; other site 391008006015 Protein of unknown function (DUF1295); Region: DUF1295; cl17837 391008006016 Protein of unknown function (DUF2878); Region: DUF2878; pfam11086 391008006017 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 391008006018 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 391008006019 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 391008006020 S-adenosylmethionine binding site [chemical binding]; other site 391008006021 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 391008006022 Flavin containing amine oxidoreductase; Region: Amino_oxidase; pfam01593 391008006023 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 391008006024 Fatty acid desaturase; Region: FA_desaturase; pfam00487 391008006025 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 391008006026 Di-iron ligands [ion binding]; other site 391008006027 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 391008006028 RNA polymerase sigma factor RpoE; Provisional; Region: PRK09652 391008006029 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391008006030 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 391008006031 DNA binding residues [nucleotide binding] 391008006032 anti-sigma factor, putative, ChrR family; Region: anti_sig_ChrR; TIGR02451 391008006033 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 391008006034 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 391008006035 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008006036 NAD(P) binding site [chemical binding]; other site 391008006037 active site 391008006038 TspO/MBR family; Region: TspO_MBR; pfam03073 391008006039 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 391008006040 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391008006041 Coenzyme A binding pocket [chemical binding]; other site 391008006042 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 391008006043 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 391008006044 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 391008006045 Predicted membrane protein [Function unknown]; Region: COG2259 391008006046 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008006047 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008006048 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 391008006049 putative effector binding pocket; other site 391008006050 dimerization interface [polypeptide binding]; other site 391008006051 Pirin; Region: Pirin; pfam02678 391008006052 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 391008006053 Plasmid replication region DNA-binding N-term; Region: KfrA_N; pfam11740 391008006054 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 391008006055 active site 391008006056 DNA binding site [nucleotide binding] 391008006057 Int/Topo IB signature motif; other site 391008006058 Restriction endonuclease; Region: Mrr_cat; pfam04471 391008006059 TIR domain; Region: TIR_2; cl17458 391008006060 Piwi-like: PIWI domain. Domain found in proteins involved in RNA silencing. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The...; Region: Piwi-like; cl00628 391008006061 5' RNA guide strand anchoring site; other site 391008006062 active site 391008006063 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 391008006064 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 391008006065 Chromate transporter; Region: Chromate_transp; pfam02417 391008006066 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 391008006067 ArsC family; Region: ArsC; pfam03960 391008006068 catalytic residues [active] 391008006069 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 391008006070 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 391008006071 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 391008006072 putative DNA binding site [nucleotide binding]; other site 391008006073 putative Zn2+ binding site [ion binding]; other site 391008006074 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 391008006075 Low molecular weight phosphatase family; Region: LMWPc; cl00105 391008006076 active site 391008006077 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 391008006078 arsenical-resistance protein; Region: acr3; TIGR00832 391008006079 thioredoxin reductase; Provisional; Region: PRK10262 391008006080 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 391008006081 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 391008006082 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 391008006083 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 391008006084 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 391008006085 Low molecular weight phosphatase family; Region: LMWPc; cd00115 391008006086 active site 391008006087 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]; Region: COG4700 391008006088 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 391008006089 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 391008006090 Ligand binding site; other site 391008006091 metal-binding site 391008006092 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 391008006093 xanthine dehydrogenase accessory protein XdhC; Region: xanthine_xdhC; TIGR02964 391008006094 XdhC Rossmann domain; Region: XdhC_C; pfam13478 391008006095 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 391008006096 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 391008006097 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 391008006098 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 391008006099 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; smart01092 391008006100 aldehyde oxidoreductase 2Fe-2S subunit; Provisional; Region: PRK11433 391008006101 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 391008006102 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 391008006103 OsmC-like protein; Region: OsmC; cl00767 391008006104 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008006105 NADH(P)-binding; Region: NAD_binding_10; pfam13460 391008006106 NAD(P) binding site [chemical binding]; other site 391008006107 active site 391008006108 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008006109 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008006110 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 391008006111 putative effector binding pocket; other site 391008006112 dimerization interface [polypeptide binding]; other site 391008006113 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 391008006114 DNA binding residues [nucleotide binding] 391008006115 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 391008006116 Uncharacterized conserved protein [Function unknown]; Region: COG2128 391008006117 Cupin domain; Region: Cupin_2; pfam07883 391008006118 RNA polymerase sigma-70 factor, TIGR02957 family; Region: SigX4 391008006119 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391008006120 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 391008006121 DNA binding residues [nucleotide binding] 391008006122 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 391008006123 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 391008006124 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3558 391008006125 SnoaL-like domain; Region: SnoaL_2; pfam12680 391008006126 putative transcriptional regulator; Provisional; Region: PRK11640 391008006127 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008006128 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 391008006129 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 391008006130 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 391008006131 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008006132 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 391008006133 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 391008006134 FMN binding site [chemical binding]; other site 391008006135 active site 391008006136 substrate binding site [chemical binding]; other site 391008006137 catalytic residue [active] 391008006138 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 391008006139 classical (c) SDRs; Region: SDR_c; cd05233 391008006140 NAD(P) binding site [chemical binding]; other site 391008006141 active site 391008006142 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 391008006143 alcohol dehydrogenase and quinone reductase-like medium chain degydrogenases/reductases; Region: MDR_like_2; cd05289 391008006144 putative NAD(P) binding site [chemical binding]; other site 391008006145 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 391008006146 Walker A/P-loop; other site 391008006147 ATP binding site [chemical binding]; other site 391008006148 Excinuclease ATPase subunit [DNA replication, recombination, and repair]; Region: UvrA; COG0178 391008006149 Q-loop/lid; other site 391008006150 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 391008006151 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 391008006152 Walker A/P-loop; other site 391008006153 ATP binding site [chemical binding]; other site 391008006154 Q-loop/lid; other site 391008006155 ABC transporter signature motif; other site 391008006156 Walker B; other site 391008006157 D-loop; other site 391008006158 H-loop/switch region; other site 391008006159 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008006160 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008006161 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 391008006162 putative effector binding pocket; other site 391008006163 putative dimerization interface [polypeptide binding]; other site 391008006164 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 391008006165 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 391008006166 putative substrate translocation pore; other site 391008006167 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 391008006168 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 391008006169 active site 391008006170 catalytic tetrad [active] 391008006171 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 391008006172 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 391008006173 BAAT / Acyl-CoA thioester hydrolase C terminal; Region: BAAT_C; pfam08840 391008006174 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 391008006175 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 391008006176 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 391008006177 Secretin and TonB N terminus short domain; Region: STN; smart00965 391008006178 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 391008006179 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 391008006180 N-terminal plug; other site 391008006181 ligand-binding site [chemical binding]; other site 391008006182 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 391008006183 KIF-1 binding protein C terminal; Region: KBP_C; pfam12309 391008006184 FecR protein; Region: FecR; pfam04773 391008006185 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 391008006186 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 391008006187 Protein of unknown function (DUF3313); Region: DUF3313; pfam11769 391008006188 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 391008006189 Helix-turn-helix domain; Region: HTH_18; pfam12833 391008006190 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 391008006191 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008006192 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008006193 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 391008006194 Protein export membrane protein; Region: SecD_SecF; cl14618 391008006195 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 391008006196 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 391008006197 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008006198 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008006199 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 391008006200 NADH dehydrogenase subunit D; Validated; Region: PRK06075 391008006201 Transcriptional regulators [Transcription]; Region: PurR; COG1609 391008006202 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 391008006203 DNA binding site [nucleotide binding] 391008006204 domain linker motif; other site 391008006205 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; Region: PBP1_LacI_like_4; cd06280 391008006206 putative dimerization interface [polypeptide binding]; other site 391008006207 putative ligand binding site [chemical binding]; other site 391008006208 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 391008006209 active site 391008006210 phosphorylation site [posttranslational modification] 391008006211 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 391008006212 dimerization domain swap beta strand [polypeptide binding]; other site 391008006213 regulatory protein interface [polypeptide binding]; other site 391008006214 active site 391008006215 regulatory phosphorylation site [posttranslational modification]; other site 391008006216 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 391008006217 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 391008006218 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 391008006219 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 391008006220 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 391008006221 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 391008006222 putative substrate binding site [chemical binding]; other site 391008006223 putative ATP binding site [chemical binding]; other site 391008006224 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 and...; Region: PTS_IIB_fructose; cd05569 391008006225 active site 391008006226 P-loop; other site 391008006227 phosphorylation site [posttranslational modification] 391008006228 Phosphotransferase system, fructose-specific IIC component [Carbohydrate transport and metabolism]; Region: FruA; cl17425 391008006229 Carbohydrate-selective porin, OprB family; Region: OprB; pfam04966 391008006230 Secreted and surface protein containing fasciclin-like repeats [Cell envelope biogenesis, outer membrane]; Region: COG2335 391008006231 Fasciclin domain; Region: Fasciclin; pfam02469 391008006232 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 391008006233 active site 391008006234 substrate binding sites [chemical binding]; other site 391008006235 Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase...; Region: MTHFR; cd00537 391008006236 FAD binding site [chemical binding]; other site 391008006237 DNA-binding transcriptional regulator MetR; Provisional; Region: PRK15421 391008006238 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008006239 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 391008006240 putative dimerization interface [polypeptide binding]; other site 391008006241 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 391008006242 FMN reductase, MsuE subfamily; Region: FMN_reduc_MsuE; TIGR03566 391008006243 Domain of unknown function (DUF1852); Region: DUF1852; pfam08908 391008006244 methionine synthase; Provisional; Region: PRK01207 391008006245 CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_C_terminal_like; cd03311 391008006246 substrate binding site [chemical binding]; other site 391008006247 THF binding site; other site 391008006248 zinc-binding site [ion binding]; other site 391008006249 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 391008006250 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 391008006251 transmembrane helices; other site 391008006252 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 391008006253 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 391008006254 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 391008006255 Walker A/P-loop; other site 391008006256 ATP binding site [chemical binding]; other site 391008006257 Q-loop/lid; other site 391008006258 ABC transporter signature motif; other site 391008006259 Walker B; other site 391008006260 D-loop; other site 391008006261 H-loop/switch region; other site 391008006262 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008006263 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008006264 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 391008006265 Domain of unknown function (DUF3526); Region: DUF3526; pfam12040 391008006266 ABC-type transport system involved in multi-copper enzyme maturation, permease component [General function prediction only]; Region: NosY; COG1277 391008006267 Domain of unknown function (DUF3526); Region: DUF3526; pfam12040 391008006268 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 391008006269 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 391008006270 Walker A/P-loop; other site 391008006271 ATP binding site [chemical binding]; other site 391008006272 Q-loop/lid; other site 391008006273 ABC transporter signature motif; other site 391008006274 Walker B; other site 391008006275 D-loop; other site 391008006276 H-loop/switch region; other site 391008006277 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 391008006278 Ligand Binding Site [chemical binding]; other site 391008006279 Molecular Tunnel; other site 391008006280 Transglutaminase-like superfamily; Region: Transglut_core3; pfam13471 391008006281 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 391008006282 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008006283 esterase, PHB depolymerase family; Region: esterase_phb; TIGR01840 391008006284 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 391008006285 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008006286 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 391008006287 N-terminal plug; other site 391008006288 ligand-binding site [chemical binding]; other site 391008006289 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 391008006290 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 391008006291 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 391008006292 active site 2 [active] 391008006293 active site 1 [active] 391008006294 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 391008006295 PAS domain; Region: PAS; smart00091 391008006296 PAS fold; Region: PAS_7; pfam12860 391008006297 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008006298 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 391008006299 ATP binding site [chemical binding]; other site 391008006300 Mg2+ binding site [ion binding]; other site 391008006301 G-X-G motif; other site 391008006302 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 391008006303 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 391008006304 active site 391008006305 phosphorylation site [posttranslational modification] 391008006306 intermolecular recognition site; other site 391008006307 dimerization interface [polypeptide binding]; other site 391008006308 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 391008006309 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 391008006310 active site 391008006311 phosphorylation site [posttranslational modification] 391008006312 intermolecular recognition site; other site 391008006313 dimerization interface [polypeptide binding]; other site 391008006314 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 391008006315 dimerization interface [polypeptide binding]; other site 391008006316 DNA binding residues [nucleotide binding] 391008006317 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 391008006318 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 391008006319 acyl-activating enzyme (AAE) consensus motif; other site 391008006320 AMP binding site [chemical binding]; other site 391008006321 active site 391008006322 CoA binding site [chemical binding]; other site 391008006323 Transcriptional regulators [Transcription]; Region: FadR; COG2186 391008006324 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 391008006325 DNA-binding site [nucleotide binding]; DNA binding site 391008006326 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 391008006327 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 391008006328 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008006329 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008006330 nitrous oxide reductase family maturation protein NosD; Region: NosD_copper_fam; TIGR04247 391008006331 Alginate Lyase A1-III; enzymatically depolymerizes alginate, a complex copolymer of beta-D-mannuronate and alpha-L-guluronate, by cleaving the beta-(1,4) glycosidic bond; Region: AlgLyase; cl00179 391008006332 Heparinase II/III-like protein; Region: Hepar_II_III; pfam07940 391008006333 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 391008006334 Major Facilitator Superfamily; Region: MFS_1; pfam07690 391008006335 putative substrate translocation pore; other site 391008006336 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 391008006337 classical (c) SDRs; Region: SDR_c; cd05233 391008006338 NAD(P) binding site [chemical binding]; other site 391008006339 active site 391008006340 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 391008006341 active site 391008006342 catalytic triad [active] 391008006343 oxyanion hole [active] 391008006344 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 391008006345 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 391008006346 substrate binding site [chemical binding]; other site 391008006347 ATP binding site [chemical binding]; other site 391008006348 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 391008006349 catalytic motif [active] 391008006350 Catalytic residue [active] 391008006351 Cellular and retroviral pepsin-like aspartate proteases; Region: pepsin_retropepsin_like; cl11403 391008006352 inhibitor binding site; inhibition site 391008006353 catalytic motif [active] 391008006354 Catalytic residue [active] 391008006355 Active site flap [active] 391008006356 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 391008006357 X-Pro dipeptidyl-peptidase (S15 family); Region: Peptidase_S15; pfam02129 391008006358 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 391008006359 X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain; Region: PepX_C; cl08482 391008006360 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 391008006361 DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases. They exists as monomers and homodimers; Region: NUC; cl00089 391008006362 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 391008006363 active site 391008006364 substrate binding site [chemical binding]; other site 391008006365 Mg2+ binding site [ion binding]; other site 391008006366 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 391008006367 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 391008006368 active site 391008006369 motif I; other site 391008006370 motif II; other site 391008006371 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 391008006372 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_16; cd07263 391008006373 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 391008006374 S-adenosylmethionine binding site [chemical binding]; other site 391008006375 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 391008006376 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 391008006377 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 391008006378 catalytic residue [active] 391008006379 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008006380 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 391008006381 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 391008006382 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008006383 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 391008006384 dimerization interface [polypeptide binding]; other site 391008006385 substrate binding pocket [chemical binding]; other site 391008006386 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 391008006387 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 391008006388 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 391008006389 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 391008006390 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008006391 Walker A motif; other site 391008006392 ATP binding site [chemical binding]; other site 391008006393 Walker B motif; other site 391008006394 arginine finger; other site 391008006395 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 391008006396 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39G; cd02423 391008006397 putative active site [active] 391008006398 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; cl01768 391008006399 Killing trait; Region: RebB; pfam11747 391008006400 Killing trait; Region: RebB; pfam11747 391008006401 Killing trait; Region: RebB; pfam11747 391008006402 Killing trait; Region: RebB; pfam11747 391008006403 Killing trait; Region: RebB; pfam11747 391008006404 Killing trait; Region: RebB; pfam11747 391008006405 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 391008006406 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008006407 Walker A motif; other site 391008006408 ATP binding site [chemical binding]; other site 391008006409 Walker B motif; other site 391008006410 arginine finger; other site 391008006411 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 391008006412 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008006413 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008006414 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 391008006415 Short C-terminal domain; Region: SHOCT; pfam09851 391008006416 Protein involved in formate dehydrogenase formation; Region: FdhE; pfam04216 391008006417 Tyrosine phosphatase family; Region: Y_phosphatase3; pfam13350 391008006418 Tyrosine phosphatase family C-terminal region; Region: Y_phosphatase3C; pfam13348 391008006419 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 391008006420 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 391008006421 N-terminal plug; other site 391008006422 ligand-binding site [chemical binding]; other site 391008006423 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 391008006424 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008006425 Bacterial transcriptional repressor; Region: TetR_C_6; pfam13977 391008006426 Protease inhibitor Inh; Region: Inh; pfam02974 391008006427 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 391008006428 GAF domain; Region: GAF; pfam01590 391008006429 PAS domain; Region: PAS_9; pfam13426 391008006430 PAS domain S-box; Region: sensory_box; TIGR00229 391008006431 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 391008006432 putative active site [active] 391008006433 heme pocket [chemical binding]; other site 391008006434 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008006435 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008006436 metal binding site [ion binding]; metal-binding site 391008006437 active site 391008006438 I-site; other site 391008006439 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 391008006440 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 391008006441 Walker A/P-loop; other site 391008006442 ATP binding site [chemical binding]; other site 391008006443 Q-loop/lid; other site 391008006444 ABC transporter signature motif; other site 391008006445 Walker B; other site 391008006446 D-loop; other site 391008006447 H-loop/switch region; other site 391008006448 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 391008006449 FtsX-like permease family; Region: FtsX; pfam02687 391008006450 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 391008006451 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008006452 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008006453 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391008006454 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 391008006455 active site 391008006456 phosphorylation site [posttranslational modification] 391008006457 intermolecular recognition site; other site 391008006458 dimerization interface [polypeptide binding]; other site 391008006459 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008006460 DNA binding site [nucleotide binding] 391008006461 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008006462 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 391008006463 dimerization interface [polypeptide binding]; other site 391008006464 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008006465 dimer interface [polypeptide binding]; other site 391008006466 phosphorylation site [posttranslational modification] 391008006467 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 391008006468 ATP binding site [chemical binding]; other site 391008006469 Mg2+ binding site [ion binding]; other site 391008006470 G-X-G motif; other site 391008006471 ABC transporter transmembrane region; Region: ABC_membrane_3; pfam13748 391008006472 tetracycline repressor protein TetR; Provisional; Region: PRK13756 391008006473 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 391008006474 FAD binding pocket [chemical binding]; other site 391008006475 FAD binding motif [chemical binding]; other site 391008006476 phosphate binding motif [ion binding]; other site 391008006477 NAD binding pocket [chemical binding]; other site 391008006478 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 391008006479 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 391008006480 N-terminal plug; other site 391008006481 ligand-binding site [chemical binding]; other site 391008006482 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 391008006483 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 391008006484 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 391008006485 Protein of unknown function (DUF3325); Region: DUF3325; pfam11804 391008006486 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3214 391008006487 Protein of unknown function (DUF1006); Region: DUF1006; pfam06224 391008006488 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 391008006489 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 391008006490 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 391008006491 N-terminal plug; other site 391008006492 ligand-binding site [chemical binding]; other site 391008006493 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 391008006494 Catalytic domain of Protein Kinases; Region: PKc; cd00180 391008006495 active site 391008006496 ATP binding site [chemical binding]; other site 391008006497 substrate binding site [chemical binding]; other site 391008006498 activation loop (A-loop); other site 391008006499 Lanthionine synthetase C-like protein; Region: LANC_like; pfam05147 391008006500 Lanthionine synthetase C-like domain associated with serine threonine kinases. Some members of this subgroup lack the zinc binding site and the active site residues, and therefore are most likely inactive. The function of this domain is unknown; Region: LanC_SerThrkinase; cd04791 391008006501 active site 391008006502 zinc binding site [ion binding]; other site 391008006503 conjugal transfer protein TrbP; Provisional; Region: PRK13882 391008006504 TraX protein; Region: TraX; pfam05857 391008006505 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 391008006506 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 391008006507 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 391008006508 magnesium-transporting ATPase MgtA; Provisional; Region: PRK10517 391008006509 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; pfam00690 391008006510 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 391008006511 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 391008006512 Soluble P-type ATPase [General function prediction only]; Region: COG4087 391008006513 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 391008006514 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 391008006515 MgtC family; Region: MgtC; pfam02308 391008006516 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008006517 dimer interface [polypeptide binding]; other site 391008006518 phosphorylation site [posttranslational modification] 391008006519 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 391008006520 ATP binding site [chemical binding]; other site 391008006521 Mg2+ binding site [ion binding]; other site 391008006522 G-X-G motif; other site 391008006523 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 391008006524 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 391008006525 active site 391008006526 phosphorylation site [posttranslational modification] 391008006527 intermolecular recognition site; other site 391008006528 dimerization interface [polypeptide binding]; other site 391008006529 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 391008006530 DNA binding residues [nucleotide binding] 391008006531 Protein of unknown function (DUF1697); Region: DUF1697; pfam08002 391008006532 Bacterial low temperature requirement A protein (LtrA); Region: LtrA; cl01754 391008006533 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 391008006534 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 391008006535 DNA binding residues [nucleotide binding] 391008006536 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 391008006537 FecR protein; Region: FecR; pfam04773 391008006538 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008006539 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 391008006540 N-terminal plug; other site 391008006541 ligand-binding site [chemical binding]; other site 391008006542 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 391008006543 Predicted metal-binding protein [General function prediction only]; Region: COG3019 391008006544 oxidoreductase alpha (molybdopterin) subunit; Region: Fdhalpha-like; TIGR01701 391008006545 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 391008006546 putative molybdopterin cofactor binding site [chemical binding]; other site 391008006547 The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region...; Region: MopB_CT_ydeP; cd02787 391008006548 putative molybdopterin cofactor binding site; other site 391008006549 formate dehydrogenase accessory protein; Reviewed; Region: PRK00724 391008006550 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 391008006551 alkylhydroperoxidase AhpD family core domain; Region: ahpD_dom; TIGR00778 391008006552 Cupin; Region: Cupin_6; pfam12852 391008006553 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008006554 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 391008006555 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008006556 transcriptional repressor BetI; Region: betaine_BetI; TIGR03384 391008006557 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008006558 methyl viologen resistance protein SmvA; Provisional; Region: PRK14995 391008006559 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 391008006560 putative substrate translocation pore; other site 391008006561 Protein of unknown function (DUF3299); Region: DUF3299; pfam11736 391008006562 Protein of unknown function (DUF3299); Region: DUF3299; pfam11736 391008006563 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 391008006564 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 391008006565 FtsX-like permease family; Region: FtsX; pfam02687 391008006566 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 391008006567 Q-loop/lid; other site 391008006568 ABC transporter signature motif; other site 391008006569 Walker B; other site 391008006570 D-loop; other site 391008006571 H-loop/switch region; other site 391008006572 Protein of unknown function (DUF2796); Region: DUF2796; pfam10986 391008006573 MerC mercury resistance protein; Region: MerC; cl03934 391008006574 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 391008006575 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 391008006576 N-terminal plug; other site 391008006577 ligand-binding site [chemical binding]; other site 391008006578 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 391008006579 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008006580 CopC domain; Region: CopC; pfam04234 391008006581 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 391008006582 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 391008006583 active site 391008006584 phosphorylation site [posttranslational modification] 391008006585 intermolecular recognition site; other site 391008006586 dimerization interface [polypeptide binding]; other site 391008006587 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008006588 DNA binding site [nucleotide binding] 391008006589 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 391008006590 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008006591 dimer interface [polypeptide binding]; other site 391008006592 phosphorylation site [posttranslational modification] 391008006593 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 391008006594 ATP binding site [chemical binding]; other site 391008006595 Mg2+ binding site [ion binding]; other site 391008006596 G-X-G motif; other site 391008006597 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008006598 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008006599 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 391008006600 putative effector binding pocket; other site 391008006601 putative dimerization interface [polypeptide binding]; other site 391008006602 short chain dehydrogenase; Provisional; Region: PRK12937 391008006603 tetrahydroxynaphthalene/trihydroxynaphthalene reductase-like, classical (c) SDRs; Region: THN_reductase-like_SDR_c; cd05362 391008006604 NADP binding site [chemical binding]; other site 391008006605 homodimer interface [polypeptide binding]; other site 391008006606 active site 391008006607 substrate binding site [chemical binding]; other site 391008006608 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 391008006609 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 391008006610 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 391008006611 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008006612 Outer membrane efflux protein; Region: OEP; pfam02321 391008006613 Outer membrane efflux protein; Region: OEP; pfam02321 391008006614 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391008006615 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 391008006616 active site 391008006617 phosphorylation site [posttranslational modification] 391008006618 intermolecular recognition site; other site 391008006619 dimerization interface [polypeptide binding]; other site 391008006620 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008006621 DNA binding site [nucleotide binding] 391008006622 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 391008006623 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008006624 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008006625 dimer interface [polypeptide binding]; other site 391008006626 phosphorylation site [posttranslational modification] 391008006627 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 391008006628 ATP binding site [chemical binding]; other site 391008006629 Mg2+ binding site [ion binding]; other site 391008006630 G-X-G motif; other site 391008006631 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 391008006632 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 391008006633 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 391008006634 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 391008006635 catalytic residues [active] 391008006636 Protein required for attachment to host cells; Region: Host_attach; pfam10116 391008006637 proline/glycine betaine transporter; Provisional; Region: PRK10642 391008006638 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 391008006639 putative substrate translocation pore; other site 391008006640 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4185 391008006641 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 391008006642 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 391008006643 PAS domain; Region: PAS_9; pfam13426 391008006644 putative active site [active] 391008006645 heme pocket [chemical binding]; other site 391008006646 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 391008006647 HWE histidine kinase; Region: HWE_HK; smart00911 391008006648 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 391008006649 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 391008006650 active site 391008006651 phosphorylation site [posttranslational modification] 391008006652 intermolecular recognition site; other site 391008006653 dimerization interface [polypeptide binding]; other site 391008006654 Tetratricopeptide repeat; Region: TPR_16; pfam13432 391008006655 Protein of unknown function (DUF560); Region: DUF560; pfam04575 391008006656 Secretin and TonB N terminus short domain; Region: STN; smart00965 391008006657 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 391008006658 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008006659 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008006660 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 391008006661 FecR protein; Region: FecR; pfam04773 391008006662 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 391008006663 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 391008006664 DNA binding residues [nucleotide binding] 391008006665 LysR family transcriptional regulator; Provisional; Region: PRK14997 391008006666 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008006667 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_4; cd08473 391008006668 putative effector binding pocket; other site 391008006669 putative dimerization interface [polypeptide binding]; other site 391008006670 Pirin-related protein [General function prediction only]; Region: COG1741 391008006671 Pirin; Region: Pirin; pfam02678 391008006672 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 391008006673 Isochorismatase family; Region: Isochorismatase; pfam00857 391008006674 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 391008006675 catalytic triad [active] 391008006676 dimer interface [polypeptide binding]; other site 391008006677 conserved cis-peptide bond; other site 391008006678 Isochorismatase family; Region: Isochorismatase; pfam00857 391008006679 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 391008006680 catalytic triad [active] 391008006681 dimer interface [polypeptide binding]; other site 391008006682 conserved cis-peptide bond; other site 391008006683 OsmC-like protein; Region: OsmC; pfam02566 391008006684 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 391008006685 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 391008006686 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 391008006687 ABC transporter; Region: ABC_tran; pfam00005 391008006688 TonB C terminal; Region: TonB_2; pfam13103 391008006689 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 391008006690 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 391008006691 Domain of unknown function (DUF2341); Region: DUF2341; pfam10102 391008006692 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 391008006693 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 391008006694 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 391008006695 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 391008006696 Surface antigen; Region: Bac_surface_Ag; pfam01103 391008006697 Type IV pilus biogenesis; Region: Pilus_PilP; pfam11356 391008006698 Prokaryotic N-terminal methylation motif; Region: N_methyl; pfam07963 391008006699 type II secretion system protein H; Region: typeII_sec_gspH; TIGR01708 391008006700 Type II transport protein GspH; Region: GspH; pfam12019 391008006701 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 391008006702 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 391008006703 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 391008006704 filamentous hemagglutinin family N-terminal domain; Region: adhes_NPXG; TIGR01901 391008006705 Filamentous haemagglutinin family outer membrane protein; Region: DUF3739; pfam12545 391008006706 PBP superfamily domain; Region: PBP_like_2; pfam12849 391008006707 PBP superfamily domain; Region: PBP_like_2; pfam12849 391008006708 type II secretion system protein F; Region: GspF; TIGR02120 391008006709 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 391008006710 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 391008006711 type II secretion system protein E; Region: type_II_gspE; TIGR02533 391008006712 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 391008006713 Walker A motif; other site 391008006714 ATP binding site [chemical binding]; other site 391008006715 Walker B motif; other site 391008006716 type II secretion system protein D; Region: type_II_gspD; TIGR02517 391008006717 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 391008006718 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 391008006719 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 391008006720 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 391008006721 Type II secretion system (T2SS), protein M; Region: T2SM; cl01222 391008006722 type II secretion system protein L; Region: typeII_sec_gspL; TIGR01709 391008006723 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 391008006724 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 391008006725 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 391008006726 FecR protein; Region: FecR; pfam04773 391008006727 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 391008006728 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391008006729 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 391008006730 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 391008006731 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 391008006732 putative DNA binding site [nucleotide binding]; other site 391008006733 putative Zn2+ binding site [ion binding]; other site 391008006734 AsnC family; Region: AsnC_trans_reg; pfam01037 391008006735 Predicted branched-chain amino acid permease (azaleucine resistance) [Amino acid transport and metabolism]; Region: AzlC; COG1296 391008006736 Predicted membrane protein [Function unknown]; Region: COG4541 391008006737 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 391008006738 PAS domain; Region: PAS_9; pfam13426 391008006739 putative active site [active] 391008006740 heme pocket [chemical binding]; other site 391008006741 Sulfite reductase, alpha subunit (flavoprotein) [Inorganic ion transport and metabolism]; Region: CysJ; COG0369 391008006742 Flavodoxin; Region: Flavodoxin_1; pfam00258 391008006743 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cl06868 391008006744 FAD binding pocket [chemical binding]; other site 391008006745 conserved FAD binding motif [chemical binding]; other site 391008006746 phosphate binding motif [ion binding]; other site 391008006747 beta-alpha-beta structure motif; other site 391008006748 NAD binding pocket [chemical binding]; other site 391008006749 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 391008006750 cell division ATP-binding protein FtsE; Region: FtsE; TIGR02673 391008006751 Walker A/P-loop; other site 391008006752 ATP binding site [chemical binding]; other site 391008006753 Q-loop/lid; other site 391008006754 ABC transporter signature motif; other site 391008006755 Walker B; other site 391008006756 D-loop; other site 391008006757 H-loop/switch region; other site 391008006758 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 391008006759 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 391008006760 dimer interface [polypeptide binding]; other site 391008006761 conserved gate region; other site 391008006762 putative PBP binding loops; other site 391008006763 ABC-ATPase subunit interface; other site 391008006764 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 391008006765 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 391008006766 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 391008006767 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 391008006768 ligand binding site [chemical binding]; other site 391008006769 flexible hinge region; other site 391008006770 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 391008006771 putative switch regulator; other site 391008006772 non-specific DNA interactions [nucleotide binding]; other site 391008006773 DNA binding site [nucleotide binding] 391008006774 sequence specific DNA binding site [nucleotide binding]; other site 391008006775 putative cAMP binding site [chemical binding]; other site 391008006776 coproporphyrinogen III oxidase; Provisional; Region: PRK13347 391008006777 HemN C-terminal domain; Region: HemN_C; pfam06969 391008006778 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 391008006779 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 391008006780 putative substrate translocation pore; other site 391008006781 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 391008006782 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; pfam02665 391008006783 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 391008006784 Nitrate reductase beta subunit [Energy production and conversion]; Region: NarY; COG1140 391008006785 4Fe-4S binding domain; Region: Fer4_6; pfam12837 391008006786 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cl00470 391008006787 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 391008006788 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 to...; Region: MopB_Nitrate-R-NarG-like; cd02750 391008006789 [4Fe-4S] binding site [ion binding]; other site 391008006790 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 391008006791 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 391008006792 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 391008006793 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 to...; Region: MopB_CT_Nitrate-R-NarG-like; cd02776 391008006794 molybdopterin cofactor binding site; other site 391008006795 nitrate/nitrite transport protein NarU; Provisional; Region: PRK15034 391008006796 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 391008006797 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 391008006798 GTP binding site; other site 391008006799 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 391008006800 MoaE homodimer interface [polypeptide binding]; other site 391008006801 MoaD interaction [polypeptide binding]; other site 391008006802 active site residues [active] 391008006803 Molybdopterin converting factor, small subunit [Coenzyme metabolism]; Region: MoaD; COG1977 391008006804 charged pocket; other site 391008006805 hydrophobic patch; other site 391008006806 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 391008006807 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 391008006808 dimer interface [polypeptide binding]; other site 391008006809 putative functional site; other site 391008006810 putative MPT binding site; other site 391008006811 bifunctional molybdenum cofactor biosynthesis protein MoaC/MogA; Provisional; Region: moaC; PRK03604 391008006812 MoaC family. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine derivative to the precursor...; Region: MoaC; cl00242 391008006813 trimer interface [polypeptide binding]; other site 391008006814 dimer interface [polypeptide binding]; other site 391008006815 putative active site [active] 391008006816 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 391008006817 MPT binding site; other site 391008006818 trimer interface [polypeptide binding]; other site 391008006819 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 391008006820 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 391008006821 FeS/SAM binding site; other site 391008006822 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 391008006823 Uncharacterized protein conserved in Bacteroidetes; Region: Bacuni_01323_like; cd12871 391008006824 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 391008006825 RHS Repeat; Region: RHS_repeat; pfam05593 391008006826 RHS Repeat; Region: RHS_repeat; cl11982 391008006827 RHS Repeat; Region: RHS_repeat; pfam05593 391008006828 RHS Repeat; Region: RHS_repeat; pfam05593 391008006829 RHS Repeat; Region: RHS_repeat; pfam05593 391008006830 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 391008006831 Helix-turn-helix domain; Region: HTH_18; pfam12833 391008006832 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008006833 Fusaric acid resistance protein family; Region: FUSC; pfam04632 391008006834 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 391008006835 p-hydroxybenzoic acid efflux subunit AaeA; Provisional; Region: PRK10559 391008006836 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008006837 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008006838 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 391008006839 Domain of unknown function (DUF3315); Region: DUF3315; pfam11776 391008006840 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 391008006841 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_4; cd06231 391008006842 putative active site [active] 391008006843 Zn binding site [ion binding]; other site 391008006844 Protein of unknown function (DUF3348); Region: DUF3348; pfam11828 391008006845 hypothetical protein; Provisional; Region: PRK09040 391008006846 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 391008006847 ligand binding site [chemical binding]; other site 391008006848 Protein of unknown function (DUF2894); Region: DUF2894; pfam11445 391008006849 Transposase; Region: DEDD_Tnp_IS110; pfam01548 391008006850 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 391008006851 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 391008006852 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008006853 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008006854 Esterase-like activity of phytase; Region: Phytase-like; pfam13449 391008006855 2,3-dihydroxybenzoate-2,3-dehydrogenase; Validated; Region: PRK08220 391008006856 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008006857 NAD(P) binding site [chemical binding]; other site 391008006858 active site 391008006859 enterobactin synthase subunit F; Provisional; Region: entF; PRK10252 391008006860 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 391008006861 acyl-activating enzyme (AAE) consensus motif; other site 391008006862 AMP binding site [chemical binding]; other site 391008006863 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 391008006864 Phosphopantetheine attachment site; Region: PP-binding; cl09936 391008006865 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; cl00220 391008006866 Isochorismatase family; Region: Isochorismatase; pfam00857 391008006867 catalytic triad [active] 391008006868 conserved cis-peptide bond; other site 391008006869 Peptide arylation enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntE; COG1021 391008006870 2,3-dihydroxybenzoate-AMP ligase; Region: 23DHB-AMP_lg; cd05920 391008006871 acyl-activating enzyme (AAE) consensus motif; other site 391008006872 active site 391008006873 AMP binding site [chemical binding]; other site 391008006874 substrate binding site [chemical binding]; other site 391008006875 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 391008006876 Major Facilitator Superfamily; Region: MFS_1; pfam07690 391008006877 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 391008006878 putative substrate translocation pore; other site 391008006879 Domain of unknown function (DUF3817); Region: DUF3817; pfam12823 391008006880 luciferase-type oxidoreductase, BA3436 family; Region: lucif_BA3436; TIGR03571 391008006881 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 391008006882 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 391008006883 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 391008006884 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391008006885 Coenzyme A binding pocket [chemical binding]; other site 391008006886 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 391008006887 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 391008006888 catalytic residues [active] 391008006889 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 391008006890 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 391008006891 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 391008006892 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 391008006893 Fatty acid desaturase [Lipid metabolism]; Region: DesA; COG3239 391008006894 The Delta6 Fatty Acid Desaturase (Delta6-FADS)-like CD includes the integral-membrane enzymes: delta-4, delta-5, delta-6, delta-8, delta-8-sphingolipid, and delta-11 desaturases found in vertebrates, higher plants, fungi, and bacteria. These desaturases...; Region: Delta6-FADS-like; cd03506 391008006895 putative di-iron ligands [ion binding]; other site 391008006896 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_2; cd06216 391008006897 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 391008006898 FAD binding pocket [chemical binding]; other site 391008006899 FAD binding motif [chemical binding]; other site 391008006900 phosphate binding motif [ion binding]; other site 391008006901 beta-alpha-beta structure motif; other site 391008006902 NAD binding pocket [chemical binding]; other site 391008006903 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 391008006904 catalytic loop [active] 391008006905 iron binding site [ion binding]; other site 391008006906 DNA-binding transcriptional repressor FabR; Provisional; Region: PRK11202 391008006907 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008006908 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 391008006909 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 391008006910 Autotransporter beta-domain; Region: Autotransporter; smart00869 391008006911 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 391008006912 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 391008006913 N-terminal plug; other site 391008006914 ligand-binding site [chemical binding]; other site 391008006915 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 391008006916 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 391008006917 manganese transport regulator MntR; Provisional; Region: PRK11050 391008006918 Iron dependent repressor, N-terminal DNA binding domain; Region: Fe_dep_repress; pfam01325 391008006919 Iron dependent repressor, metal binding and dimerisation domain; Region: Fe_dep_repr_C; pfam02742 391008006920 manganese transport protein MntH; Reviewed; Region: PRK00701 391008006921 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 391008006922 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 391008006923 catalytic residues [active] 391008006924 flavodoxin; Provisional; Region: PRK09271 391008006925 ribonucleotide-diphosphate reductase subunit beta; Provisional; Region: nrdF2; PRK13966 391008006926 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 391008006927 dimer interface [polypeptide binding]; other site 391008006928 putative radical transfer pathway; other site 391008006929 diiron center [ion binding]; other site 391008006930 tyrosyl radical; other site 391008006931 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09209 391008006932 Class I ribonucleotide reductase; Region: RNR_I; cd01679 391008006933 active site 391008006934 dimer interface [polypeptide binding]; other site 391008006935 catalytic residues [active] 391008006936 effector binding site; other site 391008006937 R2 peptide binding site; other site 391008006938 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 391008006939 2-enoyl thioester reductase (ETR) like proteins, child 2; Region: ETR_like_2; cd08292 391008006940 putative NAD(P) binding site [chemical binding]; other site 391008006941 putative dimer interface [polypeptide binding]; other site 391008006942 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008006943 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008006944 BCCT family transporter; Region: BCCT; cl00569 391008006945 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_19; cd07262 391008006946 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 391008006947 RNA polymerase sigma factor; Provisional; Region: PRK12528 391008006948 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391008006949 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 391008006950 DNA binding residues [nucleotide binding] 391008006951 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 391008006952 FecR protein; Region: FecR; pfam04773 391008006953 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008006954 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008006955 Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism]; Region: EmrE; COG2076 391008006956 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 391008006957 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008006958 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008006959 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 391008006960 dimerization interface [polypeptide binding]; other site 391008006961 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_4; cd06231 391008006962 putative active site [active] 391008006963 Zn binding site [ion binding]; other site 391008006964 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 391008006965 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 391008006966 N-terminal plug; other site 391008006967 ligand-binding site [chemical binding]; other site 391008006968 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 391008006969 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 391008006970 Cl- selectivity filter; other site 391008006971 Cl- binding residues [ion binding]; other site 391008006972 pore gating glutamate residue; other site 391008006973 dimer interface [polypeptide binding]; other site 391008006974 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 391008006975 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 391008006976 MgtC family; Region: MgtC; pfam02308 391008006977 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 391008006978 DNA binding residues [nucleotide binding] 391008006979 Methyltransferase domain; Region: Methyltransf_11; pfam08241 391008006980 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 391008006981 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 391008006982 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 391008006983 ligand binding site [chemical binding]; other site 391008006984 Extended Signal Peptide of Type V secretion system; Region: ESPR; pfam13018 391008006985 Haemagglutinin; Region: HIM; pfam05662 391008006986 Left-handed beta-roll, including virulence factors and various other proteins; Region: LbR-like; cl17507 391008006987 Autotransporter adhesin [Intracellular trafficking and secretion / Extracellular structures]; Region: Hia; COG5295 391008006988 YadA-like C-terminal region; Region: YadA; pfam03895 391008006989 Helix-turn-helix domain; Region: HTH_18; pfam12833 391008006990 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008006991 Flp/Fap pilin component; Region: Flp_Fap; cl01585 391008006992 Flp pilus assembly protein, protease CpaA [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: CpaA; COG4960 391008006993 Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]; Region: CpaB; COG3745 391008006994 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 391008006995 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 391008006996 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 391008006997 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 391008006998 AAA domain; Region: AAA_31; pfam13614 391008006999 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 391008007000 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 391008007001 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 391008007002 ATP binding site [chemical binding]; other site 391008007003 Walker A motif; other site 391008007004 hexamer interface [polypeptide binding]; other site 391008007005 Walker B motif; other site 391008007006 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 391008007007 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 391008007008 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 391008007009 Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]; Region: TadD; COG5010 391008007010 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 391008007011 binding surface 391008007012 TPR motif; other site 391008007013 Protein of unknown function (DUF3613); Region: DUF3613; pfam12266 391008007014 Predicted membrane protein [Function unknown]; Region: COG4655 391008007015 Putative Tad-like Flp pilus-assembly; Region: Tad_C; pfam09977 391008007016 Protein of unknown function (DUF2968); Region: DUF2968; pfam11180 391008007017 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 391008007018 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 391008007019 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 391008007020 Transmembrane secretion effector; Region: MFS_3; pfam05977 391008007021 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 391008007022 putative substrate translocation pore; other site 391008007023 Domain of unknown function (DUF4104); Region: DUF4104; pfam13372 391008007024 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 391008007025 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 391008007026 active site 391008007027 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 391008007028 Isochorismatase family; Region: Isochorismatase; pfam00857 391008007029 catalytic triad [active] 391008007030 dimer interface [polypeptide binding]; other site 391008007031 conserved cis-peptide bond; other site 391008007032 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008007033 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 391008007034 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008007035 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 391008007036 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 391008007037 Histidine kinase; Region: HisKA_3; pfam07730 391008007038 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 391008007039 ATP binding site [chemical binding]; other site 391008007040 Mg2+ binding site [ion binding]; other site 391008007041 G-X-G motif; other site 391008007042 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 391008007043 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 391008007044 active site 391008007045 phosphorylation site [posttranslational modification] 391008007046 intermolecular recognition site; other site 391008007047 dimerization interface [polypeptide binding]; other site 391008007048 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 391008007049 DNA binding residues [nucleotide binding] 391008007050 dimerization interface [polypeptide binding]; other site 391008007051 Acyl-CoA thioester hydrolase/BAAT N-terminal region; Region: Bile_Hydr_Trans; pfam04775 391008007052 BAAT / Acyl-CoA thioester hydrolase C terminal; Region: BAAT_C; pfam08840 391008007053 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 391008007054 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 391008007055 active site 391008007056 dimerization interface [polypeptide binding]; other site 391008007057 LytTr DNA-binding domain; Region: LytTR; smart00850 391008007058 Histidine kinase; Region: His_kinase; pfam06580 391008007059 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 391008007060 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 391008007061 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 391008007062 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 391008007063 active site 391008007064 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 391008007065 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 391008007066 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 391008007067 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008007068 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008007069 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 391008007070 dimerization interface [polypeptide binding]; other site 391008007071 Domain of unknown function (DUF3806); Region: DUF3806; pfam12713 391008007072 cytosine deaminase; Provisional; Region: PRK05985 391008007073 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 fungi; Region: Bact_CD; cd01293 391008007074 active site 391008007075 Glycosyltransferase (GlcNAc); Region: GlcNAc; pfam11397 391008007076 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008007077 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008007078 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008007079 Acetyltransferase (GNAT) domain; Region: Acetyltransf_4; pfam13420 391008007080 CDP-diacylglycerol pyrophosphatase; Provisional; Region: PRK05471 391008007081 Peptidase inhibitor I78 family; Region: Inhibitor_I78; pfam11720 391008007082 D-lactate dehydrogenase; Provisional; Region: PRK11183 391008007083 FAD binding domain; Region: FAD_binding_4; pfam01565 391008007084 D-lactate dehydrogenase, membrane binding; Region: Lact-deh-memb; pfam09330 391008007085 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 391008007086 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 391008007087 phosphate binding site [ion binding]; other site 391008007088 DNA-binding transcriptional repressor LldR; Provisional; Region: PRK10421 391008007089 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 391008007090 DNA-binding site [nucleotide binding]; DNA binding site 391008007091 FCD domain; Region: FCD; pfam07729 391008007092 L-lactate permease; Provisional; Region: PRK10420 391008007093 glycolate transporter; Provisional; Region: PRK09695 391008007094 MgtC family; Region: MgtC; pfam02308 391008007095 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 391008007096 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008007097 NAD(P) binding site [chemical binding]; other site 391008007098 active site 391008007099 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008007100 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 391008007101 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008007102 Predicted acyl esterases [General function prediction only]; Region: COG2936 391008007103 X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain; Region: PepX_C; smart00939 391008007104 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4460 391008007105 SnoaL-like domain; Region: SnoaL_3; pfam13474 391008007106 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 391008007107 Major Facilitator Superfamily; Region: MFS_1; pfam07690 391008007108 putative substrate translocation pore; other site 391008007109 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008007110 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008007111 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 391008007112 putative effector binding pocket; other site 391008007113 dimerization interface [polypeptide binding]; other site 391008007114 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 391008007115 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 391008007116 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 391008007117 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 391008007118 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 391008007119 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 391008007120 active site 391008007121 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 391008007122 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 391008007123 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 391008007124 transcriptional regulator; Provisional; Region: PRK10632 391008007125 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008007126 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 391008007127 putative effector binding pocket; other site 391008007128 dimerization interface [polypeptide binding]; other site 391008007129 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 391008007130 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 391008007131 Putative cyclase; Region: Cyclase; pfam04199 391008007132 Uncharacterized conserved protein [Function unknown]; Region: COG4544 391008007133 DNA Polymerase Y-family; Region: PolY_like; cd03468 391008007134 active site 391008007135 DNA binding site [nucleotide binding] 391008007136 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 391008007137 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; Region: PHP_PolIIIA_DnaE2; cd07434 391008007138 putative active site [active] 391008007139 putative PHP Thumb interface [polypeptide binding]; other site 391008007140 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 391008007141 generic binding surface II; other site 391008007142 generic binding surface I; other site 391008007143 transcriptional regulatory protein PtsJ; Provisional; Region: PRK15481 391008007144 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 391008007145 DNA-binding site [nucleotide binding]; DNA binding site 391008007146 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 391008007147 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008007148 homodimer interface [polypeptide binding]; other site 391008007149 catalytic residue [active] 391008007150 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 391008007151 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 391008007152 catalytic residue [active] 391008007153 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 391008007154 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 391008007155 catalytic triad [active] 391008007156 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 391008007157 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391008007158 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 391008007159 DNA binding residues [nucleotide binding] 391008007160 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 391008007161 FecR protein; Region: FecR; pfam04773 391008007162 Secretin and TonB N terminus short domain; Region: STN; smart00965 391008007163 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008007164 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 391008007165 Protein of unknown function, DUF399; Region: DUF399; cl01139 391008007166 TonB family C-terminal domain; Region: tonB_Cterm; TIGR01352 391008007167 Cation efflux family; Region: Cation_efflux; cl00316 391008007168 arginine decarboxylase; Provisional; Region: PRK15029 391008007169 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 391008007170 Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and lysine...; Region: Orn_deC_like; cd00615 391008007171 homodimer interface [polypeptide binding]; other site 391008007172 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008007173 catalytic residue [active] 391008007174 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 391008007175 arginine:agmatin antiporter; Provisional; Region: PRK10644 391008007176 Porin subfamily; Region: Porin_2; pfam02530 391008007177 disulfide isomerase/thiol-disulfide oxidase; Provisional; Region: dsbG; PRK11657 391008007178 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 391008007179 dimer interface [polypeptide binding]; other site 391008007180 catalytic residues [active] 391008007181 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 391008007182 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 391008007183 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 391008007184 catalytic residues [active] 391008007185 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 391008007186 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 391008007187 conserved cys residue [active] 391008007188 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008007189 Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; Region: HTH_HMRTR; cd04770 391008007190 DNA binding residues [nucleotide binding] 391008007191 Hg(II)-responsive transcriptional regulator; Region: MerR; TIGR02051 391008007192 dimer interface [polypeptide binding]; other site 391008007193 metal binding site [ion binding]; metal-binding site 391008007194 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391008007195 Coenzyme A binding pocket [chemical binding]; other site 391008007196 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 391008007197 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 391008007198 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 391008007199 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008007200 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008007201 metal binding site [ion binding]; metal-binding site 391008007202 active site 391008007203 I-site; other site 391008007204 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 391008007205 PAS domain; Region: PAS_9; pfam13426 391008007206 putative active site [active] 391008007207 heme pocket [chemical binding]; other site 391008007208 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 391008007209 PAS domain; Region: PAS_9; pfam13426 391008007210 putative active site [active] 391008007211 heme pocket [chemical binding]; other site 391008007212 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 391008007213 dimer interface [polypeptide binding]; other site 391008007214 putative CheW interface [polypeptide binding]; other site 391008007215 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 391008007216 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 391008007217 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 391008007218 PAS fold; Region: PAS_3; pfam08447 391008007219 putative active site [active] 391008007220 heme pocket [chemical binding]; other site 391008007221 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 391008007222 PAS domain; Region: PAS_9; pfam13426 391008007223 putative active site [active] 391008007224 heme pocket [chemical binding]; other site 391008007225 PAS domain S-box; Region: sensory_box; TIGR00229 391008007226 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 391008007227 putative active site [active] 391008007228 heme pocket [chemical binding]; other site 391008007229 PAS fold; Region: PAS_4; pfam08448 391008007230 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 391008007231 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008007232 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008007233 metal binding site [ion binding]; metal-binding site 391008007234 active site 391008007235 I-site; other site 391008007236 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 391008007237 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 391008007238 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 391008007239 S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression; Region: S1_Tex; cd05685 391008007240 RNA binding site [nucleotide binding]; other site 391008007241 PspC domain; Region: PspC; pfam04024 391008007242 hypothetical protein; Provisional; Region: PRK10318 391008007243 poly(R)-hydroxyalkanoic acid synthase, class III, PhaC subunit; Region: PHA_synth_III_C; TIGR01836 391008007244 Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E); Region: PHA_synth_III_E; pfam09712 391008007245 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 391008007246 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 391008007247 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 391008007248 S-adenosylmethionine binding site [chemical binding]; other site 391008007249 MutT homolog-1 (MTH1) is a member of the Nudix hydrolase superfamily. MTH1, the mammalian counterpart of MutT, hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to monophosphates, thereby preventing the...; Region: MTH1; cd03427 391008007250 putative active site [active] 391008007251 nucleotide binding site [chemical binding]; other site 391008007252 nudix motif; other site 391008007253 putative metal binding site [ion binding]; other site 391008007254 Protein of unknown function (DUF1249); Region: DUF1249; cl01223 391008007255 PEP synthetase regulatory protein; Provisional; Region: PRK05339 391008007256 phosphoenolpyruvate synthase; Validated; Region: PRK06464 391008007257 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 391008007258 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 391008007259 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 391008007260 Mechanosensitive ion channel; Region: MS_channel; pfam00924 391008007261 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 391008007262 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 391008007263 FMN binding site [chemical binding]; other site 391008007264 active site 391008007265 substrate binding site [chemical binding]; other site 391008007266 catalytic residue [active] 391008007267 EcsC protein family; Region: EcsC; pfam12787 391008007268 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 391008007269 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 391008007270 catalytic site [active] 391008007271 putative active site [active] 391008007272 putative substrate binding site [chemical binding]; other site 391008007273 dimer interface [polypeptide binding]; other site 391008007274 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 391008007275 nucleoside/Zn binding site; other site 391008007276 dimer interface [polypeptide binding]; other site 391008007277 catalytic motif [active] 391008007278 Predicted transcriptional regulators [Transcription]; Region: COG1733 391008007279 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 391008007280 Flavodoxin-like fold; Region: Flavodoxin_2; pfam02525 391008007281 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 391008007282 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 391008007283 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 391008007284 putative acetyltransferase; Provisional; Region: PRK03624 391008007285 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391008007286 Coenzyme A binding pocket [chemical binding]; other site 391008007287 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation", the process of...; Region: Lipase; cl14883 391008007288 nucleophilic elbow; other site 391008007289 catalytic triad; other site 391008007290 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 391008007291 catalytic residue [active] 391008007292 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; pfam04610 391008007293 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 391008007294 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 391008007295 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 391008007296 TrbC/VIRB2 family; Region: TrbC; pfam04956 391008007297 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 391008007298 N-acetyl-D-glucosamine binding site [chemical binding]; other site 391008007299 catalytic residue [active] 391008007300 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 391008007301 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 391008007302 Walker A motif; other site 391008007303 hexamer interface [polypeptide binding]; other site 391008007304 ATP binding site [chemical binding]; other site 391008007305 Walker B motif; other site 391008007306 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 391008007307 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 391008007308 VirB7 interaction site; other site 391008007309 VirB8 protein; Region: VirB8; pfam04335 391008007310 Toxin co-regulated pilus biosynthesis protein Q; Region: TcpQ; pfam10671 391008007311 Type IV secretory system Conjugative DNA transfer; Region: T4SS-DNA_transf; pfam02534 391008007312 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 391008007313 Walker A motif; other site 391008007314 ATP binding site [chemical binding]; other site 391008007315 Walker B motif; other site 391008007316 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 391008007317 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 391008007318 putative substrate translocation pore; other site 391008007319 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 391008007320 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 391008007321 DNA binding residues [nucleotide binding] 391008007322 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 391008007323 Old yellow enzyme (OYE)-related FMN binding domain, group 2. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as...; Region: OYE_like_2_FMN; cd04733 391008007324 putative active site [active] 391008007325 putative FMN binding site [chemical binding]; other site 391008007326 putative substrate binding site [chemical binding]; other site 391008007327 putative catalytic residue [active] 391008007328 hypothetical protein; Provisional; Region: PRK06834 391008007329 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 391008007330 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 391008007331 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 391008007332 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008007333 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 391008007334 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 391008007335 N-terminal plug; other site 391008007336 ligand-binding site [chemical binding]; other site 391008007337 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391008007338 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 391008007339 active site 391008007340 phosphorylation site [posttranslational modification] 391008007341 intermolecular recognition site; other site 391008007342 dimerization interface [polypeptide binding]; other site 391008007343 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008007344 DNA binding site [nucleotide binding] 391008007345 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008007346 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 391008007347 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008007348 dimer interface [polypeptide binding]; other site 391008007349 phosphorylation site [posttranslational modification] 391008007350 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 391008007351 ATP binding site [chemical binding]; other site 391008007352 Mg2+ binding site [ion binding]; other site 391008007353 G-X-G motif; other site 391008007354 macrolide transporter subunit MacA; Provisional; Region: PRK11578 391008007355 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008007356 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008007357 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 391008007358 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 391008007359 Walker A/P-loop; other site 391008007360 ATP binding site [chemical binding]; other site 391008007361 Q-loop/lid; other site 391008007362 ABC transporter signature motif; other site 391008007363 Walker B; other site 391008007364 D-loop; other site 391008007365 H-loop/switch region; other site 391008007366 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 391008007367 FtsX-like permease family; Region: FtsX; pfam02687 391008007368 BA14K-like protein; Region: BA14K; pfam07886 391008007369 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cd00051 391008007370 EF-hand domain pair; Region: EF_hand_5; pfam13499 391008007371 Ca2+ binding site [ion binding]; other site 391008007372 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cd00051 391008007373 EF-hand domain pair; Region: EF_hand_5; pfam13499 391008007374 Ca2+ binding site [ion binding]; other site 391008007375 Predicted transcriptional regulators [Transcription]; Region: COG1733 391008007376 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 391008007377 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 391008007378 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 391008007379 NADP binding site [chemical binding]; other site 391008007380 dimer interface [polypeptide binding]; other site 391008007381 DNA helicase IV / RNA helicase N terminal; Region: Nucleolin_N; pfam12462 391008007382 Part of AAA domain; Region: AAA_19; pfam13245 391008007383 Family description; Region: UvrD_C_2; pfam13538 391008007384 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 391008007385 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 391008007386 active site 391008007387 Int/Topo IB signature motif; other site 391008007388 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 391008007389 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 391008007390 tape measure domain; Region: tape_meas_nterm; TIGR02675 391008007391 Protein of unknown function (DUF3168); Region: DUF3168; pfam11367 391008007392 Bacteriophage protein of unknown function (DUF646); Region: DUF646; cl12124 391008007393 Phage head-tail joining protein; Region: Phage_H_T_join; pfam05521 391008007394 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 391008007395 oligomerization interface [polypeptide binding]; other site 391008007396 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 391008007397 Phage capsid family; Region: Phage_capsid; pfam05065 391008007398 Clp protease; Region: CLP_protease; pfam00574 391008007399 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_1; cd07016 391008007400 oligomer interface [polypeptide binding]; other site 391008007401 active site residues [active] 391008007402 Phage-related protein [Function unknown]; Region: COG4695; cl01923 391008007403 Phage portal protein; Region: Phage_portal; pfam04860 391008007404 Phage terminase-like protein, large subunit [General function prediction only]; Region: COG4626 391008007405 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 391008007406 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 391008007407 active site 391008007408 The lysozyme from bacteriophage lambda hydrolyses the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc), as do other lysozymes. But unlike other lysozymes, bacteriophage lambda does not produce a reducing...; Region: bacteriophage_lambda_lysozyme; cd00736 391008007409 N-acetyl-D-glucosamine binding site [chemical binding]; other site 391008007410 catalytic residue [active] 391008007411 Bacteriophage CI repressor helix-turn-helix domain; Region: Phage_CI_repr; pfam07022 391008007412 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 391008007413 Protein of unknown function (DUF4241); Region: DUF4241; pfam14025 391008007414 LysR family transcriptional regulator; Provisional; Region: PRK14997 391008007415 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008007416 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_4; cd08473 391008007417 putative effector binding pocket; other site 391008007418 putative dimerization interface [polypeptide binding]; other site 391008007419 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 391008007420 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 391008007421 Src Homology 3 domain superfamily; Region: SH3; cl17036 391008007422 peptide ligand binding site [polypeptide binding]; other site 391008007423 seryl-tRNA synthetase; Provisional; Region: PRK05431 391008007424 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 391008007425 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 391008007426 dimer interface [polypeptide binding]; other site 391008007427 active site 391008007428 motif 1; other site 391008007429 motif 2; other site 391008007430 motif 3; other site 391008007431 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 391008007432 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 391008007433 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 391008007434 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 391008007435 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 391008007436 EPSP synthase domain. 3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3-phosphate synthase) (EC 2.5.1.19) catalyses the reaction between shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form...; Region: EPSP_synthase; cd01556 391008007437 hinge; other site 391008007438 active site 391008007439 Chorismate mutase type II; Region: CM_2; pfam01817 391008007440 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 391008007441 Prephenate dehydratase; Region: PDT; pfam00800 391008007442 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 391008007443 putative L-Phe binding site [chemical binding]; other site 391008007444 3-phosphoserine/phosphohydroxythreonine aminotransferase; Provisional; Region: PRK05355 391008007445 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 391008007446 catalytic residue [active] 391008007447 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 391008007448 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 391008007449 phosphopeptide binding site; other site 391008007450 Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn); Region: PHA_gran_rgn; pfam09650 391008007451 Poly(hydroxyalcanoate) granule associated protein (phasin); Region: Phasin; pfam05597 391008007452 Uncharacterized protein family (UPF0150); Region: UPF0150; pfam03681 391008007453 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 391008007454 YcfA-like protein; Region: YcfA; pfam07927 391008007455 histidine utilization repressor, proteobacterial; Region: his_ut_repres; TIGR02018 391008007456 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 391008007457 DNA-binding site [nucleotide binding]; DNA binding site 391008007458 UTRA domain; Region: UTRA; pfam07702 391008007459 N-formimino-L-glutamate deiminase; Validated; Region: PRK09229 391008007460 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 391008007461 active site 391008007462 imidazolonepropionase; Validated; Region: PRK09356 391008007463 Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria; Region: Imidazolone-5PH; cd01296 391008007464 active site 391008007465 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 391008007466 active sites [active] 391008007467 tetramer interface [polypeptide binding]; other site 391008007468 N-formylglutamate amidohydrolase; Region: FGase; cl01522 391008007469 urocanate hydratase; Provisional; Region: PRK05414 391008007470 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 391008007471 Beta-lactamase; Region: Beta-lactamase; pfam00144 391008007472 Tetratricopeptide repeat; Region: TPR_12; pfam13424 391008007473 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 391008007474 TPR motif; other site 391008007475 Transposase; Region: DEDD_Tnp_IS110; pfam01548 391008007476 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 391008007477 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 391008007478 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 391008007479 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008007480 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 391008007481 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008007482 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 391008007483 active site 391008007484 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957; cl01113 391008007485 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 391008007486 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 391008007487 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008007488 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 391008007489 dimerization interface [polypeptide binding]; other site 391008007490 Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase_like_4; cd04501 391008007491 active site 391008007492 catalytic triad [active] 391008007493 oxyanion hole [active] 391008007494 Predicted Zn-dependent protease (DUF2268); Region: DUF2268; cl02316 391008007495 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 391008007496 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 391008007497 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 391008007498 Peptidase family M13; Region: Peptidase_M13; pfam01431 391008007499 Protein of unknown function (DUF3037); Region: DUF3037; pfam11236 391008007500 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 391008007501 Beta-lactamase; Region: Beta-lactamase; pfam00144 391008007502 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008007503 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008007504 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_8; cd08477 391008007505 putative effector binding pocket; other site 391008007506 putative dimerization interface [polypeptide binding]; other site 391008007507 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR2; cd08268 391008007508 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 391008007509 putative NAD(P) binding site [chemical binding]; other site 391008007510 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family; Region: PQQ_membr_DH; TIGR03074 391008007511 Membrane-bound PQQ-dependent glucose dehydrogenase; Region: PQQ_mGDH; cd10280 391008007512 Trp docking motif [polypeptide binding]; other site 391008007513 putative active site [active] 391008007514 DNA gyrase subunit A; Validated; Region: PRK05560 391008007515 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 391008007516 CAP-like domain; other site 391008007517 active site 391008007518 primary dimer interface [polypeptide binding]; other site 391008007519 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 391008007520 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 391008007521 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 391008007522 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 391008007523 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 391008007524 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 391008007525 S-methyl-5-thioribose-1-phosphate isomerase; Region: salvage_mtnA; TIGR00512 391008007526 Protein of unknown function (DUF3011); Region: DUF3011; pfam11218 391008007527 EF-P lysine aminoacylase GenX; Region: genX; TIGR00462 391008007528 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 391008007529 dimer interface [polypeptide binding]; other site 391008007530 motif 1; other site 391008007531 active site 391008007532 motif 2; other site 391008007533 motif 3; other site 391008007534 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 391008007535 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391008007536 Coenzyme A binding pocket [chemical binding]; other site 391008007537 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 391008007538 DNA ligase, NAD-dependent; Region: dnlj; TIGR00575 391008007539 nucleotide binding pocket [chemical binding]; other site 391008007540 K-X-D-G motif; other site 391008007541 catalytic site [active] 391008007542 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 391008007543 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 391008007544 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 391008007545 Dimer interface [polypeptide binding]; other site 391008007546 BRCT sequence motif; other site 391008007547 putative aminotransferase; Provisional; Region: PRK09105 391008007548 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 391008007549 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008007550 homodimer interface [polypeptide binding]; other site 391008007551 catalytic residue [active] 391008007552 cell division protein ZipA; Provisional; Region: PRK04570 391008007553 FtsZ protein binding site [polypeptide binding]; other site 391008007554 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 391008007555 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 391008007556 Walker A/P-loop; other site 391008007557 ATP binding site [chemical binding]; other site 391008007558 Q-loop/lid; other site 391008007559 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; pfam06470 391008007560 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 391008007561 ABC transporter signature motif; other site 391008007562 Walker B; other site 391008007563 D-loop; other site 391008007564 H-loop/switch region; other site 391008007565 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 391008007566 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 391008007567 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 391008007568 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 391008007569 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 391008007570 Uncharacterized protein family (UPF0167); Region: UPF0167; pfam03691 391008007571 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 391008007572 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 391008007573 EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB...; Region: EcAsnRS_like_N; cd04318 391008007574 putative anticodon binding site; other site 391008007575 putative dimer interface [polypeptide binding]; other site 391008007576 Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as...; Region: AsxRS_core; cd00776 391008007577 homodimer interface [polypeptide binding]; other site 391008007578 motif 1; other site 391008007579 motif 2; other site 391008007580 active site 391008007581 motif 3; other site 391008007582 Putative FMN-binding domain; Region: FMN_bind_2; pfam04299 391008007583 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 391008007584 active site clefts [active] 391008007585 zinc binding site [ion binding]; other site 391008007586 dimer interface [polypeptide binding]; other site 391008007587 3-hydroxyanthranilate 3,4-dioxygenase; Provisional; Region: PRK13264 391008007588 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 391008007589 kynureninase; Region: kynureninase; TIGR01814 391008007590 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 391008007591 catalytic residue [active] 391008007592 FAD binding domain; Region: FAD_binding_3; pfam01494 391008007593 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 391008007594 exonuclease I; Provisional; Region: sbcB; PRK11779 391008007595 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 391008007596 active site 391008007597 catalytic site [active] 391008007598 substrate binding site [chemical binding]; other site 391008007599 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 391008007600 TIGR02453 family protein; Region: TIGR02453 391008007601 Protein of unknown function (DUF2939); Region: DUF2939; pfam11159 391008007602 5'-nucleotidase; Region: 5-nucleotidase; pfam06189 391008007603 ATP-NAD kinase; Region: NAD_kinase; pfam01513 391008007604 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 391008007605 Glutamate dehydrogenase N terminal; Region: GDH_N; pfam12466 391008007606 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 391008007607 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 391008007608 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 391008007609 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008007610 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 391008007611 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 391008007612 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008007613 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008007614 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 391008007615 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 391008007616 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 391008007617 active site 391008007618 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 391008007619 dimerization interface [polypeptide binding]; other site 391008007620 putative DNA binding site [nucleotide binding]; other site 391008007621 putative Zn2+ binding site [ion binding]; other site 391008007622 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 391008007623 Methyltransferase domain; Region: Methyltransf_31; pfam13847 391008007624 S-adenosylmethionine binding site [chemical binding]; other site 391008007625 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 391008007626 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 391008007627 Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism]; Region: MetH; COG1410 391008007628 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 391008007629 substrate binding pocket [chemical binding]; other site 391008007630 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 391008007631 B12 binding site [chemical binding]; other site 391008007632 cobalt ligand [ion binding]; other site 391008007633 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 391008007634 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 391008007635 MFS_1 like family; Region: MFS_1_like; pfam12832 391008007636 Uncharacterized protein conserved in bacteria (DUF2058); Region: DUF2058; cl01201 391008007637 hypothetical protein; Provisional; Region: PRK00846 391008007638 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 391008007639 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 391008007640 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 391008007641 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 391008007642 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 391008007643 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 391008007644 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 391008007645 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 391008007646 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 391008007647 catalytic residues [active] 391008007648 dimer interface [polypeptide binding]; other site 391008007649 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 391008007650 DNA-binding site [nucleotide binding]; DNA binding site 391008007651 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 391008007652 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 391008007653 Walker A/P-loop; other site 391008007654 ATP binding site [chemical binding]; other site 391008007655 Q-loop/lid; other site 391008007656 ABC transporter signature motif; other site 391008007657 Walker B; other site 391008007658 D-loop; other site 391008007659 H-loop/switch region; other site 391008007660 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 391008007661 Protein of unknown function (DUF2884); Region: DUF2884; pfam11101 391008007662 Protein of unknown function (DUF2884); Region: DUF2884; pfam11101 391008007663 fumarate hydratase; Reviewed; Region: fumC; PRK00485 391008007664 Class II fumarases; Region: Fumarase_classII; cd01362 391008007665 active site 391008007666 tetramer interface [polypeptide binding]; other site 391008007667 adenylosuccinate lyase; Provisional; Region: PRK09285 391008007668 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 391008007669 tetramer interface [polypeptide binding]; other site 391008007670 active site 391008007671 Cupin superfamily protein; Region: Cupin_4; pfam08007 391008007672 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 391008007673 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391008007674 Coenzyme A binding pocket [chemical binding]; other site 391008007675 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 391008007676 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 391008007677 TPP-binding site [chemical binding]; other site 391008007678 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 391008007679 dimer interface [polypeptide binding]; other site 391008007680 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 391008007681 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 391008007682 E3 interaction surface; other site 391008007683 lipoyl attachment site [posttranslational modification]; other site 391008007684 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 391008007685 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 391008007686 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 391008007687 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 391008007688 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 391008007689 PhoD-like phosphatase; Region: PhoD; pfam09423 391008007690 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 391008007691 putative active site [active] 391008007692 putative metal binding site [ion binding]; other site 391008007693 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 391008007694 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 391008007695 N-terminal plug; other site 391008007696 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008007697 ligand-binding site [chemical binding]; other site 391008007698 replicative DNA helicase; Provisional; Region: PRK08760 391008007699 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 391008007700 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 391008007701 Walker A motif; other site 391008007702 ATP binding site [chemical binding]; other site 391008007703 Walker B motif; other site 391008007704 DNA binding loops [nucleotide binding] 391008007705 Predicted flavoprotein [General function prediction only]; Region: COG0431 391008007706 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 391008007707 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 391008007708 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 391008007709 active site 391008007710 dimer interface [polypeptide binding]; other site 391008007711 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 391008007712 Ligand Binding Site [chemical binding]; other site 391008007713 Molecular Tunnel; other site 391008007714 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 391008007715 TPP-binding site [chemical binding]; other site 391008007716 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 391008007717 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 391008007718 PYR/PP interface [polypeptide binding]; other site 391008007719 dimer interface [polypeptide binding]; other site 391008007720 TPP binding site [chemical binding]; other site 391008007721 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 391008007722 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 391008007723 GST_N family, unknown subfamily 4; 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_4; cd03056 391008007724 putative C-terminal domain interface [polypeptide binding]; other site 391008007725 putative GSH binding site (G-site) [chemical binding]; other site 391008007726 putative dimer interface [polypeptide binding]; other site 391008007727 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 391008007728 N-terminal domain interface [polypeptide binding]; other site 391008007729 dimer interface [polypeptide binding]; other site 391008007730 substrate binding pocket (H-site) [chemical binding]; other site 391008007731 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 391008007732 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 391008007733 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 391008007734 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 391008007735 active site 391008007736 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 391008007737 Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like...; Region: YgdL_like; cd00755 391008007738 putative ATP binding site [chemical binding]; other site 391008007739 putative substrate interface [chemical binding]; other site 391008007740 Cytochrome C' Region: Cytochrom_C_2; cl01610 391008007741 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 391008007742 DNA-binding site [nucleotide binding]; DNA binding site 391008007743 RNA-binding motif; other site 391008007744 Protein of unknown function (DUF456); Region: DUF456; pfam04306 391008007745 The outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of acylester bonds in phospholipids using calcium as a cofactor. The enzyme has a fold of transmembrane beta-barrels and is widespread among...; Region: OMPLA; cd00541 391008007746 dimerization interface [polypeptide binding]; other site 391008007747 substrate binding site [chemical binding]; other site 391008007748 active site 391008007749 calcium binding site [ion binding]; other site 391008007750 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 391008007751 ArsC family; Region: ArsC; pfam03960 391008007752 catalytic residues [active] 391008007753 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 391008007754 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 391008007755 C-terminal domain interface [polypeptide binding]; other site 391008007756 GSH binding site (G-site) [chemical binding]; other site 391008007757 dimer interface [polypeptide binding]; other site 391008007758 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 391008007759 dimer interface [polypeptide binding]; other site 391008007760 N-terminal domain interface [polypeptide binding]; other site 391008007761 substrate binding pocket (H-site) [chemical binding]; other site 391008007762 putative fumarate hydratase; Provisional; Region: PRK15392 391008007763 Tartrate dehydratase alpha subunit/Fumarate hydratase class I, N-terminal domain [Energy production and conversion]; Region: TtdA; COG1951 391008007764 Fumarase C-terminus; Region: Fumerase_C; pfam05683 391008007765 RNA polymerase sigma-70 factor, TIGR02957 family; Region: SigX4 391008007766 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391008007767 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 391008007768 DNA binding residues [nucleotide binding] 391008007769 Uncharacterized conserved protein [Function unknown]; Region: COG2128 391008007770 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 391008007771 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 391008007772 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 391008007773 Walker A/P-loop; other site 391008007774 ATP binding site [chemical binding]; other site 391008007775 Q-loop/lid; other site 391008007776 ABC transporter signature motif; other site 391008007777 Walker B; other site 391008007778 D-loop; other site 391008007779 H-loop/switch region; other site 391008007780 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 391008007781 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 391008007782 FAD binding pocket [chemical binding]; other site 391008007783 FAD binding motif [chemical binding]; other site 391008007784 phosphate binding motif [ion binding]; other site 391008007785 beta-alpha-beta structure motif; other site 391008007786 NAD binding pocket [chemical binding]; other site 391008007787 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 391008007788 catalytic residues [active] 391008007789 dimer interface [polypeptide binding]; other site 391008007790 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 391008007791 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 391008007792 active site 391008007793 Zn binding site [ion binding]; other site 391008007794 cyclopropane fatty acyl phospholipid synthase; Provisional; Region: PRK11705 391008007795 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 391008007796 S-adenosylmethionine binding site [chemical binding]; other site 391008007797 Domain of unknown function (DUF4163); Region: DUF4163; pfam13739 391008007798 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 391008007799 Predicted acetyltransferase [General function prediction only]; Region: COG2388 391008007800 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 391008007801 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 391008007802 POT family; Region: PTR2; cl17359 391008007803 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 391008007804 putative catalytic site [active] 391008007805 putative metal binding site [ion binding]; other site 391008007806 putative phosphate binding site [ion binding]; other site 391008007807 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 391008007808 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 391008007809 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 391008007810 microbial_RNases. Ribonucleases (RNAses) cleave phosphodiester bonds in RNA and are essential for both non-specific RNA degradation and for numerous forms of RNA processing. The alignment contains fungal RNases (U2, T1, F1, Th, Pb, N1, and Ms) and...; Region: microbial_RNases; cl00212 391008007811 active site 391008007812 Barstar_evA4336-like contains uncharacterized sequences similar to the uncharacterized, predicted RNAase inhibitor evA4336 found in Azoarcus sp. EvN1. This is a subfamily of the Barstar family of RNAase inhibitors. Barstar is an intracellular inhibitor...; Region: Barstar_evA4336-like; cd05141 391008007813 putative RNAase interaction site [polypeptide binding]; other site 391008007814 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 391008007815 IscR-regulated protein YhgI; Region: YhgI_GntY; TIGR03341 391008007816 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 391008007817 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_a; cd00913 391008007818 aromatic arch; other site 391008007819 DCoH dimer interaction site [polypeptide binding]; other site 391008007820 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 391008007821 DCoH tetramer interaction site [polypeptide binding]; other site 391008007822 substrate binding site [chemical binding]; other site 391008007823 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 391008007824 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 391008007825 zinc transporter ZupT; Provisional; Region: PRK04201 391008007826 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 391008007827 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 391008007828 RNA binding surface [nucleotide binding]; other site 391008007829 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 391008007830 active site 391008007831 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 391008007832 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 391008007833 homodimer interface [polypeptide binding]; other site 391008007834 oligonucleotide binding site [chemical binding]; other site 391008007835 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 391008007836 putative catalytic site [active] 391008007837 putative metal binding site [ion binding]; other site 391008007838 putative phosphate binding site [ion binding]; other site 391008007839 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 391008007840 sugar binding site [chemical binding]; other site 391008007841 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 391008007842 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 391008007843 dimer interface [polypeptide binding]; other site 391008007844 conserved gate region; other site 391008007845 putative PBP binding loops; other site 391008007846 ABC-ATPase subunit interface; other site 391008007847 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 391008007848 dimer interface [polypeptide binding]; other site 391008007849 conserved gate region; other site 391008007850 putative PBP binding loops; other site 391008007851 ABC-ATPase subunit interface; other site 391008007852 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 391008007853 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 391008007854 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5368 391008007855 Putative glucoamylase; Region: Glycoamylase; pfam10091 391008007856 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 391008007857 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008007858 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008007859 Transcriptional regulators [Transcription]; Region: PurR; COG1609 391008007860 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 391008007861 DNA binding site [nucleotide binding] 391008007862 domain linker motif; other site 391008007863 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 391008007864 dimerization interface [polypeptide binding]; other site 391008007865 ligand binding site [chemical binding]; other site 391008007866 BolA-like protein; Region: BolA; pfam01722 391008007867 YciI-like protein; Reviewed; Region: PRK11370 391008007868 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 391008007869 Chromosome segregation and condensation protein B [DNA replication, recombination and repair]; Region: scpB; COG1386 391008007870 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 391008007871 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 391008007872 RNA binding surface [nucleotide binding]; other site 391008007873 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 391008007874 active site 391008007875 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 391008007876 Helix-turn-helix domain; Region: HTH_18; pfam12833 391008007877 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 391008007878 putative substrate translocation pore; other site 391008007879 C-N hydrolase family amidase; Provisional; Region: PRK10438 391008007880 Xanthomonas campestris XC1258 and related proteins, members of the nitrilase superfamily (putative class 13 nitrilases); Region: Xc-1258_like; cd07575 391008007881 putative active site [active] 391008007882 catalytic triad [active] 391008007883 dimer interface [polypeptide binding]; other site 391008007884 multimer interface [polypeptide binding]; other site 391008007885 methionine aminotransferase; Validated; Region: PRK09082 391008007886 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 391008007887 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008007888 homodimer interface [polypeptide binding]; other site 391008007889 catalytic residue [active] 391008007890 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13543 391008007891 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 391008007892 Walker A/P-loop; other site 391008007893 ATP binding site [chemical binding]; other site 391008007894 Q-loop/lid; other site 391008007895 ABC transporter signature motif; other site 391008007896 Walker B; other site 391008007897 D-loop; other site 391008007898 H-loop/switch region; other site 391008007899 CcmB protein; Region: CcmB; cl17444 391008007900 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 391008007901 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 391008007902 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 391008007903 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 391008007904 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 391008007905 catalytic residues [active] 391008007906 central insert; other site 391008007907 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 391008007908 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 391008007909 Homoserine acetyltransferase [Amino acid transport and metabolism]; Region: MET2; COG2021 391008007910 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 391008007911 Protein of unknown function (DUF1294); Region: DUF1294; pfam06961 391008007912 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 391008007913 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 391008007914 Walker A/P-loop; other site 391008007915 ATP binding site [chemical binding]; other site 391008007916 Q-loop/lid; other site 391008007917 ABC transporter signature motif; other site 391008007918 Walker B; other site 391008007919 D-loop; other site 391008007920 H-loop/switch region; other site 391008007921 thiol reductant ABC exporter, CydD subunit; Region: CydD; TIGR02857 391008007922 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 391008007923 Walker A/P-loop; other site 391008007924 ATP binding site [chemical binding]; other site 391008007925 Q-loop/lid; other site 391008007926 ABC transporter signature motif; other site 391008007927 Walker B; other site 391008007928 D-loop; other site 391008007929 H-loop/switch region; other site 391008007930 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 391008007931 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 391008007932 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 391008007933 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 391008007934 Membrane bound YbgT-like protein; Region: YbgT_YccB; pfam08173 391008007935 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 391008007936 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 391008007937 poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA; Region: PGA_TPR_OMP; TIGR03939 391008007938 poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB; Region: deacetyl_PgaB; TIGR03938 391008007939 N-terminal putative catalytic polysaccharide deacetylase domain of bacterial poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, and similar proteins; Region: CE4_PgaB_5s; cd10964 391008007940 putative active site [active] 391008007941 putative metal binding site [ion binding]; other site 391008007942 N-glycosyltransferase; Provisional; Region: PRK11204 391008007943 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 391008007944 DXD motif; other site 391008007945 PgaD-like protein; Region: PgaD; pfam13994 391008007946 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 391008007947 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 391008007948 putative catalytic cysteine [active] 391008007949 gamma-glutamyl kinase; Provisional; Region: PRK05429 391008007950 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 391008007951 nucleotide binding site [chemical binding]; other site 391008007952 PUA domain; Region: PUA; pfam01472 391008007953 YCII-related domain; Region: YCII; cl00999 391008007954 argininosuccinate lyase; Provisional; Region: PRK00855 391008007955 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 391008007956 active sites [active] 391008007957 tetramer interface [polypeptide binding]; other site 391008007958 N-acetyl-gamma-glutamyl-phosphate reductase, common form; Region: argC; TIGR01850 391008007959 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 391008007960 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 391008007961 acetylglutamate kinase; Provisional; Region: PRK04531 391008007962 AAK_NAGK-fArgBP: N-Acetyl-L-glutamate kinase (NAGK) of the fungal arginine-biosynthetic pathway (fArgBP). The nuclear-encoded, mitochondrial polyprotein precursor with an N-terminal NAGK (ArgB) domain (this CD), a central DUF619 domain, and a C-terminal...; Region: AAK_NAGK-fArgBP; cd04252 391008007963 putative nucleotide binding site [chemical binding]; other site 391008007964 putative N-acetyl-L-glutamate binding site [chemical binding]; other site 391008007965 DUF619 domain of various N-acetylglutamate Synthases of the fungal arginine-biosynthetic pathway and urea cycle found in humans and fish; Region: DUF619-NAGS; cd04264 391008007966 acetylornithine deacetylase; Provisional; Region: PRK08737 391008007967 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 391008007968 metal binding site [ion binding]; metal-binding site 391008007969 putative dimer interface [polypeptide binding]; other site 391008007970 argininosuccinate synthase; Provisional; Region: PRK13820 391008007971 Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In...; Region: Argininosuccinate_Synthase; cd01999 391008007972 ANP binding site [chemical binding]; other site 391008007973 Substrate Binding Site II [chemical binding]; other site 391008007974 Substrate Binding Site I [chemical binding]; other site 391008007975 N-acetylornithine carbamoyltransferase; Reviewed; Region: PRK04523 391008007976 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 391008007977 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 391008007978 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 391008007979 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 391008007980 active site 391008007981 HIGH motif; other site 391008007982 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 391008007983 active site 391008007984 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 391008007985 KMSKS motif; other site 391008007986 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 391008007987 tRNA binding surface [nucleotide binding]; other site 391008007988 anticodon binding site; other site 391008007989 Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones]; Region: sufE; COG2166 391008007990 H+ Antiporter protein; Region: 2A0121; TIGR00900 391008007991 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 391008007992 putative substrate translocation pore; other site 391008007993 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 391008007994 hypothetical protein; Validated; Region: PRK00041 391008007995 dihydroorotase; Reviewed; Region: PRK09236 391008007996 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 391008007997 Dihydroorotase (DHOase), subgroup IIb; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This group contains the archeal members of the DHOase family; Region: DHOase_IIb; cd01318 391008007998 active site 391008007999 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 391008008000 Peptidase family M23; Region: Peptidase_M23; pfam01551 391008008001 Isoprenoid Biosynthesis enzymes, Class 1; Region: Isoprenoid_Biosyn_C1; cl00210 391008008002 phosphoglycolate phosphatase; Provisional; Region: PRK13226 391008008003 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 391008008004 active site 391008008005 motif I; other site 391008008006 motif II; other site 391008008007 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 391008008008 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 391008008009 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 391008008010 S-adenosylmethionine binding site [chemical binding]; other site 391008008011 N-ethylammeline chlorohydrolase; Provisional; Region: PRK09045 391008008012 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 391008008013 active site 391008008014 putative substrate binding pocket [chemical binding]; other site 391008008015 elongation factor P; Validated; Region: PRK00529 391008008016 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 391008008017 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_1; cd04470 391008008018 RNA binding site [nucleotide binding]; other site 391008008019 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_2; cd05794 391008008020 RNA binding site [nucleotide binding]; other site 391008008021 Lysine 2,3-aminomutase [Amino acid transport and metabolism]; Region: KamA; COG1509 391008008022 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 391008008023 FeS/SAM binding site; other site 391008008024 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 391008008025 dimerization interface [polypeptide binding]; other site 391008008026 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008008027 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008008028 metal binding site [ion binding]; metal-binding site 391008008029 active site 391008008030 I-site; other site 391008008031 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 391008008032 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 391008008033 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 391008008034 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 391008008035 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 391008008036 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 391008008037 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 391008008038 active site 391008008039 dimerization interface [polypeptide binding]; other site 391008008040 heat shock protein HtpX; Provisional; Region: PRK05457 391008008041 glutamyl-Q tRNA(Asp) synthetase; Reviewed; Region: PRK05710 391008008042 active site 391008008043 HIGH motif; other site 391008008044 nucleotide binding site [chemical binding]; other site 391008008045 KMSKS motif; other site 391008008046 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 391008008047 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 391008008048 NAD(P) binding site [chemical binding]; other site 391008008049 homotetramer interface [polypeptide binding]; other site 391008008050 homodimer interface [polypeptide binding]; other site 391008008051 active site 391008008052 polyhydroxyalkanoate synthesis repressor PhaR; Region: PHA_reg_PhaR; TIGR01848 391008008053 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 391008008054 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 391008008055 TraB family; Region: TraB; pfam01963 391008008056 Protein of unknown function (DUF1684); Region: DUF1684; cl01327 391008008057 DNA mismatch repair protein MutL; Region: mutl; TIGR00585 391008008058 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 391008008059 ATP binding site [chemical binding]; other site 391008008060 Mg2+ binding site [ion binding]; other site 391008008061 G-X-G motif; other site 391008008062 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 391008008063 ATP binding site [chemical binding]; other site 391008008064 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 391008008065 AMIN domain; Region: AMIN; pfam11741 391008008066 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 391008008067 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 391008008068 active site 391008008069 metal binding site [ion binding]; metal-binding site 391008008070 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 391008008071 YjeF-related protein N-terminus; Region: YjeF_N; pfam03853 391008008072 putative carbohydrate kinase; Provisional; Region: PRK10565 391008008073 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 391008008074 putative substrate binding site [chemical binding]; other site 391008008075 putative ATP binding site [chemical binding]; other site 391008008076 epoxyqueuosine reductase; Region: TIGR00276 391008008077 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 391008008078 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 391008008079 ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a...; Region: ExoVII_LU_OBF; cd04489 391008008080 generic binding surface II; other site 391008008081 generic binding surface I; other site 391008008082 Peptidase family M48; Region: Peptidase_M48; pfam01435 391008008083 Uncharacterized conserved protein [Function unknown]; Region: COG1262 391008008084 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 391008008085 ribonuclease D; Region: rnd; TIGR01388 391008008086 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 391008008087 catalytic site [active] 391008008088 putative active site [active] 391008008089 putative substrate binding site [chemical binding]; other site 391008008090 HRDC domain; Region: HRDC; cl02578 391008008091 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008008092 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 391008008093 N-terminal plug; other site 391008008094 ligand-binding site [chemical binding]; other site 391008008095 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 391008008096 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008008097 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 391008008098 AP endonuclease family 2 C terminus; Region: AP_endonuc_2_N; pfam07582 391008008099 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 391008008100 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 391008008101 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 391008008102 substrate binding pocket [chemical binding]; other site 391008008103 short chain dehydrogenase; Provisional; Region: PRK07478 391008008104 classical (c) SDRs; Region: SDR_c; cd05233 391008008105 NAD(P) binding site [chemical binding]; other site 391008008106 active site 391008008107 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008008108 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 391008008109 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 391008008110 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 391008008111 DNA binding site [nucleotide binding] 391008008112 active site 391008008113 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 391008008114 Prostaglandin dehydrogenases; Region: PGDH; cd05288 391008008115 NAD(P) binding site [chemical binding]; other site 391008008116 substrate binding site [chemical binding]; other site 391008008117 dimer interface [polypeptide binding]; other site 391008008118 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 391008008119 Late embryogenesis abundant protein; Region: LEA_2; pfam03168 391008008120 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 391008008121 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 391008008122 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 391008008123 active site 391008008124 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 391008008125 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 391008008126 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 391008008127 active site 391008008128 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 391008008129 Thiamine pyrophosphate (TPP) family, DXS subfamily, TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products...; Region: TPP_DXS; cd02007 391008008130 TPP-binding site; other site 391008008131 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 391008008132 PYR/PP interface [polypeptide binding]; other site 391008008133 dimer interface [polypeptide binding]; other site 391008008134 TPP binding site [chemical binding]; other site 391008008135 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 391008008136 Protein of unknown function (DUF3011); Region: DUF3011; pfam11218 391008008137 Protein of unknown function (DUF1653); Region: DUF1653; pfam07866 391008008138 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008008139 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 391008008140 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 391008008141 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 391008008142 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 391008008143 oligomer interface [polypeptide binding]; other site 391008008144 active site residues [active] 391008008145 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 391008008146 hydrophobic ligand binding site; other site 391008008147 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 391008008148 dimerization interface [polypeptide binding]; other site 391008008149 putative DNA binding site [nucleotide binding]; other site 391008008150 putative Zn2+ binding site [ion binding]; other site 391008008151 Aspartate racemase [Cell envelope biogenesis, outer membrane]; Region: RacX; COG1794 391008008152 aspartate racemase; Region: asp_race; TIGR00035 391008008153 Protein of unknown function (DUF3011); Region: DUF3011; pfam11218 391008008154 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391008008155 Coenzyme A binding pocket [chemical binding]; other site 391008008156 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 391008008157 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 391008008158 DNA binding residues [nucleotide binding] 391008008159 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 391008008160 IHF dimer interface [polypeptide binding]; other site 391008008161 IHF - DNA interface [nucleotide binding]; other site 391008008162 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 391008008163 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 391008008164 putative tRNA-binding site [nucleotide binding]; other site 391008008165 B3/4 domain; Region: B3_4; pfam03483 391008008166 tRNA synthetase B5 domain; Region: B5; smart00874 391008008167 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 391008008168 dimer interface [polypeptide binding]; other site 391008008169 motif 1; other site 391008008170 motif 3; other site 391008008171 motif 2; other site 391008008172 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 391008008173 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 391008008174 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 391008008175 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 391008008176 dimer interface [polypeptide binding]; other site 391008008177 motif 1; other site 391008008178 active site 391008008179 motif 2; other site 391008008180 motif 3; other site 391008008181 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 391008008182 23S rRNA binding site [nucleotide binding]; other site 391008008183 L21 binding site [polypeptide binding]; other site 391008008184 L13 binding site [polypeptide binding]; other site 391008008185 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 391008008186 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 391008008187 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 391008008188 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 391008008189 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 391008008190 TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and...; Region: TGS_ThrRS_N; cd01667 391008008191 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 391008008192 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 391008008193 active site 391008008194 dimer interface [polypeptide binding]; other site 391008008195 motif 1; other site 391008008196 motif 2; other site 391008008197 motif 3; other site 391008008198 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 391008008199 anticodon binding site; other site 391008008200 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 391008008201 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 391008008202 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 391008008203 The GH18 (glycosyl hydrolases, family 18) type II chitinases hydrolyze chitin, an abundant polymer of N-acetylglucosamine and have been identified in bacteria, fungi, insects, plants, viruses, and protozoan parasites. The structure of this domain is an...; Region: GH18_chitinase; cd06548 391008008204 Glyco_18 domain; Region: Glyco_18; smart00636 391008008205 active site 391008008206 TPR repeat; Region: TPR_11; pfam13414 391008008207 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 391008008208 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 391008008209 RNase E interface [polypeptide binding]; other site 391008008210 trimer interface [polypeptide binding]; other site 391008008211 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 391008008212 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 391008008213 RNase E interface [polypeptide binding]; other site 391008008214 trimer interface [polypeptide binding]; other site 391008008215 active site 391008008216 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 391008008217 putative nucleic acid binding region [nucleotide binding]; other site 391008008218 G-X-X-G motif; other site 391008008219 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 391008008220 RNA binding site [nucleotide binding]; other site 391008008221 domain interface; other site 391008008222 Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole ribosome; Region: Ribosomal_S15p_S13e; cd00353 391008008223 16S/18S rRNA binding site [nucleotide binding]; other site 391008008224 S13e-L30e interaction site [polypeptide binding]; other site 391008008225 25S rRNA binding site [nucleotide binding]; other site 391008008226 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK04642 391008008227 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 391008008228 RNA binding site [nucleotide binding]; other site 391008008229 active site 391008008230 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 391008008231 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 391008008232 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 391008008233 translation initiation factor IF-2; Region: IF-2; TIGR00487 391008008234 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 391008008235 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 391008008236 G1 box; other site 391008008237 putative GEF interaction site [polypeptide binding]; other site 391008008238 GTP/Mg2+ binding site [chemical binding]; other site 391008008239 Switch I region; other site 391008008240 G2 box; other site 391008008241 G3 box; other site 391008008242 Switch II region; other site 391008008243 G4 box; other site 391008008244 G5 box; other site 391008008245 This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell; Region: IF2_mtIF2_II; cd03702 391008008246 Translation-initiation factor 2; Region: IF-2; pfam11987 391008008247 mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor...; Region: mtIF2_IVc; cd03692 391008008248 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 391008008249 NusA N-terminal domain; Region: NusA_N; pfam08529 391008008250 S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three...; Region: S1_NusA; cd04455 391008008251 RNA binding site [nucleotide binding]; other site 391008008252 homodimer interface [polypeptide binding]; other site 391008008253 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 391008008254 G-X-X-G motif; other site 391008008255 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 391008008256 G-X-X-G motif; other site 391008008257 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 391008008258 ribosome maturation protein RimP; Reviewed; Region: PRK00092 391008008259 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 391008008260 putative oligomer interface [polypeptide binding]; other site 391008008261 putative RNA binding site [nucleotide binding]; other site 391008008262 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 391008008263 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 391008008264 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 391008008265 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 391008008266 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 391008008267 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 391008008268 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 391008008269 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 391008008270 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 391008008271 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 391008008272 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 391008008273 4Fe-4S binding domain; Region: Fer4; pfam00037 391008008274 4Fe-4S binding domain; Region: Fer4; pfam00037 391008008275 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 391008008276 NADH dehydrogenase subunit G; Validated; Region: PRK09129 391008008277 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 391008008278 catalytic loop [active] 391008008279 iron binding site [ion binding]; other site 391008008280 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 391008008281 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 391008008282 molybdopterin cofactor binding site; other site 391008008283 Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum-...; Region: MopB_CT; cd02775 391008008284 NADH-quinone oxidoreductase, F subunit; Region: nuoF_fam; TIGR01959 391008008285 SLBB domain; Region: SLBB; pfam10531 391008008286 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 391008008287 NADH-quinone oxidoreductase, E subunit; Region: nuoE_fam; TIGR01958 391008008288 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 391008008289 putative dimer interface [polypeptide binding]; other site 391008008290 [2Fe-2S] cluster binding site [ion binding]; other site 391008008291 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 391008008292 NADH dehydrogenase subunit D; Validated; Region: PRK06075 391008008293 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 391008008294 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl16917 391008008295 NADH dehydrogenase subunit B; Validated; Region: PRK06411 391008008296 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 391008008297 Preprotein translocase SecG subunit; Region: SecG; pfam03840 391008008298 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 391008008299 substrate binding site [chemical binding]; other site 391008008300 dimer interface [polypeptide binding]; other site 391008008301 catalytic triad [active] 391008008302 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 391008008303 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; pfam14226 391008008304 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 391008008305 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 391008008306 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 391008008307 Sulfatase; Region: Sulfatase; cl17466 391008008308 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 391008008309 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 391008008310 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 391008008311 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 391008008312 Putative catalytic NodB homology domain of a hypothetical protein Ecf1 from Escherichia coli and similar proteins; Region: CE4_Ecf1_like_5s; cd10969 391008008313 putative active site [active] 391008008314 putative metal binding site [ion binding]; other site 391008008315 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 391008008316 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 391008008317 NAD binding site [chemical binding]; other site 391008008318 homodimer interface [polypeptide binding]; other site 391008008319 active site 391008008320 substrate binding site [chemical binding]; other site 391008008321 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 391008008322 GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of...; Region: GlmM; cd05802 391008008323 active site 391008008324 substrate binding site [chemical binding]; other site 391008008325 metal binding site [ion binding]; metal-binding site 391008008326 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 391008008327 zinc-ribbon domain; Region: zinc_ribbon_2; pfam13240 391008008328 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 391008008329 Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both...; Region: Tryptophan_synthase_alpha; cd04724 391008008330 substrate binding site [chemical binding]; other site 391008008331 active site 391008008332 catalytic residues [active] 391008008333 heterodimer interface [polypeptide binding]; other site 391008008334 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 391008008335 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 391008008336 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008008337 catalytic residue [active] 391008008338 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 391008008339 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008008340 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 391008008341 dimerization interface [polypeptide binding]; other site 391008008342 Toxic anion resistance protein (TelA); Region: TelA; pfam05816 391008008343 ATPase involved in DNA repair; Region: DUF3686; pfam12458 391008008344 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 391008008345 Walker A motif; other site 391008008346 ATP binding site [chemical binding]; other site 391008008347 Walker B motif; other site 391008008348 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2268 391008008349 Band_7_flotillin: a subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. These two proteins are lipid raft-associated. Individual proteins of...; Region: Band_7_flotillin; cd03399 391008008350 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2268 391008008351 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are...; Region: PRAI; cd00405 391008008352 active site 391008008353 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 391008008354 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 391008008355 dimerization interface 3.5A [polypeptide binding]; other site 391008008356 active site 391008008357 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 391008008358 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 391008008359 FimV N-terminal domain; Region: FimV_core; TIGR03505 391008008360 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 391008008361 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 391008008362 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 391008008363 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 391008008364 D-glycerate dehydrogenase/hydroxypyruvate reductase (GDH); Region: GDH; cd05301 391008008365 dimerization interface [polypeptide binding]; other site 391008008366 ligand binding site [chemical binding]; other site 391008008367 NADP binding site [chemical binding]; other site 391008008368 catalytic site [active] 391008008369 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 391008008370 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 391008008371 Tetramer interface [polypeptide binding]; other site 391008008372 active site 391008008373 FMN-binding site [chemical binding]; other site 391008008374 HemK family putative methylases; Region: hemK_fam; TIGR00536 391008008375 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 391008008376 S-adenosylmethionine binding site [chemical binding]; other site 391008008377 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 391008008378 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 391008008379 Cu(I) binding site [ion binding]; other site 391008008380 phosphatidylserine decarboxylase; Reviewed; Region: psd; PRK00044 391008008381 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 391008008382 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 391008008383 N-acetyl-D-glucosamine binding site [chemical binding]; other site 391008008384 catalytic residue [active] 391008008385 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 391008008386 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 391008008387 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 391008008388 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 391008008389 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 391008008390 Protein of unknown function (DUF3025); Region: DUF3025; pfam11227 391008008391 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 391008008392 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 391008008393 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 391008008394 FeS/SAM binding site; other site 391008008395 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 391008008396 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis...; Region: HIT_like; cl00228 391008008397 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 391008008398 trimer interface [polypeptide binding]; other site 391008008399 active site 391008008400 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 391008008401 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 391008008402 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008008403 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008008404 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008008405 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008008406 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 391008008407 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 391008008408 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 391008008409 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 391008008410 active site 391008008411 Zn binding site [ion binding]; other site 391008008412 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 391008008413 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 391008008414 active site 391008008415 Zn binding site [ion binding]; other site 391008008416 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 391008008417 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008008418 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008008419 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 391008008420 dimer interface [polypeptide binding]; other site 391008008421 Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG1233 391008008422 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 391008008423 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 391008008424 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 391008008425 active site 391008008426 DNA binding site [nucleotide binding] 391008008427 EamA-like transporter family; Region: EamA; pfam00892 391008008428 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 391008008429 EamA-like transporter family; Region: EamA; pfam00892 391008008430 Transposase; Region: DEDD_Tnp_IS110; pfam01548 391008008431 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 391008008432 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 391008008433 glutathione reductase; Validated; Region: PRK06116 391008008434 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 391008008435 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 391008008436 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 391008008437 Predicted membrane protein [Function unknown]; Region: COG2311 391008008438 Protein of unknown function (DUF418); Region: DUF418; cl12135 391008008439 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 391008008440 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 391008008441 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 391008008442 NlpC/P60 family; Region: NLPC_P60; pfam00877 391008008443 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 391008008444 NlpC/P60 family; Region: NLPC_P60; pfam00877 391008008445 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 391008008446 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 391008008447 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 391008008448 Alkaline phosphatase homologues; Region: alkPPc; smart00098 391008008449 active site 391008008450 dimer interface [polypeptide binding]; other site 391008008451 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 391008008452 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 391008008453 Ligand Binding Site [chemical binding]; other site 391008008454 TilS substrate binding domain; Region: TilS; pfam09179 391008008455 TilS substrate C-terminal domain; Region: TilS_C; pfam11734 391008008456 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 391008008457 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 391008008458 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 391008008459 substrate binding pocket [chemical binding]; other site 391008008460 chain length determination region; other site 391008008461 substrate-Mg2+ binding site; other site 391008008462 catalytic residues [active] 391008008463 aspartate-rich region 1; other site 391008008464 active site lid residues [active] 391008008465 aspartate-rich region 2; other site 391008008466 Tic20-like protein; Region: Tic20; pfam09685 391008008467 peptidase PmbA; Provisional; Region: PRK11040 391008008468 hypothetical protein; Provisional; Region: PRK05255 391008008469 protease TldD; Provisional; Region: tldD; PRK10735 391008008470 TIGR02099 family protein; Region: TIGR02099 391008008471 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 391008008472 ribonuclease G; Provisional; Region: PRK11712 391008008473 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 391008008474 homodimer interface [polypeptide binding]; other site 391008008475 oligonucleotide binding site [chemical binding]; other site 391008008476 Maf-like protein; Region: Maf; pfam02545 391008008477 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 391008008478 active site 391008008479 dimer interface [polypeptide binding]; other site 391008008480 Uncharacterized conserved protein [Function unknown]; Region: COG2968 391008008481 Protein of unknown function (DUF541); Region: SIMPL; pfam04402 391008008482 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 391008008483 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 391008008484 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008008485 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008008486 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 391008008487 arginine-ornithine antiporter; Region: arg_ornith_anti; TIGR03810 391008008488 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 391008008489 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 391008008490 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 391008008491 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 391008008492 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 391008008493 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 391008008494 active site 391008008495 (T/H)XGH motif; other site 391008008496 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 391008008497 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 391008008498 Lipopolysaccharide-assembly; Region: LptE; cl01125 391008008499 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 391008008500 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 391008008501 HIGH motif; other site 391008008502 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 391008008503 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 391008008504 active site 391008008505 KMSKS motif; other site 391008008506 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 391008008507 tRNA binding surface [nucleotide binding]; other site 391008008508 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 391008008509 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 391008008510 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4254 391008008511 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 391008008512 FecR protein; Region: FecR; pfam04773 391008008513 CHASE2 domain; Region: CHASE2; pfam05226 391008008514 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008008515 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008008516 metal binding site [ion binding]; metal-binding site 391008008517 active site 391008008518 I-site; other site 391008008519 Xylose isomerase [Carbohydrate transport and metabolism]; Region: XylA; cl09945 391008008520 Uncharacterized conserved protein [Function unknown]; Region: COG2928 391008008521 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 391008008522 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 391008008523 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 391008008524 Beta-lactamase; Region: Beta-lactamase; pfam00144 391008008525 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 391008008526 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 391008008527 putative metal binding site [ion binding]; other site 391008008528 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 391008008529 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 391008008530 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 391008008531 active site 391008008532 HIGH motif; other site 391008008533 KMSKS motif; other site 391008008534 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 391008008535 anticodon binding site; other site 391008008536 tRNA binding surface [nucleotide binding]; other site 391008008537 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 391008008538 putative tRNA-binding site [nucleotide binding]; other site 391008008539 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 391008008540 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 391008008541 ferredoxin; Provisional; Region: PRK08764 391008008542 Putative Fe-S cluster; Region: FeS; pfam04060 391008008543 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 391008008544 homotrimer interaction site [polypeptide binding]; other site 391008008545 putative active site [active] 391008008546 Predicted integral membrane protein [Function unknown]; Region: COG0392 391008008547 Uncharacterized conserved protein [Function unknown]; Region: COG2898 391008008548 Uncharacterized conserved protein (DUF2156); Region: DUF2156; pfam09924 391008008549 Type IV secretory pathway, VirJ component [Intracellular trafficking and secretion]; Region: VirJ; COG3946 391008008550 Bacterial virulence protein (VirJ); Region: VirJ; pfam06057 391008008551 Protein of unknown function (DUF998); Region: DUF998; pfam06197 391008008552 Oxidoreductase-like protein, N-terminal; Region: Oxidored-like; pfam09791 391008008553 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 391008008554 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 391008008555 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 391008008556 TPR repeat; Region: TPR_11; pfam13414 391008008557 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 391008008558 binding surface 391008008559 TPR motif; other site 391008008560 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 391008008561 binding surface 391008008562 TPR motif; other site 391008008563 TPR repeat; Region: TPR_11; pfam13414 391008008564 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 391008008565 binding surface 391008008566 TPR motif; other site 391008008567 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 391008008568 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 391008008569 PhnA protein; Region: PhnA; pfam03831 391008008570 putative chaperone; Provisional; Region: PRK11678 391008008571 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 391008008572 nucleotide binding site [chemical binding]; other site 391008008573 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 391008008574 nucleotide binding site [chemical binding]; other site 391008008575 Flagellin N-methylase; Region: FliB; pfam03692 391008008576 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 391008008577 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 391008008578 RNA polymerase sigma factor SigY; Reviewed; Region: PRK09638 391008008579 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391008008580 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 391008008581 DNA binding residues [nucleotide binding] 391008008582 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 391008008583 Mechanosensitive ion channel; Region: MS_channel; pfam00924 391008008584 putative transposase OrfB; Reviewed; Region: PHA02517 391008008585 HTH-like domain; Region: HTH_21; pfam13276 391008008586 Integrase core domain; Region: rve; pfam00665 391008008587 Integrase core domain; Region: rve_2; pfam13333 391008008588 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 391008008589 Transposase; Region: HTH_Tnp_1; cl17663 391008008590 hypothetical protein; Provisional; Region: PRK11019 391008008591 Uncharacterized protein conserved in bacteria (DUF2058); Region: DUF2058; pfam09831 391008008592 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 391008008593 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 391008008594 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 391008008595 RNA binding surface [nucleotide binding]; other site 391008008596 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 391008008597 active site 391008008598 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 391008008599 PLD-like domain; Region: PLDc_2; pfam13091 391008008600 putative active site [active] 391008008601 catalytic site [active] 391008008602 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 391008008603 PLD-like domain; Region: PLDc_2; pfam13091 391008008604 putative active site [active] 391008008605 catalytic site [active] 391008008606 HDOD domain; Region: HDOD; pfam08668 391008008607 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 391008008608 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 391008008609 NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase; Region: NAD_bind_Leu_Phe_Val_DH; cd01075 391008008610 NAD binding site [chemical binding]; other site 391008008611 Phe binding site; other site 391008008612 Peptidase S8 family domain in Autotransporter serine proteases; Region: Peptidases_S8_Autotransporter_serine_protease_like; cd04848 391008008613 catalytic triad [active] 391008008614 putative active site [active] 391008008615 Uncharacterized protein with a C-terminal OMP (outer membrane protein) domain [Function unknown]; Region: COG4625 391008008616 Autotransporter beta-domain; Region: Autotransporter; smart00869 391008008617 putative acyltransferase; Provisional; Region: PRK05790 391008008618 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 391008008619 dimer interface [polypeptide binding]; other site 391008008620 active site 391008008621 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 391008008622 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 391008008623 active site 391008008624 putative exonuclease, DNA ligase-associated; Region: Xnuc_lig_assoc; TIGR04122 391008008625 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 391008008626 ATP-dependent DNA ligase; Validated; Region: PRK09247 391008008627 Adenylation domain of putative bacterial ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_Bac1; cd07897 391008008628 active site 391008008629 DNA binding site [nucleotide binding] 391008008630 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; Region: OBF_DNA_ligase_Arch_LigB; cd07972 391008008631 DNA binding site [nucleotide binding] 391008008632 DEXH box helicase, DNA ligase-associated; Region: DEXH_lig_assoc; TIGR04121 391008008633 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 391008008634 ATP binding site [chemical binding]; other site 391008008635 putative Mg++ binding site [ion binding]; other site 391008008636 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 391008008637 nucleotide binding region [chemical binding]; other site 391008008638 DEAD/H associated; Region: DEAD_assoc; pfam08494 391008008639 Pyrococcus furiosus PF1019 and related proteins, metallophosphatase domain; Region: MPP_PF1019; cd07391 391008008640 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 391008008641 putative active site [active] 391008008642 putative metal binding site [ion binding]; other site 391008008643 hypothetical protein; Provisional; Region: PRK07236 391008008644 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 391008008645 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 391008008646 DNA-binding site [nucleotide binding]; DNA binding site 391008008647 RNA-binding motif; other site 391008008648 5'-methylthioadenosine phosphorylase; Validated; Region: PRK09136 391008008649 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 391008008650 active site 391008008651 beta-hexosaminidase; Provisional; Region: PRK05337 391008008652 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 391008008653 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 391008008654 DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins; Region: DsbA_FrnE; cd03024 391008008655 catalytic residues [active] 391008008656 CYTH-like Clostridium thermocellum TTM-like subgroup 1; Region: CYTH-like_CthTTM-like_1; cd07891 391008008657 putative active site [active] 391008008658 putative metal binding residues [ion binding]; other site 391008008659 signature motif; other site 391008008660 putative dimer interface [polypeptide binding]; other site 391008008661 putative phosphate binding site [ion binding]; other site 391008008662 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 391008008663 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 391008008664 S-adenosylmethionine binding site [chemical binding]; other site 391008008665 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 391008008666 Response regulator receiver domain; Region: Response_reg; pfam00072 391008008667 active site 391008008668 phosphorylation site [posttranslational modification] 391008008669 intermolecular recognition site; other site 391008008670 dimerization interface [polypeptide binding]; other site 391008008671 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 391008008672 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 391008008673 Recombination protein O N terminal; Region: RecO_N; pfam11967 391008008674 Recombination protein O C terminal; Region: RecO_C; pfam02565 391008008675 GTPase Era; Reviewed; Region: era; PRK00089 391008008676 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 391008008677 G1 box; other site 391008008678 GTP/Mg2+ binding site [chemical binding]; other site 391008008679 Switch I region; other site 391008008680 G2 box; other site 391008008681 Switch II region; other site 391008008682 G3 box; other site 391008008683 G4 box; other site 391008008684 G5 box; other site 391008008685 KH domain; Region: KH_2; pfam07650 391008008686 ribonuclease III; Reviewed; Region: rnc; PRK00102 391008008687 RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in...; Region: RIBOc; cd00593 391008008688 dimerization interface [polypeptide binding]; other site 391008008689 active site 391008008690 metal binding site [ion binding]; metal-binding site 391008008691 Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III; Region: DSRM; cd00048 391008008692 dsRNA binding site [nucleotide binding]; other site 391008008693 signal peptidase I; Provisional; Region: PRK10861 391008008694 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 391008008695 Catalytic site [active] 391008008696 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 391008008697 GTP-binding protein LepA; Provisional; Region: PRK05433 391008008698 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 391008008699 G1 box; other site 391008008700 putative GEF interaction site [polypeptide binding]; other site 391008008701 GTP/Mg2+ binding site [chemical binding]; other site 391008008702 Switch I region; other site 391008008703 G2 box; other site 391008008704 G3 box; other site 391008008705 Switch II region; other site 391008008706 G4 box; other site 391008008707 G5 box; other site 391008008708 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu...; Region: lepA_II; cd03699 391008008709 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 391008008710 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 391008008711 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 391008008712 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 391008008713 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 391008008714 protein binding site [polypeptide binding]; other site 391008008715 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 391008008716 protein binding site [polypeptide binding]; other site 391008008717 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 391008008718 RNA polymerase sigma factor RpoE; Region: RpoE_Sigma70; TIGR02939 391008008719 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391008008720 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 391008008721 DNA binding residues [nucleotide binding] 391008008722 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 391008008723 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 391008008724 substrate binding site [chemical binding]; other site 391008008725 oxyanion hole (OAH) forming residues; other site 391008008726 trimer interface [polypeptide binding]; other site 391008008727 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 391008008728 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 391008008729 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 391008008730 Pirin-related protein [General function prediction only]; Region: COG1741 391008008731 Pirin; Region: Pirin; pfam02678 391008008732 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 391008008733 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal...; Region: MIP; cd00333 391008008734 amphipathic channel; other site 391008008735 Asn-Pro-Ala signature motifs; other site 391008008736 Pirin-related protein [General function prediction only]; Region: COG1741 391008008737 Pirin; Region: Pirin; pfam02678 391008008738 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 391008008739 carbon starvation protein A; Provisional; Region: PRK15015 391008008740 Carbon starvation protein CstA; Region: CstA; pfam02554 391008008741 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 391008008742 Protein of unknown function (DUF466); Region: DUF466; pfam04328 391008008743 Protein of unknown function (DUF819); Region: DUF819; cl02317 391008008744 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 391008008745 active site 391008008746 metal binding site [ion binding]; metal-binding site 391008008747 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 391008008748 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008008749 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 391008008750 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008008751 dimer interface [polypeptide binding]; other site 391008008752 phosphorylation site [posttranslational modification] 391008008753 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 391008008754 ATP binding site [chemical binding]; other site 391008008755 Mg2+ binding site [ion binding]; other site 391008008756 G-X-G motif; other site 391008008757 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391008008758 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 391008008759 active site 391008008760 phosphorylation site [posttranslational modification] 391008008761 intermolecular recognition site; other site 391008008762 dimerization interface [polypeptide binding]; other site 391008008763 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008008764 DNA binding site [nucleotide binding] 391008008765 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 391008008766 PAP2_like_6 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which mainly contains bacterial proteins, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_6; cd03396 391008008767 active site 391008008768 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 391008008769 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 391008008770 Sulfatase; Region: Sulfatase; pfam00884 391008008771 Peptidase family M2 Angiotensin converting enzyme (ACE); Region: M2_ACE; cd06461 391008008772 active site 391008008773 Zn binding site [ion binding]; other site 391008008774 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 391008008775 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 391008008776 FAD binding pocket [chemical binding]; other site 391008008777 FAD binding motif [chemical binding]; other site 391008008778 phosphate binding motif [ion binding]; other site 391008008779 NAD binding pocket [chemical binding]; other site 391008008780 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 391008008781 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 391008008782 putative substrate translocation pore; other site 391008008783 glycine dehydrogenase; Provisional; Region: PRK05367 391008008784 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 391008008785 tetramer interface [polypeptide binding]; other site 391008008786 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008008787 catalytic residue [active] 391008008788 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 391008008789 tetramer interface [polypeptide binding]; other site 391008008790 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008008791 catalytic residue [active] 391008008792 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 391008008793 dimer interface [polypeptide binding]; other site 391008008794 Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]; Region: AnsP; COG1113 391008008795 PAS fold; Region: PAS_4; pfam08448 391008008796 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 391008008797 putative active site [active] 391008008798 heme pocket [chemical binding]; other site 391008008799 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 391008008800 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008008801 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 391008008802 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 391008008803 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 391008008804 dimer interface [polypeptide binding]; other site 391008008805 putative CheW interface [polypeptide binding]; other site 391008008806 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 391008008807 Putative peptidoglycan-binding domain-containing protein [Cell envelope biogenesis, outer membrane]; Region: COG3409 391008008808 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 391008008809 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 391008008810 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 391008008811 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 391008008812 Peptidase family M23; Region: Peptidase_M23; pfam01551 391008008813 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 391008008814 Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosynthesis of AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the...; Region: AdSS; cd03108 391008008815 GDP-binding site [chemical binding]; other site 391008008816 ACT binding site; other site 391008008817 IMP binding site; other site 391008008818 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3242 391008008819 FtsH protease regulator HflC; Provisional; Region: PRK11029 391008008820 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 391008008821 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 391008008822 HflK protein; Region: hflK; TIGR01933 391008008823 Yhdh and yhfp-like putative quinone oxidoreductases; Region: MDR_yhdh_yhfp; cd05280 391008008824 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 391008008825 NADP binding site [chemical binding]; other site 391008008826 dimer interface [polypeptide binding]; other site 391008008827 Response regulator receiver domain; Region: Response_reg; pfam00072 391008008828 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 391008008829 active site 391008008830 phosphorylation site [posttranslational modification] 391008008831 intermolecular recognition site; other site 391008008832 dimerization interface [polypeptide binding]; other site 391008008833 curved DNA-binding protein CbpA; Provisional; Region: PRK10266 391008008834 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 391008008835 HSP70 interaction site [polypeptide binding]; other site 391008008836 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 391008008837 substrate binding site [polypeptide binding]; other site 391008008838 dimer interface [polypeptide binding]; other site 391008008839 Peroxiredoxin (PRX) family, PRX5-like subfamily; members are similar to the human protein, PRX5, a homodimeric TRX peroxidase, widely expressed in tissues and found cellularly in mitochondria, peroxisomes and the cytosol. The cellular location of PRX5...; Region: PRX5_like; cd03013 391008008840 catalytic triad [active] 391008008841 dimer interface [polypeptide binding]; other site 391008008842 Ferritin-like domain; Region: Ferritin; pfam00210 391008008843 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 391008008844 dinuclear metal binding motif [ion binding]; other site 391008008845 penicillin-binding protein 1C; Provisional; Region: PRK11240 391008008846 Transglycosylase; Region: Transgly; pfam00912 391008008847 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 391008008848 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 391008008849 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 391008008850 MG2 domain; Region: A2M_N; pfam01835 391008008851 Alpha-2-macroglobulin family; Region: A2M; pfam00207 391008008852 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 391008008853 surface patch; other site 391008008854 thioester region; other site 391008008855 specificity defining residues; other site 391008008856 2-methylcitrate dehydratase; Provisional; Region: prpD; PRK09425 391008008857 2-methylcitrate dehydratase; Region: prpD; TIGR02330 391008008858 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 391008008859 Plasmid stabilization system protein [General function prediction only]; Region: ParE; COG3668 391008008860 putative addiction module antidote protein, CC2985 family; Region: antidote_CC2985; TIGR02606 391008008861 2-methylisocitrate dehydratase, Fe/S-dependent; Region: 2met_isocit_dHY; TIGR02333 391008008862 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 391008008863 substrate binding site [chemical binding]; other site 391008008864 ligand binding site [chemical binding]; other site 391008008865 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 391008008866 substrate binding site [chemical binding]; other site 391008008867 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 391008008868 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 (CS)...; Region: Ec2MCS_like_1; cd06117 391008008869 dimer interface [polypeptide binding]; other site 391008008870 active site 391008008871 citrylCoA binding site [chemical binding]; other site 391008008872 oxalacetate/citrate binding site [chemical binding]; other site 391008008873 coenzyme A binding site [chemical binding]; other site 391008008874 catalytic triad [active] 391008008875 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 391008008876 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 391008008877 tetramer interface [polypeptide binding]; other site 391008008878 active site 391008008879 Mg2+/Mn2+ binding site [ion binding]; other site 391008008880 propionate catabolism operon regulatory protein PrpR; Provisional; Region: PRK15424 391008008881 Propionate catabolism activator; Region: PrpR_N; pfam06506 391008008882 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008008883 Walker A motif; other site 391008008884 ATP binding site [chemical binding]; other site 391008008885 Walker B motif; other site 391008008886 Predicted membrane protein [Function unknown]; Region: COG2259 391008008887 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 391008008888 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 391008008889 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 391008008890 D-glycerate 3-kinase; Region: PLN02796 391008008891 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cd01983 391008008892 Dodecin; Region: Dodecin; pfam07311 391008008893 shikimate kinase; Reviewed; Region: aroK; PRK00131 391008008894 Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis...; Region: SK; cd00464 391008008895 ADP binding site [chemical binding]; other site 391008008896 magnesium binding site [ion binding]; other site 391008008897 putative shikimate binding site; other site 391008008898 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 391008008899 active site 391008008900 dimer interface [polypeptide binding]; other site 391008008901 metal binding site [ion binding]; metal-binding site 391008008902 WGR domain of molybdate metabolism regulator and related proteins; Region: WGR_MMR_like; cd07996 391008008903 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction...; Region: URO-D; cd00717 391008008904 substrate binding site [chemical binding]; other site 391008008905 active site 391008008906 putative transporter; Provisional; Region: PRK10504 391008008907 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 391008008908 putative substrate translocation pore; other site 391008008909 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 391008008910 Two component regulator propeller; Region: Reg_prop; pfam07494 391008008911 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 391008008912 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008008913 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008008914 dimer interface [polypeptide binding]; other site 391008008915 phosphorylation site [posttranslational modification] 391008008916 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 391008008917 ATP binding site [chemical binding]; other site 391008008918 Mg2+ binding site [ion binding]; other site 391008008919 G-X-G motif; other site 391008008920 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 391008008921 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 391008008922 active site 391008008923 phosphorylation site [posttranslational modification] 391008008924 intermolecular recognition site; other site 391008008925 dimerization interface [polypeptide binding]; other site 391008008926 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 391008008927 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 391008008928 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008008929 dimer interface [polypeptide binding]; other site 391008008930 phosphorylation site [posttranslational modification] 391008008931 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 391008008932 ATP binding site [chemical binding]; other site 391008008933 Mg2+ binding site [ion binding]; other site 391008008934 G-X-G motif; other site 391008008935 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 391008008936 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 391008008937 active site 391008008938 phosphorylation site [posttranslational modification] 391008008939 intermolecular recognition site; other site 391008008940 dimerization interface [polypeptide binding]; other site 391008008941 Uncharacterized conserved protein [Function unknown]; Region: COG2353 391008008942 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 391008008943 Uncharacterized conserved protein [Function unknown]; Region: COG2353 391008008944 Glutaredoxin-like domain (DUF836); Region: DUF836; pfam05768 391008008945 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 391008008946 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 391008008947 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 391008008948 Alpha/beta hydrolase of unknown function (DUF1057); Region: DUF1057; pfam06342 391008008949 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 391008008950 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 391008008951 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 391008008952 cystathionine gamma-synthase; Provisional; Region: PRK08776 391008008953 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 391008008954 homodimer interface [polypeptide binding]; other site 391008008955 substrate-cofactor binding pocket; other site 391008008956 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008008957 catalytic residue [active] 391008008958 homoserine O-acetyltransferase; Provisional; Region: PRK08775 391008008959 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 391008008960 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 391008008961 Peptidase family M23; Region: Peptidase_M23; pfam01551 391008008962 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 391008008963 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 391008008964 G1 box; other site 391008008965 putative GEF interaction site [polypeptide binding]; other site 391008008966 GTP/Mg2+ binding site [chemical binding]; other site 391008008967 Switch I region; other site 391008008968 G2 box; other site 391008008969 G3 box; other site 391008008970 Switch II region; other site 391008008971 G4 box; other site 391008008972 G5 box; other site 391008008973 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 391008008974 Haemolysin-III related; Region: HlyIII; cl03831 391008008975 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 391008008976 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 391008008977 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 391008008978 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 391008008979 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_10; cd04623 391008008980 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 391008008981 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 391008008982 Ligand binding site; other site 391008008983 Putative Catalytic site; other site 391008008984 DXD motif; other site 391008008985 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 391008008986 Transglycosylase; Region: Transgly; cl17702 391008008987 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 391008008988 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 391008008989 dimerization interface [polypeptide binding]; other site 391008008990 domain crossover interface; other site 391008008991 redox-dependent activation switch; other site 391008008992 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 391008008993 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008008994 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008008995 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 391008008996 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008008997 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 391008008998 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 391008008999 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 391008009000 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 391008009001 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 391008009002 active site 391008009003 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 391008009004 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 391008009005 CoenzymeA binding site [chemical binding]; other site 391008009006 subunit interaction site [polypeptide binding]; other site 391008009007 PHB binding site; other site 391008009008 Protein of unknown function (DUF1304); Region: DUF1304; pfam06993 391008009009 TLC ATP/ADP transporter; Region: TLC; cl03940 391008009010 Major Facilitator Superfamily; Region: MFS_1; pfam07690 391008009011 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 391008009012 Beta-lactamase; Region: Beta-lactamase; pfam00144 391008009013 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 391008009014 putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR; Region: BKR_like_SDR_like; cd05344 391008009015 putative NAD(P) binding site [chemical binding]; other site 391008009016 putative active site [active] 391008009017 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008009018 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008009019 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_8; cd08477 391008009020 putative effector binding pocket; other site 391008009021 putative dimerization interface [polypeptide binding]; other site 391008009022 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and...; Region: GCS_H; cd06848 391008009023 lipoyl attachment site [posttranslational modification]; other site 391008009024 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 391008009025 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 391008009026 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 391008009027 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 391008009028 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 391008009029 Protein of unknown function (DUF962); Region: DUF962; pfam06127 391008009030 hypothetical protein; Provisional; Region: PRK02237 391008009031 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 391008009032 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs; Region: NTP-PPase_MazG_Nterm; cd11528 391008009033 homodimer interface [polypeptide binding]; other site 391008009034 metal binding site [ion binding]; metal-binding site 391008009035 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs' Region: NTP-PPase_MazG_Cterm; cd11529 391008009036 homodimer interface [polypeptide binding]; other site 391008009037 active site 391008009038 putative chemical substrate binding site [chemical binding]; other site 391008009039 metal binding site [ion binding]; metal-binding site 391008009040 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 391008009041 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 391008009042 active site 391008009043 adenosine nucleotide hydrolase NudE; Provisional; Region: nudE; PRK11762 391008009044 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+; Region: ADPRase_NUDT5; cd03424 391008009045 dimer interface [polypeptide binding]; other site 391008009046 ADP-ribose binding site [chemical binding]; other site 391008009047 active site 391008009048 nudix motif; other site 391008009049 metal binding site [ion binding]; metal-binding site 391008009050 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK08742 391008009051 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 391008009052 inhibitor-cofactor binding pocket; inhibition site 391008009053 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008009054 catalytic residue [active] 391008009055 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 391008009056 CheW-like domain; Region: CheW; pfam01584 391008009057 CheB methylesterase; Region: CheB_methylest; pfam01339 391008009058 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 391008009059 putative binding surface; other site 391008009060 active site 391008009061 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 391008009062 putative binding surface; other site 391008009063 active site 391008009064 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 391008009065 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 391008009066 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 391008009067 ATP binding site [chemical binding]; other site 391008009068 Mg2+ binding site [ion binding]; other site 391008009069 G-X-G motif; other site 391008009070 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 391008009071 Response regulator receiver domain; Region: Response_reg; pfam00072 391008009072 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 391008009073 active site 391008009074 phosphorylation site [posttranslational modification] 391008009075 intermolecular recognition site; other site 391008009076 dimerization interface [polypeptide binding]; other site 391008009077 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 391008009078 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 391008009079 dimer interface [polypeptide binding]; other site 391008009080 putative CheW interface [polypeptide binding]; other site 391008009081 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cd00588 391008009082 Response regulator receiver domain; Region: Response_reg; pfam00072 391008009083 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 391008009084 active site 391008009085 phosphorylation site [posttranslational modification] 391008009086 intermolecular recognition site; other site 391008009087 dimerization interface [polypeptide binding]; other site 391008009088 Response regulator receiver domain; Region: Response_reg; pfam00072 391008009089 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 391008009090 active site 391008009091 phosphorylation site [posttranslational modification] 391008009092 intermolecular recognition site; other site 391008009093 dimerization interface [polypeptide binding]; other site 391008009094 glutathione synthetase; Provisional; Region: PRK05246 391008009095 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 391008009096 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 391008009097 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 391008009098 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 391008009099 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 391008009100 Glycoprotease family; Region: Peptidase_M22; pfam00814 391008009101 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 391008009102 DEAD/DEAH box helicase; Region: DEAD; pfam00270 391008009103 ATP binding site [chemical binding]; other site 391008009104 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 391008009105 penicillin-binding protein 1B; Region: PBP_1b; TIGR02071 391008009106 Transglycosylase; Region: Transgly; pfam00912 391008009107 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 391008009108 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 391008009109 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_d; cd04196 391008009110 Probable Catalytic site; other site 391008009111 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008009112 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 391008009113 NAD(P) binding site [chemical binding]; other site 391008009114 active site 391008009115 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 391008009116 HD domain; Region: HD_4; pfam13328 391008009117 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 391008009118 synthetase active site [active] 391008009119 NTP binding site [chemical binding]; other site 391008009120 metal binding site [ion binding]; metal-binding site 391008009121 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after...; Region: TGS_RelA_SpoT; cd01668 391008009122 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 391008009123 DEAD-like helicases superfamily; Region: DEXDc; smart00487 391008009124 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 391008009125 ATP binding site [chemical binding]; other site 391008009126 putative Mg++ binding site [ion binding]; other site 391008009127 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 391008009128 nucleotide binding region [chemical binding]; other site 391008009129 ATP-binding site [chemical binding]; other site 391008009130 Helicase associated domain (HA2); Region: HA2; pfam04408 391008009131 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 391008009132 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 391008009133 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 391008009134 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 391008009135 dimerization interface [polypeptide binding]; other site 391008009136 DPS ferroxidase diiron center [ion binding]; other site 391008009137 ion pore; other site 391008009138 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 391008009139 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 391008009140 ATP binding site [chemical binding]; other site 391008009141 putative Mg++ binding site [ion binding]; other site 391008009142 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 391008009143 nucleotide binding region [chemical binding]; other site 391008009144 ATP-binding site [chemical binding]; other site 391008009145 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 391008009146 HRDC domain; Region: HRDC; pfam00570 391008009147 copper-resistance protein, CopA family; Region: copper_res_A; TIGR01480 391008009148 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 391008009149 Multicopper oxidase; Region: Cu-oxidase; pfam00394 391008009150 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 391008009151 Copper resistance protein B precursor (CopB); Region: CopB; pfam05275 391008009152 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 391008009153 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391008009154 Coenzyme A binding pocket [chemical binding]; other site 391008009155 Transcription factor zinc-finger; Region: zf-TFIIB; cl01565 391008009156 Response regulator receiver domain; Region: Response_reg; pfam00072 391008009157 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 391008009158 active site 391008009159 phosphorylation site [posttranslational modification] 391008009160 intermolecular recognition site; other site 391008009161 dimerization interface [polypeptide binding]; other site 391008009162 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819 391008009163 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819 391008009164 Predicted Zn-dependent protease (DUF2268); Region: DUF2268; cl02316 391008009165 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 391008009166 Ligand Binding Site [chemical binding]; other site 391008009167 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type; Region: rSAM_QueE_gams; TIGR04349 391008009168 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 391008009169 FeS/SAM binding site; other site 391008009170 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 391008009171 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 391008009172 binding surface 391008009173 TPR motif; other site 391008009174 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 391008009175 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 391008009176 ligand binding site [chemical binding]; other site 391008009177 translocation protein TolB; Provisional; Region: tolB; PRK04922 391008009178 TolB amino-terminal domain; Region: TolB_N; pfam04052 391008009179 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 391008009180 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 391008009181 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 391008009182 TolA protein; Region: tolA_full; TIGR02794 391008009183 TonB C terminal; Region: TonB_2; pfam13103 391008009184 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 391008009185 TolR protein; Region: tolR; TIGR02801 391008009186 TolQ protein; Region: tolQ; TIGR02796 391008009187 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 391008009188 active site 391008009189 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 391008009190 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008009191 Walker A motif; other site 391008009192 ATP binding site [chemical binding]; other site 391008009193 Walker B motif; other site 391008009194 arginine finger; other site 391008009195 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 391008009196 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 391008009197 potassium uptake protein; Region: kup; TIGR00794 391008009198 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 391008009199 RuvA N terminal domain; Region: RuvA_N; pfam01330 391008009200 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 391008009201 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD...; Region: RuvC_resolvase; cd00529 391008009202 active site 391008009203 putative DNA-binding cleft [nucleotide binding]; other site 391008009204 dimer interface [polypeptide binding]; other site 391008009205 hypothetical protein; Validated; Region: PRK00110 391008009206 Acetyltransferase (GNAT) domain; Region: Acetyltransf_8; pfam13523 391008009207 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391008009208 Coenzyme A binding pocket [chemical binding]; other site 391008009209 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 391008009210 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 391008009211 dimer interface [polypeptide binding]; other site 391008009212 anticodon binding site; other site 391008009213 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 391008009214 homodimer interface [polypeptide binding]; other site 391008009215 motif 1; other site 391008009216 active site 391008009217 motif 2; other site 391008009218 GAD domain; Region: GAD; pfam02938 391008009219 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 391008009220 motif 3; other site 391008009221 Protein of unknown function (DUF3011); Region: DUF3011; pfam11218 391008009222 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 391008009223 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 391008009224 Beta-lactamase enzyme family; Region: Beta-lactamase2; pfam13354 391008009225 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 391008009226 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008009227 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 391008009228 dimerization interface [polypeptide binding]; other site 391008009229 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 391008009230 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 391008009231 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 391008009232 ABC transporter; Region: ABC_tran_2; pfam12848 391008009233 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 391008009234 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008009235 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 391008009236 N-terminal plug; other site 391008009237 ligand-binding site [chemical binding]; other site 391008009238 putative cation:proton antiport protein; Provisional; Region: PRK10669 391008009239 Kef-type K+ transport system, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: RosB; COG4651 391008009240 TrkA-N domain; Region: TrkA_N; pfam02254 391008009241 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 391008009242 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 391008009243 homodimer interface [polypeptide binding]; other site 391008009244 substrate-cofactor binding pocket; other site 391008009245 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008009246 catalytic residue [active] 391008009247 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391008009248 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 391008009249 active site 391008009250 phosphorylation site [posttranslational modification] 391008009251 intermolecular recognition site; other site 391008009252 dimerization interface [polypeptide binding]; other site 391008009253 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008009254 DNA binding site [nucleotide binding] 391008009255 sensor protein RstB; Provisional; Region: PRK10604 391008009256 HAMP domain; Region: HAMP; pfam00672 391008009257 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008009258 dimer interface [polypeptide binding]; other site 391008009259 phosphorylation site [posttranslational modification] 391008009260 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 391008009261 ATP binding site [chemical binding]; other site 391008009262 Mg2+ binding site [ion binding]; other site 391008009263 G-X-G motif; other site 391008009264 Outer membrane protein V [Cell envelope biogenesis, outer membrane]; Region: OmpV; COG3713 391008009265 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 391008009266 Clp amino terminal domain; Region: Clp_N; pfam02861 391008009267 Clp amino terminal domain; Region: Clp_N; pfam02861 391008009268 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008009269 Walker A motif; other site 391008009270 ATP binding site [chemical binding]; other site 391008009271 Walker B motif; other site 391008009272 arginine finger; other site 391008009273 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008009274 Walker A motif; other site 391008009275 ATP binding site [chemical binding]; other site 391008009276 Walker B motif; other site 391008009277 arginine finger; other site 391008009278 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 391008009279 Protein of unknown function (DUF3014); Region: DUF3014; pfam11219 391008009280 GST_N family, Class Sigma_like; composed of GSTs belonging to class Sigma and similar proteins, including GSTs from class Mu, Pi and Alpha. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of...; Region: GST_N_Sigma_like; cd03039 391008009281 glutathione s-transferase; Provisional; Region: PTZ00057 391008009282 GSH binding site (G-site) [chemical binding]; other site 391008009283 C-terminal domain interface [polypeptide binding]; other site 391008009284 dimer interface [polypeptide binding]; other site 391008009285 C-terminal, alpha helical domain of Class Sigma-like Glutathione S-transferases; Region: GST_C_Sigma_like; cd03192 391008009286 dimer interface [polypeptide binding]; other site 391008009287 N-terminal domain interface [polypeptide binding]; other site 391008009288 substrate binding pocket (H-site) [chemical binding]; other site 391008009289 pyruvate dehydrogenase; Provisional; Region: PRK09124 391008009290 Pyrimidine (PYR) binding domain of POX; Region: TPP_PYR_POX; cd07039 391008009291 PYR/PP interface [polypeptide binding]; other site 391008009292 dimer interface [polypeptide binding]; other site 391008009293 tetramer interface [polypeptide binding]; other site 391008009294 TPP binding site [chemical binding]; other site 391008009295 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 391008009296 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 391008009297 TPP-binding site [chemical binding]; other site 391008009298 Protein of unknown function (DUF3574); Region: DUF3574; pfam12098 391008009299 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008009300 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 391008009301 N-terminal plug; other site 391008009302 ligand-binding site [chemical binding]; other site 391008009303 trehalose-6-phosphate phosphatase; Provisional; Region: PRK10187; cl17105 391008009304 Trehalose-phosphatase; Region: Trehalose_PPase; pfam02358 391008009305 Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: SGA1; COG3387 391008009306 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 391008009307 Trehalose-6-Phosphate Synthase (TPS) is a glycosyltransferase that catalyses the synthesis of alpha,alpha-1,1-trehalose-6-phosphate from glucose-6-phosphate using a UDP-glucose donor. It is a key enzyme in the trehalose synthesis pathway. Trehalose is a...; Region: GT1_TPS; cd03788 391008009308 alpha,alpha-trehalose-phosphate synthase [UDP-forming]; Region: trehalose_OtsA; TIGR02400 391008009309 active site 391008009310 homotetramer interface [polypeptide binding]; other site 391008009311 Predicted thiol-disulfide oxidoreductase [General function prediction only]; Region: COG3011 391008009312 Domain of unknown function (DUF4166); Region: DUF4166; pfam13761 391008009313 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 391008009314 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 391008009315 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 391008009316 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 391008009317 RNA binding surface [nucleotide binding]; other site 391008009318 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 391008009319 active site 391008009320 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 391008009321 NAD synthetase; Provisional; Region: PRK13981 391008009322 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 391008009323 multimer interface [polypeptide binding]; other site 391008009324 active site 391008009325 catalytic triad [active] 391008009326 protein interface 1 [polypeptide binding]; other site 391008009327 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD...; Region: NAD_synthase; cd00553 391008009328 homodimer interface [polypeptide binding]; other site 391008009329 NAD binding pocket [chemical binding]; other site 391008009330 ATP binding pocket [chemical binding]; other site 391008009331 Mg binding site [ion binding]; other site 391008009332 active-site loop [active] 391008009333 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 391008009334 CoA binding domain; Region: CoA_binding; smart00881 391008009335 CoA-ligase; Region: Ligase_CoA; pfam00549 391008009336 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 391008009337 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 391008009338 CoA-ligase; Region: Ligase_CoA; pfam00549 391008009339 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 391008009340 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008009341 dimer interface [polypeptide binding]; other site 391008009342 phosphorylation site [posttranslational modification] 391008009343 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 391008009344 ATP binding site [chemical binding]; other site 391008009345 Mg2+ binding site [ion binding]; other site 391008009346 G-X-G motif; other site 391008009347 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 391008009348 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 391008009349 active site 391008009350 phosphorylation site [posttranslational modification] 391008009351 intermolecular recognition site; other site 391008009352 dimerization interface [polypeptide binding]; other site 391008009353 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008009354 Walker A motif; other site 391008009355 ATP binding site [chemical binding]; other site 391008009356 Walker B motif; other site 391008009357 arginine finger; other site 391008009358 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 391008009359 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 391008009360 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 391008009361 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 391008009362 Walker A motif; other site 391008009363 ATP binding site [chemical binding]; other site 391008009364 Walker B motif; other site 391008009365 glycosyltransferase, TIGR04182 family; Region: glyco_TIGR04182 391008009366 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 391008009367 Ligand binding site; other site 391008009368 Putative Catalytic site; other site 391008009369 DXD motif; other site 391008009370 This family is most closely related to the GT1 family of glycosyltransferases. wlbH in Bordetella parapertussis has been shown to be required for the biosynthesis of a trisaccharide that, when attached to the B. pertussis lipopolysaccharide (LPS) core; Region: GT1_wlbH_like; cd03798 391008009371 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 391008009372 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 391008009373 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 391008009374 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 391008009375 putative ADP-binding pocket [chemical binding]; other site 391008009376 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 391008009377 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 391008009378 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 391008009379 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 391008009380 Pilin (bacterial filament); Region: Pilin; pfam00114 391008009381 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 391008009382 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 391008009383 Pilin (bacterial filament); Region: Pilin; pfam00114 391008009384 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 391008009385 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 391008009386 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 391008009387 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 391008009388 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 391008009389 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 391008009390 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 391008009391 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 391008009392 CoA-binding site [chemical binding]; other site 391008009393 ATP-binding [chemical binding]; other site 391008009394 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008009395 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 391008009396 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008009397 dimer interface [polypeptide binding]; other site 391008009398 phosphorylation site [posttranslational modification] 391008009399 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 391008009400 ATP binding site [chemical binding]; other site 391008009401 Mg2+ binding site [ion binding]; other site 391008009402 G-X-G motif; other site 391008009403 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391008009404 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 391008009405 active site 391008009406 phosphorylation site [posttranslational modification] 391008009407 intermolecular recognition site; other site 391008009408 dimerization interface [polypeptide binding]; other site 391008009409 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008009410 DNA binding site [nucleotide binding] 391008009411 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 391008009412 ATP-grasp domain; Region: ATP-grasp_4; cl17255 391008009413 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 391008009414 active site 391008009415 Protein of unknown function (DUF805); Region: DUF805; pfam05656 391008009416 Phospholipase/lecithinase/hemolysin [Lipid metabolism / General function prediction only]; Region: COG3240 391008009417 Triacylglycerol lipase-like subfamily of the SGNH hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its...; Region: Triacylglycerol_lipase_like; cd01847 391008009418 active site 391008009419 catalytic triad [active] 391008009420 oxyanion hole [active] 391008009421 Autotransporter beta-domain; Region: Autotransporter; cl17461 391008009422 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 391008009423 thiS-thiF/thiG interaction site; other site 391008009424 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 391008009425 ThiS interaction site; other site 391008009426 putative active site [active] 391008009427 tetramer interface [polypeptide binding]; other site 391008009428 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 391008009429 S-adenosylmethionine binding site [chemical binding]; other site 391008009430 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 391008009431 transmembrane helices; other site 391008009432 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 391008009433 TrkA-C domain; Region: TrkA_C; pfam02080 391008009434 TrkA-C domain; Region: TrkA_C; pfam02080 391008009435 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 391008009436 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cd03467 391008009437 iron-sulfur cluster [ion binding]; other site 391008009438 [2Fe-2S] cluster binding site [ion binding]; other site 391008009439 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 391008009440 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 391008009441 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 391008009442 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 391008009443 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 391008009444 PA_M28_2: Protease-associated (PA) domain, peptidase family M28, subfamily-2. A subfamily of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions; Region: PA_M28_2; cd04815 391008009445 PA/protease or protease-like domain interface [polypeptide binding]; other site 391008009446 M28 Zn-Peptidase Plasma glutamate carboxypeptidase; Region: M28_Pgcp_like; cd03883 391008009447 Peptidase family M28; Region: Peptidase_M28; pfam04389 391008009448 metal binding site [ion binding]; metal-binding site 391008009449 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 391008009450 amino acid carrier protein; Region: agcS; TIGR00835 391008009451 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 391008009452 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 391008009453 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 391008009454 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 391008009455 Sodium:alanine symporter family; Region: Na_Ala_symp; pfam01235 391008009456 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 391008009457 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 391008009458 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 391008009459 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 391008009460 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008009461 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 391008009462 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 391008009463 N-terminal plug; other site 391008009464 ligand-binding site [chemical binding]; other site 391008009465 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 391008009466 Transposase; Region: HTH_Tnp_1; cl17663 391008009467 putative transposase OrfB; Reviewed; Region: PHA02517 391008009468 HTH-like domain; Region: HTH_21; pfam13276 391008009469 Integrase core domain; Region: rve; pfam00665 391008009470 Integrase core domain; Region: rve_2; pfam13333 391008009471 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12680 391008009472 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008009473 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 391008009474 dimerization interface [polypeptide binding]; other site 391008009475 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 391008009476 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 391008009477 dimer interface [polypeptide binding]; other site 391008009478 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008009479 catalytic residue [active] 391008009480 Macro domain, Appr-1"-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly...; Region: Macro_Appr_pase_like; cd02908 391008009481 putative ADP-ribose binding site [chemical binding]; other site 391008009482 putative active site [active] 391008009483 Fructose-1,6-bisphosphate aldolase; Region: FBP_aldolase_I_a; cd00948 391008009484 active site 391008009485 intersubunit interface [polypeptide binding]; other site 391008009486 catalytic residue [active] 391008009487 pyruvate kinase; Provisional; Region: PRK05826 391008009488 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 391008009489 domain interfaces; other site 391008009490 active site 391008009491 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 391008009492 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 391008009493 motif II; other site 391008009494 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 391008009495 Phosphoglycerate kinase; Region: PGK; pfam00162 391008009496 substrate binding site [chemical binding]; other site 391008009497 hinge regions; other site 391008009498 ADP binding site [chemical binding]; other site 391008009499 catalytic site [active] 391008009500 Protein of unknown function (DUF3999); Region: DUF3999; pfam13163 391008009501 Predicted membrane protein (DUF2339); Region: DUF2339; pfam10101 391008009502 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 391008009503 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 391008009504 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 391008009505 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 391008009506 S1/P1 nucleases and related enzymes; Region: S1-P1_nuclease; cd11010 391008009507 active site 391008009508 Zn binding site [ion binding]; other site 391008009509 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 391008009510 BlaR1 peptidase M56; Region: Peptidase_M56; pfam05569 391008009511 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 391008009512 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 391008009513 Penicillinase repressor; Region: Pencillinase_R; pfam03965 391008009514 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 391008009515 Acetyl-CoA hydrolase [Energy production and conversion]; Region: ACH1; COG0427 391008009516 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 391008009517 transketolase; Reviewed; Region: PRK12753 391008009518 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 391008009519 TPP-binding site [chemical binding]; other site 391008009520 dimer interface [polypeptide binding]; other site 391008009521 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 391008009522 PYR/PP interface [polypeptide binding]; other site 391008009523 dimer interface [polypeptide binding]; other site 391008009524 TPP binding site [chemical binding]; other site 391008009525 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 391008009526 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 391008009527 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 391008009528 Oxygen tolerance; Region: BatD; pfam13584 391008009529 Oxygen tolerance; Region: BatD; pfam13584 391008009530 von Willebrand factor type A domain; Region: VWA_2; pfam13519 391008009531 metal ion-dependent adhesion site (MIDAS); other site 391008009532 Tetratricopeptide repeat; Region: TPR_16; pfam13432 391008009533 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 391008009534 TPR motif; other site 391008009535 VWA BatA type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b...; Region: vWA_BatA_type; cd01467 391008009536 metal ion-dependent adhesion site (MIDAS); other site 391008009537 Protein of unknown function DUF58; Region: DUF58; pfam01882 391008009538 MoxR-like ATPases [General function prediction only]; Region: COG0714 391008009539 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008009540 Walker A motif; other site 391008009541 ATP binding site [chemical binding]; other site 391008009542 Walker B motif; other site 391008009543 arginine finger; other site 391008009544 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 391008009545 Secretin and TonB N terminus short domain; Region: STN; smart00965 391008009546 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 391008009547 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 391008009548 Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilP; COG3168 391008009549 Pilus assembly protein, PilP; Region: PilP; pfam04351 391008009550 Tfp pilus assembly protein PilO [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilO; COG3167 391008009551 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 391008009552 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 391008009553 Competence protein A; Region: Competence_A; pfam11104 391008009554 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 391008009555 Transglycosylase; Region: Transgly; pfam00912 391008009556 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 391008009557 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 391008009558 Transposase; Region: DEDD_Tnp_IS110; pfam01548 391008009559 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 391008009560 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 391008009561 Extended Signal Peptide of Type V secretion system; Region: ESPR; pfam13018 391008009562 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 391008009563 trimer interface [polypeptide binding]; other site 391008009564 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 391008009565 trimer interface [polypeptide binding]; other site 391008009566 Left-handed beta-roll, including virulence factors and various other proteins; Region: LbR-like; cl17507 391008009567 trimer interface [polypeptide binding]; other site 391008009568 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 391008009569 trimer interface [polypeptide binding]; other site 391008009570 YadA-like C-terminal region; Region: YadA; pfam03895 391008009571 putative fimbrial protein TcfA; Provisional; Region: PRK15308 391008009572 CblD like pilus biogenesis initiator; Region: CblD; cl06460 391008009573 fimbrial outer membrane usher protein TcfC; Provisional; Region: PRK15310 391008009574 CS1 type fimbrial major subunit; Region: Fimbrial_CS1; pfam04449 391008009575 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 391008009576 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 391008009577 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 391008009578 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 391008009579 dimer interface [polypeptide binding]; other site 391008009580 Citrate synthase; Region: Citrate_synt; pfam00285 391008009581 active site 391008009582 citrylCoA binding site [chemical binding]; other site 391008009583 NADH binding [chemical binding]; other site 391008009584 cationic pore residues; other site 391008009585 oxalacetate/citrate binding site [chemical binding]; other site 391008009586 coenzyme A binding site [chemical binding]; other site 391008009587 catalytic triad [active] 391008009588 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 391008009589 nuc_hydro_CeIAG: Nucleoside hydrolases similar to the inosine-adenosine-guanosine-preferring nucleoside hydrolase from Caenorhabditis elegans. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base; Region: nuc_hydro_CeIAG; cd02649 391008009590 active site 391008009591 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 391008009592 RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a...; Region: RecG_wedge_OBF; cd04488 391008009593 generic binding surface II; other site 391008009594 ssDNA binding site; other site 391008009595 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 391008009596 ATP binding site [chemical binding]; other site 391008009597 putative Mg++ binding site [ion binding]; other site 391008009598 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 391008009599 nucleotide binding region [chemical binding]; other site 391008009600 ATP-binding site [chemical binding]; other site 391008009601 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 391008009602 homotrimer interaction site [polypeptide binding]; other site 391008009603 putative active site [active] 391008009604 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 391008009605 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 391008009606 Zn2+ binding site [ion binding]; other site 391008009607 Mg2+ binding site [ion binding]; other site 391008009608 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 391008009609 synthetase active site [active] 391008009610 NTP binding site [chemical binding]; other site 391008009611 metal binding site [ion binding]; metal-binding site 391008009612 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after...; Region: TGS_RelA_SpoT; cd01668 391008009613 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 391008009614 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 391008009615 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 391008009616 Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine...; Region: GMPK; cd00071 391008009617 catalytic site [active] 391008009618 G-X2-G-X-G-K; other site 391008009619 formate dehydrogenase, alpha subunit, proteobacterial-type; Region: formate-DH-alph; TIGR01553 391008009620 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 391008009621 [4Fe-4S] binding site [ion binding]; other site 391008009622 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 391008009623 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 391008009624 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 391008009625 molybdopterin cofactor binding site; other site 391008009626 formate dehydrogenase, beta subunit, Fe-S containing; Region: FDH-beta; TIGR01582 391008009627 Formate dehydrogenase N, transmembrane; Region: Form-deh_trans; pfam09163 391008009628 Cytochrome b subunit of formate dehydrogenase [Energy production and conversion]; Region: FdnI; COG2864 391008009629 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 391008009630 Protein involved in formate dehydrogenase formation; Region: FdhE; pfam04216 391008009631 formate dehydrogenase accessory protein FdhE; Region: FdhE; TIGR01562 391008009632 selenocysteine synthase; Provisional; Region: PRK04311 391008009633 Selenocysteine synthase [seryl-tRNASer selenium transferase] [Amino acid transport and metabolism]; Region: SelA; COG1921 391008009634 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 391008009635 catalytic residue [active] 391008009636 selenocysteinyl-tRNA-specific translation factor; Provisional; Region: PRK10512 391008009637 SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; Region: SelB; cd04171 391008009638 G1 box; other site 391008009639 putative GEF interaction site [polypeptide binding]; other site 391008009640 GTP/Mg2+ binding site [chemical binding]; other site 391008009641 Switch I region; other site 391008009642 G2 box; other site 391008009643 G3 box; other site 391008009644 Switch II region; other site 391008009645 G4 box; other site 391008009646 G5 box; other site 391008009647 selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several...; Region: selB_II; cd03696 391008009648 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 391008009649 Elongation factor SelB, winged helix; Region: SelB-wing_2; pfam09106 391008009650 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 391008009651 selenophosphate synthetase; Provisional; Region: PRK00943 391008009652 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 391008009653 dimerization interface [polypeptide binding]; other site 391008009654 putative ATP binding site [chemical binding]; other site 391008009655 Fic family protein [Function unknown]; Region: COG3177 391008009656 Fic/DOC family N-terminal; Region: Fic_N; pfam13784 391008009657 Fic/DOC family; Region: Fic; pfam02661 391008009658 hypothetical protein; Provisional; Region: PRK11820 391008009659 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 391008009660 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 391008009661 ribonuclease PH; Reviewed; Region: rph; PRK00173 391008009662 Ribonuclease PH; Region: RNase_PH_bact; cd11362 391008009663 hexamer interface [polypeptide binding]; other site 391008009664 active site 391008009665 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 391008009666 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_16; cd07263 391008009667 NTPase/HAM1. This family consists of the HAM1 protein and pyrophosphate-releasing xanthosine/ inosine triphosphatase. HAM1 protects the cell against mutagenesis by the base analog 6-N-hydroxylaminopurine (HAP) in E. Coli and S. cerevisiae. A...; Region: HAM1; cd00515 391008009668 active site 391008009669 dimerization interface [polypeptide binding]; other site 391008009670 HemN family oxidoreductase; Provisional; Region: PRK05660 391008009671 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 391008009672 FeS/SAM binding site; other site 391008009673 HemN C-terminal domain; Region: HemN_C; pfam06969 391008009674 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 391008009675 PilZ domain; Region: PilZ; pfam07238 391008009676 proline dipeptidase; Provisional; Region: PRK13607 391008009677 Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on...; Region: Prolidase; cd01087 391008009678 active site 391008009679 Aminopeptidase P, N-terminal domain; Region: AMP_N; pfam05195 391008009680 proline aminopeptidase P II; Provisional; Region: PRK10879 391008009681 Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on...; Region: Prolidase; cd01087 391008009682 active site 391008009683 hypothetical protein; Validated; Region: PRK04758 391008009684 TIGR02449 family protein; Region: TIGR02449 391008009685 Cell division protein ZapA; Region: ZapA; pfam05164 391008009686 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 391008009687 Uncharacterized conserved protein [Function unknown]; Region: COG2947 391008009688 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 391008009689 tetramer (dimer of dimers) interface [polypeptide binding]; other site 391008009690 active site 391008009691 dimer interface [polypeptide binding]; other site 391008009692 Uncharacterized ACR, COG1430; Region: DUF192; pfam02643 391008009693 Uncharacterized conserved protein [Function unknown]; Region: COG2912 391008009694 Transglutaminase-like superfamily; Region: Transglut_core2; pfam13369 391008009695 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 391008009696 binding surface 391008009697 TPR motif; other site 391008009698 Rubredoxin [Energy production and conversion]; Region: COG1773 391008009699 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 391008009700 iron binding site [ion binding]; other site 391008009701 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 391008009702 thiamine phosphate binding site [chemical binding]; other site 391008009703 active site 391008009704 pyrophosphate binding site [ion binding]; other site 391008009705 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 391008009706 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 391008009707 inhibitor-cofactor binding pocket; inhibition site 391008009708 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008009709 catalytic residue [active] 391008009710 Cupredoxin-like domain; Region: Cupredoxin_1; cl17234 391008009711 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 391008009712 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 391008009713 acetylornithine transaminase protein; Provisional; Region: argD; PRK04612 391008009714 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 391008009715 inhibitor-cofactor binding pocket; inhibition site 391008009716 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008009717 catalytic residue [active] 391008009718 Ion transport protein; Region: Ion_trans; pfam00520 391008009719 Ion channel; Region: Ion_trans_2; pfam07885 391008009720 Double zinc ribbon; Region: DZR; pfam12773 391008009721 zinc-ribbon domain; Region: zinc_ribbon_2; pfam13240 391008009722 Protein of unknown function (DUF3829); Region: DUF3829; pfam12889 391008009723 Protein of unknown function (DUF3829); Region: DUF3829; pfam12889 391008009724 short chain dehydrogenase; Provisional; Region: PRK08278 391008009725 human hydroxysteroid dehydrogenase-like protein 2 (HSDL2), classical (c) SDRs; Region: HSDL2_SDR_c; cd09762 391008009726 NAD(P) binding site [chemical binding]; other site 391008009727 homodimer interface [polypeptide binding]; other site 391008009728 active site 391008009729 Protein of unknown function (DUF2867); Region: DUF2867; pfam11066 391008009730 serine/threonine protein kinase; Provisional; Region: PRK12274 391008009731 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 391008009732 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 391008009733 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 391008009734 active site 391008009735 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 391008009736 LssY C-terminus; Region: LssY_C; pfam14067 391008009737 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 391008009738 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 391008009739 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 391008009740 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 391008009741 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 391008009742 adenylate kinase; Reviewed; Region: adk; PRK00279 391008009743 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 391008009744 AMP-binding site [chemical binding]; other site 391008009745 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 391008009746 6-phosphofructokinase; Provisional; Region: PRK14072 391008009747 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 391008009748 active site 391008009749 ADP/pyrophosphate binding site [chemical binding]; other site 391008009750 dimerization interface [polypeptide binding]; other site 391008009751 allosteric effector site; other site 391008009752 fructose-1,6-bisphosphate binding site; other site 391008009753 tRNA_anti-like; Region: tRNA_anti-like; pfam12869 391008009754 Protein of unknown function, DUF488; Region: DUF488; cl01246 391008009755 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 391008009756 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 391008009757 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 391008009758 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 391008009759 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 391008009760 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 391008009761 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 391008009762 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2832 391008009763 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cd00232 391008009764 heme binding pocket [chemical binding]; other site 391008009765 heme ligand [chemical binding]; other site 391008009766 Protein of unknown function (DUF2789); Region: DUF2789; pfam10982 391008009767 Secretin and TonB N terminus short domain; Region: STN; smart00965 391008009768 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008009769 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008009770 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008009771 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 391008009772 FecR protein; Region: FecR; pfam04773 391008009773 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 391008009774 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 391008009775 DNA binding residues [nucleotide binding] 391008009776 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 391008009777 substrate binding site [chemical binding]; other site 391008009778 metal binding sites [ion binding]; metal-binding site 391008009779 dimer interface [polypeptide binding]; other site 391008009780 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 391008009781 active site 391008009782 phosphorylation site [posttranslational modification] 391008009783 intermolecular recognition site; other site 391008009784 HDOD domain; Region: HDOD; pfam08668 391008009785 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 391008009786 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008009787 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008009788 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008009789 Helix-turn-helix domain; Region: HTH_18; pfam12833 391008009790 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391008009791 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008009792 DNA binding site [nucleotide binding] 391008009793 tol-pal system beta propeller repeat protein TolB; Region: propeller_TolB; TIGR02800 391008009794 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 391008009795 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 391008009796 ThiC-associated domain; Region: ThiC-associated; pfam13667 391008009797 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 391008009798 BCCT family transporter; Region: BCCT; pfam02028 391008009799 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 391008009800 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 391008009801 ketol-acid reductoisomerase; Provisional; Region: PRK05479 391008009802 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 391008009803 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 391008009804 acetolactate synthase 2 catalytic subunit; Reviewed; Region: PRK08978 391008009805 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 391008009806 PYR/PP interface [polypeptide binding]; other site 391008009807 dimer interface [polypeptide binding]; other site 391008009808 TPP binding site [chemical binding]; other site 391008009809 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 391008009810 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 391008009811 TPP-binding site [chemical binding]; other site 391008009812 dimer interface [polypeptide binding]; other site 391008009813 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 391008009814 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 391008009815 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 391008009816 tetramer interface [polypeptide binding]; other site 391008009817 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008009818 catalytic residue [active] 391008009819 2-isopropylmalate synthase; Validated; Region: PRK00915 391008009820 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 391008009821 active site 391008009822 catalytic residues [active] 391008009823 metal binding site [ion binding]; metal-binding site 391008009824 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; pfam08502 391008009825 Methyltransferase domain; Region: Methyltransf_23; pfam13489 391008009826 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 391008009827 S-adenosylmethionine binding site [chemical binding]; other site 391008009828 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 391008009829 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 391008009830 substrate binding site [chemical binding]; other site 391008009831 ligand binding site [chemical binding]; other site 391008009832 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 391008009833 Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate...; Region: IPMI_Swivel; cd01577 391008009834 substrate binding site [chemical binding]; other site 391008009835 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 391008009836 tartrate dehydrogenase; Region: TTC; TIGR02089 391008009837 short chain dehydrogenase; Provisional; Region: PRK12744 391008009838 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008009839 NAD(P) binding site [chemical binding]; other site 391008009840 active site 391008009841 transcriptional regulator; Provisional; Region: PRK10632 391008009842 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008009843 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 391008009844 putative effector binding pocket; other site 391008009845 putative dimerization interface [polypeptide binding]; other site 391008009846 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 391008009847 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 391008009848 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008009849 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 391008009850 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008009851 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 391008009852 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 391008009853 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 391008009854 S-adenosylmethionine binding site [chemical binding]; other site 391008009855 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 391008009856 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 391008009857 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 391008009858 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 391008009859 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 391008009860 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 391008009861 putative acyl-acceptor binding pocket; other site 391008009862 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 391008009863 O-Antigen ligase; Region: Wzy_C; pfam04932 391008009864 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 391008009865 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 391008009866 Zinc-finger domain; Region: zf-CHCC; cl01821 391008009867 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 391008009868 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 391008009869 Peptidase of plants and bacteria; Region: BSP; pfam04450 391008009870 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 391008009871 Malic enzyme, N-terminal domain; Region: malic; pfam00390 391008009872 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 391008009873 putative NAD(P) binding site [chemical binding]; other site 391008009874 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 391008009875 C4-dicarboxylate transporter DctA; Reviewed; Region: PRK01663 391008009876 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 391008009877 Phosphate-selective porin [Inorganic ion transport and metabolism]; Region: OprP; COG3746 391008009878 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 391008009879 PAS domain; Region: PAS; smart00091 391008009880 PAS fold; Region: PAS_7; pfam12860 391008009881 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008009882 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008009883 dimer interface [polypeptide binding]; other site 391008009884 phosphorylation site [posttranslational modification] 391008009885 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 391008009886 ATP binding site [chemical binding]; other site 391008009887 Mg2+ binding site [ion binding]; other site 391008009888 G-X-G motif; other site 391008009889 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 391008009890 Response regulator receiver domain; Region: Response_reg; pfam00072 391008009891 active site 391008009892 phosphorylation site [posttranslational modification] 391008009893 intermolecular recognition site; other site 391008009894 dimerization interface [polypeptide binding]; other site 391008009895 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 391008009896 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 391008009897 active site 391008009898 phosphorylation site [posttranslational modification] 391008009899 intermolecular recognition site; other site 391008009900 dimerization interface [polypeptide binding]; other site 391008009901 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 391008009902 DNA binding residues [nucleotide binding] 391008009903 dimerization interface [polypeptide binding]; other site 391008009904 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 391008009905 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 391008009906 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 391008009907 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008009908 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008009909 dimer interface [polypeptide binding]; other site 391008009910 phosphorylation site [posttranslational modification] 391008009911 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 391008009912 ATP binding site [chemical binding]; other site 391008009913 Mg2+ binding site [ion binding]; other site 391008009914 G-X-G motif; other site 391008009915 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391008009916 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 391008009917 active site 391008009918 phosphorylation site [posttranslational modification] 391008009919 intermolecular recognition site; other site 391008009920 dimerization interface [polypeptide binding]; other site 391008009921 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008009922 DNA binding site [nucleotide binding] 391008009923 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 391008009924 H+/citrate symporter [Energy production and conversion]; Region: CitM; COG2851 391008009925 Citrate transporter; Region: CitMHS; pfam03600 391008009926 acetyacetyl-CoA reductase; Provisional; Region: PRK12938 391008009927 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008009928 NAD(P) binding site [chemical binding]; other site 391008009929 active site 391008009930 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 391008009931 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 391008009932 N-terminal plug; other site 391008009933 ligand-binding site [chemical binding]; other site 391008009934 Domain of unknown function (DUF1704); Region: DUF1704; cl06858 391008009935 GTPase RsgA; Reviewed; Region: PRK01889 391008009936 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 391008009937 GTPase/Zn-binding domain interface [polypeptide binding]; other site 391008009938 GTP/Mg2+ binding site [chemical binding]; other site 391008009939 G4 box; other site 391008009940 G5 box; other site 391008009941 G1 box; other site 391008009942 Switch I region; other site 391008009943 G2 box; other site 391008009944 G3 box; other site 391008009945 Switch II region; other site 391008009946 aminotransferase AlaT; Validated; Region: PRK09265 391008009947 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 391008009948 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008009949 homodimer interface [polypeptide binding]; other site 391008009950 catalytic residue [active] 391008009951 Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase_like_1; cd01832 391008009952 active site 391008009953 catalytic triad [active] 391008009954 oxyanion hole [active] 391008009955 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 391008009956 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 391008009957 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 391008009958 NodB motif; other site 391008009959 active site 391008009960 catalytic site [active] 391008009961 metal binding site [ion binding]; metal-binding site 391008009962 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 391008009963 putative GSH binding site [chemical binding]; other site 391008009964 catalytic residues [active] 391008009965 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 391008009966 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 391008009967 active site residue [active] 391008009968 Bacterial protein of unknown function (DUF924); Region: DUF924; pfam06041 391008009969 AMP nucleosidase; Provisional; Region: PRK07115 391008009970 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 391008009971 Metallo-dependent hydrolases, subgroup C is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_C; cd01309 391008009972 active site 391008009973 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 391008009974 active site 391008009975 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1; Region: DsbA_HCCA_Iso; cd03022 391008009976 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 391008009977 putative catalytic residue [active] 391008009978 Uncharacterized protein conserved in bacteria [Function unknown]; Region: DegV; COG1307 391008009979 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 391008009980 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 391008009981 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 391008009982 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008009983 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008009984 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 391008009985 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 391008009986 putative substrate translocation pore; other site 391008009987 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008009988 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008009989 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_like_1; cd08460 391008009990 putative substrate binding pocket [chemical binding]; other site 391008009991 putative dimerization interface [polypeptide binding]; other site 391008009992 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 391008009993 Ligand Binding Site [chemical binding]; other site 391008009994 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008009995 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008009996 metal binding site [ion binding]; metal-binding site 391008009997 active site 391008009998 I-site; other site 391008009999 S-formylglutathione hydrolase; Region: PLN02442 391008010000 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 391008010001 tRNA pseudouridine synthase C; Region: DUF446; cl01187 391008010002 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 391008010003 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 391008010004 substrate binding site [chemical binding]; other site 391008010005 catalytic Zn binding site [ion binding]; other site 391008010006 NAD binding site [chemical binding]; other site 391008010007 structural Zn binding site [ion binding]; other site 391008010008 dimer interface [polypeptide binding]; other site 391008010009 Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156; Region: RcnR-FrmR-like_DUF156; cd10153 391008010010 putative metal binding site [ion binding]; other site 391008010011 putative homodimer interface [polypeptide binding]; other site 391008010012 putative homotetramer interface [polypeptide binding]; other site 391008010013 putative homodimer-homodimer interface [polypeptide binding]; other site 391008010014 putative allosteric switch controlling residues; other site 391008010015 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008010016 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008010017 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_6; cd08475 391008010018 putative effector binding pocket; other site 391008010019 putative dimerization interface [polypeptide binding]; other site 391008010020 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 391008010021 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 391008010022 FMN binding site [chemical binding]; other site 391008010023 active site 391008010024 substrate binding site [chemical binding]; other site 391008010025 catalytic residue [active] 391008010026 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 391008010027 active site 391008010028 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3226 391008010029 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008010030 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008010031 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008010032 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 391008010033 putative effector binding pocket; other site 391008010034 putative dimerization interface [polypeptide binding]; other site 391008010035 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 391008010036 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 391008010037 putative NAD(P) binding site [chemical binding]; other site 391008010038 putative substrate binding site [chemical binding]; other site 391008010039 catalytic Zn binding site [ion binding]; other site 391008010040 structural Zn binding site [ion binding]; other site 391008010041 dimer interface [polypeptide binding]; other site 391008010042 NnrS protein; Region: NnrS; pfam05940 391008010043 glutamate--cysteine ligase; Region: PLN02611 391008010044 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432 391008010045 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 391008010046 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008010047 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 391008010048 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 391008010049 G1 box; other site 391008010050 GTP/Mg2+ binding site [chemical binding]; other site 391008010051 Switch I region; other site 391008010052 G2 box; other site 391008010053 G3 box; other site 391008010054 Switch II region; other site 391008010055 G4 box; other site 391008010056 G5 box; other site 391008010057 Cytochrome c553 [Energy production and conversion]; Region: COG2863 391008010058 Cytochrome c; Region: Cytochrom_C; cl11414 391008010059 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 391008010060 catalytic residues [active] 391008010061 hinge region; other site 391008010062 alpha helical domain; other site 391008010063 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 391008010064 catalytic residues [active] 391008010065 hinge region; other site 391008010066 alpha helical domain; other site 391008010067 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 391008010068 putative catalytic site [active] 391008010069 putative metal binding site [ion binding]; other site 391008010070 putative phosphate binding site [ion binding]; other site 391008010071 threonine and homoserine efflux system; Provisional; Region: PRK10532 391008010072 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 391008010073 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 391008010074 putative DNA binding site [nucleotide binding]; other site 391008010075 putative Zn2+ binding site [ion binding]; other site 391008010076 AsnC family; Region: AsnC_trans_reg; pfam01037 391008010077 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 391008010078 Peptidase family M23; Region: Peptidase_M23; pfam01551 391008010079 ferric-rhodotorulic acid outer membrane transporter; Provisional; Region: PRK10003 391008010080 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 391008010081 N-terminal plug; other site 391008010082 ligand-binding site [chemical binding]; other site 391008010083 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 391008010084 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008010085 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008010086 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 391008010087 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 391008010088 lytic murein transglycosylase; Provisional; Region: PRK11619 391008010089 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 391008010090 N-acetyl-D-glucosamine binding site [chemical binding]; other site 391008010091 catalytic residue [active] 391008010092 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 391008010093 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 391008010094 active site 391008010095 NTP binding site [chemical binding]; other site 391008010096 metal binding triad [ion binding]; metal-binding site 391008010097 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 391008010098 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 391008010099 Zn2+ binding site [ion binding]; other site 391008010100 Mg2+ binding site [ion binding]; other site 391008010101 SseB protein; Region: SseB; cl06279 391008010102 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 391008010103 Active site serine [active] 391008010104 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 391008010105 Autotransporter beta-domain; Region: Autotransporter; smart00869 391008010106 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4299 391008010107 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4299 391008010108 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 391008010109 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 391008010110 active site 391008010111 dimer interface [polypeptide binding]; other site 391008010112 Predicted phosphosugar isomerases [Cell envelope biogenesis, outer membrane]; Region: AgaS; COG2222 391008010113 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 391008010114 dimer interface [polypeptide binding]; other site 391008010115 active site 391008010116 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 391008010117 dimer interface [polypeptide binding]; other site 391008010118 active site 391008010119 Transcriptional regulators [Transcription]; Region: PurR; COG1609 391008010120 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 391008010121 DNA binding site [nucleotide binding] 391008010122 domain linker motif; other site 391008010123 Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_SalR; cd01545 391008010124 putative dimerization interface [polypeptide binding]; other site 391008010125 putative ligand binding site [chemical binding]; other site 391008010126 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 391008010127 Major Facilitator Superfamily; Region: MFS_1; pfam07690 391008010128 putative substrate translocation pore; other site 391008010129 glucose/galactose transporter; Region: gluP; TIGR01272 391008010130 glucokinase; Provisional; Region: PRK12408 391008010131 glucokinase, proteobacterial type; Region: glk; TIGR00749 391008010132 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 391008010133 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008010134 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 391008010135 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 391008010136 The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i)...; Region: GH20_chitobiase-like; cd06563 391008010137 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 391008010138 active site 391008010139 Chitobiase/beta-hexosaminidase C-terminal domain; Region: CHB_HEX_C; pfam03174 391008010140 VanZ like family; Region: VanZ; cl01971 391008010141 Uncharacterized conserved protein [Function unknown]; Region: COG1565 391008010142 pteridine reductase; Provisional; Region: PRK09135 391008010143 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008010144 NAD(P) binding site [chemical binding]; other site 391008010145 active site 391008010146 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 391008010147 catalytic center binding site [active] 391008010148 ATP binding site [chemical binding]; other site 391008010149 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 391008010150 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 391008010151 active site 391008010152 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 391008010153 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 391008010154 active site 391008010155 phosphorylation site [posttranslational modification] 391008010156 intermolecular recognition site; other site 391008010157 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008010158 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 391008010159 ATP binding site [chemical binding]; other site 391008010160 Mg2+ binding site [ion binding]; other site 391008010161 G-X-G motif; other site 391008010162 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 391008010163 cheY-homologous receiver domain; Region: REC; smart00448 391008010164 active site 391008010165 phosphorylation site [posttranslational modification] 391008010166 intermolecular recognition site; other site 391008010167 dimerization interface [polypeptide binding]; other site 391008010168 Response regulator receiver domain; Region: Response_reg; pfam00072 391008010169 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 391008010170 active site 391008010171 phosphorylation site [posttranslational modification] 391008010172 intermolecular recognition site; other site 391008010173 dimerization interface [polypeptide binding]; other site 391008010174 CHASE3 domain; Region: CHASE3; pfam05227 391008010175 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 391008010176 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008010177 dimer interface [polypeptide binding]; other site 391008010178 phosphorylation site [posttranslational modification] 391008010179 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 391008010180 ATP binding site [chemical binding]; other site 391008010181 Mg2+ binding site [ion binding]; other site 391008010182 G-X-G motif; other site 391008010183 BON domain; Region: BON; pfam04972 391008010184 putative oxidoreductase; Provisional; Region: PRK11579 391008010185 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 391008010186 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 391008010187 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK12490 391008010188 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 391008010189 Uncharacterized protein conserved in bacteria (DUF2242); Region: DUF2242; pfam10001 391008010190 carboxy-terminal protease; Provisional; Region: PRK11186 391008010191 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 391008010192 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 391008010193 protein binding site [polypeptide binding]; other site 391008010194 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 391008010195 Catalytic dyad [active] 391008010196 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 391008010197 lipoyl synthase; Provisional; Region: PRK05481 391008010198 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 391008010199 FeS/SAM binding site; other site 391008010200 lipoate-protein ligase B; Provisional; Region: PRK14342 391008010201 hypothetical protein; Provisional; Region: PRK00907 391008010202 Uncharacterized protein conserved in bacteria (DUF2219); Region: DUF2219; pfam09982 391008010203 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 391008010204 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 391008010205 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 391008010206 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 391008010207 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 391008010208 Sporulation related domain; Region: SPOR; pfam05036 391008010209 Transglycosylase SLT domain; Region: SLT_2; pfam13406 391008010210 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 391008010211 N-acetyl-D-glucosamine binding site [chemical binding]; other site 391008010212 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 391008010213 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 391008010214 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 391008010215 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 391008010216 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 391008010217 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreD; COG2891 391008010218 rod shape-determining protein MreC; Provisional; Region: PRK13922 391008010219 rod shape-determining protein MreC; Region: MreC; pfam04085 391008010220 rod shape-determining protein MreB; Provisional; Region: PRK13927 391008010221 MreB and similar proteins; Region: MreB_like; cd10225 391008010222 nucleotide binding site [chemical binding]; other site 391008010223 Mg binding site [ion binding]; other site 391008010224 putative protofilament interaction site [polypeptide binding]; other site 391008010225 RodZ interaction site [polypeptide binding]; other site 391008010226 Ribokinase-like subgroup A. Found in bacteria and archaea, this subgroup is part of the ribokinase/pfkB superfamily. Its oligomerization state is unknown at this time; Region: ribokinase_group_A; cd01942 391008010227 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 391008010228 substrate binding site [chemical binding]; other site 391008010229 ATP binding site [chemical binding]; other site 391008010230 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 391008010231 Sulfatase; Region: Sulfatase; pfam00884 391008010232 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 391008010233 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 391008010234 active site 391008010235 motif I; other site 391008010236 motif II; other site 391008010237 leukotriene A-4 hydrolase/aminopeptidase; Region: leuko_A4_hydro; TIGR02411 391008010238 Peptidase M1 family contains leukotriene A4 hydrolase; Region: M1_LTA4H; cd09599 391008010239 active site 391008010240 Zn binding site [ion binding]; other site 391008010241 Leukotriene A4 hydrolase, C-terminal; Region: Leuk-A4-hydro_C; pfam09127 391008010242 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 391008010243 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 391008010244 S-adenosylmethionine binding site [chemical binding]; other site 391008010245 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 391008010246 nucleoside/Zn binding site; other site 391008010247 dimer interface [polypeptide binding]; other site 391008010248 catalytic motif [active] 391008010249 Low affinity iron permease; Region: Iron_permease; pfam04120 391008010250 Transposase IS200 like; Region: Y1_Tnp; pfam01797 391008010251 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 391008010252 Domain of unknown function, E. rectale Gene description (DUF3881); Region: DUF3881; pfam12997 391008010253 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 391008010254 Protein export membrane protein; Region: SecD_SecF; cl14618 391008010255 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 391008010256 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008010257 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008010258 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 391008010259 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008010260 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 391008010261 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 391008010262 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 391008010263 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 391008010264 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008010265 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 391008010266 Walker A motif; other site 391008010267 ATP binding site [chemical binding]; other site 391008010268 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008010269 Walker B motif; other site 391008010270 arginine finger; other site 391008010271 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 391008010272 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 391008010273 active site 391008010274 HslU subunit interaction site [polypeptide binding]; other site 391008010275 Protein of unknown function (DUF3079); Region: DUF3079; pfam11278 391008010276 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 391008010277 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 391008010278 active site 391008010279 DNA binding site [nucleotide binding] 391008010280 Int/Topo IB signature motif; other site 391008010281 Protein of unknown function, DUF484; Region: DUF484; cl17449 391008010282 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 391008010283 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 391008010284 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 391008010285 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2832 391008010286 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 391008010287 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 391008010288 hypothetical protein; Provisional; Region: PRK08960 391008010289 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 391008010290 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008010291 homodimer interface [polypeptide binding]; other site 391008010292 catalytic residue [active] 391008010293 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 391008010294 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 391008010295 Bacterial lipocalin [Cell envelope biogenesis, outer membrane]; Region: Blc; COG3040 391008010296 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 391008010297 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 391008010298 dimer interface [polypeptide binding]; other site 391008010299 conserved gate region; other site 391008010300 ABC-ATPase subunit interface; other site 391008010301 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 391008010302 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 391008010303 Walker A/P-loop; other site 391008010304 ATP binding site [chemical binding]; other site 391008010305 Q-loop/lid; other site 391008010306 ABC transporter signature motif; other site 391008010307 Walker B; other site 391008010308 D-loop; other site 391008010309 H-loop/switch region; other site 391008010310 This domain is found at the C-terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins; Region: NIL; smart00930 391008010311 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 391008010312 EamA-like transporter family; Region: EamA; pfam00892 391008010313 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 391008010314 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 391008010315 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 391008010316 Benzyl alcohol dehydrogenase; Region: benzyl_alcohol_DH; cd08278 391008010317 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 391008010318 catalytic Zn binding site [ion binding]; other site 391008010319 NAD binding site [chemical binding]; other site 391008010320 structural Zn binding site [ion binding]; other site 391008010321 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 391008010322 NAD-dependent benzaldehyde dehydrogenase II-like; Region: ALDH_BenzADH; cd07152 391008010323 NAD(P) binding site [chemical binding]; other site 391008010324 catalytic residues [active] 391008010325 Protein of unknown function (DUF1415); Region: DUF1415; pfam07209 391008010326 oxidoreductase; Validated; Region: PRK05717 391008010327 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008010328 NAD(P) binding site [chemical binding]; other site 391008010329 active site 391008010330 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 391008010331 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 391008010332 active site 391008010333 Zn binding site [ion binding]; other site 391008010334 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 391008010335 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 391008010336 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 391008010337 catalytic residue [active] 391008010338 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 391008010339 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 391008010340 dimer interface [polypeptide binding]; other site 391008010341 active site 391008010342 metal binding site [ion binding]; metal-binding site 391008010343 glutathione binding site [chemical binding]; other site 391008010344 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_19; cd07262 391008010345 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 391008010346 FOG: CBS domain [General function prediction only]; Region: COG0517 391008010347 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 391008010348 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 391008010349 Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In...; Region: GFAT; cd00714 391008010350 glutaminase active site [active] 391008010351 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 391008010352 dimer interface [polypeptide binding]; other site 391008010353 active site 391008010354 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 391008010355 dimer interface [polypeptide binding]; other site 391008010356 active site 391008010357 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 391008010358 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008010359 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008010360 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 391008010361 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 391008010362 Walker A/P-loop; other site 391008010363 ATP binding site [chemical binding]; other site 391008010364 Q-loop/lid; other site 391008010365 ABC transporter signature motif; other site 391008010366 Walker B; other site 391008010367 D-loop; other site 391008010368 H-loop/switch region; other site 391008010369 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 391008010370 FtsX-like permease family; Region: FtsX; pfam02687 391008010371 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 391008010372 FtsX-like permease family; Region: FtsX; pfam02687 391008010373 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 391008010374 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 391008010375 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 391008010376 active site 391008010377 phosphorylation site [posttranslational modification] 391008010378 intermolecular recognition site; other site 391008010379 dimerization interface [polypeptide binding]; other site 391008010380 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008010381 Walker A motif; other site 391008010382 ATP binding site [chemical binding]; other site 391008010383 Walker B motif; other site 391008010384 arginine finger; other site 391008010385 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 391008010386 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008010387 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 391008010388 ATP binding site [chemical binding]; other site 391008010389 Mg2+ binding site [ion binding]; other site 391008010390 G-X-G motif; other site 391008010391 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391008010392 Coenzyme A binding pocket [chemical binding]; other site 391008010393 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 391008010394 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 391008010395 Substrate binding site; other site 391008010396 Mg++ binding site; other site 391008010397 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 391008010398 active site 391008010399 substrate binding site [chemical binding]; other site 391008010400 CoA binding site [chemical binding]; other site 391008010401 GtrA-like protein; Region: GtrA; pfam04138 391008010402 Predicted membrane protein [Function unknown]; Region: COG2246 391008010403 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 391008010404 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 391008010405 gamma subunit interface [polypeptide binding]; other site 391008010406 epsilon subunit interface [polypeptide binding]; other site 391008010407 LBP interface [polypeptide binding]; other site 391008010408 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 391008010409 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 391008010410 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 391008010411 alpha subunit interaction interface [polypeptide binding]; other site 391008010412 Walker A motif; other site 391008010413 ATP binding site [chemical binding]; other site 391008010414 Walker B motif; other site 391008010415 inhibitor binding site; inhibition site 391008010416 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 391008010417 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 391008010418 core domain interface [polypeptide binding]; other site 391008010419 delta subunit interface [polypeptide binding]; other site 391008010420 epsilon subunit interface [polypeptide binding]; other site 391008010421 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 391008010422 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 391008010423 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 391008010424 beta subunit interaction interface [polypeptide binding]; other site 391008010425 Walker A motif; other site 391008010426 ATP binding site [chemical binding]; other site 391008010427 Walker B motif; other site 391008010428 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 391008010429 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 391008010430 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 391008010431 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 391008010432 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 391008010433 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 391008010434 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 391008010435 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 391008010436 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 391008010437 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 391008010438 E3 interaction surface; other site 391008010439 lipoyl attachment site [posttranslational modification]; other site 391008010440 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 391008010441 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 391008010442 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 391008010443 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 391008010444 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 391008010445 E3 interaction surface; other site 391008010446 lipoyl attachment site [posttranslational modification]; other site 391008010447 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 391008010448 E3 interaction surface; other site 391008010449 lipoyl attachment site [posttranslational modification]; other site 391008010450 e3 binding domain; Region: E3_binding; pfam02817 391008010451 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 391008010452 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 391008010453 putative active site [active] 391008010454 OmpW family; Region: OmpW; cl17427 391008010455 glycerol-3-phosphate dehydrogenase; Reviewed; Region: glpD; PRK12266 391008010456 glycerol kinase; Provisional; Region: glpK; PRK00047 391008010457 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 391008010458 N- and C-terminal domain interface [polypeptide binding]; other site 391008010459 active site 391008010460 MgATP binding site [chemical binding]; other site 391008010461 catalytic site [active] 391008010462 metal binding site [ion binding]; metal-binding site 391008010463 glycerol binding site [chemical binding]; other site 391008010464 homotetramer interface [polypeptide binding]; other site 391008010465 homodimer interface [polypeptide binding]; other site 391008010466 FBP binding site [chemical binding]; other site 391008010467 protein IIAGlc interface [polypeptide binding]; other site 391008010468 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 391008010469 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 391008010470 Predicted transcriptional regulator [Transcription]; Region: COG2378 391008010471 HTH domain; Region: HTH_11; pfam08279 391008010472 WYL domain; Region: WYL; pfam13280 391008010473 Protein of unknown function, DUF481; Region: DUF481; pfam04338 391008010474 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 391008010475 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cl17708 391008010476 domain interfaces; other site 391008010477 active site 391008010478 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 391008010479 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 391008010480 active site 391008010481 phosphorylation site [posttranslational modification] 391008010482 intermolecular recognition site; other site 391008010483 dimerization interface [polypeptide binding]; other site 391008010484 LytTr DNA-binding domain; Region: LytTR; pfam04397 391008010485 Histidine kinase; Region: His_kinase; pfam06580 391008010486 putative hydrolase; Provisional; Region: PRK11460 391008010487 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 391008010488 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 391008010489 Glucan_BSP_ModH catalyzes the elongation of beta-1,2 polyglucose chains of glucan; Region: Glucan_BSP_ModH; cd04191 391008010490 Ligand binding site; other site 391008010491 DXD motif; other site 391008010492 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 391008010493 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 391008010494 N-terminal plug; other site 391008010495 ligand-binding site [chemical binding]; other site 391008010496 Cache domain; Region: Cache_1; pfam02743 391008010497 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 391008010498 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 391008010499 dimerization interface [polypeptide binding]; other site 391008010500 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 391008010501 dimer interface [polypeptide binding]; other site 391008010502 putative CheW interface [polypeptide binding]; other site 391008010503 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 391008010504 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008010505 NAD(P) binding site [chemical binding]; other site 391008010506 active site 391008010507 Interphotoreceptor retinoid-binding protein; serine protease family S41; Region: Peptidase_S41_IRBP; cd07563 391008010508 active site triad [active] 391008010509 MarR family; Region: MarR_2; pfam12802 391008010510 A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity...; Region: APP_MetAP; cd01066 391008010511 active site 391008010512 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008010513 Domain of unknown function (DUF1956); Region: DUF1956; pfam09209 391008010514 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 391008010515 Major Facilitator Superfamily; Region: MFS_1; pfam07690 391008010516 putative substrate translocation pore; other site 391008010517 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 391008010518 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008010519 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_5; cd07238 391008010520 dimer interface [polypeptide binding]; other site 391008010521 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 391008010522 Peptidase S8 family domain in Autotransporter serine proteases; Region: Peptidases_S8_Autotransporter_serine_protease_like; cd04848 391008010523 catalytic triad [active] 391008010524 putative active site [active] 391008010525 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 391008010526 Autotransporter beta-domain; Region: Autotransporter; smart00869 391008010527 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 391008010528 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 391008010529 putative substrate translocation pore; other site 391008010530 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 391008010531 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008010532 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 391008010533 dimerization interface [polypeptide binding]; other site 391008010534 substrate binding pocket [chemical binding]; other site 391008010535 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 391008010536 putative substrate translocation pore; other site 391008010537 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 391008010538 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 391008010539 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 391008010540 Domain of unknown function (DUF2383); Region: DUF2383; cl17556 391008010541 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 391008010542 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008010543 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008010544 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008010545 MarR family; Region: MarR_2; pfam12802 391008010546 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 391008010547 EamA-like transporter family; Region: EamA; pfam00892 391008010548 Cupin domain; Region: Cupin_2; pfam07883 391008010549 Helix-turn-helix domain; Region: HTH_18; pfam12833 391008010550 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008010551 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 391008010552 putative C-terminal domain interface [polypeptide binding]; other site 391008010553 putative GSH binding site (G-site) [chemical binding]; other site 391008010554 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 391008010555 putative dimer interface [polypeptide binding]; other site 391008010556 C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases; Region: GST_C_8; cd03207 391008010557 dimer interface [polypeptide binding]; other site 391008010558 N-terminal domain interface [polypeptide binding]; other site 391008010559 putative substrate binding pocket (H-site) [chemical binding]; other site 391008010560 H-NS histone family; Region: Histone_HNS; pfam00816 391008010561 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 391008010562 Predicted membrane protein [Function unknown]; Region: COG2259 391008010563 CHAT domain; Region: CHAT; cl17868 391008010564 Predicted ATPase [General function prediction only]; Region: COG4637 391008010565 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 391008010566 Walker A/P-loop; other site 391008010567 ATP binding site [chemical binding]; other site 391008010568 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 391008010569 putative active site [active] 391008010570 putative metal-binding site [ion binding]; other site 391008010571 Integrase core domain; Region: rve; pfam00665 391008010572 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 391008010573 AAA domain; Region: AAA_22; pfam13401 391008010574 Walker A motif; other site 391008010575 ATP binding site [chemical binding]; other site 391008010576 Walker B motif; other site 391008010577 TniQ; Region: TniQ; pfam06527 391008010578 putative DNA-binding transcriptional regulator; Provisional; Region: PRK09775 391008010579 WAHD domain of WASH complex; Region: WASH_WAHD; pfam11945 391008010580 HipA-like N-terminal domain; Region: HipA_N; pfam07805 391008010581 HipA-like C-terminal domain; Region: HipA_C; pfam07804 391008010582 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 391008010583 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 391008010584 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 391008010585 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 391008010586 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391008010587 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 391008010588 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 391008010589 DNA binding residues [nucleotide binding] 391008010590 D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not...; Region: Dtyr_deacylase; cd00563 391008010591 putative active site [active] 391008010592 dimerization interface [polypeptide binding]; other site 391008010593 putative tRNAtyr binding site [nucleotide binding]; other site 391008010594 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 391008010595 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 391008010596 putative acyl-acceptor binding pocket; other site 391008010597 GTP cyclohydrolase; Provisional; Region: PRK08815 391008010598 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 391008010599 dimerization interface [polypeptide binding]; other site 391008010600 active site 391008010601 Bacterial PH domain; Region: DUF304; cl01348 391008010602 Predicted membrane protein [Function unknown]; Region: COG3428 391008010603 Bacterial PH domain; Region: DUF304; pfam03703 391008010604 Bacterial PH domain; Region: DUF304; pfam03703 391008010605 Bacterial PH domain; Region: DUF304; pfam03703 391008010606 Putative glycosyl/glycerophosphate transferases involved in teichoic acid biosynthesis TagF/TagB/EpsJ/RodC [Cell envelope biogenesis, outer membrane]; Region: TagB; COG1887 391008010607 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 391008010608 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 391008010609 putative metal binding site; other site 391008010610 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 391008010611 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 391008010612 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 391008010613 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 391008010614 16S rRNA methyltransferase B; Provisional; Region: PRK10901 391008010615 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 391008010616 putative RNA binding site [nucleotide binding]; other site 391008010617 NOL1/NOP2/sun family putative RNA methylase; Region: nop2p; TIGR00446 391008010618 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 391008010619 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 391008010620 putative active site [active] 391008010621 substrate binding site [chemical binding]; other site 391008010622 putative cosubstrate binding site; other site 391008010623 catalytic site [active] 391008010624 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 391008010625 substrate binding site [chemical binding]; other site 391008010626 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II)...; Region: Pep_deformylase; cd00487 391008010627 active site 391008010628 catalytic residues [active] 391008010629 metal binding site [ion binding]; metal-binding site 391008010630 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 391008010631 Uncharacterized protein containing LysM domain [Function unknown]; Region: XkdP; COG1652 391008010632 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 391008010633 DNA protecting protein DprA; Region: dprA; TIGR00732 391008010634 hypothetical protein; Validated; Region: PRK03430 391008010635 Domain of unknown function (DUF4339); Region: DUF4339; pfam14237 391008010636 Pilin (bacterial filament); Region: Pilin; pfam00114 391008010637 Domain of unknown function (DUF4339); Region: DUF4339; pfam14237 391008010638 RDD family; Region: RDD; pfam06271 391008010639 DNA topoisomerase I; Provisional; Region: PRK08780 391008010640 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the...; Region: TOPRIM_TopoIA_TopoI; cd03363 391008010641 active site 391008010642 interdomain interaction site; other site 391008010643 putative metal-binding site [ion binding]; other site 391008010644 nucleotide binding site [chemical binding]; other site 391008010645 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA...; Region: TOP1Ac; cd00186 391008010646 domain I; other site 391008010647 DNA binding groove [nucleotide binding] 391008010648 phosphate binding site [ion binding]; other site 391008010649 domain II; other site 391008010650 domain III; other site 391008010651 nucleotide binding site [chemical binding]; other site 391008010652 catalytic site [active] 391008010653 domain IV; other site 391008010654 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 391008010655 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 391008010656 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 391008010657 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 391008010658 tropinone reductase; Provisional; Region: PRK09242 391008010659 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008010660 NAD(P) binding site [chemical binding]; other site 391008010661 active site 391008010662 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 391008010663 tandem repeat interface [polypeptide binding]; other site 391008010664 oligomer interface [polypeptide binding]; other site 391008010665 active site residues [active] 391008010666 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 391008010667 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 391008010668 tandem repeat interface [polypeptide binding]; other site 391008010669 oligomer interface [polypeptide binding]; other site 391008010670 active site residues [active] 391008010671 multidrug efflux protein; Reviewed; Region: PRK01766 391008010672 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 391008010673 cation binding site [ion binding]; other site 391008010674 primosome assembly protein PriA; Validated; Region: PRK05580 391008010675 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 391008010676 ATP binding site [chemical binding]; other site 391008010677 putative Mg++ binding site [ion binding]; other site 391008010678 helicase superfamily c-terminal domain; Region: HELICc; smart00490 391008010679 nucleotide binding region [chemical binding]; other site 391008010680 ATP-binding site [chemical binding]; other site 391008010681 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 391008010682 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 391008010683 putative C-terminal domain interface [polypeptide binding]; other site 391008010684 putative GSH binding site (G-site) [chemical binding]; other site 391008010685 putative dimer interface [polypeptide binding]; other site 391008010686 C-terminal, alpha helical domain of an unknown subfamily 2 of Glutathione S-transferases; Region: GST_C_2; cd03180 391008010687 putative N-terminal domain interface [polypeptide binding]; other site 391008010688 putative dimer interface [polypeptide binding]; other site 391008010689 putative substrate binding pocket (H-site) [chemical binding]; other site 391008010690 Uncharacterized conserved protein [Function unknown]; Region: COG1432 391008010691 Uncharacterized subfamily of N-terminal LabA-like domains; Region: LabA_like_N_1; cd11297 391008010692 putative metal binding site [ion binding]; other site 391008010693 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cd10146 391008010694 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 391008010695 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 391008010696 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 391008010697 Putative lumazine-binding; Region: Lumazine_bd_2; pfam12893 391008010698 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 391008010699 GIY-YIG motif/motif A; other site 391008010700 putative active site [active] 391008010701 putative metal binding site [ion binding]; other site 391008010702 Predicted membrane protein [Function unknown]; Region: COG2860 391008010703 UPF0126 domain; Region: UPF0126; pfam03458 391008010704 UPF0126 domain; Region: UPF0126; pfam03458 391008010705 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 391008010706 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008010707 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008010708 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 391008010709 Protein export membrane protein; Region: SecD_SecF; cl14618 391008010710 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 391008010711 MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin; Region: MoCF_BD; cl00451 391008010712 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 391008010713 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 391008010714 DNA alkylation repair enzyme [DNA replication, recombination, and repair]; Region: COG4335 391008010715 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 391008010716 MarR family; Region: MarR; pfam01047 391008010717 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008010718 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008010719 dimer interface [polypeptide binding]; other site 391008010720 phosphorylation site [posttranslational modification] 391008010721 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 391008010722 ATP binding site [chemical binding]; other site 391008010723 Mg2+ binding site [ion binding]; other site 391008010724 G-X-G motif; other site 391008010725 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391008010726 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 391008010727 active site 391008010728 phosphorylation site [posttranslational modification] 391008010729 intermolecular recognition site; other site 391008010730 dimerization interface [polypeptide binding]; other site 391008010731 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008010732 DNA binding site [nucleotide binding] 391008010733 Aspartyl protease; Region: Asp_protease_2; pfam13650 391008010734 catalytic motif [active] 391008010735 Catalytic residue [active] 391008010736 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 391008010737 catalytic motif [active] 391008010738 Catalytic residue [active] 391008010739 luciferase-type oxidoreductase, BA3436 family; Region: lucif_BA3436; TIGR03571 391008010740 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 391008010741 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 391008010742 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 391008010743 C-terminal domain interface [polypeptide binding]; other site 391008010744 GSH binding site (G-site) [chemical binding]; other site 391008010745 dimer interface [polypeptide binding]; other site 391008010746 C-terminal, alpha helical domain of Ure2p and related Glutathione S-transferase-like proteins; Region: GST_C_Ure2p_like; cd03178 391008010747 dimer interface [polypeptide binding]; other site 391008010748 N-terminal domain interface [polypeptide binding]; other site 391008010749 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 391008010750 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008010751 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 391008010752 dimerization interface [polypeptide binding]; other site 391008010753 substrate binding pocket [chemical binding]; other site 391008010754 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 391008010755 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 391008010756 ring oligomerisation interface [polypeptide binding]; other site 391008010757 ATP/Mg binding site [chemical binding]; other site 391008010758 stacking interactions; other site 391008010759 hinge regions; other site 391008010760 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It...; Region: cpn10; cd00320 391008010761 oligomerisation interface [polypeptide binding]; other site 391008010762 mobile loop; other site 391008010763 roof hairpin; other site 391008010764 Bacterial Ig-like domain; Region: Big_5; pfam13205 391008010765 Endonuclease I; Region: Endonuclease_1; pfam04231 391008010766 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 391008010767 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 391008010768 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 391008010769 Thiol:disulfide interchange protein [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]; Region: COG4232 391008010770 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 391008010771 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 391008010772 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 391008010773 catalytic residues [active] 391008010774 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 391008010775 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 391008010776 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 391008010777 Sulfite reductase, alpha subunit (flavoprotein) [Inorganic ion transport and metabolism]; Region: CysJ; COG0369 391008010778 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 391008010779 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_like1; cd06200 391008010780 FAD binding pocket [chemical binding]; other site 391008010781 FAD binding motif [chemical binding]; other site 391008010782 catalytic residues [active] 391008010783 NAD binding pocket [chemical binding]; other site 391008010784 phosphate binding motif [ion binding]; other site 391008010785 beta-alpha-beta structure motif; other site 391008010786 HAMP domain; Region: HAMP; pfam00672 391008010787 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 391008010788 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 391008010789 dimer interface [polypeptide binding]; other site 391008010790 putative CheW interface [polypeptide binding]; other site 391008010791 N-acetyltransferase; Region: Acetyltransf_2; pfam00797 391008010792 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 391008010793 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 391008010794 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 391008010795 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 391008010796 substrate binding pocket [chemical binding]; other site 391008010797 membrane-bound complex binding site; other site 391008010798 hinge residues; other site 391008010799 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 391008010800 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008010801 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 391008010802 dimerization interface [polypeptide binding]; other site 391008010803 substrate binding pocket [chemical binding]; other site 391008010804 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cl15837 391008010805 active site 391008010806 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 391008010807 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 391008010808 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 391008010809 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391008010810 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 391008010811 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 391008010812 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 391008010813 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 391008010814 tetramer interface [polypeptide binding]; other site 391008010815 active site 391008010816 Mg2+/Mn2+ binding site [ion binding]; other site 391008010817 Dopa 4,5-dioxygenase family; Region: DOPA_dioxygen; pfam08883 391008010818 Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway...; Region: DHQase_II; cd00466 391008010819 Dehydroquinase class II; Region: DHquinase_II; pfam01220 391008010820 active site 391008010821 trimer interface [polypeptide binding]; other site 391008010822 dimer interface [polypeptide binding]; other site 391008010823 Protein of unknown function (DUF1311); Region: DUF1311; pfam07007 391008010824 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 391008010825 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 391008010826 carboxyltransferase (CT) interaction site; other site 391008010827 biotinylation site [posttranslational modification]; other site 391008010828 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 391008010829 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 391008010830 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 391008010831 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 391008010832 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 391008010833 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 391008010834 global DNA-binding transcriptional dual regulator Fis; Provisional; Region: fis; PRK00430 391008010835 Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]; Region: Fis; COG2901 391008010836 Predicted CDP-diglyceride synthetase/phosphatidate cytidylyltransferase [General function prediction only]; Region: COG4589 391008010837 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 391008010838 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 391008010839 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 391008010840 putative acyl-acceptor binding pocket; other site 391008010841 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 391008010842 active site 391008010843 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr; Region: PTPc; cl00053 391008010844 active site 391008010845 catalytic residues [active] 391008010846 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 391008010847 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 391008010848 Putative methyltransferase; Region: Methyltransf_20; pfam12147 391008010849 Phosphatidylglycerophosphate synthase [Lipid metabolism]; Region: PgsA; COG0558 391008010850 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 391008010851 Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates...; Region: IMPCH; cd01421 391008010852 purine monophosphate binding site [chemical binding]; other site 391008010853 dimer interface [polypeptide binding]; other site 391008010854 putative catalytic residues [active] 391008010855 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 391008010856 Virulence protein [General function prediction only]; Region: COG3943 391008010857 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 391008010858 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 391008010859 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 391008010860 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 391008010861 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 391008010862 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 391008010863 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 391008010864 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391008010865 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 391008010866 DNA binding residues [nucleotide binding] 391008010867 Penicillinase repressor; Region: Pencillinase_R; pfam03965 391008010868 BlaR1 peptidase M56; Region: Peptidase_M56; pfam05569 391008010869 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 391008010870 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 391008010871 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 391008010872 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 391008010873 Beta-lactamase; Region: Beta-lactamase; pfam00144 391008010874 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 391008010875 ligand binding site [chemical binding]; other site 391008010876 active site 391008010877 UGI interface [polypeptide binding]; other site 391008010878 catalytic site [active] 391008010879 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 391008010880 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 391008010881 active site 391008010882 phosphorylation site [posttranslational modification] 391008010883 intermolecular recognition site; other site 391008010884 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 391008010885 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 391008010886 active site 391008010887 phosphorylation site [posttranslational modification] 391008010888 intermolecular recognition site; other site 391008010889 dimerization interface [polypeptide binding]; other site 391008010890 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 391008010891 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 391008010892 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 391008010893 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 391008010894 Walker A/P-loop; other site 391008010895 ATP binding site [chemical binding]; other site 391008010896 Q-loop/lid; other site 391008010897 ABC transporter signature motif; other site 391008010898 Walker B; other site 391008010899 D-loop; other site 391008010900 H-loop/switch region; other site 391008010901 helicase 45; Provisional; Region: PTZ00424 391008010902 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 391008010903 ATP binding site [chemical binding]; other site 391008010904 Mg++ binding site [ion binding]; other site 391008010905 motif III; other site 391008010906 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 391008010907 nucleotide binding region [chemical binding]; other site 391008010908 ATP-binding site [chemical binding]; other site 391008010909 Protein of unknown function (DUF3628); Region: DUF3628; pfam12300 391008010910 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 391008010911 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 391008010912 catalytic residues [active] 391008010913 transcription termination factor Rho; Provisional; Region: rho; PRK09376 391008010914 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 391008010915 Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA...; Region: Rho_CSD; cd04459 391008010916 RNA binding site [nucleotide binding]; other site 391008010917 Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the...; Region: rho_factor; cd01128 391008010918 multimer interface [polypeptide binding]; other site 391008010919 Walker A motif; other site 391008010920 ATP binding site [chemical binding]; other site 391008010921 Walker B motif; other site 391008010922 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 391008010923 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008010924 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008010925 metal binding site [ion binding]; metal-binding site 391008010926 active site 391008010927 I-site; other site 391008010928 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 391008010929 bifunctional isocitrate dehydrogenase kinase/phosphatase protein; Validated; Region: aceK; PRK02946 391008010930 Isocitrate dehydrogenase kinase/phosphatase [Signal transduction mechanisms]; Region: COG4579 391008010931 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 391008010932 Conserved hypothetical ATP binding protein; Region: ATP_bind_1; pfam03029 391008010933 G1 box; other site 391008010934 GTP/Mg2+ binding site [chemical binding]; other site 391008010935 G2 box; other site 391008010936 Switch I region; other site 391008010937 G3 box; other site 391008010938 Switch II region; other site 391008010939 G4 box; other site 391008010940 G5 box; other site 391008010941 Monomeric isocitrate dehydrogenase [Energy production and conversion]; Region: Icd; COG2838 391008010942 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 391008010943 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 391008010944 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 391008010945 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 391008010946 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 391008010947 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like2; cd05667 391008010948 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 391008010949 metal binding site [ion binding]; metal-binding site 391008010950 putative dimer interface [polypeptide binding]; other site 391008010951 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 391008010952 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008010953 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008010954 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 391008010955 Protein export membrane protein; Region: SecD_SecF; cl14618 391008010956 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 391008010957 Protein export membrane protein; Region: SecD_SecF; cl14618 391008010958 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 391008010959 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 391008010960 N-terminal plug; other site 391008010961 ligand-binding site [chemical binding]; other site 391008010962 integral membrane protein, YccS/YhfK family; Region: YCCS_YHJK; TIGR01667 391008010963 FUSC-like inner membrane protein yccS; Region: FUSC-like; pfam12805 391008010964 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 391008010965 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 391008010966 classical (c) SDRs; Region: SDR_c; cd05233 391008010967 NAD(P) binding site [chemical binding]; other site 391008010968 active site 391008010969 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 391008010970 putative substrate translocation pore; other site 391008010971 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 391008010972 putative acyl-acceptor binding pocket; other site 391008010973 Interferon-induced transmembrane protein; Region: CD225; pfam04505 391008010974 Interferon-induced transmembrane protein; Region: CD225; pfam04505 391008010975 Protein of unknown function (DUF2752); Region: DUF2752; pfam10825 391008010976 Membrane protein required for beta-lactamase induction [Defense mechanisms]; Region: AmpE; cl17896 391008010977 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 391008010978 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]; Region: NPY1; COG2816 391008010979 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 391008010980 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 391008010981 putative NADH binding site [chemical binding]; other site 391008010982 putative active site [active] 391008010983 nudix motif; other site 391008010984 putative metal binding site [ion binding]; other site 391008010985 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 391008010986 Integral membrane protein CcmA involved in cell shape determination [Cell envelope biogenesis, outer membrane]; Region: CcmA; COG1664 391008010987 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 391008010988 TATA element modulatory factor 1 TATA binding; Region: TMF_TATA_bd; pfam12325 391008010989 Domain of unknown function (DUF4126); Region: DUF4126; pfam13548 391008010990 Response regulator receiver domain; Region: Response_reg; pfam00072 391008010991 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 391008010992 active site 391008010993 phosphorylation site [posttranslational modification] 391008010994 intermolecular recognition site; other site 391008010995 dimerization interface [polypeptide binding]; other site 391008010996 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008010997 metal binding site [ion binding]; metal-binding site 391008010998 active site 391008010999 I-site; other site 391008011000 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 391008011001 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008011002 dimer interface [polypeptide binding]; other site 391008011003 phosphorylation site [posttranslational modification] 391008011004 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 391008011005 ATP binding site [chemical binding]; other site 391008011006 Mg2+ binding site [ion binding]; other site 391008011007 G-X-G motif; other site 391008011008 Response regulator receiver domain; Region: Response_reg; pfam00072 391008011009 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 391008011010 active site 391008011011 phosphorylation site [posttranslational modification] 391008011012 intermolecular recognition site; other site 391008011013 dimerization interface [polypeptide binding]; other site 391008011014 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 391008011015 putative binding surface; other site 391008011016 active site 391008011017 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 391008011018 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 391008011019 heme binding site [chemical binding]; other site 391008011020 ferroxidase pore; other site 391008011021 ferroxidase diiron center [ion binding]; other site 391008011022 Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]; Region: Bfd; COG2906 391008011023 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 391008011024 putative active site [active] 391008011025 Ap4A binding site [chemical binding]; other site 391008011026 nudix motif; other site 391008011027 putative metal binding site [ion binding]; other site 391008011028 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 391008011029 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 391008011030 23S rRNA interface [nucleotide binding]; other site 391008011031 L3 interface [polypeptide binding]; other site 391008011032 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 391008011033 diiron binding motif [ion binding]; other site 391008011034 Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism]; Region: EmrE; COG2076 391008011035 S-adenosylmethionine decarboxylase; Provisional; Region: PRK05462 391008011036 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 391008011037 DNA-binding transcriptional dual regulator Crp; Provisional; Region: PRK11753 391008011038 ligand binding site [chemical binding]; other site 391008011039 flexible hinge region; other site 391008011040 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 391008011041 putative switch regulator; other site 391008011042 non-specific DNA interactions [nucleotide binding]; other site 391008011043 DNA binding site [nucleotide binding] 391008011044 sequence specific DNA binding site [nucleotide binding]; other site 391008011045 putative cAMP binding site [chemical binding]; other site 391008011046 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 391008011047 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 391008011048 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 391008011049 active site 391008011050 ribulose/triose binding site [chemical binding]; other site 391008011051 phosphate binding site [ion binding]; other site 391008011052 substrate (anthranilate) binding pocket [chemical binding]; other site 391008011053 product (indole) binding pocket [chemical binding]; other site 391008011054 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 391008011055 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 391008011056 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 391008011057 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 391008011058 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 391008011059 glutamine binding [chemical binding]; other site 391008011060 catalytic triad [active] 391008011061 Protein of unknown function (DUF541); Region: SIMPL; pfam04402 391008011062 anthranilate synthase component I; Provisional; Region: PRK13565 391008011063 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 391008011064 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 391008011065 lipid kinase; Reviewed; Region: PRK13054 391008011066 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 391008011067 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391008011068 Coenzyme A binding pocket [chemical binding]; other site 391008011069 Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative pentose...; Region: RPE; cd00429 391008011070 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 391008011071 substrate binding site [chemical binding]; other site 391008011072 hexamer interface [polypeptide binding]; other site 391008011073 metal binding site [ion binding]; metal-binding site 391008011074 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 391008011075 HSP70 interaction site [polypeptide binding]; other site 391008011076 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 391008011077 ATP binding site [chemical binding]; other site 391008011078 active site 391008011079 substrate binding site [chemical binding]; other site 391008011080 Protein of unknown function (DUF962); Region: DUF962; cl01879 391008011081 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12648 391008011082 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 391008011083 Multisubunit Na+/H+ antiporter, MnhB subunit [Inorganic ion transport and metabolism]; Region: MnhB; COG2111 391008011084 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 391008011085 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12573 391008011086 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK09094 391008011087 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12666 391008011088 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 391008011089 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK08965 391008011090 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK06161 391008011091 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 391008011092 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]; Region: ECM27; COG0530 391008011093 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 391008011094 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 391008011095 homogentisate 1,2-dioxygenase; Provisional; Region: PRK05341 391008011096 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]; Region: COG3185 391008011097 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 391008011098 dimer interface [polypeptide binding]; other site 391008011099 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 391008011100 active site 391008011101 Fe binding site [ion binding]; other site 391008011102 Transcriptional regulators [Transcription]; Region: MarR; COG1846 391008011103 MarR family; Region: MarR_2; pfam12802 391008011104 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 391008011105 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 391008011106 Flagellar L-ring protein; Region: FlgH; cl17277 391008011107 Thioredoxin-like; Region: Thioredoxin_7; pfam13899 391008011108 POT family; Region: PTR2; cl17359 391008011109 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 391008011110 tryptophan 2,3-dioxygenase; Region: trp_2_3_diox; TIGR03036 391008011111 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_x; TIGR03181 391008011112 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 391008011113 TPP-binding site [chemical binding]; other site 391008011114 tetramer interface [polypeptide binding]; other site 391008011115 heterodimer interface [polypeptide binding]; other site 391008011116 phosphorylation loop region [posttranslational modification] 391008011117 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 391008011118 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 391008011119 alpha subunit interface [polypeptide binding]; other site 391008011120 TPP binding site [chemical binding]; other site 391008011121 heterodimer interface [polypeptide binding]; other site 391008011122 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 391008011123 Variant SH3 domain; Region: SH3_2; pfam07653 391008011124 Src Homology 3 domain superfamily; Region: SH3; cl17036 391008011125 peptide ligand binding site [polypeptide binding]; other site 391008011126 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 391008011127 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 391008011128 E3 interaction surface; other site 391008011129 lipoyl attachment site [posttranslational modification]; other site 391008011130 e3 binding domain; Region: E3_binding; pfam02817 391008011131 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 391008011132 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_11; cd07261 391008011133 putative dimer interface [polypeptide binding]; other site 391008011134 HTH domain; Region: HTH_11; pfam08279 391008011135 Predicted transcriptional regulator [Transcription]; Region: COG2378 391008011136 WYL domain; Region: WYL; pfam13280 391008011137 CC3(TIP30)-like, atypical (a) SDRs; Region: CC3_like_SDR_a; cd05250 391008011138 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 391008011139 NAD binding site [chemical binding]; other site 391008011140 active site 391008011141 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008011142 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008011143 metal binding site [ion binding]; metal-binding site 391008011144 active site 391008011145 I-site; other site 391008011146 Protein of unknown function (DUF808); Region: DUF808; pfam05661 391008011147 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 391008011148 ABC1 family; Region: ABC1; cl17513 391008011149 phosphoglycerol transferase I; Provisional; Region: PRK12363 391008011150 Sulfatase; Region: Sulfatase; cl17466 391008011151 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 391008011152 Protein of unknown function (DUF3772); Region: DUF3772; pfam12607 391008011153 Mechanosensitive ion channel; Region: MS_channel; pfam00924 391008011154 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 391008011155 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 391008011156 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 391008011157 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 391008011158 Peptidase propeptide and YPEB domain; Region: PepSY_2; cl17877 391008011159 Predicted membrane protein [Function unknown]; Region: COG3212 391008011160 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 391008011161 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391008011162 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 391008011163 active site 391008011164 phosphorylation site [posttranslational modification] 391008011165 intermolecular recognition site; other site 391008011166 dimerization interface [polypeptide binding]; other site 391008011167 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008011168 DNA binding site [nucleotide binding] 391008011169 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008011170 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 391008011171 ATP binding site [chemical binding]; other site 391008011172 Mg2+ binding site [ion binding]; other site 391008011173 G-X-G motif; other site 391008011174 arginine decarboxylase; Provisional; Region: PRK05354 391008011175 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 391008011176 dimer interface [polypeptide binding]; other site 391008011177 active site 391008011178 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 391008011179 catalytic residues [active] 391008011180 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 391008011181 spermidine synthase; Provisional; Region: PRK00811 391008011182 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 391008011183 S-adenosylmethionine binding site [chemical binding]; other site 391008011184 Aspartyl/asparaginyl beta-hydroxylase and related dioxygenases [Posttranslational modification, protein turnover, chaperones]; Region: COG3555 391008011185 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 391008011186 active site 391008011187 ATP binding site [chemical binding]; other site 391008011188 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 391008011189 Nitrogen regulatory protein P-II; Region: P-II; smart00938 391008011190 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2960 391008011191 Rifampin ADP-ribosyl transferase; Region: Arr-ms; pfam12120 391008011192 Domain of unknown function (DUF4279); Region: DUF4279; pfam14106 391008011193 Restriction endonuclease; Region: Mrr_cat; pfam04471 391008011194 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 391008011195 Walker A motif; other site 391008011196 ATP binding site [chemical binding]; other site 391008011197 Walker B motif; other site 391008011198 Protein of unknown function (DUF998); Region: DUF998; pfam06197 391008011199 Protein of unknown function (DUF1629); Region: DUF1629; pfam07791 391008011200 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 391008011201 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 391008011202 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 391008011203 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 391008011204 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008011205 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008011206 sugar phosphate phosphatase; Provisional; Region: PRK10513 391008011207 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 391008011208 active site 391008011209 motif I; other site 391008011210 motif II; other site 391008011211 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 391008011212 Exopolysaccharide synthesis, ExoD; Region: ExoD; pfam06055 391008011213 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 391008011214 Predicted membrane protein (DUF2231); Region: DUF2231; cl01730 391008011215 Peptidase S8 family domain in Protein convertases; Region: Peptidases_S8_Protein_convertases_Kexins_Furin-lik; cd04059 391008011216 calcium binding site 1 [ion binding]; other site 391008011217 active site 391008011218 catalytic triad [active] 391008011219 calcium binding site 2 [ion binding]; other site 391008011220 calcium binding site 3 [ion binding]; other site 391008011221 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 391008011222 catalytic residues [active] 391008011223 Proprotein convertase P-domain; Region: P_proprotein; pfam01483 391008011224 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 391008011225 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 391008011226 Cu(I) binding site [ion binding]; other site 391008011227 cytochrome o ubiquinol oxidase subunit IV; Region: CyoD; TIGR02847 391008011228 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 391008011229 Subunit I/III interface [polypeptide binding]; other site 391008011230 Subunit III/IV interface [polypeptide binding]; other site 391008011231 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 391008011232 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 391008011233 D-pathway; other site 391008011234 Putative ubiquinol binding site [chemical binding]; other site 391008011235 Low-spin heme (heme b) binding site [chemical binding]; other site 391008011236 Putative water exit pathway; other site 391008011237 Binuclear center (heme o3/CuB) [ion binding]; other site 391008011238 K-pathway; other site 391008011239 Putative proton exit pathway; other site 391008011240 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 391008011241 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 391008011242 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 391008011243 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 391008011244 DNA-binding site [nucleotide binding]; DNA binding site 391008011245 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 391008011246 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008011247 homodimer interface [polypeptide binding]; other site 391008011248 catalytic residue [active] 391008011249 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 391008011250 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 391008011251 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 391008011252 DNA-binding site [nucleotide binding]; DNA binding site 391008011253 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 391008011254 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008011255 homodimer interface [polypeptide binding]; other site 391008011256 catalytic residue [active] 391008011257 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 391008011258 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 391008011259 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 391008011260 catalytic residue [active] 391008011261 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 391008011262 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 391008011263 N-terminal plug; other site 391008011264 ligand-binding site [chemical binding]; other site 391008011265 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 391008011266 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 391008011267 Zn binding site [ion binding]; other site 391008011268 Orthopoxvirus protein of unknown function (DUF830); Region: DUF830; pfam05708 391008011269 Short chain fatty acids transporter [Lipid metabolism]; Region: AtoE; COG2031 391008011270 4-hydroxybenzoate octaprenyltransferase; Reviewed; Region: ubiA; PRK12848 391008011271 UbiA prenyltransferase family; Region: UbiA; pfam01040 391008011272 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 391008011273 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008011274 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 391008011275 catalytic motif [active] 391008011276 Catalytic residue [active] 391008011277 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 391008011278 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 391008011279 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 391008011280 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008011281 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 391008011282 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 391008011283 CPE1046 is an uncharacterized Clostridium perfringens protein with a glycosyl hydrolase family 31 (GH31) domain. The domain architecture of CPE1046 and its orthologs includes a C-terminal fibronectin type 3 (FN3) domain and a coagulation factor 5/8 type...; Region: GH31_CPE1046; cd06596 391008011284 putative active site [active] 391008011285 Alpha-glucosidases, family 31 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: COG1501 391008011286 putative catalytic site [active] 391008011287 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 391008011288 NPCBM/NEW2 domain; Region: NPCBM; pfam08305 391008011289 putative sugar isomerase, AgaS family; Region: agaS_fam; TIGR02815 391008011290 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 391008011291 dimer interface [polypeptide binding]; other site 391008011292 active site 391008011293 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 391008011294 putative active site [active] 391008011295 fructokinase; Reviewed; Region: PRK09557 391008011296 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 391008011297 nucleotide binding site [chemical binding]; other site 391008011298 Tagatose 6 phosphate kinase; Region: Tagatose_6_P_K; pfam08013 391008011299 DNA-binding transcriptional regulator AgaR; Provisional; Region: PRK09802 391008011300 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 391008011301 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 391008011302 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 391008011303 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 391008011304 active site 391008011305 Sugar (and other) transporter; Region: Sugar_tr; pfam00083 391008011306 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 391008011307 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 391008011308 Uncharacterized conserved protein [Function unknown]; Region: HdeD; COG3247 391008011309 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 391008011310 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 391008011311 active site 391008011312 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 391008011313 ClC chloride channel family. These protein sequences, closely related to the ClC Eric family, are putative halogen ion (Cl-, Br- and I-) transport proteins found in eubacteria. They belong to the ClC superfamily of chloride ion channels, which share a...; Region: EriC_like; cd01034 391008011314 putative ion selectivity filter; other site 391008011315 putative pore gating glutamate residue; other site 391008011316 putative H+/Cl- coupling transport residue; other site 391008011317 biotin synthase; Provisional; Region: PRK15108 391008011318 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 391008011319 FeS/SAM binding site; other site 391008011320 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 391008011321 8-amino-7-oxononanoate synthase; Reviewed; Region: PRK05958 391008011322 Aminotransferase class I and II; Region: Aminotran_1_2; pfam00155 391008011323 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 391008011324 catalytic residue [active] 391008011325 pimelyl-[acyl-carrier protein] methyl ester esterase; Region: bioH; TIGR01738 391008011326 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK12825 391008011327 putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR; Region: BKR_like_SDR_like; cd05344 391008011328 putative NAD(P) binding site [chemical binding]; other site 391008011329 putative active site [active] 391008011330 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 391008011331 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 391008011332 S-adenosylmethionine binding site [chemical binding]; other site 391008011333 Uncharacterized conserved protein [Function unknown]; Region: COG1434 391008011334 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 391008011335 putative active site [active] 391008011336 serine racemase; Region: PLN02970 391008011337 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 391008011338 tetramer interface [polypeptide binding]; other site 391008011339 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391008011340 catalytic residue [active] 391008011341 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 391008011342 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 391008011343 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 391008011344 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 391008011345 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 391008011346 Protein export membrane protein; Region: SecD_SecF; cl14618 391008011347 Protein export membrane protein; Region: SecD_SecF; cl14618 391008011348 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 391008011349 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008011350 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008011351 signal transduction histidine-protein kinase BaeS; Provisional; Region: PRK10549 391008011352 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 391008011353 dimerization interface [polypeptide binding]; other site 391008011354 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008011355 dimer interface [polypeptide binding]; other site 391008011356 phosphorylation site [posttranslational modification] 391008011357 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 391008011358 ATP binding site [chemical binding]; other site 391008011359 Mg2+ binding site [ion binding]; other site 391008011360 G-X-G motif; other site 391008011361 DNA-binding transcriptional regulator BaeR; Provisional; Region: PRK10710 391008011362 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 391008011363 active site 391008011364 phosphorylation site [posttranslational modification] 391008011365 intermolecular recognition site; other site 391008011366 dimerization interface [polypeptide binding]; other site 391008011367 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 391008011368 DNA binding site [nucleotide binding] 391008011369 Predicted nucleotidyltransferase; Region: Nuc-transf; pfam10127 391008011370 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 391008011371 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 391008011372 trimer interface [polypeptide binding]; other site 391008011373 putative metal binding site [ion binding]; other site 391008011374 RDD family; Region: RDD; pfam06271 391008011375 Integral membrane protein DUF95; Region: DUF95; pfam01944 391008011376 Domain of unknown function (DUF4129); Region: DUF4129; pfam13559 391008011377 Domain of unknown function (DUF4350); Region: DUF4350; pfam14258 391008011378 MoxR-like ATPases [General function prediction only]; Region: COG0714 391008011379 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 391008011380 Walker A motif; other site 391008011381 ATP binding site [chemical binding]; other site 391008011382 Walker B motif; other site 391008011383 arginine finger; other site 391008011384 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 391008011385 Protein of unknown function DUF58; Region: DUF58; pfam01882 391008011386 Glutathionylspermidine synthase [Amino acid transport and metabolism]; Region: Gsp; COG0754 391008011387 Protein of unknown function (DUF1190); Region: DUF1190; pfam06693 391008011388 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 391008011389 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 391008011390 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 391008011391 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 391008011392 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 391008011393 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 391008011394 shikimate binding site; other site 391008011395 NAD(P) binding site [chemical binding]; other site 391008011396 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 391008011397 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 391008011398 DMAP1-binding Domain; Region: DMAP_binding; pfam06464 391008011399 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS_aspartate_rich; cd04823 391008011400 dimer interface [polypeptide binding]; other site 391008011401 allosteric magnesium binding site [ion binding]; other site 391008011402 active site 391008011403 aspartate-rich active site metal binding site; other site 391008011404 Schiff base residues; other site 391008011405 Bestrophin, RFP-TM, chloride channel; Region: Bestrophin; pfam01062 391008011406 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 391008011407 Cytochrome oxidase complex assembly protein 1; Region: Coa1; pfam08695 391008011408 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 391008011409 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 391008011410 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 391008011411 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 391008011412 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 391008011413 C-terminal domain interface [polypeptide binding]; other site 391008011414 GSH binding site (G-site) [chemical binding]; other site 391008011415 dimer interface [polypeptide binding]; other site 391008011416 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 391008011417 N-terminal domain interface [polypeptide binding]; other site 391008011418 putative dimer interface [polypeptide binding]; other site 391008011419 active site 391008011420 hypothetical protein; Provisional; Region: PRK05208 391008011421 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 391008011422 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 391008011423 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 391008011424 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 391008011425 Transposase IS200 like; Region: Y1_Tnp; pfam01797 391008011426 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 391008011427 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 391008011428 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 391008011429 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 391008011430 Walker A/P-loop; other site 391008011431 ATP binding site [chemical binding]; other site 391008011432 Q-loop/lid; other site 391008011433 ABC transporter signature motif; other site 391008011434 Walker B; other site 391008011435 D-loop; other site 391008011436 H-loop/switch region; other site 391008011437 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 391008011438 TAP-like protein; Region: Abhydrolase_4; pfam08386 391008011439 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008011440 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008011441 metal binding site [ion binding]; metal-binding site 391008011442 active site 391008011443 I-site; other site 391008011444 Protein of unknown function (DUF1203); Region: DUF1203; pfam06718 391008011445 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3397 391008011446 Chitin binding domain; Region: Chitin_bind_3; pfam03067 391008011447 Chitin binding domain; Region: Chitin_bind_3; pfam03067 391008011448 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 391008011449 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 391008011450 FAD binding pocket [chemical binding]; other site 391008011451 FAD binding motif [chemical binding]; other site 391008011452 phosphate binding motif [ion binding]; other site 391008011453 beta-alpha-beta structure motif; other site 391008011454 NAD binding pocket [chemical binding]; other site 391008011455 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 391008011456 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 391008011457 Walker A/P-loop; other site 391008011458 ATP binding site [chemical binding]; other site 391008011459 Q-loop/lid; other site 391008011460 ABC transporter signature motif; other site 391008011461 Walker B; other site 391008011462 D-loop; other site 391008011463 H-loop/switch region; other site 391008011464 inner membrane transport permease; Provisional; Region: PRK15066 391008011465 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 391008011466 2-dehydropantoate 2-reductase; Provisional; Region: PRK12921 391008011467 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 391008011468 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 391008011469 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 391008011470 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 391008011471 putative NAD(P) binding site [chemical binding]; other site 391008011472 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 391008011473 active site 391008011474 ATP-dependent helicase HrpB; Region: DEAH_box_HrpB; TIGR01970 391008011475 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 391008011476 ATP binding site [chemical binding]; other site 391008011477 putative Mg++ binding site [ion binding]; other site 391008011478 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 391008011479 nucleotide binding region [chemical binding]; other site 391008011480 Helicase associated domain (HA2); Region: HA2; pfam04408 391008011481 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 391008011482 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 391008011483 pseudouridine synthase; Region: TIGR00093 391008011484 active site 391008011485 Methyltransferase domain; Region: Methyltransf_23; pfam13489 391008011486 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 391008011487 S-adenosylmethionine binding site [chemical binding]; other site 391008011488 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 391008011489 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 391008011490 active site 391008011491 catalytic tetrad [active] 391008011492 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 391008011493 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 391008011494 Uncharacterized protein family UPF0027; Region: UPF0027; pfam01139 391008011495 hypothetical protein; Reviewed; Region: PRK09588 391008011496 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 391008011497 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 391008011498 Predicted transcriptional regulator [Transcription]; Region: COG1959 391008011499 Transcriptional regulator; Region: Rrf2; pfam02082 391008011500 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 391008011501 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 391008011502 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 391008011503 dimer interface [polypeptide binding]; other site 391008011504 putative CheW interface [polypeptide binding]; other site 391008011505 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008011506 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008011507 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 391008011508 dimerization interface [polypeptide binding]; other site 391008011509 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 391008011510 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 391008011511 putative substrate translocation pore; other site 391008011512 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 391008011513 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 391008011514 active site 391008011515 catalytic tetrad [active] 391008011516 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 391008011517 Putative heavy-metal-binding; Region: YbjQ_1; cl00426 391008011518 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 391008011519 CoA binding domain; Region: CoA_binding_2; pfam13380 391008011520 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 391008011521 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 391008011522 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 391008011523 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 391008011524 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 391008011525 MgtE intracellular N domain; Region: MgtE_N; smart00924 391008011526 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 391008011527 Divalent cation transporter; Region: MgtE; pfam01769 391008011528 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 391008011529 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 391008011530 TrkA-N domain; Region: TrkA_N; pfam02254 391008011531 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 391008011532 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 391008011533 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 391008011534 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 391008011535 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 391008011536 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 391008011537 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 391008011538 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 391008011539 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 391008011540 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 391008011541 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 391008011542 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 391008011543 YcgL domain; Region: YcgL; pfam05166 391008011544 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK09116 391008011545 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 391008011546 dimer interface [polypeptide binding]; other site 391008011547 active site 391008011548 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008011549 3-oxoacyl-(acyl-carrier-protein) reductase, putative; Region: fabG_rel; TIGR01831 391008011550 NAD(P) binding site [chemical binding]; other site 391008011551 active site 391008011552 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 391008011553 active site 2 [active] 391008011554 active site 1 [active] 391008011555 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK09185 391008011556 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 391008011557 dimer interface [polypeptide binding]; other site 391008011558 active site 391008011559 Protein of unknown function (DUF3261); Region: DUF3261; pfam11659 391008011560 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 391008011561 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 391008011562 Predicted exporter [General function prediction only]; Region: COG4258 391008011563 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl17548 391008011564 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 391008011565 active site 391008011566 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 391008011567 active sites [active] 391008011568 tetramer interface [polypeptide binding]; other site 391008011569 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 391008011570 putative acyl-acceptor binding pocket; other site 391008011571 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 391008011572 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 391008011573 Ligand binding site; other site 391008011574 Putative Catalytic site; other site 391008011575 DXD motif; other site 391008011576 O-succinylbenzoic acid--CoA ligase; Provisional; Region: PRK07824 391008011577 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 391008011578 AMP binding site [chemical binding]; other site 391008011579 active site 391008011580 acyl-activating enzyme (AAE) consensus motif; other site 391008011581 CoA binding site [chemical binding]; other site 391008011582 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 391008011583 active site 2 [active] 391008011584 active site 1 [active] 391008011585 Predicted membrane protein [Function unknown]; Region: COG4648 391008011586 acyl carrier protein; Provisional; Region: PRK05350 391008011587 Phosphopantetheine attachment site; Region: PP-binding; cl09936 391008011588 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 391008011589 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 391008011590 putative acyl-acceptor binding pocket; other site 391008011591 Beta-ketoacyl synthase, N-terminal domain; Region: Ketoacyl-synt_2; pfam13723 391008011592 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 391008011593 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 391008011594 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 391008011595 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 391008011596 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 391008011597 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 391008011598 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391008011599 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 391008011600 DNA binding residues [nucleotide binding] 391008011601 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 391008011602 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 391008011603 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_31; cd04690 391008011604 nudix motif; other site 391008011605 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 391008011606 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 391008011607 Predicted membrane protein [Function unknown]; Region: COG2323 391008011608 DNA polymerase I; Provisional; Region: PRK05755 391008011609 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 391008011610 active site 391008011611 metal binding site 1 [ion binding]; metal-binding site 391008011612 putative 5' ssDNA interaction site; other site 391008011613 metal binding site 3; metal-binding site 391008011614 metal binding site 2 [ion binding]; metal-binding site 391008011615 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 391008011616 putative DNA binding site [nucleotide binding]; other site 391008011617 putative metal binding site [ion binding]; other site 391008011618 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 391008011619 active site 391008011620 catalytic site [active] 391008011621 substrate binding site [chemical binding]; other site 391008011622 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 391008011623 active site 391008011624 DNA binding site [nucleotide binding] 391008011625 catalytic site [active] 391008011626 Protein of unknown function (DUF2782); Region: DUF2782; pfam11191 391008011627 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 391008011628 Ligand Binding Site [chemical binding]; other site 391008011629 Predicted protein tyrosine phosphatase [General function prediction only]; Region: COG4551 391008011630 active site 391008011631 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 391008011632 Part of AAA domain; Region: AAA_19; pfam13245 391008011633 Family description; Region: UvrD_C_2; pfam13538 391008011634 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4529 391008011635 FAD-NAD(P)-binding; Region: NAD_binding_9; pfam13454 391008011636 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 391008011637 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 391008011638 Catalytic domain, repeat 1, of Escherichia coli cardiolipin synthase and similar proteins; Region: PLDc_EcCLS_like_1; cd09152 391008011639 putative active site [active] 391008011640 catalytic site [active] 391008011641 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins; Region: PLDc_EcCLS_like_2; cd09158 391008011642 putative active site [active] 391008011643 catalytic site [active] 391008011644 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 391008011645 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 391008011646 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 391008011647 active site 391008011648 catalytic site [active] 391008011649 substrate binding site [chemical binding]; other site 391008011650 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008011651 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008011652 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 391008011653 putative effector binding pocket; other site 391008011654 putative dimerization interface [polypeptide binding]; other site 391008011655 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 391008011656 homotrimer interaction site [polypeptide binding]; other site 391008011657 putative active site [active] 391008011658 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 391008011659 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 391008011660 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 391008011661 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 391008011662 leucine-zipper of insertion element IS481; Region: LZ_Tnp_IS481; pfam13011 391008011663 Winged helix-turn helix; Region: HTH_29; pfam13551 391008011664 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 391008011665 Integrase core domain; Region: rve; pfam00665 391008011666 Integrase core domain; Region: rve_3; pfam13683 391008011667 Lipid A Biosynthesis N-terminal domain; Region: LAB_N; cl01627 391008011668 dolichyl-phosphate beta-D-mannosyltransferase; Region: PLN02726 391008011669 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 391008011670 Ligand binding site; other site 391008011671 Putative Catalytic site; other site 391008011672 DXD motif; other site 391008011673 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 391008011674 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391008011675 NAD(P) binding site [chemical binding]; other site 391008011676 active site 391008011677 Suppressor of fused protein (SUFU); Region: SUFU; pfam05076 391008011678 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 391008011679 ParB-like nuclease domain; Region: ParBc; pfam02195 391008011680 KorB domain; Region: KorB; pfam08535 391008011681 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 391008011682 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 391008011683 P-loop; other site 391008011684 Magnesium ion binding site [ion binding]; other site 391008011685 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 391008011686 Magnesium ion binding site [ion binding]; other site 391008011687 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 391008011688 rRNA small subunit methyltransferase G; Region: GidB; pfam02527 391008011689 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; pfam01648 391008011690 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 391008011691 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 391008011692 putative catalytic site [active] 391008011693 putative phosphate binding site [ion binding]; other site 391008011694 active site 391008011695 metal binding site A [ion binding]; metal-binding site 391008011696 DNA binding site [nucleotide binding] 391008011697 putative AP binding site [nucleotide binding]; other site 391008011698 putative metal binding site B [ion binding]; other site 391008011699 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 391008011700 NAD(P) binding site [chemical binding]; other site 391008011701 catalytic residues [active] 391008011702 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 391008011703 putative substrate translocation pore; other site 391008011704 acetyl-CoA synthetase; Provisional; Region: PRK00174 391008011705 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 391008011706 active site 391008011707 CoA binding site [chemical binding]; other site 391008011708 acyl-activating enzyme (AAE) consensus motif; other site 391008011709 AMP binding site [chemical binding]; other site 391008011710 acetate binding site [chemical binding]; other site 391008011711 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 391008011712 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 391008011713 active site 391008011714 phosphorylation site [posttranslational modification] 391008011715 intermolecular recognition site; other site 391008011716 dimerization interface [polypeptide binding]; other site 391008011717 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 391008011718 DNA binding residues [nucleotide binding] 391008011719 dimerization interface [polypeptide binding]; other site 391008011720 Transposase IS200 like; Region: Y1_Tnp; pfam01797 391008011721 Predicted membrane protein [Function unknown]; Region: COG1971 391008011722 Domain of unknown function DUF; Region: DUF204; pfam02659 391008011723 Domain of unknown function DUF; Region: DUF204; pfam02659 391008011724 Na+/proline symporter [Amino acid transport and metabolism / General function prediction only]; Region: PutP; COG0591 391008011725 Na binding site [ion binding]; other site 391008011726 PAS fold; Region: PAS_7; pfam12860 391008011727 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 391008011728 putative active site [active] 391008011729 heme pocket [chemical binding]; other site 391008011730 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391008011731 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 391008011732 dimer interface [polypeptide binding]; other site 391008011733 phosphorylation site [posttranslational modification] 391008011734 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 391008011735 ATP binding site [chemical binding]; other site 391008011736 Mg2+ binding site [ion binding]; other site 391008011737 G-X-G motif; other site 391008011738 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 391008011739 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 391008011740 active site 391008011741 phosphorylation site [posttranslational modification] 391008011742 intermolecular recognition site; other site 391008011743 dimerization interface [polypeptide binding]; other site 391008011744 Peptidase S46; Region: Peptidase_S46; pfam10459 391008011745 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 391008011746 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 391008011747 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 391008011748 Family of unknown function (DUF490); Region: DUF490; pfam04357 391008011749 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 391008011750 Surface antigen; Region: Bac_surface_Ag; pfam01103 391008011751 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 391008011752 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 391008011753 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 391008011754 dimer interface [polypeptide binding]; other site 391008011755 motif 1; other site 391008011756 active site 391008011757 motif 2; other site 391008011758 motif 3; other site 391008011759 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 391008011760 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 391008011761 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 391008011762 Walker A motif; other site 391008011763 ATP binding site [chemical binding]; other site 391008011764 Walker B motif; other site 391008011765 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 391008011766 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 391008011767 catalytic triad [active] 391008011768 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 391008011769 sec-independent translocase; Provisional; Region: tatB; PRK00404 391008011770 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 391008011771 twin arginine translocase protein A; Provisional; Region: tatA; PRK04561 391008011772 The SYLF domain (also called DUF500), a novel lipid-binding module; Region: SYLF; cd11524 391008011773 putative amphipathic alpha helix; other site 391008011774 ferrochelatase; Reviewed; Region: hemH; PRK00035 391008011775 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 391008011776 C-terminal domain interface [polypeptide binding]; other site 391008011777 active site 391008011778 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 391008011779 active site 391008011780 N-terminal domain interface [polypeptide binding]; other site 391008011781 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 391008011782 PAS domain; Region: PAS_9; pfam13426 391008011783 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 391008011784 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 391008011785 dimer interface [polypeptide binding]; other site 391008011786 putative CheW interface [polypeptide binding]; other site 391008011787 Benzoate membrane transport protein; Region: BenE; pfam03594 391008011788 benzoate transporter; Region: benE; TIGR00843 391008011789 Domain of unknown function (DUF4339); Region: DUF4339; pfam14237 391008011790 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 391008011791 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 391008011792 active site 391008011793 phosphate binding residues; other site 391008011794 catalytic residues [active] 391008011795 Transglycosylase SLT domain; Region: SLT_2; pfam13406 391008011796 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 391008011797 N-acetyl-D-glucosamine binding site [chemical binding]; other site 391008011798 dimethylhistidine N-methyltransferase; Region: egtD_ergothio; TIGR03438 391008011799 Methyltransferase domain; Region: Methyltransf_25; pfam13649 391008011800 Uncharacterized conserved protein (DUF2260); Region: DUF2260; pfam10017 391008011801 ergothioneine biosynthesis protein EgtB; Region: egtB_TIGR03440 391008011802 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 391008011803 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 391008011804 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391008011805 metal binding site [ion binding]; metal-binding site 391008011806 active site 391008011807 I-site; other site 391008011808 hypothetical protein; Provisional; Region: PRK04233 391008011809 hypothetical protein; Provisional; Region: PRK10621 391008011810 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 391008011811 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4913 391008011812 P-loop containing region of AAA domain; Region: AAA_29; pfam13555 391008011813 Putative exonuclease SbcCD, C subunit; Region: SbcCD_C; pfam13558 391008011814 Domain of unknown function (DUF4194); Region: DUF4194; pfam13835 391008011815 Protein of unknown function (DUF3375); Region: DUF3375; pfam11855 391008011816 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 391008011817 GTP cyclohydrolase I; Provisional; Region: PLN03044 391008011818 active site 391008011819 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 391008011820 MarR family; Region: MarR_2; pfam12802 391008011821 Protein of unknown function (DUF1656); Region: DUF1656; pfam07869 391008011822 p-hydroxybenzoic acid efflux subunit AaeA; Provisional; Region: PRK10559 391008011823 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 391008011824 HlyD family secretion protein; Region: HlyD_3; pfam13437 391008011825 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 391008011826 Fusaric acid resistance protein family; Region: FUSC; pfam04632 391008011827 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 391008011828 exodeoxyribonuclease V, alpha subunit; Region: recD; TIGR01447 391008011829 AAA domain; Region: AAA_30; pfam13604 391008011830 Family description; Region: UvrD_C_2; pfam13538 391008011831 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 391008011832 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 391008011833 exodeoxyribonuclease V, gamma subunit; Region: recC; TIGR01450 391008011834 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 391008011835 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 391008011836 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 391008011837 Walker A/P-loop; other site 391008011838 ATP binding site [chemical binding]; other site 391008011839 Q-loop/lid; other site 391008011840 ABC transporter signature motif; other site 391008011841 Walker B; other site 391008011842 D-loop; other site 391008011843 H-loop/switch region; other site 391008011844 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 391008011845 Permease; Region: Permease; pfam02405 391008011846 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 391008011847 mce related protein; Region: MCE; pfam02470 391008011848 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; cl01074 391008011849 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 391008011850 Surface lipoprotein [Cell envelope biogenesis, outer membrane]; Region: VacJ; COG2853 391008011851 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 391008011852 catalytic residues [active] 391008011853 dimer interface [polypeptide binding]; other site 391008011854 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 391008011855 RmuC family; Region: RmuC; pfam02646 391008011856 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 391008011857 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 391008011858 C-terminal, alpha helical domain of an unknown subfamily 2 of Glutathione S-transferases; Region: GST_C_2; cd03180 391008011859 putative N-terminal domain interface [polypeptide binding]; other site 391008011860 putative dimer interface [polypeptide binding]; other site 391008011861 putative substrate binding pocket (H-site) [chemical binding]; other site 391008011862 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 391008011863 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 391008011864 putative NAD(P) binding site [chemical binding]; other site 391008011865 dimer interface [polypeptide binding]; other site 391008011866 Transcriptional regulator [Transcription]; Region: LysR; COG0583 391008011867 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 391008011868 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 391008011869 putative effector binding pocket; other site 391008011870 dimerization interface [polypeptide binding]; other site 391008011871 LysE type translocator; Region: LysE; cl00565 391008011872 Suppressor of fused protein (SUFU); Region: SUFU; pfam05076 391008011873 amino acid transporter; Region: 2A0306; TIGR00909 391008011874 C-terminus of AA_permease; Region: AA_permease_C; pfam13906 391008011875 Zn-dependent dipeptidase, microsomal dipeptidase homolog [Amino acid transport and metabolism]; Region: COG2355 391008011876 renal dipeptidase (rDP), best studied in mammals and also called membrane or microsomal dipeptidase, is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics; Region: rDP_like; cd01301 391008011877 active site 391008011878 dimer interface [polypeptide binding]; other site 391008011879 Toxic anion resistance protein (TelA); Region: TelA; pfam05816 391008011880 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 391008011881 Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase; Region: PUA; smart00359 391008011882 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 391008011883 putative RNA binding site [nucleotide binding]; other site 391008011884 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 391008011885 S-adenosylmethionine binding site [chemical binding]; other site 391008011886 integral membrane protein, TerC family; Region: R_switched_Alx; TIGR03718 391008011887 Rhomboid family; Region: Rhomboid; cl11446 391008011888 glycerophosphodiester phosphodiesterase; Provisional; Region: glpQ; PRK11143 391008011889 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 391008011890 active site 391008011891 catalytic site [active] 391008011892 Beta protein; Region: Beta_protein; pfam14350 391008011893 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 391008011894 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 391008011895 trmE is a tRNA modification GTPase; Region: trmE; cd04164 391008011896 G1 box; other site 391008011897 GTP/Mg2+ binding site [chemical binding]; other site 391008011898 Switch I region; other site 391008011899 G2 box; other site 391008011900 Switch II region; other site 391008011901 G3 box; other site 391008011902 G4 box; other site 391008011903 G5 box; other site 391008011904 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 391008011905 delta-lactam-biosynthetic de-N-acetylase; Region: spore_pdaA; TIGR02884 391008011906 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 391008011907 NodB motif; other site 391008011908 active site 391008011909 catalytic site [active] 391008011910 metal binding site [ion binding]; metal-binding site 391008011911 Uncharacterized protein containing caspase domain [General function prediction only]; Region: COG4249 391008011912 Caspase domain; Region: Peptidase_C14; pfam00656 391008011913 TPR repeat; Region: TPR_11; pfam13414 391008011914 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 391008011915 TPR motif; other site 391008011916 binding surface 391008011917 TPR repeat; Region: TPR_11; pfam13414 391008011918 membrane protein insertase, YidC/Oxa1 family, N-terminal domain; Region: yidC_nterm; TIGR03593 391008011919 Preprotein translocase subunit YidC [Intracellular trafficking and secretion]; Region: YidC; COG0706 391008011920 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 391008011921 ribonuclease P; Reviewed; Region: rnpA; PRK04820 391008011922 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399