-- dump date 20140619_094121 -- class Genbank::misc_feature -- table misc_feature_note -- id note 402612000001 ribonuclease R; Region: RNase_R; TIGR02063 402612000002 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 402612000003 RNB domain; Region: RNB; pfam00773 402612000004 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 402612000005 RNA binding site [nucleotide binding]; other site 402612000006 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 402612000007 LysE type translocator; Region: LysE; cl00565 402612000008 Dihydroneopterin aldolase; Region: FolB; pfam02152 402612000009 active site 402612000010 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 402612000011 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 402612000012 active site 402612000013 HIGH motif; other site 402612000014 KMSKS motif; other site 402612000015 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 402612000016 YtxH-like protein; Region: YtxH; pfam12732 402612000017 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 402612000018 Uncharacterized family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily; Region: SPFH_like_u4; cd03407 402612000019 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 402612000020 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 402612000021 active site 402612000022 HIGH motif; other site 402612000023 KMSKS motif; other site 402612000024 Apolipophorin-III and similar insect proteins; Region: ApoLp-III_like; cl19113 402612000025 Ciliary protein causing Leber congenital amaurosis disease; Region: Lebercilin; pfam15619 402612000026 Invariant surface glycoprotein; Region: ISG65-75; cl19916 402612000027 Uncharacterized protein family UPF0054; Region: UPF0054; pfam02130 402612000028 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 402612000029 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 402612000030 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 402612000031 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 402612000032 S-adenosylmethionine binding site [chemical binding]; other site 402612000033 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 402612000034 SprB repeat; Region: SprB; pfam13573 402612000035 SprB repeat; Region: SprB; pfam13573 402612000036 SprB repeat; Region: SprB; pfam13573 402612000037 SprB repeat; Region: SprB; pfam13573 402612000038 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000039 PIF1-like helicase; Region: PIF1; pfam05970 402612000040 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 402612000041 Walker A motif; other site 402612000042 ATP binding site [chemical binding]; other site 402612000043 Walker B motif; other site 402612000044 UvrD-like helicase C-terminal domain; Region: UvrD_C_2; pfam13538 402612000045 Helix-turn-helix domain; Region: HTH_40; pfam14493 402612000046 DinB superfamily; Region: DinB_2; pfam12867 402612000047 Cyclic nucleotide-binding domain; Region: cNMP_binding; pfam00027 402612000048 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 402612000049 ligand binding site [chemical binding]; other site 402612000050 flexible hinge region; other site 402612000051 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 402612000052 DNA polymerase III subunit delta'; Validated; Region: PRK08485 402612000053 ATPase involved in DNA replication [DNA replication, recombination, and repair]; Region: HolB; COG0470 402612000054 C-terminal domain of CHU protein family; Region: CHU_C; cl17875 402612000055 Protein of unknown function (DUF3308); Region: DUF3308; pfam11751 402612000056 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 402612000057 SprB repeat; Region: SprB; pfam13573 402612000058 SprB repeat; Region: SprB; pfam13573 402612000059 C-terminal domain of CHU protein family; Region: CHU_C; cl17875 402612000060 Protein of unknown function (DUF3308); Region: DUF3308; pfam11751 402612000061 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cd00318 402612000062 substrate binding site [chemical binding]; other site 402612000063 hinge regions; other site 402612000064 ADP binding site [chemical binding]; other site 402612000065 catalytic site [active] 402612000066 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 402612000067 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 402612000068 N-acetyl-D-glucosamine binding site [chemical binding]; other site 402612000069 catalytic residue [active] 402612000070 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 402612000071 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 402612000072 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 402612000073 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 402612000074 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 402612000075 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 402612000076 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 402612000077 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 402612000078 Coenzyme A binding pocket [chemical binding]; other site 402612000079 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 402612000080 ligand binding site [chemical binding]; other site 402612000081 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 402612000082 ligand binding site [chemical binding]; other site 402612000083 putative rhodanese-related sulfurtransferase; Provisional; Region: PRK00142 402612000084 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 402612000085 active site residue [active] 402612000086 PSP1 C-terminal conserved region; Region: PSP1; cl00770 402612000087 GldH lipoprotein; Region: GldH_lipo; pfam14109 402612000088 Transglycosylase; Region: Transgly; pfam00912 402612000089 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 402612000090 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 402612000091 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 402612000092 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 402612000093 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 402612000094 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 402612000095 Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]; Region: SpmA; COG2715 402612000096 Uncharacterized membrane protein [Function unknown]; Region: SpmB; cl17667 402612000097 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 402612000098 active site 402612000099 catalytic site [active] 402612000100 substrate binding site [chemical binding]; other site 402612000101 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 402612000102 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 402612000103 DNA binding site [nucleotide binding] 402612000104 active site 402612000105 Cytochrome c; Region: Cytochrom_C; cl11414 402612000106 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 402612000107 dimer interface [polypeptide binding]; other site 402612000108 allosteric magnesium binding site [ion binding]; other site 402612000109 active site 402612000110 aspartate-rich active site metal binding site; other site 402612000111 Schiff base residues; other site 402612000112 Domain of unknown function (DUF4421); Region: DUF4421; pfam14391 402612000113 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 402612000114 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 402612000115 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 402612000116 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 402612000117 META domain; Region: META; pfam03724 402612000118 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 402612000119 substrate binding site [chemical binding]; other site 402612000120 active site 402612000121 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 402612000122 active site 402612000123 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 402612000124 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cd00494 402612000125 domain interfaces; other site 402612000126 active site 402612000127 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 402612000128 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 402612000129 NAD(P) binding pocket [chemical binding]; other site 402612000130 Glutamyl-tRNAGlu reductase, dimerization domain; Region: GlutR_dimer; pfam00745 402612000131 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 402612000132 Ferrochelatase; Region: Ferrochelatase; pfam00762 402612000133 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 402612000134 C-terminal domain interface [polypeptide binding]; other site 402612000135 active site 402612000136 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 402612000137 active site 402612000138 N-terminal domain interface [polypeptide binding]; other site 402612000139 Uncharacterized protein family (UPF0093); Region: UPF0093; pfam03653 402612000140 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 402612000141 HAMP domain; Region: HAMP; pfam00672 402612000142 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 402612000143 dimer interface [polypeptide binding]; other site 402612000144 phosphorylation site [posttranslational modification] 402612000145 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 402612000146 ATP binding site [chemical binding]; other site 402612000147 Mg2+ binding site [ion binding]; other site 402612000148 G-X-G motif; other site 402612000149 enoyl-CoA hydratase; Provisional; Region: PRK07658 402612000150 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 402612000151 substrate binding site [chemical binding]; other site 402612000152 oxyanion hole (OAH) forming residues; other site 402612000153 trimer interface [polypeptide binding]; other site 402612000154 Predicted HD superfamily hydrolase [General function prediction only]; Region: COG1418 402612000155 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 402612000156 Zn2+ binding site [ion binding]; other site 402612000157 Mg2+ binding site [ion binding]; other site 402612000158 Acyl ACP desaturase, ferritin-like diiron-binding domain; Region: Acyl_ACP_Desat; cd01050 402612000159 homodimer interface [polypeptide binding]; other site 402612000160 putative substrate binding pocket [chemical binding]; other site 402612000161 diiron center [ion binding]; other site 402612000162 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 402612000163 putative acyl-acceptor binding pocket; other site 402612000164 Disulphide isomerase; Region: Disulph_isomer; pfam06491 402612000165 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 402612000166 haloacid dehalogenase-like hydrolase; Region: HAD; cl19137 402612000167 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 402612000168 motif II; other site 402612000169 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 402612000170 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 402612000171 active site 402612000172 HIGH motif; other site 402612000173 KMSKS motif; other site 402612000174 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 402612000175 tRNA binding surface [nucleotide binding]; other site 402612000176 anticodon binding site; other site 402612000177 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 402612000178 dimer interface [polypeptide binding]; other site 402612000179 putative tRNA-binding site [nucleotide binding]; other site 402612000180 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 402612000181 dimer interface [polypeptide binding]; other site 402612000182 catalytic triad [active] 402612000183 hypothetical protein; Provisional; Region: PRK14686 402612000184 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 402612000185 voltage-dependent potassium channel beta subunit, animal; Region: Kv_beta; TIGR01293 402612000186 active site 402612000187 catalytic tetrad [active] 402612000188 Trypsin-like peptidase domain; Region: Trypsin_2; cl19303 402612000189 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 402612000190 ligand binding site [chemical binding]; other site 402612000191 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 402612000192 putative active site [active] 402612000193 putative catalytic site [active] 402612000194 putative DNA binding site [nucleotide binding]; other site 402612000195 putative phosphate binding site [ion binding]; other site 402612000196 metal binding site A [ion binding]; metal-binding site 402612000197 putative AP binding site [nucleotide binding]; other site 402612000198 putative metal binding site B [ion binding]; other site 402612000199 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ACT14924; Region: LPLAT_ACT14924-like; cd07986 402612000200 putative acyl-acceptor binding pocket; other site 402612000201 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; pfam13444 402612000202 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 402612000203 Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains; Region: 2-Hacid_dh_14; cd12179 402612000204 putative ligand binding site [chemical binding]; other site 402612000205 putative NAD binding site [chemical binding]; other site 402612000206 catalytic site [active] 402612000207 Ion channel; Region: Ion_trans_2; pfam07885 402612000208 Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism]; Region: ProC; COG0345 402612000209 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; pfam03807 402612000210 Pyrroline-5-carboxylate reductase dimerization; Region: P5CR_dimer; pfam14748 402612000211 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 402612000212 MgtE intracellular N domain; Region: MgtE_N; pfam03448 402612000213 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 402612000214 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 402612000215 Divalent cation transporter; Region: MgtE; pfam01769 402612000216 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 402612000217 Abi-like protein; Region: Abi_2; pfam07751 402612000218 Domain of unknown function (DUF4286); Region: DUF4286; pfam14114 402612000219 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 402612000220 binding surface 402612000221 TPR motif; other site 402612000222 seryl-tRNA synthetase; Provisional; Region: PRK05431 402612000223 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 402612000224 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 402612000225 motif 1; other site 402612000226 dimer interface [polypeptide binding]; other site 402612000227 active site 402612000228 motif 2; other site 402612000229 motif 3; other site 402612000230 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 402612000231 iron-sulfur cluster [ion binding]; other site 402612000232 [2Fe-2S] cluster binding site [ion binding]; other site 402612000233 Protein of unknown function (DUF1111); Region: DUF1111; pfam06537 402612000234 Predicted thiol oxidoreductase [Energy production and conversion]; Region: COG3488 402612000235 manganese transport protein MntH; Reviewed; Region: PRK00701 402612000236 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 402612000237 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 402612000238 Ligand Binding Site [chemical binding]; other site 402612000239 Iron dependent repressor, N-terminal DNA binding domain; Region: Fe_dep_repress; pfam01325 402612000240 Helix-turn-helix diphteria tox regulatory element; Region: HTH_DTXR; smart00529 402612000241 Iron dependent repressor, metal binding and dimerization domain; Region: Fe_dep_repr_C; pfam02742 402612000242 FeoA domain; Region: FeoA; pfam04023 402612000243 SnoaL-like domain; Region: SnoaL_3; pfam13474 402612000244 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; pfam13640 402612000245 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 402612000246 RIP metalloprotease RseP; Region: TIGR00054 402612000247 active site 402612000248 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 402612000249 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 402612000250 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 402612000251 putative substrate binding region [chemical binding]; other site 402612000252 Peptidase M1 family Aminopeptidase N; Region: M1_APN_4; cd09603 402612000253 Zn binding site [ion binding]; other site 402612000254 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000255 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 402612000256 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 402612000257 dimer interface [polypeptide binding]; other site 402612000258 ssDNA binding site [nucleotide binding]; other site 402612000259 tetramer (dimer of dimers) interface [polypeptide binding]; other site 402612000260 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 402612000261 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 402612000262 NAD(P) binding site [chemical binding]; other site 402612000263 active site 402612000264 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 402612000265 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 402612000266 active site 402612000267 Zn binding site [ion binding]; other site 402612000268 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 402612000269 Immune inhibitor A peptidase M6; Region: Peptidase_M6; cl11525 402612000270 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000271 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 402612000272 Cu(I) binding site [ion binding]; other site 402612000273 FeoA domain; Region: FeoA; pfam04023 402612000274 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 402612000275 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 402612000276 G1 box; other site 402612000277 GTP/Mg2+ binding site [chemical binding]; other site 402612000278 Switch I region; other site 402612000279 G2 box; other site 402612000280 G3 box; other site 402612000281 Switch II region; other site 402612000282 G4 box; other site 402612000283 G5 box; other site 402612000284 Nucleoside recognition; Region: Gate; pfam07670 402612000285 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 402612000286 Nucleoside recognition; Region: Gate; pfam07670 402612000287 succinate dehydrogenase (or fumarate reductase) cytochrome b subunit, b558 family; Region: sdhC_b558_fam; TIGR02046 402612000288 Succinate:quinone oxidoreductase (SQR)-like Type B subfamily 2, transmembrane subunit; composed of proteins with similarity to the SQRs of Geobacter metallireducens and Corynebacterium glutamicum. SQR catalyzes the oxidation of succinate to fumarate...; Region: SQR_TypeB_2_TM; cd03498 402612000289 putative Iron-sulfur protein interface [polypeptide binding]; other site 402612000290 proximal heme binding site [chemical binding]; other site 402612000291 distal heme binding site [chemical binding]; other site 402612000292 putative dimer interface [polypeptide binding]; other site 402612000293 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07573 402612000294 L-aspartate oxidase; Provisional; Region: PRK06175 402612000295 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 402612000296 23S rRNA-intervening sequence protein; Region: 23S_rRNA_IVP; pfam05635 402612000297 succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Validated; Region: PRK07570 402612000298 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 402612000299 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 402612000300 Thiol-activated cytolysin; Region: Thiol_cytolysin; pfam01289 402612000301 N-terminal domain of unknown function (DUF4140); Region: DUF4140; pfam13600 402612000302 Domain of unknown function (DUF4139); Region: DUF4139; pfam13598 402612000303 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 402612000304 Transglycosylase; Region: Transgly; pfam00912 402612000305 Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane]; Region: MrcB; COG0744 402612000306 Plasmid stabilisation system protein; Region: Plasmid_stabil; pfam05016 402612000307 DNA repair protein RadA; Provisional; Region: PRK11823 402612000308 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 402612000309 Walker A motif/ATP binding site; other site 402612000310 ATP binding site [chemical binding]; other site 402612000311 Walker B motif; other site 402612000312 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 402612000313 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819; cl19187 402612000314 Uncharacterized protein family (UPF0104); Region: UPF0104; pfam03706 402612000315 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 402612000316 tetramerization interface [polypeptide binding]; other site 402612000317 active site 402612000318 Pantoate-beta-alanine ligase; Region: PanC; cd00560 402612000319 active site 402612000320 ATP-binding site [chemical binding]; other site 402612000321 pantoate-binding site; other site 402612000322 HXXH motif; other site 402612000323 Starch synthase catalytic domain; Region: Glyco_transf_5; pfam08323 402612000324 Domain of unknown function (DUF4270); Region: DUF4270; pfam14092 402612000325 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 402612000326 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 402612000327 glutaminase active site [active] 402612000328 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 402612000329 dimer interface [polypeptide binding]; other site 402612000330 active site 402612000331 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 402612000332 dimer interface [polypeptide binding]; other site 402612000333 active site 402612000334 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612000335 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 402612000336 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 402612000337 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 402612000338 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 402612000339 catalytic triad [active] 402612000340 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 402612000341 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 402612000342 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 402612000343 alpha subunit interaction interface [polypeptide binding]; other site 402612000344 Walker A motif; other site 402612000345 ATP binding site [chemical binding]; other site 402612000346 Walker B motif; other site 402612000347 inhibitor binding site; inhibition site 402612000348 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 402612000349 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 402612000350 gamma subunit interface [polypeptide binding]; other site 402612000351 LBP interface [polypeptide binding]; other site 402612000352 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 402612000353 8-amino-7-oxononanoate synthase; Region: bioF; TIGR00858 402612000354 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 402612000355 catalytic residue [active] 402612000356 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000357 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000358 Acyl-protein synthetase, LuxE; Region: LuxE; pfam04443 402612000359 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 402612000360 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 402612000361 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 402612000362 dimer interface [polypeptide binding]; other site 402612000363 motif 1; other site 402612000364 active site 402612000365 motif 2; other site 402612000366 motif 3; other site 402612000367 Colicin V production protein; Region: Colicin_V; pfam02674 402612000368 TPR repeat; Region: TPR_11; pfam13414 402612000369 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 402612000370 binding surface 402612000371 TPR motif; other site 402612000372 TPR repeat; Region: TPR_11; pfam13414 402612000373 Oxygen tolerance; Region: BatD; pfam13584 402612000374 TPR repeat; Region: TPR_11; pfam13414 402612000375 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 402612000376 binding surface 402612000377 TPR motif; other site 402612000378 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 402612000379 metal ion-dependent adhesion site (MIDAS); other site 402612000380 GxxExxY protein; Region: GxxExxY; TIGR04256 402612000381 Aerotolerance regulator N-terminal; Region: BatA; pfam07584 402612000382 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 402612000383 metal ion-dependent adhesion site (MIDAS); other site 402612000384 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 402612000385 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 402612000386 metal ion-dependent adhesion site (MIDAS); other site 402612000387 MoxR-like ATPases [General function prediction only]; Region: COG0714 402612000388 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 402612000389 Walker A motif; other site 402612000390 ATP binding site [chemical binding]; other site 402612000391 Walker B motif; other site 402612000392 arginine finger; other site 402612000393 Divergent AAA domain; Region: AAA_4; pfam04326 402612000394 phosphoprotein phosphatases of the metallophosphatase superfamily, metallophosphatase domain; Region: MPP_PPP_family; cd00144 402612000395 active site 402612000396 metal binding site [ion binding]; metal-binding site 402612000397 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 402612000398 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; smart00782 402612000399 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 402612000400 PhnA protein; Region: PhnA; pfam03831 402612000401 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GpsA; COG0240 402612000402 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 402612000403 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 402612000404 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 402612000405 dimer interface [polypeptide binding]; other site 402612000406 active site 402612000407 metal binding site [ion binding]; metal-binding site 402612000408 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 402612000409 active site 402612000410 (T/H)XGH motif; other site 402612000411 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612000412 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 402612000413 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 402612000414 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 402612000415 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 402612000416 active site 402612000417 dimer interface [polypeptide binding]; other site 402612000418 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 402612000419 dimer interface [polypeptide binding]; other site 402612000420 active site 402612000421 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 402612000422 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 402612000423 5S rRNA interface [nucleotide binding]; other site 402612000424 CTC domain interface [polypeptide binding]; other site 402612000425 L16 interface [polypeptide binding]; other site 402612000426 Ribosomal protein TL5, C-terminal domain; Region: Ribosomal_TL5_C; pfam14693 402612000427 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 402612000428 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 402612000429 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 402612000430 active site 402612000431 hypothetical protein; Provisional; Region: PRK08201 402612000432 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_3; cd05680 402612000433 metal binding site [ion binding]; metal-binding site 402612000434 putative dimer interface [polypeptide binding]; other site 402612000435 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 402612000436 S-adenosylmethionine binding site [chemical binding]; other site 402612000437 Domain of unknown function (DUF4407); Region: DUF4407; pfam14362 402612000438 proline aminopeptidase P II; Provisional; Region: PRK10879 402612000439 Aminopeptidase P, N-terminal domain; Region: AMP_N; smart01011 402612000440 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 402612000441 active site 402612000442 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 402612000443 Putative lysophospholipase; Region: Hydrolase_4; cl19140 402612000444 UvrD-like helicase C-terminal domain; Region: UvrD_C_2; cl19402 402612000445 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 402612000446 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 402612000447 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 402612000448 ligand binding site [chemical binding]; other site 402612000449 8-amino-7-oxononanoate synthase; Region: bioF; TIGR00858 402612000450 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 402612000451 substrate-cofactor binding pocket; other site 402612000452 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612000453 catalytic residue [active] 402612000454 Protein of unknown function DUF262; Region: DUF262; pfam03235 402612000455 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 402612000456 putative recombination protein RecB; Provisional; Region: PRK13909 402612000457 UvrD-like helicase C-terminal domain; Region: UvrD_C_2; pfam13538 402612000458 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 402612000459 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 402612000460 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 402612000461 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 402612000462 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 402612000463 active site 402612000464 HIGH motif; other site 402612000465 dimer interface [polypeptide binding]; other site 402612000466 KMSKS motif; other site 402612000467 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 402612000468 RNA binding surface [nucleotide binding]; other site 402612000469 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 402612000470 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 402612000471 NAD(P) binding site [chemical binding]; other site 402612000472 active site 402612000473 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 402612000474 Domain of unknown function (DUF4296); Region: DUF4296; pfam14129 402612000475 dihydroorotase; Reviewed; Region: PRK09236 402612000476 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 402612000477 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 402612000478 active site 402612000479 DPM1_like represents putative enzymes similar to eukaryotic DPM1; Region: DPM1_like; cd06442 402612000480 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 402612000481 Ligand binding site; other site 402612000482 Putative Catalytic site; other site 402612000483 DXD motif; other site 402612000484 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 402612000485 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000486 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 402612000487 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 402612000488 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000489 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 402612000490 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 402612000491 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000492 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 402612000493 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000494 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 402612000495 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000496 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 402612000497 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000498 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 402612000499 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000500 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 402612000501 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 402612000502 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 402612000503 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000504 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 402612000505 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000506 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 402612000507 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 402612000508 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000509 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 402612000510 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000511 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 402612000512 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000513 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 402612000514 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000515 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 402612000516 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000517 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 402612000518 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000519 Domain of unknown function (DUF4271); Region: DUF4271; pfam14093 402612000520 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 402612000521 active site 402612000522 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 402612000523 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 402612000524 substrate binding site [chemical binding]; other site 402612000525 oxyanion hole (OAH) forming residues; other site 402612000526 trimer interface [polypeptide binding]; other site 402612000527 hypothetical protein; Provisional; Region: PRK09256 402612000528 AAA domain; Region: AAA_28; pfam13521 402612000529 Domain of unknown function (DUF4301); Region: DUF4301; pfam14134 402612000530 Nicotinamide mononucleotide transporter; Region: NMN_transporter; pfam04973 402612000531 geranylgeranylglyceryl phosphate synthase-like protein; Reviewed; Region: PRK04169 402612000532 phosphate binding site [ion binding]; other site 402612000533 Phosphopantetheinyl transferase [Coenzyme metabolism]; Region: Sfp; COG2091 402612000534 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; pfam01648 402612000535 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 402612000536 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 402612000537 homotetramer interface [polypeptide binding]; other site 402612000538 ligand binding site [chemical binding]; other site 402612000539 catalytic site [active] 402612000540 NAD binding site [chemical binding]; other site 402612000541 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 402612000542 L-threonine dehydrogenase, extended (e) SDRs; Region: TDH_SDR_e; cd05272 402612000543 NAD binding site [chemical binding]; other site 402612000544 homodimer interface [polypeptide binding]; other site 402612000545 active site 402612000546 putative substrate binding site [chemical binding]; other site 402612000547 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 402612000548 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 402612000549 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 402612000550 ATP binding site [chemical binding]; other site 402612000551 putative Mg++ binding site [ion binding]; other site 402612000552 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 402612000553 nucleotide binding region [chemical binding]; other site 402612000554 ATP-binding site [chemical binding]; other site 402612000555 TRCF domain; Region: TRCF; pfam03461 402612000556 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 402612000557 CYTH-like Clostridium thermocellum TTM-like subgroup 1; Region: CYTH-like_CthTTM-like_1; cd07891 402612000558 putative active site [active] 402612000559 putative metal binding residues [ion binding]; other site 402612000560 signature motif; other site 402612000561 putative dimer interface [polypeptide binding]; other site 402612000562 putative phosphate binding site [ion binding]; other site 402612000563 Glutamine phosphoribosylpyrophosphate amidotransferase [Nucleotide transport and metabolism]; Region: PurF; COG0034 402612000564 Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to...; Region: Gn_AT_II; cl00319 402612000565 active site 402612000566 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 402612000567 active site 402612000568 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase; Region: ribokinase_pfkB_like; cl00192 402612000569 substrate binding site [chemical binding]; other site 402612000570 ATP binding site [chemical binding]; other site 402612000571 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 402612000572 RNA/DNA hybrid binding site [nucleotide binding]; other site 402612000573 active site 402612000574 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 402612000575 active site 402612000576 substrate binding site [chemical binding]; other site 402612000577 cosubstrate binding site; other site 402612000578 catalytic site [active] 402612000579 acyl carrier protein; Provisional; Region: acpP; PRK00982 402612000580 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 402612000581 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 402612000582 dimer interface [polypeptide binding]; other site 402612000583 active site 402612000584 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 402612000585 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 402612000586 dimerization interface [polypeptide binding]; other site 402612000587 active site 402612000588 metal binding site [ion binding]; metal-binding site 402612000589 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 402612000590 dsRNA binding site [nucleotide binding]; other site 402612000591 Pyruvate kinase [Carbohydrate transport and metabolism]; Region: PykF; COG0469 402612000592 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cd00288 402612000593 domain interfaces; other site 402612000594 active site 402612000595 Bacterial PH domain; Region: bPH_3; pfam14470 402612000596 YjbR; Region: YjbR; pfam04237 402612000597 Putative cyclase; Region: Cyclase; pfam04199 402612000598 Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]; Region: HemN; COG0635 402612000599 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 402612000600 FeS/SAM binding site; other site 402612000601 HemN C-terminal domain; Region: HemN_C; pfam06969 402612000602 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 402612000603 active site 402612000604 putative DNA-binding cleft [nucleotide binding]; other site 402612000605 dimer interface [polypeptide binding]; other site 402612000606 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 402612000607 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_e; cd04192 402612000608 Protein of unknown function (DUF456); Region: DUF456; pfam04306 402612000609 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 402612000610 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 402612000611 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 402612000612 active site 402612000613 HIGH motif; other site 402612000614 nucleotide binding site [chemical binding]; other site 402612000615 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 402612000616 active site 402612000617 KMSKS motif; other site 402612000618 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 402612000619 tRNA binding surface [nucleotide binding]; other site 402612000620 anticodon binding site; other site 402612000621 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 402612000622 lipoprotein signal peptidase; Provisional; Region: PRK14788 402612000623 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 402612000624 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup; Region: M14_ASTE_ASPA_like_1; cd06251 402612000625 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 402612000626 putative active site [active] 402612000627 Zn binding site [ion binding]; other site 402612000628 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 402612000629 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 402612000630 GIY-YIG motif/motif A; other site 402612000631 active site 402612000632 catalytic site [active] 402612000633 putative DNA binding site [nucleotide binding]; other site 402612000634 metal binding site [ion binding]; metal-binding site 402612000635 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 402612000636 Helix-hairpin-helix domain; Region: HHH_5; pfam14520 402612000637 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 402612000638 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 402612000639 active site 402612000640 nucleophile elbow; other site 402612000641 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 402612000642 Surface antigen; Region: Bac_surface_Ag; pfam01103 402612000643 amino acid transporter; Region: 2A0306; TIGR00909 402612000644 Transmembrane amino acid transporter protein; Region: Aa_trans; cl17468 402612000645 C-terminus of AA_permease; Region: AA_permease_C; pfam13906 402612000646 homogentisate 1,2-dioxygenase; Region: HgmA; cl17306 402612000647 4-hydroxyphenylpyruvate dioxygenase; Region: 4HPPD; TIGR01263 402612000648 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 402612000649 dimer interface [polypeptide binding]; other site 402612000650 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 402612000651 active site 402612000652 Fe binding site [ion binding]; other site 402612000653 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 402612000654 Tryptophan 2,3-dioxygenase; Region: Trp_dioxygenase; cl03994 402612000655 putative peptidase; Provisional; Region: PRK11649 402612000656 Peptidase family M23; Region: Peptidase_M23; pfam01551 402612000657 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 402612000658 putative active site [active] 402612000659 catalytic residue [active] 402612000660 Metallo-peptidase family M12B Reprolysin-like; Region: Reprolysin_2; pfam13574 402612000661 Proprotein convertase P-domain; Region: P_proprotein; pfam01483 402612000662 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000663 Zinc-dependent metalloprotease, pappalysin_like subfamily. The pregnancy-associated plasma protein A (PAPP-A or pappalysin-1) cleaves insulin-like growth factor-binding proteins 4 and 5, thereby promoting cell growth by releasing bound growth factor; Region: ZnMc_pappalysin_like; cd04275 402612000664 active site 402612000665 Cleaved Adhesin Domain; Region: Cleaved_Adhesin; pfam07675 402612000666 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000667 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 402612000668 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 402612000669 active site 402612000670 Riboflavin kinase; Region: Flavokinase; pfam01687 402612000671 biotin synthase; Region: bioB; TIGR00433 402612000672 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 402612000673 FeS/SAM binding site; other site 402612000674 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 402612000675 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 402612000676 dimer interface [polypeptide binding]; other site 402612000677 substrate binding site [chemical binding]; other site 402612000678 metal binding site [ion binding]; metal-binding site 402612000679 Ribosome-binding factor A; Region: RBFA; pfam02033 402612000680 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 402612000681 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 402612000682 FtsX-like permease family; Region: FtsX; pfam02687 402612000683 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 402612000684 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 402612000685 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 402612000686 hinge; other site 402612000687 active site 402612000688 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain putative pyrophosphatase YpjD from Bacillus subtilis and its bacterial homologs; Region: NTP-PPase_BsYpjD; cd11531 402612000689 homodimer interface [polypeptide binding]; other site 402612000690 metal binding site [ion binding]; metal-binding site 402612000691 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 402612000692 GIY-YIG motif/motif A; other site 402612000693 putative active site [active] 402612000694 putative metal binding site [ion binding]; other site 402612000695 DNA-damage-inducible protein D; Provisional; Region: dinD; PRK11525 402612000696 BRO family, N-terminal domain; Region: Bro-N; pfam02498 402612000697 type II restriction m6 adenine DNA methyltransferase, Alw26I/Eco31I/Esp3I family; Region: met_A_Alw26; TIGR02987 402612000698 Methyltransferase domain; Region: Methyltransf_26; pfam13659 402612000699 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 402612000700 TaqI-like C-terminal specificity domain; Region: TaqI_C; pfam12950 402612000701 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 402612000702 putative active site [active] 402612000703 dimerization interface [polypeptide binding]; other site 402612000704 putative tRNAtyr binding site [nucleotide binding]; other site 402612000705 GTPase RsgA; Reviewed; Region: PRK00098 402612000706 S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of...; Region: S1_YloQ_GTPase; cd04466 402612000707 RNA binding site [nucleotide binding]; other site 402612000708 homodimer interface [polypeptide binding]; other site 402612000709 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 402612000710 GTPase/Zn-binding domain interface [polypeptide binding]; other site 402612000711 GTP/Mg2+ binding site [chemical binding]; other site 402612000712 G4 box; other site 402612000713 G5 box; other site 402612000714 G1 box; other site 402612000715 Switch I region; other site 402612000716 G2 box; other site 402612000717 G3 box; other site 402612000718 Switch II region; other site 402612000719 DAHP synthetase I family; Region: DAHP_synth_1; cl17225 402612000720 Chorismate mutase type II; Region: CM_2; smart00830 402612000721 LL-diaminopimelate aminotransferase; Provisional; Region: PRK09276 402612000722 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 402612000723 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612000724 homodimer interface [polypeptide binding]; other site 402612000725 catalytic residue [active] 402612000726 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 402612000727 Prephenate dehydratase; Region: PDT; pfam00800 402612000728 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 402612000729 putative L-Phe binding site [chemical binding]; other site 402612000730 gliding motility-associated ABC transporter ATP-binding subunit GldA; Region: GldA_ABC_ATP; TIGR03522 402612000731 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 402612000732 Walker A/P-loop; other site 402612000733 ATP binding site [chemical binding]; other site 402612000734 Q-loop/lid; other site 402612000735 ABC transporter signature motif; other site 402612000736 Walker B; other site 402612000737 D-loop; other site 402612000738 H-loop/switch region; other site 402612000739 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 402612000740 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 402612000741 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 402612000742 Homoserine dehydrogenase [Amino acid transport and metabolism]; Region: ThrA; COG0460 402612000743 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 402612000744 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 402612000745 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 402612000746 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 402612000747 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 402612000748 homodimer interface [polypeptide binding]; other site 402612000749 substrate-cofactor binding pocket; other site 402612000750 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612000751 catalytic residue [active] 402612000752 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 402612000753 metal ion-dependent adhesion site (MIDAS); other site 402612000754 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 402612000755 catalytic residues [active] 402612000756 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 402612000757 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 402612000758 Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1; Region: dNK; cd01673 402612000759 Substrate-binding site [chemical binding]; other site 402612000760 Substrate specificity [chemical binding]; other site 402612000761 putative transposase OrfB; Reviewed; Region: PHA02517 402612000762 HTH-like domain; Region: HTH_21; pfam13276 402612000763 Integrase core domain; Region: rve; pfam00665 402612000764 Integrase core domain; Region: rve_3; pfam13683 402612000765 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 402612000766 Transposase; Region: HTH_Tnp_1; cl17663 402612000767 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612000768 GLPGLI family protein; Region: GLPGLI; TIGR01200 402612000769 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 402612000770 TonB dependent receptor; Region: TonB_dep_Rec; cl17754 402612000771 S-adenosylmethionine synthetase; Validated; Region: PRK05250 402612000772 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 402612000773 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 402612000774 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 402612000775 Recombination protein O N terminal; Region: RecO_N; pfam11967 402612000776 DNA repair protein RecO; Region: reco; TIGR00613 402612000777 Recombination protein O C terminal; Region: RecO_C; pfam02565 402612000778 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 402612000779 glutamate dehydrogenase; Provisional; Region: PRK09414 402612000780 Glu/Leu/Phe/Val dehydrogenase, dimerization domain; Region: ELFV_dehydrog_N; pfam02812 402612000781 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 402612000782 NAD(P) binding site [chemical binding]; other site 402612000783 Protein of unknown function (DUF3050); Region: DUF3050; pfam11251 402612000784 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 402612000785 catalytic residues [active] 402612000786 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 402612000787 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 402612000788 dimer interface [polypeptide binding]; other site 402612000789 anticodon binding site; other site 402612000790 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 402612000791 homodimer interface [polypeptide binding]; other site 402612000792 motif 1; other site 402612000793 active site 402612000794 motif 2; other site 402612000795 GAD domain; Region: GAD; pfam02938 402612000796 motif 3; other site 402612000797 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 402612000798 DNA-binding site [nucleotide binding]; DNA binding site 402612000799 RNA-binding motif; other site 402612000800 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 402612000801 nucleoside/Zn binding site; other site 402612000802 dimer interface [polypeptide binding]; other site 402612000803 catalytic motif [active] 402612000804 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 402612000805 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 402612000806 TPP-binding site; other site 402612000807 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 402612000808 PYR/PP interface [polypeptide binding]; other site 402612000809 dimer interface [polypeptide binding]; other site 402612000810 TPP binding site [chemical binding]; other site 402612000811 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 402612000812 Fungalysin metallopeptidase (M36); Region: Peptidase_M36; pfam02128 402612000813 Peptidase M36 family also known as fungalysin family; Region: M36; cd09596 402612000814 PA_subtilisin_1: Protease-associated domain containing subtilisin-like proteases, subgroup 1. A subgroup of PA domain-containing subtilisin-like proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined; Region: PA_subtilisin_1; cd04818 402612000815 PA/protease or protease-like domain interface [polypeptide binding]; other site 402612000816 Zn binding site [ion binding]; other site 402612000817 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000818 Fungalysin metallopeptidase (M36); Region: Peptidase_M36; pfam02128 402612000819 Peptidase M36 family also known as fungalysin family; Region: M36; cd09596 402612000820 PA_subtilisin_1: Protease-associated domain containing subtilisin-like proteases, subgroup 1. A subgroup of PA domain-containing subtilisin-like proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined; Region: PA_subtilisin_1; cd04818 402612000821 PA/protease or protease-like domain interface [polypeptide binding]; other site 402612000822 Zn binding site [ion binding]; other site 402612000823 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612000824 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01096 402612000825 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 402612000826 Zn2+ binding site [ion binding]; other site 402612000827 Mg2+ binding site [ion binding]; other site 402612000828 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 402612000829 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 402612000830 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 402612000831 Beta-lactamase; Region: Beta-lactamase; pfam00144 402612000832 Domain of unknown function (DUF3471); Region: DUF3471; pfam11954 402612000833 DNA polymerase I; Provisional; Region: PRK05755 402612000834 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 402612000835 active site 402612000836 metal binding site 1 [ion binding]; metal-binding site 402612000837 putative 5' ssDNA interaction site; other site 402612000838 metal binding site 3; metal-binding site 402612000839 metal binding site 2 [ion binding]; metal-binding site 402612000840 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 402612000841 putative DNA binding site [nucleotide binding]; other site 402612000842 putative metal binding site [ion binding]; other site 402612000843 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 402612000844 active site 402612000845 catalytic site [active] 402612000846 substrate binding site [chemical binding]; other site 402612000847 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 402612000848 active site 402612000849 DNA binding site [nucleotide binding] 402612000850 catalytic site [active] 402612000851 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 402612000852 Predicted phosphohydrolases [General function prediction only]; Region: Icc; COG1409 402612000853 putative active site [active] 402612000854 putative metal binding site [ion binding]; other site 402612000855 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 402612000856 catalytic residues [active] 402612000857 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 402612000858 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 402612000859 NodB motif; other site 402612000860 active site 402612000861 catalytic site [active] 402612000862 metal binding site [ion binding]; metal-binding site 402612000863 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; cl19580 402612000864 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 402612000865 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 402612000866 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 402612000867 ABC exporter membrane fusion protein, DevB family; Region: heterocyst_DevB; TIGR02971 402612000868 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 402612000869 Outer membrane efflux protein; Region: OEP; pfam02321 402612000870 Outer membrane efflux protein; Region: OEP; pfam02321 402612000871 Protein of unknown function (DUF2723); Region: DUF2723; pfam11028 402612000872 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; cl09440 402612000873 Tetratricopeptide repeat; Region: TPR_19; pfam14559 402612000874 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 402612000875 AMP binding site [chemical binding]; other site 402612000876 metal binding site [ion binding]; metal-binding site 402612000877 active site 402612000878 Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]; Region: HtpX; COG0501 402612000879 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 402612000880 Coenzyme A binding pocket [chemical binding]; other site 402612000881 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 402612000882 nucleotide binding site [chemical binding]; other site 402612000883 substrate binding site [chemical binding]; other site 402612000884 Conserved hypothetical protein 2217 (DUF2460); Region: DUF2460; cl02268 402612000885 Alpha amylase catalytic domain found in archaeal and bacterial Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase); Region: AmyAc_arch_bac_AmyA; cd11313 402612000886 Alpha amylase, catalytic domain; Region: Alpha-amylase; pfam00128 402612000887 active site 402612000888 catalytic site [active] 402612000889 flavoprotein, HI0933 family; Region: TIGR00275 402612000890 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl19134 402612000891 TspO/MBR family; Region: TspO_MBR; pfam03073 402612000892 Mevalonate pyrophosphate decarboxylase [Lipid metabolism]; Region: MVD1; COG3407 402612000893 diphosphomevalonate decarboxylase; Region: PLN02407 402612000894 Mevalonate kinase [Lipid metabolism]; Region: ERG12; COG1577 402612000895 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 402612000896 Geranylgeranylglycerol-phosphate geranylgeranyltransferase; Region: PT_UbiA_DGGGPS; cd13961 402612000897 putative active site [active] 402612000898 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 402612000899 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 402612000900 RNA binding surface [nucleotide binding]; other site 402612000901 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 402612000902 active site 402612000903 SnoaL-like domain; Region: SnoaL_2; pfam12680 402612000904 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 402612000905 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 402612000906 non-specific DNA binding site [nucleotide binding]; other site 402612000907 salt bridge; other site 402612000908 sequence-specific DNA binding site [nucleotide binding]; other site 402612000909 Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton]; Region: ATS1; COG5184 402612000910 Calx-beta domain; Region: Calx-beta; cl02522 402612000911 C-terminal domain of CHU protein family; Region: CHU_C; pfam13585 402612000912 Protein of unknown function (DUF3308); Region: DUF3308; pfam11751 402612000913 FOG: TPR repeat [General function prediction only]; Region: NrfG; COG0457 402612000914 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 402612000915 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 402612000916 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 402612000917 ligand binding site [chemical binding]; other site 402612000918 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 402612000919 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 402612000920 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 402612000921 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 402612000922 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 402612000923 SurA N-terminal domain; Region: SurA_N; pfam09312 402612000924 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 402612000925 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 402612000926 MoxR-like ATPases [General function prediction only]; Region: COG0714 402612000927 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 402612000928 Walker A motif; other site 402612000929 ATP binding site [chemical binding]; other site 402612000930 Walker B motif; other site 402612000931 arginine finger; other site 402612000932 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 402612000933 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 402612000934 NAD(P) binding site [chemical binding]; other site 402612000935 active site 402612000936 aconitate hydratase, mitochondrial; Region: aconitase_mito; TIGR01340 402612000937 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 402612000938 substrate binding site [chemical binding]; other site 402612000939 ligand binding site [chemical binding]; other site 402612000940 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 402612000941 substrate binding site [chemical binding]; other site 402612000942 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 402612000943 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 402612000944 FeS/SAM binding site; other site 402612000945 HemN C-terminal domain; Region: HemN_C; pfam06969 402612000946 Protein of unknown function (DUF465); Region: DUF465; cl01070 402612000947 Cytochrome C biogenesis protein transmembrane region; Region: DsbD_2; pfam13386 402612000948 FixH; Region: FixH; pfam05751 402612000949 Predicted membrane protein (DUF2207); Region: DUF2207; cl19878 402612000950 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 402612000951 4Fe-4S binding domain; Region: Fer4_5; pfam12801 402612000952 4Fe-4S dicluster domain; Region: Fer4_18; pfam13746 402612000953 IG-like fold at C-terminal of FixG, putative oxidoreductase; Region: FixG_C; pfam11614 402612000954 N-terminal domain of cytochrome oxidase-cbb3, FixP; Region: FixP_N; pfam14715 402612000955 Cytochrome c; Region: Cytochrom_C; pfam00034 402612000956 Cbb3-type cytochrome oxidase component FixQ; Region: FixQ; pfam05545 402612000957 putative bifunctional cbb3-type cytochrome c oxidase subunit I/II; Provisional; Region: PRK14485 402612000958 cbb3-type cytochrome c oxidase subunit I; Provisional; Region: PRK14488 402612000959 Low-spin heme binding site [chemical binding]; other site 402612000960 D-pathway; other site 402612000961 Putative water exit pathway; other site 402612000962 Binuclear center (active site) [active] 402612000963 K-pathway; other site 402612000964 Putative proton exit pathway; other site 402612000965 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; pfam02433 402612000966 Acyl ACP desaturase, ferritin-like diiron-binding domain; Region: Acyl_ACP_Desat; cd01050 402612000967 homodimer interface [polypeptide binding]; other site 402612000968 putative substrate binding pocket [chemical binding]; other site 402612000969 diiron center [ion binding]; other site 402612000970 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; pfam03597 402612000971 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 402612000972 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 402612000973 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 402612000974 metal-binding site [ion binding] 402612000975 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 402612000976 Soluble P-type ATPase [General function prediction only]; Region: COG4087 402612000977 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 402612000978 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 402612000979 ligand binding site [chemical binding]; other site 402612000980 flexible hinge region; other site 402612000981 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 402612000982 putative switch regulator; other site 402612000983 non-specific DNA interactions [nucleotide binding]; other site 402612000984 DNA binding site [nucleotide binding] 402612000985 sequence specific DNA binding site [nucleotide binding]; other site 402612000986 putative cAMP binding site [chemical binding]; other site 402612000987 Protein of unknown function (DUF2805); Region: DUF2805; pfam10985 402612000988 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl19158 402612000989 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; Region: EEP-2; cd09084 402612000990 putative catalytic site [active] 402612000991 putative metal binding site [ion binding]; other site 402612000992 putative phosphate binding site [ion binding]; other site 402612000993 Rhomboid family; Region: Rhomboid; cl11446 402612000994 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 402612000995 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 402612000996 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 402612000997 ATP binding site [chemical binding]; other site 402612000998 Mg2+ binding site [ion binding]; other site 402612000999 G-X-G motif; other site 402612001000 MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is...; Region: MutL_Trans; cd00782 402612001001 ATP binding site [chemical binding]; other site 402612001002 MutL C terminal dimerisation domain; Region: MutL_C; smart00853 402612001003 phosphodiesterase; Provisional; Region: PRK12704 402612001004 Cdc37 N terminal kinase binding; Region: CDC37_N; cl03951 402612001005 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cd00105 402612001006 nucleic acid binding region [nucleotide binding]; other site 402612001007 G-X-X-G motif; other site 402612001008 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 402612001009 Zn2+ binding site [ion binding]; other site 402612001010 Mg2+ binding site [ion binding]; other site 402612001011 Cell division protein ZapA; Region: ZapA; pfam05164 402612001012 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 402612001013 Peptidase family M23; Region: Peptidase_M23; pfam01551 402612001014 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612001015 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 402612001016 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 402612001017 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 402612001018 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 402612001019 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 402612001020 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 402612001021 Walker A/P-loop; other site 402612001022 ATP binding site [chemical binding]; other site 402612001023 Q-loop/lid; other site 402612001024 ABC transporter signature motif; other site 402612001025 Walker B; other site 402612001026 D-loop; other site 402612001027 H-loop/switch region; other site 402612001028 phosphoglucomutase-2-like protein; Provisional; Region: PTZ00150 402612001029 This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and...; Region: PGM2; cd05799 402612001030 active site 402612001031 substrate binding site [chemical binding]; other site 402612001032 metal binding site [ion binding]; metal-binding site 402612001033 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 402612001034 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 402612001035 Ligand binding site; other site 402612001036 Putative Catalytic site; other site 402612001037 DXD motif; other site 402612001038 Protein of unknown function (DUF4199); Region: DUF4199; pfam13858 402612001039 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 402612001040 UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase; Region: alt_bact_glmU; TIGR03991 402612001041 Sugar nucleotidyl transferase; Region: NTP_transf_4; pfam13562 402612001042 Uncharacterized proteins, Left-handed parallel beta-Helix (LbH) domain: Members in this group are uncharacterized bacterial proteins containing a LbH domain with multiple turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif...; Region: LbH_unknown; cd05635 402612001043 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 402612001044 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 402612001045 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 402612001046 Trans-2-enoyl-CoA reductase (TER) and 2,4-dienoyl-CoA reductase (DECR), atypical (a) SDR; Region: TER_DECR_SDR_a; cd05369 402612001047 short chain dehydrogenase; Provisional; Region: PRK07677 402612001048 NAD(P) binding site [chemical binding]; other site 402612001049 substrate binding site [chemical binding]; other site 402612001050 homotetramer interface [polypeptide binding]; other site 402612001051 active site 402612001052 homodimer interface [polypeptide binding]; other site 402612001053 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 402612001054 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 402612001055 P-loop; other site 402612001056 Magnesium ion binding site [ion binding]; other site 402612001057 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 402612001058 ParB-like nuclease domain; Region: ParBc; pfam02195 402612001059 dihydrodipicolinate reductase; Provisional; Region: PRK00048 402612001060 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 402612001061 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 402612001062 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 402612001063 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 402612001064 Catalytic site [active] 402612001065 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 402612001066 23S rRNA-intervening sequence protein; Region: 23S_rRNA_IVP; pfam05635 402612001067 WbqC-like protein family; Region: WbqC; pfam08889 402612001068 methylmalonyl-CoA mutase; Reviewed; Region: PRK09426 402612001069 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Alpha subunit-like subfamily; contains proteins similar to the alpha subunit of Propionbacterium shermanni MCM, as well as human and E. coli MCM. Members of this subfamily contain...; Region: MM_CoA_mutase_alpha_like; cd03679 402612001070 active site 402612001071 substrate binding site [chemical binding]; other site 402612001072 coenzyme B12 binding site [chemical binding]; other site 402612001073 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 402612001074 B12 binding site [chemical binding]; other site 402612001075 cobalt ligand [ion binding]; other site 402612001076 Glycine-zipper containing OmpA-like membrane domain; Region: Gly-zipper_OmpA; pfam13436 402612001077 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Beta subunit-like subfamily; contains bacterial proteins similar to the beta subunit of MCMs from Propionbacterium shermanni and Streptomyces cinnamonensis, which are alpha/beta...; Region: MM_CoA_mutase_beta; cd03677 402612001078 heterodimer interface [polypeptide binding]; other site 402612001079 substrate interaction site [chemical binding]; other site 402612001080 Septum formation initiator; Region: DivIC; cl17659 402612001081 Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway; Region: UMPK; cd02023 402612001082 AAA domain; Region: AAA_33; pfam13671 402612001083 ATP-binding site [chemical binding]; other site 402612001084 Sugar specificity; other site 402612001085 Pyrimidine base specificity; other site 402612001086 Predicted membrane protein (DUF2339); Region: DUF2339; pfam10101 402612001087 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 402612001088 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 402612001089 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 402612001090 cyanophycin synthetase; Provisional; Region: PRK14016 402612001091 ATP-grasp domain; Region: ATP-grasp_4; cl17255 402612001092 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 402612001093 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 402612001094 Type 1 glutamine amidotransferase (GATase1)-like domain found in cyanophycinase; Region: GAT1_cyanophycinase; cd03145 402612001095 proposed catalytic triad [active] 402612001096 Asparaginase [Amino acid transport and metabolism]; Region: COG1446 402612001097 active site 402612001098 dimer interface [polypeptide binding]; other site 402612001099 catalytic nucleophile [active] 402612001100 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 402612001101 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 402612001102 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 402612001103 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 402612001104 Walker A/P-loop; other site 402612001105 ATP binding site [chemical binding]; other site 402612001106 Q-loop/lid; other site 402612001107 ABC transporter signature motif; other site 402612001108 Walker B; other site 402612001109 D-loop; other site 402612001110 H-loop/switch region; other site 402612001111 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 402612001112 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 402612001113 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 402612001114 DNA binding residues [nucleotide binding] 402612001115 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 402612001116 PAS fold; Region: PAS_3; pfam08447 402612001117 putative active site [active] 402612001118 heme pocket [chemical binding]; other site 402612001119 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 402612001120 PAS fold; Region: PAS_3; pfam08447 402612001121 putative active site [active] 402612001122 heme pocket [chemical binding]; other site 402612001123 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 402612001124 Major Facilitator Superfamily; Region: MFS_1; pfam07690 402612001125 putative substrate translocation pore; other site 402612001126 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 402612001127 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 402612001128 minor groove reading motif; other site 402612001129 helix-hairpin-helix signature motif; other site 402612001130 substrate binding pocket [chemical binding]; other site 402612001131 active site 402612001132 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 402612001133 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 402612001134 catalytic triad [active] 402612001135 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 402612001136 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 402612001137 Prolyl oligopeptidase family; Region: Peptidase_S9; cl19144 402612001138 dihydroorotase; Validated; Region: pyrC; PRK09357 402612001139 Dihydroorotase (DHOase), subgroup IIa; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This subgroup also contains proteins that lack the active site, like unc-33, a C; Region: DHOase_IIa; cd01317 402612001140 active site 402612001141 Aerotolerance regulator N-terminal; Region: BatA; pfam07584 402612001142 von Willebrand factor type A domain; Region: VWA_2; pfam13519 402612001143 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 402612001144 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 402612001145 ATP binding site [chemical binding]; other site 402612001146 putative Mg++ binding site [ion binding]; other site 402612001147 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 402612001148 nucleotide binding region [chemical binding]; other site 402612001149 ATP-binding site [chemical binding]; other site 402612001150 DNA polymerase III subunit beta; Validated; Region: PRK05643 402612001151 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 402612001152 putative DNA binding surface [nucleotide binding]; other site 402612001153 dimer interface [polypeptide binding]; other site 402612001154 beta-clamp/clamp loader binding surface; other site 402612001155 beta-clamp/translesion DNA polymerase binding surface; other site 402612001156 gliding-associated putative ABC transporter substrate-binding component GldG; Region: GldG; TIGR03521 402612001157 ABC-type uncharacterized transport system; Region: ABC_transp_aux; pfam09822 402612001158 gliding motility-associated ABC transporter permease protein GldF; Region: ABC_perm_GldF; TIGR03518 402612001159 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 402612001160 Methyltransferase domain; Region: Methyltransf_18; pfam12847 402612001161 Antibiotic biosynthesis monooxygenase; Region: ABM; pfam03992 402612001162 ATP-NAD kinase; Region: NAD_kinase; cl01255 402612001163 SPFH domain / Band 7 family; Region: Band_7; pfam01145 402612001164 S-adenosyl-l-methionine hydroxide adenosyltransferase; Region: SAM_adeno_trans; pfam01887 402612001165 PhoH-like protein; Region: PhoH; pfam02562 402612001166 short chain dehydrogenase; Provisional; Region: PRK06179 402612001167 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 402612001168 NAD(P) binding site [chemical binding]; other site 402612001169 active site 402612001170 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 402612001171 ATP binding site [chemical binding]; other site 402612001172 active site 402612001173 phosphoribosylaminoimidazole-succinocarboxamide synthase; Provisional; Region: PRK13959 402612001174 substrate binding site [chemical binding]; other site 402612001175 M42 Peptidase, Endoglucanases; Region: M42_Frv; cd05656 402612001176 oligomer interface [polypeptide binding]; other site 402612001177 active site 402612001178 metal binding site [ion binding]; metal-binding site 402612001179 Domain of unknown function (DUF4294); Region: DUF4294; pfam14127 402612001180 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 402612001181 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 402612001182 active site 402612001183 phosphorylation site [posttranslational modification] 402612001184 intermolecular recognition site; other site 402612001185 dimerization interface [polypeptide binding]; other site 402612001186 LytTr DNA-binding domain; Region: LytTR; smart00850 402612001187 Histidine kinase; Region: His_kinase; pfam06580 402612001188 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 402612001189 Protein of unknown function (DUF1501); Region: DUF1501; cl19855 402612001190 Protein of unknown function (DUF1800); Region: DUF1800; cl19889 402612001191 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 402612001192 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 402612001193 Outer membrane protein beta-barrel family; Region: OMP_b-brl_3; pfam14905 402612001194 heat shock protein 90; Provisional; Region: PRK05218 402612001195 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 402612001196 ATP binding site [chemical binding]; other site 402612001197 Mg2+ binding site [ion binding]; other site 402612001198 G-X-G motif; other site 402612001199 Hsp90 protein; Region: HSP90; pfam00183 402612001200 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 402612001201 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 402612001202 ligand binding site [chemical binding]; other site 402612001203 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 402612001204 active site 402612001205 ATP binding site [chemical binding]; other site 402612001206 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 402612001207 substrate binding site [chemical binding]; other site 402612001208 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 402612001209 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 402612001210 Walker A/P-loop; other site 402612001211 ATP binding site [chemical binding]; other site 402612001212 Q-loop/lid; other site 402612001213 ABC transporter signature motif; other site 402612001214 Walker B; other site 402612001215 D-loop; other site 402612001216 H-loop/switch region; other site 402612001217 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 402612001218 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 402612001219 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 402612001220 dimer interface [polypeptide binding]; other site 402612001221 active site 402612001222 CoA binding pocket [chemical binding]; other site 402612001223 Transposase, Mutator family; Region: Transposase_mut; cl19537 402612001224 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3328 402612001225 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612001226 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 402612001227 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 402612001228 Outer membrane protein beta-barrel family; Region: OMP_b-brl_3; pfam14905 402612001229 gliding motility-associated C-terminal domain; Region: Bac_Flav_CTERM; TIGR04131 402612001230 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 402612001231 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 402612001232 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 402612001233 active site 402612001234 nucleotide binding site [chemical binding]; other site 402612001235 HIGH motif; other site 402612001236 KMSKS motif; other site 402612001237 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 402612001238 tRNA binding surface [nucleotide binding]; other site 402612001239 anticodon binding site; other site 402612001240 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 402612001241 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 402612001242 N-terminal plug; other site 402612001243 ligand-binding site [chemical binding]; other site 402612001244 Bacterial proteins similar to Porphyromonas gingivalis HmuY; Region: HmuY; cd12105 402612001245 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 402612001246 PAS domain; Region: PAS_9; pfam13426 402612001247 putative active site [active] 402612001248 heme pocket [chemical binding]; other site 402612001249 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 402612001250 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612001251 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 402612001252 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 402612001253 Horizontally Transferred TransMembrane Domain; Region: HTTM; smart00752 402612001254 Vitamin K-dependent gamma-carboxylase; Region: VKG_Carbox; pfam05090 402612001255 Imelysin; Region: Peptidase_M75; pfam09375 402612001256 Thioredoxin-like domain; Region: Thioredoxin_2; pfam13098 402612001257 ApbE family; Region: ApbE; pfam02424 402612001258 Protein of unknown function (DUF3570); Region: DUF3570; pfam12094 402612001259 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 402612001260 Photosynthesis system II assembly factor YCF48; Region: PSII_BNR; pfam14870 402612001261 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 402612001262 Photosynthesis system II assembly factor YCF48; Region: PSII_BNR; pfam14870 402612001263 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 402612001264 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 402612001265 DOMON-like domain of copper-dependent monooxygenases and related proteins; Region: DOMON_DOH; cd09631 402612001266 putative ligand binding site [chemical binding]; other site 402612001267 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612001268 Imelysin; Region: Peptidase_M75; cl09159 402612001269 Predicted thiol oxidoreductase [Energy production and conversion]; Region: COG3488 402612001270 Protein of unknown function (DUF1111); Region: DUF1111; pfam06537 402612001271 signal recognition particle protein; Provisional; Region: PRK10867 402612001272 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 402612001273 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 402612001274 P loop; other site 402612001275 GTP binding site [chemical binding]; other site 402612001276 Signal peptide binding domain; Region: SRP_SPB; pfam02978 402612001277 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14185 402612001278 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 402612001279 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 402612001280 homodimer interface [polypeptide binding]; other site 402612001281 NADP binding site [chemical binding]; other site 402612001282 substrate binding site [chemical binding]; other site 402612001283 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 402612001284 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 402612001285 Coenzyme A binding pocket [chemical binding]; other site 402612001286 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; pfam02606 402612001287 purine nucleoside phosphorylase; Provisional; Region: PRK08202 402612001288 Purine nucleoside phosphorylase [Nucleotide transport and metabolism]; Region: Pnp; COG0005 402612001289 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 402612001290 binding surface 402612001291 TPR motif; other site 402612001292 Tetratricopeptide repeat; Region: TPR_12; pfam13424 402612001293 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 402612001294 binding surface 402612001295 TPR motif; other site 402612001296 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 402612001297 dimer interface [polypeptide binding]; other site 402612001298 phosphorylation site [posttranslational modification] 402612001299 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 402612001300 ATP binding site [chemical binding]; other site 402612001301 Mg2+ binding site [ion binding]; other site 402612001302 G-X-G motif; other site 402612001303 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 402612001304 active site 402612001305 phosphorylation site [posttranslational modification] 402612001306 intermolecular recognition site; other site 402612001307 dimerization interface [polypeptide binding]; other site 402612001308 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 402612001309 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 402612001310 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 402612001311 lipoyl synthase; Provisional; Region: PRK05481 402612001312 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 402612001313 FeS/SAM binding site; other site 402612001314 Gram-negative bacterial TonB protein C-terminal; Region: TonB_C; cl10048 402612001315 RNA polymerase sigma factor; Provisional; Region: PRK11924 402612001316 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 402612001317 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 402612001318 DNA binding residues [nucleotide binding] 402612001319 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 402612001320 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 402612001321 active site 402612001322 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 402612001323 ABC-ATPase subunit interface; other site 402612001324 dimer interface [polypeptide binding]; other site 402612001325 putative PBP binding regions; other site 402612001326 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 402612001327 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 402612001328 intersubunit interface [polypeptide binding]; other site 402612001329 Cysteine-rich CWC; Region: Cys_rich_CWC; pfam14375 402612001330 Cobinamide kinase / cobinamide phosphate guanyltransferase; Region: CobU; pfam02283 402612001331 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cl00514 402612001332 FMN binding site [chemical binding]; other site 402612001333 dimer interface [polypeptide binding]; other site 402612001334 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 402612001335 putative dimer interface [polypeptide binding]; other site 402612001336 active site pocket [active] 402612001337 putative cataytic base [active] 402612001338 cobalamin synthase; Reviewed; Region: cobS; PRK00235 402612001339 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 402612001340 catalytic core [active] 402612001341 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 402612001342 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 402612001343 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 402612001344 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 402612001345 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 402612001346 DNA binding residues [nucleotide binding] 402612001347 Domain of unknown function (DUF4252); Region: DUF4252; pfam14060 402612001348 Domain of unknown function (DUF4252); Region: DUF4252; pfam14060 402612001349 beta-carotene hydroxylase; Region: PLN02601 402612001350 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 402612001351 active site lid residues [active] 402612001352 substrate binding pocket [chemical binding]; other site 402612001353 catalytic residues [active] 402612001354 substrate-Mg2+ binding site; other site 402612001355 aspartate-rich region 1; other site 402612001356 aspartate-rich region 2; other site 402612001357 phytoene desaturase; Region: crtI_fam; TIGR02734 402612001358 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 402612001359 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 402612001360 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 402612001361 DNA binding residues [nucleotide binding] 402612001362 B12 binding domain; Region: B12-binding_2; pfam02607 402612001363 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl19134 402612001364 Shikimate kinase [Amino acid transport and metabolism]; Region: AroK; COG0703 402612001365 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 402612001366 ADP binding site [chemical binding]; other site 402612001367 magnesium binding site [ion binding]; other site 402612001368 putative shikimate binding site; other site 402612001369 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 402612001370 active site 402612001371 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 402612001372 S-adenosylmethionine binding site [chemical binding]; other site 402612001373 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 402612001374 RNA binding surface [nucleotide binding]; other site 402612001375 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 402612001376 DNA polymerase III subunit epsilon; Validated; Region: PRK06309 402612001377 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 402612001378 active site 402612001379 catalytic site [active] 402612001380 substrate binding site [chemical binding]; other site 402612001381 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 402612001382 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 402612001383 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 402612001384 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl19483 402612001385 competence damage-inducible protein A; Provisional; Region: PRK00549 402612001386 Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of...; Region: cinA; cd00885 402612001387 putative MPT binding site; other site 402612001388 Competence-damaged protein; Region: CinA; pfam02464 402612001389 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 402612001390 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 402612001391 Domain of unknown function (DUF4295); Region: DUF4295; pfam14128 402612001392 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 402612001393 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 402612001394 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 402612001395 P loop; other site 402612001396 GTP binding site [chemical binding]; other site 402612001397 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 402612001398 substrate binding site [chemical binding]; other site 402612001399 dimer interface [polypeptide binding]; other site 402612001400 catalytic triad [active] 402612001401 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 402612001402 catalytic residues [active] 402612001403 Domain of Unknown Function (DUF1599); Region: DUF1599; pfam07659 402612001404 Domain of Unknown Function (DUF1599); Region: DUF1599; pfam07659 402612001405 Dihydropteroate synthase and related enzymes [Coenzyme metabolism]; Region: FolP; COG0294 402612001406 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 402612001407 substrate binding pocket [chemical binding]; other site 402612001408 dimer interface [polypeptide binding]; other site 402612001409 inhibitor binding site; inhibition site 402612001410 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 402612001411 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 402612001412 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 402612001413 Walker A/P-loop; other site 402612001414 ATP binding site [chemical binding]; other site 402612001415 Q-loop/lid; other site 402612001416 ABC transporter signature motif; other site 402612001417 Walker B; other site 402612001418 D-loop; other site 402612001419 H-loop/switch region; other site 402612001420 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 402612001421 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 402612001422 dimerization interface 3.5A [polypeptide binding]; other site 402612001423 active site 402612001424 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 402612001425 active site 402612001426 dimer interface [polypeptide binding]; other site 402612001427 Geranylgeranylglycerol-phosphate geranylgeranyltransferase; Region: PT_UbiA_DGGGPS; cd13961 402612001428 putative active site [active] 402612001429 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 402612001430 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 402612001431 active site 402612001432 motif I; other site 402612001433 motif II; other site 402612001434 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl19126 402612001435 Domain of unknown function (DUF2520); Region: DUF2520; pfam10728 402612001436 ResB-like family; Region: ResB; cl09125 402612001437 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 402612001438 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 402612001439 catalytic residues [active] 402612001440 dimer interface [polypeptide binding]; other site 402612001441 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 402612001442 Lipocalin-like domain; Region: Lipocalin_4; pfam13648 402612001443 Protein of unknown function (DUF721); Region: DUF721; pfam05258 402612001444 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 402612001445 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 402612001446 Nucleoside diphosphate kinase; Region: NDK; pfam00334 402612001447 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 402612001448 active site 402612001449 multimer interface [polypeptide binding]; other site 402612001450 Uncharacterized protein conserved in bacteria (DUF2317); Region: DUF2317; pfam10079 402612001451 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 402612001452 Radical SAM superfamily; Region: Radical_SAM; pfam04055 402612001453 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 402612001454 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 402612001455 active site 402612001456 phosphorylation site [posttranslational modification] 402612001457 intermolecular recognition site; other site 402612001458 dimerization interface [polypeptide binding]; other site 402612001459 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 402612001460 DNA binding site [nucleotide binding] 402612001461 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 402612001462 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 402612001463 dimer interface [polypeptide binding]; other site 402612001464 phosphorylation site [posttranslational modification] 402612001465 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 402612001466 ATP binding site [chemical binding]; other site 402612001467 Mg2+ binding site [ion binding]; other site 402612001468 G-X-G motif; other site 402612001469 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 402612001470 Transposase; Region: HTH_Tnp_1; cl17663 402612001471 putative transposase OrfB; Reviewed; Region: PHA02517 402612001472 HTH-like domain; Region: HTH_21; pfam13276 402612001473 Integrase core domain; Region: rve; pfam00665 402612001474 Integrase core domain; Region: rve_3; pfam13683 402612001475 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 402612001476 ribosomal protein S12 methylthiotransferase RimO; Region: TIGR01125 402612001477 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 402612001478 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 402612001479 FeS/SAM binding site; other site 402612001480 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 402612001481 prolyl-tRNA synthetase; Provisional; Region: PRK08661 402612001482 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_arch_euk; cd00778 402612001483 dimer interface [polypeptide binding]; other site 402612001484 motif 1; other site 402612001485 active site 402612001486 motif 2; other site 402612001487 motif 3; other site 402612001488 ProRS Prolyl-anticodon binding domain, long version found predominantly in eukaryotes and archaea. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in...; Region: ProRS_anticodon_zinc; cd00862 402612001489 anticodon binding site; other site 402612001490 zinc-binding site [ion binding]; other site 402612001491 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 402612001492 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 402612001493 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 402612001494 G1 box; other site 402612001495 putative GEF interaction site [polypeptide binding]; other site 402612001496 GTP/Mg2+ binding site [chemical binding]; other site 402612001497 Switch I region; other site 402612001498 G2 box; other site 402612001499 G3 box; other site 402612001500 Switch II region; other site 402612001501 G4 box; other site 402612001502 G5 box; other site 402612001503 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 402612001504 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 402612001505 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 402612001506 S1 domain; Region: S1_2; pfam13509 402612001507 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 402612001508 RNA binding site [nucleotide binding]; other site 402612001509 Dihydroxynaphthoic acid synthase [Coenzyme metabolism]; Region: MenB; COG0447 402612001510 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 402612001511 substrate binding site [chemical binding]; other site 402612001512 oxyanion hole (OAH) forming residues; other site 402612001513 trimer interface [polypeptide binding]; other site 402612001514 1,4-Dihydroxy-2-naphthoate octaprenyltransferase; Region: PT_UbiA_UBIAD1; cd13962 402612001515 putative active site [active] 402612001516 M28 Zn-Peptidase Plasma glutamate carboxypeptidase; Region: M28_Pgcp_like; cd03883 402612001517 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 402612001518 PA/protease or protease-like domain interface [polypeptide binding]; other site 402612001519 metal binding site [ion binding]; metal-binding site 402612001520 Saccharopine Dehydrogenase like proteins; Region: SDH_like; cd05199 402612001521 active site 402612001522 ligand binding site [chemical binding]; other site 402612001523 NAD(P) binding site [chemical binding]; other site 402612001524 Beta-lactamase; Region: Beta-lactamase; pfam00144 402612001525 BRO family, N-terminal domain; Region: Bro-N; smart01040 402612001526 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 402612001527 AAA-like domain; Region: AAA_10; pfam12846 402612001528 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 402612001529 TraM recognition site of TraD and TraG; Region: TraG-D_C; pfam12696 402612001530 Walker B motif; other site 402612001531 Transposase, Mutator family; Region: Transposase_mut; cl19537 402612001532 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3328 402612001533 Relaxase/Mobilisation nuclease domain; Region: Relaxase; cl19391 402612001534 CHC2 zinc finger; Region: zf-CHC2; cl17510 402612001535 Toprim-like; Region: Toprim_2; pfam13155 402612001536 active site 402612001537 metal binding site [ion binding]; metal-binding site 402612001538 Virulence-associated protein E; Region: VirE; pfam05272 402612001539 Helix-turn-helix domain; Region: HTH_17; pfam12728 402612001540 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 402612001541 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 402612001542 active site 402612001543 DNA binding site [nucleotide binding] 402612001544 Int/Topo IB signature motif; other site 402612001545 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 402612001546 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 402612001547 o-Succinylbenzoate synthase (OSBS) catalyzes the conversion of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 4-(2'-carboxyphenyl)-4-oxobutyrate (o-succinylbenzoate or OSB), a reaction in the menaquinone biosynthetic pathway; Region: OSBS; cd03320 402612001548 o-succinylbenzoate synthase; Region: menC_gamma/gm+; TIGR01927 402612001549 active site 402612001550 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 402612001551 binding surface 402612001552 TPR motif; other site 402612001553 Transposase zinc-ribbon domain; Region: Zn_Tnp_IS1595; pfam12760 402612001554 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; pfam12762 402612001555 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 402612001556 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 402612001557 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 402612001558 putative substrate translocation pore; other site 402612001559 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 402612001560 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 402612001561 HlyD family secretion protein; Region: HlyD_3; pfam13437 402612001562 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 402612001563 Outer membrane efflux protein; Region: OEP; pfam02321 402612001564 Outer membrane efflux protein; Region: OEP; pfam02321 402612001565 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 402612001566 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 402612001567 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; cl19825 402612001568 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 402612001569 substrate binding site [chemical binding]; other site 402612001570 active site 402612001571 catalytic residues [active] 402612001572 heterodimer interface [polypeptide binding]; other site 402612001573 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 402612001574 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612001575 catalytic residue [active] 402612001576 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 402612001577 active site 402612001578 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 402612001579 active site 402612001580 ribulose/triose binding site [chemical binding]; other site 402612001581 phosphate binding site [ion binding]; other site 402612001582 substrate (anthranilate) binding pocket [chemical binding]; other site 402612001583 product (indole) binding pocket [chemical binding]; other site 402612001584 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 402612001585 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 402612001586 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 402612001587 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 402612001588 Glutamine amidotransferase class-I; Region: GATase; pfam00117 402612001589 glutamine binding [chemical binding]; other site 402612001590 catalytic triad [active] 402612001591 Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]; Region: TrpE; COG0147 402612001592 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 402612001593 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 402612001594 YceI-like domain; Region: YceI; pfam04264 402612001595 NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family...; Region: NfsB_like_nitroreductase; cd02149 402612001596 dimer interface [polypeptide binding]; other site 402612001597 FMN binding site [chemical binding]; other site 402612001598 Transcriptional regulators [Transcription]; Region: MarR; COG1846 402612001599 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; cl17220 402612001600 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 402612001601 active site residue [active] 402612001602 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 402612001603 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl19134 402612001604 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 402612001605 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 402612001606 Walker A/P-loop; other site 402612001607 ATP binding site [chemical binding]; other site 402612001608 Q-loop/lid; other site 402612001609 ABC transporter signature motif; other site 402612001610 Walker B; other site 402612001611 D-loop; other site 402612001612 H-loop/switch region; other site 402612001613 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 402612001614 binding surface 402612001615 TPR motif; other site 402612001616 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 402612001617 TPR motif; other site 402612001618 binding surface 402612001619 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 402612001620 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 402612001621 binding surface 402612001622 TPR motif; other site 402612001623 Tetratricopeptide repeat; Region: TPR_6; pfam13174 402612001624 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 402612001625 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 402612001626 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612001627 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 402612001628 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 402612001629 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 402612001630 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; pfam01118 402612001631 Semialdehyde dehydrogenase, dimerization domain; Region: Semialdhyde_dhC; pfam02774 402612001632 Uncharacterized conserved protein, YhbC family [Function unknown]; Region: COG0782 402612001633 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 402612001634 asparagine synthetase B; Provisional; Region: asnB; PRK09431 402612001635 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 402612001636 active site 402612001637 dimer interface [polypeptide binding]; other site 402612001638 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 402612001639 Ligand Binding Site [chemical binding]; other site 402612001640 Molecular Tunnel; other site 402612001641 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 402612001642 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 402612001643 ATP binding site [chemical binding]; other site 402612001644 Mg2+ binding site [ion binding]; other site 402612001645 G-X-G motif; other site 402612001646 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 402612001647 anchoring element; other site 402612001648 dimer interface [polypeptide binding]; other site 402612001649 ATP binding site [chemical binding]; other site 402612001650 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 402612001651 active site 402612001652 putative metal-binding site [ion binding]; other site 402612001653 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 402612001654 malate dehydrogenase; Reviewed; Region: PRK06223 402612001655 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 402612001656 NAD(P) binding site [chemical binding]; other site 402612001657 dimer interface [polypeptide binding]; other site 402612001658 tetramer (dimer of dimers) interface [polypeptide binding]; other site 402612001659 substrate binding site [chemical binding]; other site 402612001660 bifunctional preprotein translocase subunit SecD/SecF; Reviewed; Region: PRK13024 402612001661 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 402612001662 Protein export membrane protein; Region: SecD_SecF; pfam02355 402612001663 tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain; Region: tRNA_bind_CsaA; cd02798 402612001664 dimer interface [polypeptide binding]; other site 402612001665 putative tRNA-binding site [nucleotide binding]; other site 402612001666 Protein of unknown function (DUF3276); Region: DUF3276; pfam11680 402612001667 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 402612001668 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 402612001669 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 402612001670 Walker A/P-loop; other site 402612001671 ATP binding site [chemical binding]; other site 402612001672 Q-loop/lid; other site 402612001673 ABC transporter signature motif; other site 402612001674 Walker B; other site 402612001675 D-loop; other site 402612001676 H-loop/switch region; other site 402612001677 Glu/Leu/Phe/Val dehydrogenase, dimerization domain; Region: ELFV_dehydrog_N; pfam02812 402612001678 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; pfam00208 402612001679 NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase; Region: NAD_bind_Leu_Phe_Val_DH; cd01075 402612001680 NAD binding site [chemical binding]; other site 402612001681 Phe binding site; other site 402612001682 transcription antitermination factor NusB; Region: nusB; TIGR01951 402612001683 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 402612001684 Preprotein translocase subunit; Region: YajC; pfam02699 402612001685 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 402612001686 active site 402612001687 dimer interface [polypeptide binding]; other site 402612001688 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 402612001689 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 402612001690 intersubunit interface [polypeptide binding]; other site 402612001691 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 402612001692 Putative lysophospholipase; Region: Hydrolase_4; cl19140 402612001693 Putative lysophospholipase; Region: Hydrolase_4; cl19140 402612001694 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 402612001695 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 402612001696 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 402612001697 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 402612001698 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 402612001699 integral membrane protein, TerC family; Region: R_switched_Alx; TIGR03718 402612001700 Uncharacterized protein related to glutamine synthetase [General function prediction only]; Region: COG3968 402612001701 Glutamine synthetase type III N terminal; Region: GSIII_N; pfam12437 402612001702 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 402612001703 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 402612001704 ligand binding site [chemical binding]; other site 402612001705 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 402612001706 ligand binding site [chemical binding]; other site 402612001707 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 402612001708 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 402612001709 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 402612001710 DNA binding residues [nucleotide binding] 402612001711 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 402612001712 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612001713 von Willebrand factor; Region: vWF_A; pfam12450 402612001714 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG2304 402612001715 VWA subgroup: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b...; Region: vWA_subgroup; cd01465 402612001716 metal ion-dependent adhesion site (MIDAS); other site 402612001717 Domain of unknown function (DUF3520); Region: DUF3520; pfam12034 402612001718 WYL domain; Region: WYL; pfam13280 402612001719 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 402612001720 Divergent AAA domain; Region: AAA_4; pfam04326 402612001721 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 402612001722 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 402612001723 putative transposase OrfB; Reviewed; Region: PHA02517 402612001724 HTH-like domain; Region: HTH_21; pfam13276 402612001725 Integrase core domain; Region: rve; pfam00665 402612001726 Integrase core domain; Region: rve_3; pfam13683 402612001727 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 402612001728 Transposase; Region: HTH_Tnp_1; cl17663 402612001729 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 402612001730 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 402612001731 ABC transporter; Region: ABC_tran_2; pfam12848 402612001732 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 402612001733 HRDC domain; Region: HRDC; pfam00570 402612001734 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 402612001735 catalytic residue [active] 402612001736 Scramblase; Region: Scramblase; pfam03803 402612001737 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 402612001738 Bacterial protein of unknown function (DUF839); Region: DUF839; pfam05787 402612001739 di-heme enzyme, MXAN_0977 family; Region: MXAN_0977_Heme2; TIGR04039 402612001740 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 402612001741 multidrug efflux protein; Reviewed; Region: PRK01766 402612001742 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 402612001743 cation binding site [ion binding]; other site 402612001744 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 402612001745 Prohibitin family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily; Region: SPFH_prohibitin; cd03401 402612001746 Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]; Region: ArgK; COG1703 402612001747 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 402612001748 Walker A; other site 402612001749 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 402612001750 Major Facilitator Superfamily; Region: MFS_1; pfam07690 402612001751 putative substrate translocation pore; other site 402612001752 FAD binding domain; Region: FAD_binding_4; pfam01565 402612001753 glycolate oxidase, subunit GlcD; Region: glcD; TIGR00387 402612001754 FAD linked oxidases, C-terminal domain; Region: FAD-oxidase_C; pfam02913 402612001755 AZL_007920/MXAN_0976 family protein; Region: AZL_007920_fam; TIGR04052 402612001756 di-heme enzyme, MXAN_0977 family; Region: MXAN_0977_Heme2; TIGR04039 402612001757 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 402612001758 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 402612001759 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; cl01768 402612001760 preprotein translocase subunit SecA; Reviewed; Region: secA; PRK12901 402612001761 SecA preprotein cross-linking domain; Region: SecA_PP_bind; pfam01043 402612001762 helicase superfamily c-terminal domain; Region: HELICc; smart00490 402612001763 SecA Wing and Scaffold domain; Region: SecA_SW; pfam07516 402612001764 Protein of unknown function (DUF2795); Region: DUF2795; pfam11387 402612001765 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 402612001766 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 402612001767 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 402612001768 Walker A/P-loop; other site 402612001769 ATP binding site [chemical binding]; other site 402612001770 Q-loop/lid; other site 402612001771 ABC transporter signature motif; other site 402612001772 Walker B; other site 402612001773 D-loop; other site 402612001774 H-loop/switch region; other site 402612001775 Methyltransferase domain; Region: Methyltransf_24; pfam13578 402612001776 Helix-turn-helix domain; Region: HTH_19; pfam12844 402612001777 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 402612001778 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 402612001779 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 402612001780 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 402612001781 Walker A/P-loop; other site 402612001782 ATP binding site [chemical binding]; other site 402612001783 Q-loop/lid; other site 402612001784 ABC transporter signature motif; other site 402612001785 Walker B; other site 402612001786 D-loop; other site 402612001787 ABC transporter; Region: ABC_tran_2; pfam12848 402612001788 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 402612001789 ABC transporter; Region: ABC_tran_2; pfam12848 402612001790 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 402612001791 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 402612001792 Probable Catalytic site; other site 402612001793 metal-binding site 402612001794 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 402612001795 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 402612001796 E3 interaction surface; other site 402612001797 lipoyl attachment site [posttranslational modification]; other site 402612001798 e3 binding domain; Region: E3_binding; pfam02817 402612001799 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 402612001800 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 402612001801 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 402612001802 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 402612001803 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 402612001804 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 402612001805 gliding motility-associated C-terminal domain; Region: Bac_Flav_CTERM; TIGR04131 402612001806 GTP cyclohydrolase I; Region: GTP_cyclohydroI; pfam01227 402612001807 active site 402612001808 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 402612001809 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 402612001810 active site 402612001811 HIGH motif; other site 402612001812 KMSKS motif; other site 402612001813 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 402612001814 tRNA binding surface [nucleotide binding]; other site 402612001815 anticodon binding site; other site 402612001816 Haemolytic domain; Region: Haemolytic; pfam01809 402612001817 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 402612001818 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 402612001819 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 402612001820 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 402612001821 FtsH Extracellular; Region: FtsH_ext; pfam06480 402612001822 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 402612001823 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 402612001824 Walker A motif; other site 402612001825 ATP binding site [chemical binding]; other site 402612001826 Walker B motif; other site 402612001827 arginine finger; other site 402612001828 Peptidase family M41; Region: Peptidase_M41; pfam01434 402612001829 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; cl00674 402612001830 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 402612001831 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 402612001832 Acyl CoA binding protein (ACBP) binds thiol esters of long fatty acids and coenzyme A in a one-to-one binding mode with high specificity and affinity. Acyl-CoAs are important intermediates in fatty lipid synthesis and fatty acid degradation and play a...; Region: ACBP; cl00221 402612001833 acyl-CoA binding pocket [chemical binding]; other site 402612001834 CoA binding site [chemical binding]; other site 402612001835 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 402612001836 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 402612001837 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 402612001838 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 402612001839 Active site serine [active] 402612001840 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 402612001841 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 402612001842 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 402612001843 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 402612001844 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 402612001845 replicative DNA helicase; Region: DnaB; TIGR00665 402612001846 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 402612001847 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 402612001848 Walker A motif; other site 402612001849 ATP binding site [chemical binding]; other site 402612001850 Walker B motif; other site 402612001851 DNA binding loops [nucleotide binding] 402612001852 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 402612001853 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl19134 402612001854 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 402612001855 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612001856 BDLF3; Provisional; Region: PHA03255 402612001857 Bestrophin, RFP-TM, chloride channel; Region: Bestrophin; pfam01062 402612001858 K+ potassium transporter; Region: K_trans; pfam02705 402612001859 Sialidases or neuraminidases function to bind and hydrolyze terminal sialic acid residues from various glycoconjugates as well as playing roles in pathogenesis, bacterial nutrition and cellular interactions. They have a six-bladed, beta-propeller fold...; Region: Sialidase; cd00260 402612001860 Asp-box motif; other site 402612001861 RNA polymerase sigma factor RpoE; Provisional; Region: PRK09652 402612001862 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 402612001863 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 402612001864 DNA binding residues [nucleotide binding] 402612001865 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 402612001866 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 402612001867 motif II; other site 402612001868 Helix-turn-helix domain; Region: HTH_17; pfam12728 402612001869 Phage integrase SAM-like domain; Region: Phage_int_SAM_5; pfam13102 402612001870 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 402612001871 active site 402612001872 DNA binding site [nucleotide binding] 402612001873 Int/Topo IB signature motif; other site 402612001874 Winged helix-turn helix; Region: HTH_29; pfam13551 402612001875 Helix-turn-helix domain; Region: HTH_17; pfam12728 402612001876 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 402612001877 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 402612001878 trmE is a tRNA modification GTPase; Region: trmE; cd04164 402612001879 G1 box; other site 402612001880 GTP/Mg2+ binding site [chemical binding]; other site 402612001881 Switch I region; other site 402612001882 G2 box; other site 402612001883 Switch II region; other site 402612001884 G3 box; other site 402612001885 G4 box; other site 402612001886 G5 box; other site 402612001887 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 402612001888 Protein of unknown function (DUF2400); Region: DUF2400; pfam09674 402612001889 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 402612001890 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 402612001891 Walker A/P-loop; other site 402612001892 ATP binding site [chemical binding]; other site 402612001893 Q-loop/lid; other site 402612001894 ABC transporter signature motif; other site 402612001895 Walker B; other site 402612001896 D-loop; other site 402612001897 H-loop/switch region; other site 402612001898 methionine sulfoxide reductase A; Provisional; Region: PRK14054 402612001899 GTP cyclohydrolase I; Region: GTP_cyclohydroI; pfam01227 402612001900 active site 402612001901 Bacterial protein of unknown function (DUF937); Region: DUF937; pfam06078 402612001902 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 402612001903 Phosphoglycerate dehydrogenase (PGDH) NAD-binding and catalytic domains; Region: PGDH_2; cd05303 402612001904 putative ligand binding site [chemical binding]; other site 402612001905 NAD binding site [chemical binding]; other site 402612001906 dimerization interface [polypeptide binding]; other site 402612001907 catalytic site [active] 402612001908 3-phosphoserine/phosphohydroxythreonine aminotransferase; Provisional; Region: PRK05355 402612001909 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 402612001910 catalytic residue [active] 402612001911 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 402612001912 NAD(P) binding site [chemical binding]; other site 402612001913 4Fe-4S binding domain; Region: Fer4; pfam00037 402612001914 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612001915 GTP-binding protein YchF; Reviewed; Region: PRK09601 402612001916 YchF GTPase; Region: YchF; cd01900 402612001917 G1 box; other site 402612001918 GTP/Mg2+ binding site [chemical binding]; other site 402612001919 Switch I region; other site 402612001920 G2 box; other site 402612001921 Switch II region; other site 402612001922 G3 box; other site 402612001923 G4 box; other site 402612001924 G5 box; other site 402612001925 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 402612001926 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612001927 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 402612001928 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 402612001929 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 402612001930 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 402612001931 ATP binding site [chemical binding]; other site 402612001932 Mg2+ binding site [ion binding]; other site 402612001933 G-X-G motif; other site 402612001934 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 402612001935 anchoring element; other site 402612001936 dimer interface [polypeptide binding]; other site 402612001937 ATP binding site [chemical binding]; other site 402612001938 TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands...; Region: TOPRIM_TopoIIA_like; cd01030 402612001939 active site 402612001940 putative metal-binding site [ion binding]; other site 402612001941 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 402612001942 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; pfam08780 402612001943 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 402612001944 active site 402612001945 NTP binding site [chemical binding]; other site 402612001946 metal binding triad [ion binding]; metal-binding site 402612001947 antibiotic binding site [chemical binding]; other site 402612001948 DNA topoisomerase IV subunit A; Provisional; Region: PRK12758 402612001949 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 402612001950 CAP-like domain; other site 402612001951 active site 402612001952 primary dimer interface [polypeptide binding]; other site 402612001953 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA; cd03877 402612001954 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 402612001955 metal binding site [ion binding]; metal-binding site 402612001956 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 402612001957 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 402612001958 RNA binding surface [nucleotide binding]; other site 402612001959 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 402612001960 active site 402612001961 PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis; Region: PASTA_pknB; cd06577 402612001962 PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis; Region: PASTA_pknB; cd06577 402612001963 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 402612001964 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 402612001965 ATP-grasp domain; Region: ATP-grasp_4; cl17255 402612001966 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 402612001967 active site 402612001968 (T/H)XGH motif; other site 402612001969 bacillithiol biosynthesis deacetylase BshB1; Region: thiol_BshB1; TIGR04001 402612001970 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 402612001971 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 402612001972 CoenzymeA binding site [chemical binding]; other site 402612001973 subunit interaction site [polypeptide binding]; other site 402612001974 PHB binding site; other site 402612001975 Right handed beta helix region; Region: Beta_helix; pfam13229 402612001976 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 402612001977 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 402612001978 ATP binding site [chemical binding]; other site 402612001979 putative Mg++ binding site [ion binding]; other site 402612001980 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 402612001981 nucleotide binding region [chemical binding]; other site 402612001982 ATP-binding site [chemical binding]; other site 402612001983 DbpA RNA binding domain; Region: DbpA; pfam03880 402612001984 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 402612001985 nudix motif; other site 402612001986 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 402612001987 active site 402612001988 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 402612001989 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 402612001990 DEAD-like helicases superfamily; Region: DEXDc; smart00487 402612001991 ATP binding site [chemical binding]; other site 402612001992 putative Mg++ binding site [ion binding]; other site 402612001993 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 402612001994 active site 402612001995 phosphorylation site [posttranslational modification] 402612001996 intermolecular recognition site; other site 402612001997 dimerization interface [polypeptide binding]; other site 402612001998 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 402612001999 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 402612002000 Walker A motif; other site 402612002001 ATP binding site [chemical binding]; other site 402612002002 Walker B motif; other site 402612002003 arginine finger; other site 402612002004 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 402612002005 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: COG4152 402612002006 ATP-binding cassette domain of an uncharacterized transporter; Region: ABC_putative_ATPase; cd03269 402612002007 Walker A/P-loop; other site 402612002008 ATP binding site [chemical binding]; other site 402612002009 Q-loop/lid; other site 402612002010 ABC transporter signature motif; other site 402612002011 Walker B; other site 402612002012 D-loop; other site 402612002013 H-loop/switch region; other site 402612002014 Domain of unknown function (DUF4162); Region: DUF4162; pfam13732 402612002015 chaperone protein DnaJ; Provisional; Region: PRK14289 402612002016 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 402612002017 HSP70 interaction site [polypeptide binding]; other site 402612002018 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 402612002019 substrate binding site [polypeptide binding]; other site 402612002020 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 402612002021 dimer interface [polypeptide binding]; other site 402612002022 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 402612002023 dimer interface [polypeptide binding]; other site 402612002024 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 402612002025 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 402612002026 TIGR01777 family protein; Region: yfcH 402612002027 NAD(P) binding site [chemical binding]; other site 402612002028 active site 402612002029 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 402612002030 Tic20-like protein; Region: Tic20; pfam09685 402612002031 Predicted transcriptional regulators [Transcription]; Region: COG1695 402612002032 putative Zn2+ binding site [ion binding]; other site 402612002033 putative DNA binding site [nucleotide binding]; other site 402612002034 PspC domain; Region: PspC; pfam04024 402612002035 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 402612002036 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 402612002037 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 402612002038 fumarylacetoacetase; Region: PLN02856 402612002039 Fumarylacetoacetase N-terminal; Region: FAA_hydrolase_N; pfam09298 402612002040 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 402612002041 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 402612002042 dimer interface [polypeptide binding]; other site 402612002043 active site 402612002044 glycine-pyridoxal phosphate binding site [chemical binding]; other site 402612002045 folate binding site [chemical binding]; other site 402612002046 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 402612002047 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 402612002048 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 402612002049 TPP-binding site [chemical binding]; other site 402612002050 dimer interface [polypeptide binding]; other site 402612002051 Transketolase, C-terminal subunit [Carbohydrate transport and metabolism]; Region: COG3958 402612002052 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 402612002053 PYR/PP interface [polypeptide binding]; other site 402612002054 dimer interface [polypeptide binding]; other site 402612002055 TPP binding site [chemical binding]; other site 402612002056 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 402612002057 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 402612002058 ligand binding site [chemical binding]; other site 402612002059 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 402612002060 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 402612002061 ligand binding site [chemical binding]; other site 402612002062 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 402612002063 AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain...; Region: PurM-like; cl10019 402612002064 dimerization interface [polypeptide binding]; other site 402612002065 ATP binding site [chemical binding]; other site 402612002066 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 402612002067 Immunoglobulin domain; Region: Ig_2; pfam13895 402612002068 gliding motility-associated C-terminal domain; Region: Bac_Flav_CTERM; TIGR04131 402612002069 Protein of unknown function (DUF3308); Region: DUF3308; pfam11751 402612002070 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612002071 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 402612002072 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 402612002073 Domain of unknown function (DUF4249); Region: DUF4249; pfam14054 402612002074 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 402612002075 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 402612002076 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 402612002077 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 402612002078 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 402612002079 AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain...; Region: PurM-like; cl10019 402612002080 dimerization interface [polypeptide binding]; other site 402612002081 ATP binding site [chemical binding]; other site 402612002082 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 402612002083 dimerization interface [polypeptide binding]; other site 402612002084 ATP binding site [chemical binding]; other site 402612002085 CobB/CobQ-like glutamine amidotransferase domain; Region: GATase_5; pfam13507 402612002086 conserved cys residue [active] 402612002087 Endonuclease I; Region: Endonuclease_1; pfam04231 402612002088 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612002089 16S rRNA methyltransferase B; Provisional; Region: PRK14902 402612002090 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 402612002091 S-adenosylmethionine binding site [chemical binding]; other site 402612002092 carbamoyl phosphate synthase-like protein; Provisional; Region: PRK12767 402612002093 cyanophycin synthetase; Provisional; Region: PRK14016 402612002094 NRDE protein; Region: NRDE; cl01315 402612002095 Peroxiredoxin (PRX)-like 2 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a CXXC motif, similar to TRX. The second cysteine in the motif corresponds to the peroxidatic cysteine of PRX, however, these...; Region: PRX_like2; cd02970 402612002096 putative catalytic residues [active] 402612002097 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 402612002098 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 402612002099 ligand binding site [chemical binding]; other site 402612002100 Bacterial transcriptional repressor; Region: TetR; pfam13972 402612002101 flexible hinge region; other site 402612002102 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 402612002103 putative switch regulator; other site 402612002104 non-specific DNA interactions [nucleotide binding]; other site 402612002105 DNA binding site [nucleotide binding] 402612002106 sequence specific DNA binding site [nucleotide binding]; other site 402612002107 putative cAMP binding site [chemical binding]; other site 402612002108 Electron transfer DM13; Region: DM13; pfam10517 402612002109 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 402612002110 putative FAD-binding dehydrogenase; Reviewed; Region: PRK12834 402612002111 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 402612002112 Pyridine nucleotide-disulphide oxidoreductase, dimerization domain; Region: Pyr_redox_dim; pfam02852 402612002113 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2268 402612002114 SPFH domain / Band 7 family; Region: Band_7; pfam01145 402612002115 Apolipophorin-III and similar insect proteins; Region: ApoLp-III_like; cl19113 402612002116 core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily; Region: SPFH_like; cl19107 402612002117 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 402612002118 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 402612002119 catalytic residue [active] 402612002120 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 402612002121 active site 402612002122 metal binding site [ion binding]; metal-binding site 402612002123 homotetramer interface [polypeptide binding]; other site 402612002124 Histidine kinase; Region: HisKA_3; pfam07730 402612002125 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 402612002126 ATP binding site [chemical binding]; other site 402612002127 Mg2+ binding site [ion binding]; other site 402612002128 G-X-G motif; other site 402612002129 Uncharacterized conserved protein [Function unknown]; Region: COG4748 402612002130 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 402612002131 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 402612002132 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 402612002133 active site 402612002134 phosphorylation site [posttranslational modification] 402612002135 intermolecular recognition site; other site 402612002136 dimerization interface [polypeptide binding]; other site 402612002137 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 402612002138 DNA binding residues [nucleotide binding] 402612002139 dimerization interface [polypeptide binding]; other site 402612002140 Domain of unknown function (DUF4293); Region: DUF4293; pfam14126 402612002141 transcription termination factor Rho; Provisional; Region: PRK12678 402612002142 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 402612002143 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 402612002144 RNA binding site [nucleotide binding]; other site 402612002145 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 402612002146 multimer interface [polypeptide binding]; other site 402612002147 Walker A motif; other site 402612002148 ATP binding site [chemical binding]; other site 402612002149 Walker B motif; other site 402612002150 hypothetical protein; Validated; Region: PRK02101 402612002151 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 402612002152 tetramer interface [polypeptide binding]; other site 402612002153 TPP-binding site [chemical binding]; other site 402612002154 heterodimer interface [polypeptide binding]; other site 402612002155 phosphorylation loop region [posttranslational modification] 402612002156 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 402612002157 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 402612002158 PYR/PP interface [polypeptide binding]; other site 402612002159 dimer interface [polypeptide binding]; other site 402612002160 TPP binding site [chemical binding]; other site 402612002161 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 402612002162 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 402612002163 Zn binding site [ion binding]; other site 402612002164 Endonuclease I; Region: Endonuclease_1; cl01003 402612002165 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612002166 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 402612002167 N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid...; Region: SIS_Etherase; cd05007 402612002168 putative active site [active] 402612002169 Pleckstrin homology (PH)-like domains in bacteria (PHb); Region: PH-like_bacteria; cd13225 402612002170 pentamer interface [polypeptide binding]; other site 402612002171 dodecaamer interface [polypeptide binding]; other site 402612002172 ZIP Zinc transporter; Region: Zip; cl00437 402612002173 Methyltransferase domain; Region: Methyltransf_31; pfam13847 402612002174 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 402612002175 S-adenosylmethionine binding site [chemical binding]; other site 402612002176 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 402612002177 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 402612002178 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 402612002179 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 402612002180 TRAM domain; Region: TRAM; cl01282 402612002181 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 402612002182 S-adenosylmethionine binding site [chemical binding]; other site 402612002183 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 402612002184 non-specific DNA binding site [nucleotide binding]; other site 402612002185 salt bridge; other site 402612002186 sequence-specific DNA binding site [nucleotide binding]; other site 402612002187 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cl19095 402612002188 cofactor binding site; other site 402612002189 DNA binding site [nucleotide binding] 402612002190 substrate interaction site [chemical binding]; other site 402612002191 Restriction endonuclease BglII; Region: Endonuc-BglII; pfam09195 402612002192 Protein of unknown function (DUF1697); Region: DUF1697; pfam08002 402612002193 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 402612002194 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase [Coenzyme metabolism]; Region: BioA; COG0161 402612002195 inhibitor-cofactor binding pocket; inhibition site 402612002196 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612002197 catalytic residue [active] 402612002198 Protein of unknown function (DUF2752); Region: DUF2752; pfam10825 402612002199 MiaE tRNA-modifying nonheme diiron monooxygenase, ferritin-like diiron-binding domain; Region: MiaE; cd07910 402612002200 active site 402612002201 dinuclear metal binding site [ion binding]; other site 402612002202 dimerization interface [polypeptide binding]; other site 402612002203 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 402612002204 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 402612002205 Glycosyl transferases group 1; Region: Glyco_trans_1_4; pfam13692 402612002206 Predicted metalloprotease [General function prediction only]; Region: COG2321 402612002207 Predicted membrane protein [Function unknown]; Region: COG2323 402612002208 Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones]; Region: COG4067 402612002209 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 402612002210 ATP-grasp domain; Region: ATP-grasp_4; cl17255 402612002211 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 402612002212 Clp amino terminal domain; Region: Clp_N; pfam02861 402612002213 Clp amino terminal domain; Region: Clp_N; pfam02861 402612002214 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 402612002215 Walker A motif; other site 402612002216 ATP binding site [chemical binding]; other site 402612002217 Walker B motif; other site 402612002218 arginine finger; other site 402612002219 UvrB/uvrC motif; Region: UVR; pfam02151 402612002220 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 402612002221 Walker A motif; other site 402612002222 ATP binding site [chemical binding]; other site 402612002223 Walker B motif; other site 402612002224 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 402612002225 DNA gyrase subunit A; Validated; Region: PRK05560 402612002226 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 402612002227 CAP-like domain; other site 402612002228 active site 402612002229 primary dimer interface [polypeptide binding]; other site 402612002230 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 402612002231 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 402612002232 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 402612002233 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 402612002234 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 402612002235 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 402612002236 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 402612002237 Tetratricopeptide repeat; Region: TPR_16; pfam13432 402612002238 TPR motif; other site 402612002239 binding surface 402612002240 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 402612002241 homotrimer interaction site [polypeptide binding]; other site 402612002242 putative active site [active] 402612002243 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 402612002244 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 402612002245 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 402612002246 active site 402612002247 metal binding site [ion binding]; metal-binding site 402612002248 virulence factor Mce family protein; Region: Mtu_fam_mce; TIGR00996 402612002249 mce related protein; Region: MCE; pfam02470 402612002250 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 402612002251 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 402612002252 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 402612002253 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 402612002254 Cysteine-rich domain; Region: CCG; pfam02754 402612002255 Cysteine-rich domain; Region: CCG; pfam02754 402612002256 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 402612002257 Beta-lactamase; Region: Beta-lactamase; cl17358 402612002258 CCC1-related family of proteins; Region: CCC1_like; cl00278 402612002259 Lipocalin-like domain; Region: Lipocalin_5; pfam13924 402612002260 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 402612002261 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_5; cd04962 402612002262 N-acetyl-alpha-D-glucosaminyl L-malate synthase BshA; Region: thiol_BshA; TIGR03999 402612002263 Transcriptional regulator [Transcription]; Region: LysR; COG0583 402612002264 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 402612002265 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 402612002266 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein; Region: GATase1_Hsp31_like; cd03141 402612002267 potential catalytic triad [active] 402612002268 conserved cys residue [active] 402612002269 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 402612002270 Tetramer interface [polypeptide binding]; other site 402612002271 active site 402612002272 FMN-binding site [chemical binding]; other site 402612002273 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 402612002274 Protein of unknown function, DUF393; Region: DUF393; pfam04134 402612002275 Bacterial SH3 domain; Region: SH3_3; pfam08239 402612002276 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 402612002277 NlpC/P60 family; Region: NLPC_P60; pfam00877 402612002278 acetyl-CoA C-acetyltransferase; Region: PLN02644 402612002279 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 402612002280 dimer interface [polypeptide binding]; other site 402612002281 active site 402612002282 Phage integrase SAM-like domain; Region: Phage_int_SAM_5; pfam13102 402612002283 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 402612002284 active site 402612002285 DNA binding site [nucleotide binding] 402612002286 Int/Topo IB signature motif; other site 402612002287 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cl19050 402612002288 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 402612002289 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 402612002290 Uncharacterized proteins similar to Bacteroides ovatus 4320; Region: Bacova_04320_like; cd12190 402612002291 Toxin SymE, type I toxin-antitoxin system; Region: SymE_toxin; cl07446 402612002292 Domain of unknown function (DUF932); Region: DUF932; cl12129 402612002293 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 402612002294 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 402612002295 putative active site [active] 402612002296 catalytic site [active] 402612002297 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 402612002298 non-specific DNA binding site [nucleotide binding]; other site 402612002299 salt bridge; other site 402612002300 sequence-specific DNA binding site [nucleotide binding]; other site 402612002301 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 402612002302 Active Sites [active] 402612002303 Domain of unknown function (DUF3440); Region: DUF3440; pfam11922 402612002304 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 402612002305 ParB-like nuclease domain; Region: ParB; smart00470 402612002306 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 402612002307 DEAD-like helicases superfamily; Region: DEXDc; smart00487 402612002308 ALIX V-shaped domain binding to HIV; Region: ALIX_LYPXL_bnd; pfam13949 402612002309 Caseinolytic protease (ClpP) is an ATP-dependent protease; Region: Clp_protease_like; cl15763 402612002310 active site 402612002311 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; cl02712 402612002312 amidase catalytic site [active] 402612002313 Zn binding residues [ion binding]; other site 402612002314 substrate binding site [chemical binding]; other site 402612002315 YopX protein; Region: YopX; pfam09643 402612002316 Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; Region: Adenylation_DNA_ligase_like; cl12015 402612002317 RNA ligase; Region: RNA_ligase; cl19220 402612002318 cinnamyl-alcohol dehydrogenase family protein; Region: PLN02986 402612002319 DNA primase (bacterial type) [DNA replication, recombination, and repair]; Region: DnaG; COG0358 402612002320 CHC2 zinc finger; Region: zf-CHC2; cl17510 402612002321 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 402612002322 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 402612002323 active site 402612002324 metal binding site [ion binding]; metal-binding site 402612002325 interdomain interaction site; other site 402612002326 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; cl17315 402612002327 Helix-turn-helix XRE-family like proteins; Region: HTH_XRE; smart00530 402612002328 non-specific DNA binding site [nucleotide binding]; other site 402612002329 salt bridge; other site 402612002330 sequence-specific DNA binding site [nucleotide binding]; other site 402612002331 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 402612002332 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 402612002333 ATP-binding cassette domain of a mitochondrial protein MTABC3 and related proteins; Region: ABC_MTABC3_MDL1_MDL2; cd03249 402612002334 Walker A/P-loop; other site 402612002335 ATP binding site [chemical binding]; other site 402612002336 Q-loop/lid; other site 402612002337 ABC transporter signature motif; other site 402612002338 Walker B; other site 402612002339 D-loop; other site 402612002340 H-loop/switch region; other site 402612002341 hypothetical protein; Provisional; Region: PRK12378 402612002342 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 402612002343 Aminomethyltransferase folate-binding domain; Region: GCV_T; pfam01571 402612002344 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 402612002345 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 402612002346 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 402612002347 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 402612002348 putative substrate binding site [chemical binding]; other site 402612002349 putative ATP binding site [chemical binding]; other site 402612002350 Aromatic amino acid lyase; Region: Lyase_aromatic; pfam00221 402612002351 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 402612002352 active sites [active] 402612002353 tetramer interface [polypeptide binding]; other site 402612002354 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 402612002355 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 402612002356 putative acyl-acceptor binding pocket; other site 402612002357 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 402612002358 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 402612002359 non-specific DNA binding site [nucleotide binding]; other site 402612002360 salt bridge; other site 402612002361 sequence-specific DNA binding site [nucleotide binding]; other site 402612002362 Peptidase M14-like domain; uncharacterized subgroup; Region: M14-like_1_2; cd06239 402612002363 putative active site [active] 402612002364 Zn binding site [ion binding]; other site 402612002365 DNA-binding transcriptional regulator AsnC; Provisional; Region: PRK11179 402612002366 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 402612002367 putative DNA binding site [nucleotide binding]; other site 402612002368 putative Zn2+ binding site [ion binding]; other site 402612002369 AsnC family; Region: AsnC_trans_reg; pfam01037 402612002370 DinB superfamily; Region: DinB_2; pfam12867 402612002371 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 402612002372 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 402612002373 McrBC 5-methylcytosine restriction system component; Region: McrBC; cl01737 402612002374 Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; Region: SPEC; cd00176 402612002375 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 402612002376 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; cl18944 402612002377 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 402612002378 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 402612002379 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 402612002380 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 402612002381 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 402612002382 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 402612002383 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 402612002384 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 402612002385 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 402612002386 N-terminal plug; other site 402612002387 ligand-binding site [chemical binding]; other site 402612002388 Protein of unknown function, DUF479; Region: DUF479; cl01203 402612002389 phosphoglucosamine mutase; Region: Arch_GlmM; TIGR03990 402612002390 The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine...; Region: phosphohexomutase; cl03757 402612002391 active site 402612002392 substrate binding site [chemical binding]; other site 402612002393 metal binding site [ion binding]; metal-binding site 402612002394 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl19078 402612002395 active site 402612002396 phosphorylation site [posttranslational modification] 402612002397 intermolecular recognition site; other site 402612002398 dimerization interface [polypeptide binding]; other site 402612002399 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 402612002400 ATP binding site [chemical binding]; other site 402612002401 Mg2+ binding site [ion binding]; other site 402612002402 G-X-G motif; other site 402612002403 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 402612002404 non-specific DNA binding site [nucleotide binding]; other site 402612002405 salt bridge; other site 402612002406 sequence-specific DNA binding site [nucleotide binding]; other site 402612002407 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cl19095 402612002408 cofactor binding site; other site 402612002409 DNA binding site [nucleotide binding] 402612002410 substrate interaction site [chemical binding]; other site 402612002411 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 402612002412 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 402612002413 catalytic residue [active] 402612002414 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 402612002415 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 402612002416 putative acyl-acceptor binding pocket; other site 402612002417 Rhomboid family; Region: Rhomboid; cl11446 402612002418 Protein of unknown function (DUF541); Region: SIMPL; pfam04402 402612002419 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 402612002420 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 402612002421 nucleotide binding site [chemical binding]; other site 402612002422 NEF interaction site [polypeptide binding]; other site 402612002423 SBD interface [polypeptide binding]; other site 402612002424 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 402612002425 hypothetical protein; Provisional; Region: PRK06149 402612002426 active site 402612002427 ATP binding site [chemical binding]; other site 402612002428 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 402612002429 inhibitor-cofactor binding pocket; inhibition site 402612002430 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612002431 catalytic residue [active] 402612002432 T5orf172 domain; Region: T5orf172; pfam10544 402612002433 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 402612002434 Part of AAA domain; Region: AAA_19; pfam13245 402612002435 UvrD-like helicase C-terminal domain; Region: UvrD_C_2; pfam13538 402612002436 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 402612002437 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 402612002438 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 402612002439 cysteine synthase; Region: PLN02565 402612002440 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 402612002441 dimer interface [polypeptide binding]; other site 402612002442 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612002443 catalytic residue [active] 402612002444 HNH endonuclease; Region: HNH_3; pfam13392 402612002445 Helix-turn-helix domain of Hin and related proteins; Region: HTH_Hin_like; cl17393 402612002446 PCRF domain; Region: PCRF; pfam03462 402612002447 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 402612002448 RF-1 domain; Region: RF-1; pfam00472 402612002449 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; cl18945 402612002450 Beta-eliminating lyase; Region: Beta_elim_lyase; pfam01212 402612002451 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 402612002452 catalytic residue [active] 402612002453 hypothetical protein; Provisional; Region: PRK14623 402612002454 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 402612002455 DHH family; Region: DHH; pfam01368 402612002456 DHHA1 domain; Region: DHHA1; pfam02272 402612002457 Smr domain; Region: Smr; pfam01713 402612002458 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 402612002459 MMPL family; Region: MMPL; cl14618 402612002460 Outer membrane efflux protein; Region: OEP; pfam02321 402612002461 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 402612002462 Outer membrane efflux protein; Region: OEP; pfam02321 402612002463 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 402612002464 HlyD family secretion protein; Region: HlyD_3; pfam13437 402612002465 Dual specificity phosphatases (DSP); Ser/Thr and Tyr protein phosphatases. Structurally similar to tyrosine-specific phosphatases but with a shallower active site cleft and a distinctive active site signature motif, HCxxGxxR. Characterized as VHR- or...; Region: DSPc; cl00053 402612002466 arylsulfatase; Provisional; Region: PRK13759 402612002467 Sulfatase; Region: Sulfatase; pfam00884 402612002468 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 402612002469 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 402612002470 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 402612002471 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 402612002472 oligomerization interface [polypeptide binding]; other site 402612002473 active site 402612002474 metal binding site [ion binding]; metal-binding site 402612002475 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 402612002476 Tricorn protease C1 domain; Region: Tricorn_C1; pfam14684 402612002477 Interphotoreceptor retinoid-binding protein; serine protease family S41; Region: Peptidase_S41_IRBP; cd07563 402612002478 active site triad [active] 402612002479 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 402612002480 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 402612002481 active site 402612002482 Bacillus subtilis aldehyde dehydrogenase ywdH-like; Region: ALDH_YwdH-P39616; cd07136 402612002483 NAD(P) binding site [chemical binding]; other site 402612002484 catalytic residues [active] 402612002485 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cl00454 402612002486 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 402612002487 Mechanosensitive ion channel; Region: MS_channel; pfam00924 402612002488 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 402612002489 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 402612002490 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 402612002491 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 402612002492 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 402612002493 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 402612002494 23S rRNA binding site [nucleotide binding]; other site 402612002495 L21 binding site [polypeptide binding]; other site 402612002496 L13 binding site [polypeptide binding]; other site 402612002497 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 402612002498 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 402612002499 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 402612002500 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 402612002501 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 402612002502 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 402612002503 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 402612002504 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 402612002505 active site 402612002506 dimer interface [polypeptide binding]; other site 402612002507 motif 1; other site 402612002508 motif 2; other site 402612002509 motif 3; other site 402612002510 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 402612002511 anticodon binding site; other site 402612002512 Transposase zinc-ribbon domain; Region: Zn_Tnp_IS1595; pfam12760 402612002513 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; pfam12762 402612002514 Transposase, Mutator family; Region: Transposase_mut; cl19537 402612002515 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3328 402612002516 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 402612002517 Transposase; Region: DDE_Tnp_ISL3; pfam01610 402612002518 Helix-turn-helix domain; Region: HTH_38; pfam13936 402612002519 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 402612002520 Integrase core domain; Region: rve; pfam00665 402612002521 Domain of unknown function (DUF4258); Region: DUF4258; pfam14076 402612002522 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 402612002523 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 402612002524 hexamer interface [polypeptide binding]; other site 402612002525 ligand binding site [chemical binding]; other site 402612002526 putative active site [active] 402612002527 NAD(P) binding site [chemical binding]; other site 402612002528 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 402612002529 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 402612002530 active site 402612002531 phosphorylation site [posttranslational modification] 402612002532 intermolecular recognition site; other site 402612002533 dimerization interface [polypeptide binding]; other site 402612002534 PglZ domain; Region: PglZ; pfam08665 402612002535 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 402612002536 putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional; Region: PRK11930 402612002537 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 402612002538 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 402612002539 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 402612002540 active site 402612002541 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 402612002542 dimer interface [polypeptide binding]; other site 402612002543 substrate binding site [chemical binding]; other site 402612002544 catalytic residues [active] 402612002545 thymidine kinase; Provisional; Region: PRK04296 402612002546 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 402612002547 putative SAM binding site [chemical binding]; other site 402612002548 putative homodimer interface [polypeptide binding]; other site 402612002549 HopJ type III effector protein; Region: HopJ; pfam08888 402612002550 Adenine deaminase [Nucleotide transport and metabolism]; Region: AdeC; COG1001 402612002551 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 402612002552 Adenine deaminase (AdeC) directly deaminates adenine to form hypoxanthine. This reaction is part of one of the adenine salvage pathways, as well as the degradation pathway. It is important for adenine utilization as a purine, as well as a nitrogen source...; Region: AdeC; cd01295 402612002553 active site 402612002554 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 402612002555 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 402612002556 Probable Catalytic site; other site 402612002557 metal-binding site 402612002558 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N_2; pfam13588 402612002559 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; cl19912 402612002560 DNA polymerase III, delta subunit; Region: holA; TIGR01128 402612002561 Glutamine cyclotransferase; Region: Glu_cyclase_2; cl19848 402612002562 Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion; Region: enolase_like; cl17188 402612002563 short chain dehydrogenase; Validated; Region: PRK06182 402612002564 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 402612002565 NADP binding site [chemical binding]; other site 402612002566 active site 402612002567 steroid binding site; other site 402612002568 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 402612002569 active site 402612002570 intersubunit interactions; other site 402612002571 catalytic residue [active] 402612002572 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 402612002573 Predicted Fe-S oxidoreductases [General function prediction only]; Region: COG1964 402612002574 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 402612002575 FeS/SAM binding site; other site 402612002576 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 402612002577 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 402612002578 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 402612002579 ABC transporter; Region: ABC_tran_2; pfam12848 402612002580 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 402612002581 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 402612002582 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 402612002583 putative tRNA-binding site [nucleotide binding]; other site 402612002584 B3/4 domain; Region: B3_4; pfam03483 402612002585 tRNA synthetase B5 domain; Region: B5; smart00874 402612002586 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 402612002587 dimer interface [polypeptide binding]; other site 402612002588 motif 1; other site 402612002589 motif 3; other site 402612002590 motif 2; other site 402612002591 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 402612002592 MutS domain III; Region: MutS_III; pfam05192 402612002593 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 402612002594 Walker A/P-loop; other site 402612002595 ATP binding site [chemical binding]; other site 402612002596 Q-loop/lid; other site 402612002597 ABC transporter signature motif; other site 402612002598 Walker B; other site 402612002599 D-loop; other site 402612002600 H-loop/switch region; other site 402612002601 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 402612002602 ligand binding site [chemical binding]; other site 402612002603 active site 402612002604 UGI interface [polypeptide binding]; other site 402612002605 catalytic site [active] 402612002606 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 402612002607 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; cl19131 402612002608 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 402612002609 Male sterility protein; Region: NAD_binding_4; pfam07993 402612002610 NAD(P) binding site [chemical binding]; other site 402612002611 active site 402612002612 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 402612002613 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 402612002614 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 402612002615 Homologs of eIF1/SUI1 including Escherichia coli YciH; Region: YciH_like; cd11567 402612002616 putative rRNA binding site [nucleotide binding]; other site 402612002617 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_3; pfam13366 402612002618 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 402612002619 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; pfam14226 402612002620 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 402612002621 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 402612002622 tetramer interface [polypeptide binding]; other site 402612002623 TPP-binding site [chemical binding]; other site 402612002624 heterodimer interface [polypeptide binding]; other site 402612002625 phosphorylation loop region [posttranslational modification] 402612002626 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 402612002627 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 402612002628 alpha subunit interface [polypeptide binding]; other site 402612002629 TPP binding site [chemical binding]; other site 402612002630 heterodimer interface [polypeptide binding]; other site 402612002631 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 402612002632 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 402612002633 Collagenase; Region: DUF3656; pfam12392 402612002634 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 402612002635 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 402612002636 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 402612002637 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 402612002638 active site 402612002639 FMN binding site [chemical binding]; other site 402612002640 substrate binding site [chemical binding]; other site 402612002641 3Fe-4S cluster binding site [ion binding]; other site 402612002642 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 402612002643 Homeodomain-like domain; Region: HTH_23; pfam13384 402612002644 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 402612002645 binding surface 402612002646 TPR motif; other site 402612002647 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 402612002648 binding surface 402612002649 TPR motif; other site 402612002650 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 402612002651 binding surface 402612002652 TPR motif; other site 402612002653 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 402612002654 binding surface 402612002655 TPR motif; other site 402612002656 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 402612002657 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 402612002658 active site 402612002659 phosphorylation site [posttranslational modification] 402612002660 intermolecular recognition site; other site 402612002661 dimerization interface [polypeptide binding]; other site 402612002662 LytTr DNA-binding domain; Region: LytTR; smart00850 402612002663 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 402612002664 dimer interface [polypeptide binding]; other site 402612002665 phosphorylation site [posttranslational modification] 402612002666 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 402612002667 ATP binding site [chemical binding]; other site 402612002668 Mg2+ binding site [ion binding]; other site 402612002669 G-X-G motif; other site 402612002670 Uncharacterized conserved protein [Function unknown]; Region: COG3287 402612002671 FIST N domain; Region: FIST; pfam08495 402612002672 FIST C domain; Region: FIST_C; pfam10442 402612002673 Heme NO binding associated; Region: HNOBA; pfam07701 402612002674 PAS domain; Region: PAS_9; pfam13426 402612002675 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 402612002676 putative active site [active] 402612002677 heme pocket [chemical binding]; other site 402612002678 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 402612002679 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 402612002680 putative active site [active] 402612002681 heme pocket [chemical binding]; other site 402612002682 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 402612002683 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 402612002684 putative active site [active] 402612002685 heme pocket [chemical binding]; other site 402612002686 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 402612002687 dimer interface [polypeptide binding]; other site 402612002688 phosphorylation site [posttranslational modification] 402612002689 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 402612002690 ATP binding site [chemical binding]; other site 402612002691 Mg2+ binding site [ion binding]; other site 402612002692 G-X-G motif; other site 402612002693 Heme NO binding; Region: HNOB; pfam07700 402612002694 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 402612002695 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 402612002696 active site 402612002697 phosphorylation site [posttranslational modification] 402612002698 intermolecular recognition site; other site 402612002699 dimerization interface [polypeptide binding]; other site 402612002700 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 402612002701 DNA photolyase; Region: DNA_photolyase; pfam00875 402612002702 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 402612002703 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 402612002704 classical (c) SDRs; Region: SDR_c; cd05233 402612002705 NAD(P) binding site [chemical binding]; other site 402612002706 active site 402612002707 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_3; cd07820 402612002708 putative hydrophobic ligand binding site [chemical binding]; other site 402612002709 Protein of unknown function (DUF2911); Region: DUF2911; pfam11138 402612002710 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 402612002711 TPR repeat; Region: TPR_11; pfam13414 402612002712 binding surface 402612002713 TPR motif; other site 402612002714 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 402612002715 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 402612002716 generic binding surface II; other site 402612002717 ssDNA binding site; other site 402612002718 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 402612002719 ATP binding site [chemical binding]; other site 402612002720 putative Mg++ binding site [ion binding]; other site 402612002721 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 402612002722 nucleotide binding region [chemical binding]; other site 402612002723 ATP-binding site [chemical binding]; other site 402612002724 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_IV; cd01994 402612002725 Ligand Binding Site [chemical binding]; other site 402612002726 Peptidase M1 family Aminopeptidase N; Region: M1_APN_4; cd09603 402612002727 Zn binding site [ion binding]; other site 402612002728 HEAT repeats; Region: HEAT_2; pfam13646 402612002729 Hexameric tyrosine-coordinated heme protein (HTHP); Region: HTHP; pfam11534 402612002730 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 402612002731 substrate binding site [chemical binding]; other site 402612002732 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 402612002733 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 402612002734 Peptidase M1 family Aminopeptidase N; Region: M1_APN_4; cd09603 402612002735 Zn binding site [ion binding]; other site 402612002736 Peptidase family S41; Region: Peptidase_S41; cl19216 402612002737 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 402612002738 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl19172 402612002739 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 402612002740 TIGR00153 family protein; Region: TIGR00153 402612002741 Phosphate transporter family; Region: PHO4; pfam01384 402612002742 myosin-cross-reactive antigen; Provisional; Region: PRK13977 402612002743 Streptococcal 67 kDa myosin-cross-reactive antigen like family; Region: Strep_67kDa_ant; pfam06100 402612002744 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK08293 402612002745 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 402612002746 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 402612002747 Helix-turn-helix domain; Region: HTH_18; pfam12833 402612002748 Predicted membrane protein [Function unknown]; Region: COG4270 402612002749 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 402612002750 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 402612002751 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 402612002752 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 402612002753 dimer interface [polypeptide binding]; other site 402612002754 phosphorylation site [posttranslational modification] 402612002755 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 402612002756 ATP binding site [chemical binding]; other site 402612002757 Mg2+ binding site [ion binding]; other site 402612002758 G-X-G motif; other site 402612002759 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 402612002760 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 402612002761 Outer membrane protein beta-barrel family; Region: OMP_b-brl_3; pfam14905 402612002762 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 402612002763 S-adenosylmethionine binding site [chemical binding]; other site 402612002764 Protein of unknown function (DUF3822); Region: DUF3822; pfam12864 402612002765 Helix-turn-helix domain; Region: HTH_18; pfam12833 402612002766 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612002767 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 402612002768 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 402612002769 Outer membrane protein beta-barrel family; Region: OMP_b-brl_3; pfam14905 402612002770 AAA domain; Region: AAA_30; pfam13604 402612002771 UvrD-like helicase C-terminal domain; Region: UvrD_C_2; pfam13538 402612002772 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 402612002773 Ligand binding site; other site 402612002774 oligomer interface; other site 402612002775 Ion channel; Region: Ion_trans_2; pfam07885 402612002776 HD superfamily phosphohydrolases [General function prediction only]; Region: COG1078 402612002777 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 402612002778 Zn2+ binding site [ion binding]; other site 402612002779 Mg2+ binding site [ion binding]; other site 402612002780 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 402612002781 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 402612002782 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 402612002783 trimer interface [polypeptide binding]; other site 402612002784 active site 402612002785 UDP-GlcNAc binding site [chemical binding]; other site 402612002786 lipid binding site [chemical binding]; lipid-binding site 402612002787 bifunctional UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase/(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase; Reviewed; Region: PRK13188 402612002788 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 402612002789 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 402612002790 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 402612002791 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 402612002792 active site 402612002793 elongation factor P; Validated; Region: PRK00529 402612002794 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 402612002795 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 402612002796 RNA binding site [nucleotide binding]; other site 402612002797 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 402612002798 RNA binding site [nucleotide binding]; other site 402612002799 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 402612002800 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 402612002801 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 402612002802 trimer interface [polypeptide binding]; other site 402612002803 active site 402612002804 UDP-GlcNAc binding site [chemical binding]; other site 402612002805 lipid binding site [chemical binding]; lipid-binding site 402612002806 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 402612002807 CoA binding domain; Region: CoA_binding; smart00881 402612002808 CoA-ligase; Region: Ligase_CoA; pfam00549 402612002809 polyphosphate kinase; Provisional; Region: PRK05443 402612002810 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 402612002811 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 402612002812 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 402612002813 putative active site [active] 402612002814 catalytic site [active] 402612002815 Catalytic C-terminal domain, second repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C2_like; cd09167 402612002816 domain interface [polypeptide binding]; other site 402612002817 active site 402612002818 catalytic site [active] 402612002819 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl19483 402612002820 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14971 402612002821 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14970 402612002822 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 402612002823 Walker A motif; other site 402612002824 ATP binding site [chemical binding]; other site 402612002825 Walker B motif; other site 402612002826 arginine finger; other site 402612002827 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 402612002828 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 402612002829 NAD(P) binding site [chemical binding]; other site 402612002830 homotetramer interface [polypeptide binding]; other site 402612002831 homodimer interface [polypeptide binding]; other site 402612002832 active site 402612002833 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl19158 402612002834 Sulfatase; Region: Sulfatase; pfam00884 402612002835 ATP phosphoribosyltransferase; Reviewed; Region: hisG; PRK00489 402612002836 ATP phosphoribosyltransferase; Region: hisG; TIGR00070 402612002837 ATP phosphoribosyltransferase, C-terminal domain; Region: HisG_C-term; TIGR03455 402612002838 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 402612002839 histidinol dehydrogenase; Region: hisD; TIGR00069 402612002840 NAD binding site [chemical binding]; other site 402612002841 dimerization interface [polypeptide binding]; other site 402612002842 product binding site; other site 402612002843 substrate binding site [chemical binding]; other site 402612002844 zinc binding site [ion binding]; other site 402612002845 catalytic residues [active] 402612002846 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 402612002847 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 402612002848 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612002849 homodimer interface [polypeptide binding]; other site 402612002850 catalytic residue [active] 402612002851 imidazole glycerol-phosphate dehydratase/histidinol phosphatase; Provisional; Region: PRK05446 402612002852 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 402612002853 active site 402612002854 motif I; other site 402612002855 motif II; other site 402612002856 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 402612002857 putative active site pocket [active] 402612002858 4-fold oligomerization interface [polypeptide binding]; other site 402612002859 metal binding residues [ion binding]; metal-binding site 402612002860 3-fold/trimer interface [polypeptide binding]; other site 402612002861 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13142 402612002862 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 402612002863 putative active site [active] 402612002864 oxyanion strand; other site 402612002865 catalytic triad [active] 402612002866 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 402612002867 catalytic residues [active] 402612002868 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 402612002869 substrate binding site [chemical binding]; other site 402612002870 glutamase interaction surface [polypeptide binding]; other site 402612002871 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 402612002872 Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]; Region: HisI; COG0139 402612002873 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 402612002874 metal binding site [ion binding]; metal-binding site 402612002875 ADP-ribose pyrophosphatase [Nucleotide transport and metabolism]; Region: COG1051 402612002876 nudix motif; other site 402612002877 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 402612002878 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 402612002879 Mechanosensitive ion channel; Region: MS_channel; pfam00924 402612002880 Domain of unknown function (DUF3817); Region: DUF3817; pfam12823 402612002881 DEAD-like helicases superfamily; Region: DEXDc; smart00487 402612002882 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 402612002883 ATP binding site [chemical binding]; other site 402612002884 putative Mg++ binding site [ion binding]; other site 402612002885 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 402612002886 nucleotide binding region [chemical binding]; other site 402612002887 ATP-binding site [chemical binding]; other site 402612002888 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 402612002889 DEAD-like helicases superfamily; Region: DEXDc; smart00487 402612002890 ATP binding site [chemical binding]; other site 402612002891 Mg++ binding site [ion binding]; other site 402612002892 motif III; other site 402612002893 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 402612002894 nucleotide binding region [chemical binding]; other site 402612002895 ATP-binding site [chemical binding]; other site 402612002896 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 402612002897 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 402612002898 ligand binding site [chemical binding]; other site 402612002899 flexible hinge region; other site 402612002900 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain; Region: CBS_pair_CAP-ED_DUF294_PBI_assoc2; cd04800 402612002901 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 402612002902 metal binding triad; other site 402612002903 Putative nucleotidyltransferase substrate binding domain; Region: DUF294_C; pfam10335 402612002904 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 402612002905 active site 402612002906 substrate binding site [chemical binding]; other site 402612002907 acetyl-CoA synthetase; Provisional; Region: PRK00174 402612002908 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 402612002909 active site 402612002910 CoA binding site [chemical binding]; other site 402612002911 acyl-activating enzyme (AAE) consensus motif; other site 402612002912 AMP binding site [chemical binding]; other site 402612002913 acetate binding site [chemical binding]; other site 402612002914 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 402612002915 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 402612002916 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 402612002917 Cellulase (glycosyl hydrolase family 5); Region: Cellulase; pfam00150 402612002918 Sugar-binding cellulase-like; Region: Cellulase-like; cl19200 402612002919 6-pyruvoyl-tetrahydropterin synthase related domain; membrane protein; Region: PTPS_related; pfam10131 402612002920 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 402612002921 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 402612002922 active site 402612002923 phosphorylation site [posttranslational modification] 402612002924 intermolecular recognition site; other site 402612002925 dimerization interface [polypeptide binding]; other site 402612002926 DPG_synthase is involved in protein N-linked glycosylation; Region: DPG_synthase; cd04188 402612002927 Ligand binding site; other site 402612002928 Ligand binding site; other site 402612002929 Ligand binding site; other site 402612002930 Putative Catalytic site; other site 402612002931 DXD motif; other site 402612002932 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 402612002933 Ligand Binding Site [chemical binding]; other site 402612002934 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 402612002935 Outer membrane efflux protein; Region: OEP; pfam02321 402612002936 Outer membrane efflux protein; Region: OEP; pfam02321 402612002937 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 402612002938 MMPL family; Region: MMPL; cl14618 402612002939 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 402612002940 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 402612002941 HlyD family secretion protein; Region: HlyD_3; pfam13437 402612002942 SEC-C motif; Region: SEC-C; cl19389 402612002943 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 402612002944 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 402612002945 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 402612002946 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 402612002947 ligand binding site [chemical binding]; other site 402612002948 flexible hinge region; other site 402612002949 helix_turn_helix, cAMP Regulatory protein; Region: HTH_CRP; smart00419 402612002950 non-specific DNA interactions [nucleotide binding]; other site 402612002951 DNA binding site [nucleotide binding] 402612002952 sequence specific DNA binding site [nucleotide binding]; other site 402612002953 putative cAMP binding site [chemical binding]; other site 402612002954 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 402612002955 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 402612002956 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 402612002957 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 402612002958 HlyD family secretion protein; Region: HlyD_3; pfam13437 402612002959 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 402612002960 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 402612002961 FtsX-like permease family; Region: FtsX; pfam02687 402612002962 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 402612002963 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 402612002964 Walker A/P-loop; other site 402612002965 ATP binding site [chemical binding]; other site 402612002966 Q-loop/lid; other site 402612002967 ABC transporter signature motif; other site 402612002968 Walker B; other site 402612002969 D-loop; other site 402612002970 H-loop/switch region; other site 402612002971 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 402612002972 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 402612002973 Low-spin heme binding site [chemical binding]; other site 402612002974 D-pathway; other site 402612002975 Putative water exit pathway; other site 402612002976 Binuclear center (active site) [active] 402612002977 K-pathway; other site 402612002978 Putative proton exit pathway; other site 402612002979 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 402612002980 putative bifunctional cbb3-type cytochrome c oxidase subunit II/cytochrome c; Provisional; Region: PRK14486 402612002981 Cytochrome c; Region: Cytochrom_C; pfam00034 402612002982 Helix-turn-helix domain; Region: HTH_18; pfam12833 402612002983 peroxiredoxin; Provisional; Region: PRK13189 402612002984 Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by...; Region: PRX_1cys; cd03016 402612002985 dimer interface [polypeptide binding]; other site 402612002986 decamer (pentamer of dimers) interface [polypeptide binding]; other site 402612002987 catalytic triad [active] 402612002988 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; cl17315 402612002989 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 402612002990 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 402612002991 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 402612002992 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 402612002993 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 402612002994 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 402612002995 CoA-ligase; Region: Ligase_CoA; pfam00549 402612002996 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 402612002997 Methyltransferase domain; Region: Methyltransf_24; pfam13578 402612002998 excinuclease ABC subunit B; Provisional; Region: PRK05298 402612002999 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 402612003000 ATP binding site [chemical binding]; other site 402612003001 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 402612003002 nucleotide binding region [chemical binding]; other site 402612003003 ATP-binding site [chemical binding]; other site 402612003004 Ultra-violet resistance protein B; Region: UvrB; pfam12344 402612003005 UvrB/uvrC motif; Region: UVR; pfam02151 402612003006 Peptidase family M48; Region: Peptidase_M48; cl12018 402612003007 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 402612003008 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 402612003009 active site 402612003010 phosphorylation site [posttranslational modification] 402612003011 intermolecular recognition site; other site 402612003012 dimerization interface [polypeptide binding]; other site 402612003013 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 402612003014 DNA binding site [nucleotide binding] 402612003015 CRISPR/Cas system-associated protein Cas9; Region: Csn1; cd09643 402612003016 CRISPR-associated protein Cas9/Csn1, subtype II/NMEMI; Region: cas_Csn1; TIGR01865 402612003017 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-II-III; cl00656 402612003018 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cl11442 402612003019 CRISPR spacer 402612003020 CRISPR spacer 402612003021 CRISPR spacer 402612003022 CRISPR spacer 402612003023 CRISPR spacer 402612003024 CRISPR spacer 402612003025 CRISPR spacer 402612003026 CRISPR spacer 402612003027 CRISPR spacer 402612003028 CRISPR spacer 402612003029 CRISPR spacer 402612003030 CRISPR spacer 402612003031 CRISPR spacer 402612003032 CRISPR spacer 402612003033 CRISPR spacer 402612003034 CRISPR spacer 402612003035 CRISPR spacer 402612003036 CRISPR spacer 402612003037 CRISPR spacer 402612003038 CRISPR spacer 402612003039 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 402612003040 Transposase; Region: HTH_Tnp_1; cl17663 402612003041 putative transposase OrfB; Reviewed; Region: PHA02517 402612003042 HTH-like domain; Region: HTH_21; pfam13276 402612003043 Integrase core domain; Region: rve; pfam00665 402612003044 Integrase core domain; Region: rve_3; pfam13683 402612003045 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 402612003046 active site 402612003047 metal binding site [ion binding]; metal-binding site 402612003048 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 402612003049 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 402612003050 Walker A/P-loop; other site 402612003051 ATP binding site [chemical binding]; other site 402612003052 AAA domain; Region: AAA_21; pfam13304 402612003053 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 402612003054 Walker A/P-loop; other site 402612003055 ATP binding site [chemical binding]; other site 402612003056 AAA domain; Region: AAA_21; pfam13304 402612003057 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 402612003058 Predicted transcriptional regulator [Transcription]; Region: COG5340 402612003059 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 402612003060 AAA domain; Region: AAA_17; pfam13207 402612003061 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 402612003062 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 402612003063 Walker A motif; other site 402612003064 ATP binding site [chemical binding]; other site 402612003065 Walker B motif; other site 402612003066 Helix-turn-helix domain; Region: HTH_36; pfam13730 402612003067 Helix-turn-helix domain; Region: HTH_17; pfam12728 402612003068 RteC protein; Region: RteC; pfam09357 402612003069 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 402612003070 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 402612003071 putative substrate translocation pore; other site 402612003072 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 402612003073 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl19134 402612003074 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 402612003075 Tn4399 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases, including cLV25, a Bacteroides fragilis chromosomal transfer factor integrase similar to the...; Region: INT_Tn4399; cd01185 402612003076 Int/Topo IB signature motif; other site 402612003077 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]; Region: COG2865 402612003078 Divergent AAA domain; Region: AAA_4; pfam04326 402612003079 ATP-dependent DNA helicase recG C-terminal; Region: HATPase_c_4; pfam13749 402612003080 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 402612003081 Domain of unknown function (DUF4263); Region: DUF4263; pfam14082 402612003082 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 402612003083 AAA domain; Region: AAA_21; pfam13304 402612003084 AAA domain; Region: AAA_21; pfam13304 402612003085 Protein of unknown function (DUF3812); Region: DUF3812; pfam12757 402612003086 Nuclease-related domain; Region: NERD; pfam08378 402612003087 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 402612003088 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 402612003089 ATP binding site [chemical binding]; other site 402612003090 AAA ATPase domain; Region: AAA_15; pfam13175 402612003091 AAA domain; Region: AAA_23; pfam13476 402612003092 AAA domain; Region: AAA_21; pfam13304 402612003093 Walker A/P-loop; other site 402612003094 ATP binding site [chemical binding]; other site 402612003095 Q-loop/lid; other site 402612003096 AAA domain; Region: AAA_21; pfam13304 402612003097 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 402612003098 putative active site [active] 402612003099 putative metal-binding site [ion binding]; other site 402612003100 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 402612003101 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 402612003102 S-adenosylmethionine binding site [chemical binding]; other site 402612003103 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 402612003104 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 402612003105 Type II restriction enzyme, methylase subunits [Defense mechanisms]; Region: COG1002 402612003106 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 402612003107 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 402612003108 non-specific DNA binding site [nucleotide binding]; other site 402612003109 salt bridge; other site 402612003110 sequence-specific DNA binding site [nucleotide binding]; other site 402612003111 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 402612003112 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 402612003113 Walker A motif; other site 402612003114 ATP binding site [chemical binding]; other site 402612003115 Walker B motif; other site 402612003116 Helix-turn-helix domain; Region: HTH_36; pfam13730 402612003117 Helix-turn-helix domain; Region: HTH_17; pfam12728 402612003118 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 402612003119 Thioesterase-like superfamily; Region: 4HBT_3; pfam13622 402612003120 CoenzymeA binding site [chemical binding]; other site 402612003121 subunit interaction site [polypeptide binding]; other site 402612003122 PHB binding site; other site 402612003123 HD domain protein, cyanamide hydratase family; Region: cyanamide_fam; TIGR03401 402612003124 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 402612003125 Zn2+ binding site [ion binding]; other site 402612003126 Mg2+ binding site [ion binding]; other site 402612003127 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 402612003128 active site 402612003129 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 402612003130 oligomerization interface [polypeptide binding]; other site 402612003131 active site 402612003132 metal binding site [ion binding]; metal-binding site 402612003133 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 402612003134 Ketopantoate reductase [Coenzyme metabolism]; Region: ApbA; COG1893 402612003135 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 402612003136 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 402612003137 Coenzyme A binding pocket [chemical binding]; other site 402612003138 DinB superfamily; Region: DinB_2; pfam12867 402612003139 Protein of unknown function (DUF1572); Region: DUF1572; pfam07609 402612003140 acetyl-CoA C-acetyltransferase; Region: PLN02644 402612003141 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 402612003142 dimer interface [polypeptide binding]; other site 402612003143 active site 402612003144 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 402612003145 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 402612003146 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 402612003147 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 402612003148 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 402612003149 dimerization interface [polypeptide binding]; other site 402612003150 active site 402612003151 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 402612003152 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl19192 402612003153 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 402612003154 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 402612003155 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 402612003156 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 402612003157 Integral membrane undecaprenol kinase and similar enzymes; Region: UDPK_IM_like; cd14265 402612003158 trimer interface [polypeptide binding]; other site 402612003159 putative active site [active] 402612003160 Zn binding site [ion binding]; other site 402612003161 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 402612003162 dimer interface [polypeptide binding]; other site 402612003163 catalytic triad [active] 402612003164 peroxidatic and resolving cysteines [active] 402612003165 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 402612003166 dimerization interface [polypeptide binding]; other site 402612003167 putative DNA binding site [nucleotide binding]; other site 402612003168 putative Zn2+ binding site [ion binding]; other site 402612003169 Methyltransferase domain; Region: Methyltransf_31; pfam13847 402612003170 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 402612003171 S-adenosylmethionine binding site [chemical binding]; other site 402612003172 Low molecular weight phosphatase family; Region: LMWPc; cd00115 402612003173 active site 402612003174 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 402612003175 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 402612003176 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 402612003177 trimer interface [polypeptide binding]; other site 402612003178 active site 402612003179 UDP-GlcNAc binding site [chemical binding]; other site 402612003180 lipid binding site [chemical binding]; lipid-binding site 402612003181 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 402612003182 AMP binding site [chemical binding]; other site 402612003183 active site 402612003184 acyl-activating enzyme (AAE) consensus motif; other site 402612003185 CoA binding site [chemical binding]; other site 402612003186 CAAX protease self-immunity; Region: Abi; pfam02517 402612003187 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 402612003188 catalytic residues [active] 402612003189 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612003190 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 402612003191 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 402612003192 Outer membrane protein beta-barrel family; Region: OMP_b-brl_3; pfam14905 402612003193 fumarate hydratase; Reviewed; Region: fumC; PRK00485 402612003194 Class II fumarases; Region: Fumarase_classII; cd01362 402612003195 active site 402612003196 tetramer interface [polypeptide binding]; other site 402612003197 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 402612003198 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 402612003199 putative substrate translocation pore; other site 402612003200 L-fucose transporter; Provisional; Region: PRK10133; cl17665 402612003201 Predicted permeases [General function prediction only]; Region: RarD; COG2962 402612003202 EamA-like transporter family; Region: EamA; pfam00892 402612003203 EamA-like transporter family; Region: EamA; pfam00892 402612003204 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 402612003205 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 402612003206 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; cl18944 402612003207 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 402612003208 Walker A motif; other site 402612003209 ATP binding site [chemical binding]; other site 402612003210 Walker B motif; other site 402612003211 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 402612003212 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 402612003213 glyceraldehyde-3-phosphate dehydrogenase; Provisional; Region: PTZ00023 402612003214 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 402612003215 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 402612003216 6-phosphofructokinase; Provisional; Region: PRK03202 402612003217 active site 402612003218 ADP/pyrophosphate binding site [chemical binding]; other site 402612003219 dimerization interface [polypeptide binding]; other site 402612003220 allosteric effector site; other site 402612003221 fructose-1,6-bisphosphate binding site; other site 402612003222 Family of unknown function (DUF490); Region: DUF490; pfam04357 402612003223 UGMP family protein; Validated; Region: PRK09604 402612003224 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 402612003225 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 402612003226 Domain of unknown function (DUF4159); Region: DUF4159; pfam13709 402612003227 Zinc-dependent metalloprotease, pappalysin_like subfamily. The pregnancy-associated plasma protein A (PAPP-A or pappalysin-1) cleaves insulin-like growth factor-binding proteins 4 and 5, thereby promoting cell growth by releasing bound growth factor; Region: ZnMc_pappalysin_like; cd04275 402612003228 active site 402612003229 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 402612003230 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 402612003231 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 402612003232 Domain of unknown function (DUF4349); Region: DUF4349; pfam14257 402612003233 Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]; Region: TrpE; COG0147 402612003234 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 402612003235 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 402612003236 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 402612003237 Ligand Binding Site [chemical binding]; other site 402612003238 TilS substrate C-terminal domain; Region: TilS_C; smart00977 402612003239 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 402612003240 Sulfite exporter TauE/SafE; Region: TauE; cl19196 402612003241 Thioredoxin-like; Region: Thioredoxin_7; pfam13899 402612003242 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 402612003243 Tetrahydrodipicolinate N-succinyltransferase N-terminal; Region: THDPS_N_2; pfam14805 402612003244 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 402612003245 trimer interface [polypeptide binding]; other site 402612003246 active site 402612003247 substrate binding site [chemical binding]; other site 402612003248 CoA binding site [chemical binding]; other site 402612003249 Exostosin family; Region: Exostosin; pfam03016 402612003250 Putative lipopolysaccharide-modifying enzyme; Region: CAP10; smart00672 402612003251 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 402612003252 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 402612003253 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 402612003254 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 402612003255 putative metal binding site; other site 402612003256 Putative catalytic domain of uncharacterized prokaryotic polysaccharide deacetylases similar to bacterial PuuE allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA); Region: CE4_PuuE_HpPgdA_like_2; cd10941 402612003257 polysaccharide deacetylase family protein, PEP-CTERM locus subfamily; Region: pepcterm_polyde; TIGR03006 402612003258 putative active site [active] 402612003259 putative catalytic site [active] 402612003260 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 402612003261 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 402612003262 Ligand binding site; other site 402612003263 Putative Catalytic site; other site 402612003264 DXD motif; other site 402612003265 Protein of unknown function (DUF2029); Region: DUF2029; pfam09594 402612003266 The Sema domain, a protein interacting module, of semaphorins and plexins; Region: Sema; cl15693 402612003267 Glycosyl transferases group 1; Region: Glyco_trans_1_4; pfam13692 402612003268 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 402612003269 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 402612003270 active site 402612003271 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 402612003272 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 402612003273 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 402612003274 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 402612003275 NADP-binding site; other site 402612003276 homotetramer interface [polypeptide binding]; other site 402612003277 substrate binding site [chemical binding]; other site 402612003278 homodimer interface [polypeptide binding]; other site 402612003279 active site 402612003280 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 402612003281 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 402612003282 NAD(P) binding site [chemical binding]; other site 402612003283 active site 402612003284 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 402612003285 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 402612003286 active site 402612003287 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 402612003288 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 402612003289 tRNA adenylyltransferase; Region: tRNA_CCA_actino; TIGR02692 402612003290 active site 402612003291 NTP binding site [chemical binding]; other site 402612003292 metal binding triad [ion binding]; metal-binding site 402612003293 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 402612003294 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 402612003295 Zn2+ binding site [ion binding]; other site 402612003296 Mg2+ binding site [ion binding]; other site 402612003297 tRNA nucleotidyltransferase domain 2 putative; Region: tRNA_NucTran2_2; pfam13735 402612003298 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 402612003299 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 402612003300 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 402612003301 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 402612003302 active site 402612003303 phosphorylation site [posttranslational modification] 402612003304 intermolecular recognition site; other site 402612003305 dimerization interface [polypeptide binding]; other site 402612003306 LytTr DNA-binding domain; Region: LytTR; smart00850 402612003307 2TM domain; Region: 2TM; pfam13239 402612003308 2TM domain; Region: 2TM; pfam13239 402612003309 2TM domain; Region: 2TM; pfam13239 402612003310 Histidine kinase; Region: His_kinase; pfam06580 402612003311 2TM domain; Region: 2TM; pfam13239 402612003312 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612003313 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 402612003314 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 402612003315 Plasmid pRiA4b ORF-3-like protein; Region: PRiA4_ORF3; pfam07929 402612003316 23S rRNA-intervening sequence protein; Region: 23S_rRNA_IVP; pfam05635 402612003317 37-kD nucleoid-associated bacterial protein; Region: NA37; pfam04245 402612003318 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 402612003319 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 402612003320 Walker A/P-loop; other site 402612003321 ATP binding site [chemical binding]; other site 402612003322 Q-loop/lid; other site 402612003323 ABC transporter signature motif; other site 402612003324 Walker B; other site 402612003325 D-loop; other site 402612003326 H-loop/switch region; other site 402612003327 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 402612003328 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 402612003329 gliding motility-associated C-terminal domain; Region: Bac_Flav_CTERM; TIGR04131 402612003330 gliding motility-associated C-terminal domain; Region: Bac_Flav_CTERM; TIGR04131 402612003331 gliding motility-associated lipoprotein GldD; Region: GldD_lipo; TIGR03512 402612003332 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 402612003333 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 402612003334 dimer interface [polypeptide binding]; other site 402612003335 ssDNA binding site [nucleotide binding]; other site 402612003336 tetramer (dimer of dimers) interface [polypeptide binding]; other site 402612003337 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 402612003338 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 402612003339 minor groove reading motif; other site 402612003340 helix-hairpin-helix signature motif; other site 402612003341 substrate binding pocket [chemical binding]; other site 402612003342 active site 402612003343 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 402612003344 DNA binding and oxoG recognition site [nucleotide binding] 402612003345 Beta subunit of integration host factor (IHFB); Region: IHF_B; cd13836 402612003346 dimer interface [polypeptide binding]; other site 402612003347 DNA binding site [nucleotide binding] 402612003348 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 402612003349 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 402612003350 homodimer interface [polypeptide binding]; other site 402612003351 oligonucleotide binding site [chemical binding]; other site 402612003352 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 402612003353 Domain of unknown function DUF59; Region: DUF59; pfam01883 402612003354 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 402612003355 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 402612003356 Walker A motif; other site 402612003357 NifU-like domain; Region: NifU; pfam01106 402612003358 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 402612003359 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl19134 402612003360 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 402612003361 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 402612003362 dinuclear metal binding motif [ion binding]; other site 402612003363 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 402612003364 EamA-like transporter family; Region: EamA; pfam00892 402612003365 EamA-like transporter family; Region: EamA; pfam00892 402612003366 Protein of unknown function (DUF2853); Region: DUF2853; pfam11015 402612003367 Pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1- carboxylate synthase (MenD) and related proteins; Region: TPP_PYR_MenD; cd07037 402612003368 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase; Validated; Region: PRK07449 402612003369 dimer interface [polypeptide binding]; other site 402612003370 tetramer interface [polypeptide binding]; other site 402612003371 PYR/PP interface [polypeptide binding]; other site 402612003372 TPP binding site [chemical binding]; other site 402612003373 Thiamine pyrophosphate (TPP) family, SHCHC synthase subfamily, TPP-binding module; composed of proteins similar to Escherichia coli 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) synthase (also called MenD). SHCHC synthase plays a key...; Region: TPP_SHCHC_synthase; cd02009 402612003374 TPP-binding site; other site 402612003375 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 402612003376 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 402612003377 ribosomal protein L11 methyltransferase; Reviewed; Region: prmA; PRK00517 402612003378 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 402612003379 S-adenosylmethionine binding site [chemical binding]; other site 402612003380 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; pfam02617 402612003381 YhhN-like protein; Region: YhhN; pfam07947 402612003382 Sulphur transport; Region: Sulf_transp; pfam04143 402612003383 Uncharacterized conserved protein [Function unknown]; Region: COG1284 402612003384 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 402612003385 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 402612003386 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 402612003387 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 402612003388 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 402612003389 dimerization interface [polypeptide binding]; other site 402612003390 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 402612003391 putative active site [active] 402612003392 heme pocket [chemical binding]; other site 402612003393 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 402612003394 dimer interface [polypeptide binding]; other site 402612003395 phosphorylation site [posttranslational modification] 402612003396 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 402612003397 ATP binding site [chemical binding]; other site 402612003398 Mg2+ binding site [ion binding]; other site 402612003399 G-X-G motif; other site 402612003400 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 402612003401 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 402612003402 Ligand Binding Site [chemical binding]; other site 402612003403 Outer membrane protein family (DUF1597); Region: DUF1597; pfam07642 402612003404 potassium-transporting ATPase subunit C; Provisional; Region: PRK14002 402612003405 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 402612003406 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 402612003407 haloacid dehalogenase-like hydrolase; Region: HAD; cl19137 402612003408 potassium-transporting ATPase subunit A; Provisional; Region: PRK05482 402612003409 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 402612003410 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 402612003411 active site 402612003412 phosphorylation site [posttranslational modification] 402612003413 intermolecular recognition site; other site 402612003414 dimerization interface [polypeptide binding]; other site 402612003415 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 402612003416 Walker A motif; other site 402612003417 ATP binding site [chemical binding]; other site 402612003418 Walker B motif; other site 402612003419 arginine finger; other site 402612003420 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 402612003421 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 402612003422 aspartate aminotransferase; Provisional; Region: PRK07568 402612003423 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 402612003424 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612003425 homodimer interface [polypeptide binding]; other site 402612003426 catalytic residue [active] 402612003427 N-terminal domain of glycoside hydrolase family 94 and related domains; Region: GH94N_like; cl17067 402612003428 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 402612003429 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 402612003430 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 402612003431 active site 402612003432 HIGH motif; other site 402612003433 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 402612003434 KMSKS motif; other site 402612003435 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 402612003436 tRNA binding surface [nucleotide binding]; other site 402612003437 anticodon binding site; other site 402612003438 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 402612003439 Monopolin complex subunit LRS4; Region: LRS4; pfam10422 402612003440 Formimidoylglutamase or HutE; Region: Formimidoylglutamase; cd09988 402612003441 putative active site [active] 402612003442 putative metal binding site [ion binding]; other site 402612003443 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 402612003444 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 402612003445 ATP binding site [chemical binding]; other site 402612003446 Mg++ binding site [ion binding]; other site 402612003447 motif III; other site 402612003448 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 402612003449 nucleotide binding region [chemical binding]; other site 402612003450 ATP-binding site [chemical binding]; other site 402612003451 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 402612003452 Predicted membrane protein (DUF2207); Region: DUF2207; pfam09972 402612003453 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 402612003454 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 402612003455 Pyridoxine 5'-phosphate oxidase C-terminal dimerization region; Region: PNPOx_C; pfam10590 402612003456 ribonuclease Z; Reviewed; Region: PRK00055 402612003457 proline dehydrogenase; Region: PLN02681 402612003458 Proline dehydrogenase; Region: Pro_dh; pfam01619 402612003459 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 402612003460 active site 402612003461 dimer interface [polypeptide binding]; other site 402612003462 metal binding site [ion binding]; metal-binding site 402612003463 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 402612003464 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 402612003465 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 402612003466 catalytic residue [active] 402612003467 Deoxyhypusine synthase; Region: DS; cl00826 402612003468 lysophospholipid transporter LplT; Provisional; Region: PRK11195; cl19150 402612003469 Nucleoside H+ symporter; Region: Nuc_H_symport; pfam03825 402612003470 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 402612003471 cytidylate kinase; Provisional; Region: cmk; PRK00023 402612003472 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 402612003473 AAA domain; Region: AAA_17; pfam13207 402612003474 CMP-binding site; other site 402612003475 The sites determining sugar specificity; other site 402612003476 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 402612003477 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 402612003478 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 402612003479 Walker A motif; other site 402612003480 ATP binding site [chemical binding]; other site 402612003481 Walker B motif; other site 402612003482 arginine finger; other site 402612003483 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 402612003484 Vacuole effluxer Atg22 like; Region: ATG22; pfam11700 402612003485 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 402612003486 putative substrate translocation pore; other site 402612003487 Peptidase family M48; Region: Peptidase_M48; pfam01435 402612003488 Putative lysophospholipase; Region: Hydrolase_4; cl19140 402612003489 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 402612003490 Putative lysophospholipase; Region: Hydrolase_4; cl19140 402612003491 methionine sulfoxide reductase B; Provisional; Region: PRK00222 402612003492 SelR domain; Region: SelR; cl15841 402612003493 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 402612003494 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 402612003495 acyl-activating enzyme (AAE) consensus motif; other site 402612003496 putative AMP binding site [chemical binding]; other site 402612003497 putative active site [active] 402612003498 putative CoA binding site [chemical binding]; other site 402612003499 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 402612003500 Transcriptional regulators [Transcription]; Region: MarR; COG1846 402612003501 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; cl17220 402612003502 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 402612003503 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 402612003504 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 402612003505 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 402612003506 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 402612003507 substrate binding site [chemical binding]; other site 402612003508 oxyanion hole (OAH) forming residues; other site 402612003509 trimer interface [polypeptide binding]; other site 402612003510 23S rRNA-intervening sequence protein; Region: 23S_rRNA_IVP; pfam05635 402612003511 acetyl-CoA acetyltransferase; Provisional; Region: PRK09052 402612003512 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 402612003513 dimer interface [polypeptide binding]; other site 402612003514 active site 402612003515 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 402612003516 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 402612003517 active site 402612003518 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 402612003519 catalytic residues [active] 402612003520 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 402612003521 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 402612003522 dimer interface [polypeptide binding]; other site 402612003523 decamer (pentamer of dimers) interface [polypeptide binding]; other site 402612003524 catalytic triad [active] 402612003525 peroxidatic and resolving cysteines [active] 402612003526 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 402612003527 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 402612003528 dimer interface [polypeptide binding]; other site 402612003529 active site 402612003530 heme binding site [chemical binding]; other site 402612003531 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 402612003532 Putative lysophospholipase; Region: Hydrolase_4; cl19140 402612003533 Putative lysophospholipase; Region: Hydrolase_4; cl19140 402612003534 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612003535 amino acid transporter; Region: 2A0306; TIGR00909 402612003536 Transmembrane amino acid transporter protein; Region: Aa_trans; cl17468 402612003537 C-terminus of AA_permease; Region: AA_permease_C; pfam13906 402612003538 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; cl18945 402612003539 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 402612003540 catalytic residue [active] 402612003541 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 402612003542 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 402612003543 putative DNA binding site [nucleotide binding]; other site 402612003544 putative Zn2+ binding site [ion binding]; other site 402612003545 AsnC family; Region: AsnC_trans_reg; pfam01037 402612003546 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 402612003547 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl19134 402612003548 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 402612003549 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl19134 402612003550 Pyridine nucleotide-disulphide oxidoreductase, dimerization domain; Region: Pyr_redox_dim; pfam02852 402612003551 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 402612003552 E-class dimer interface [polypeptide binding]; other site 402612003553 P-class dimer interface [polypeptide binding]; other site 402612003554 active site 402612003555 Cu2+ binding site [ion binding]; other site 402612003556 Zn2+ binding site [ion binding]; other site 402612003557 LETM1-like protein; Region: LETM1; pfam07766 402612003558 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 402612003559 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 402612003560 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 402612003561 dimerization interface [polypeptide binding]; other site 402612003562 S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_30; cl17711 402612003563 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 402612003564 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and...; Region: PLPDE_IV; cl00224 402612003565 homodimer interface [polypeptide binding]; other site 402612003566 substrate-cofactor binding pocket; other site 402612003567 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612003568 catalytic residue [active] 402612003569 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Deinococcus radiodurans DR2231 protein and its bacterial homologs; Region: NTP-PPase_DR2231_like; cd11530 402612003570 metal binding site [ion binding]; metal-binding site 402612003571 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 402612003572 hydrophobic ligand binding site; other site 402612003573 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 402612003574 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 402612003575 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 402612003576 putative ATP binding site [chemical binding]; other site 402612003577 putative substrate interface [chemical binding]; other site 402612003578 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 402612003579 active site 402612003580 Protein of unknown function (DUF1684); Region: DUF1684; pfam07920 402612003581 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 402612003582 Major Facilitator Superfamily; Region: MFS_1; pfam07690 402612003583 putative substrate translocation pore; other site 402612003584 Penicillinase repressor; Region: Penicillinase_R; pfam03965 402612003585 BlaR1 peptidase M56; Region: Peptidase_M56; pfam05569 402612003586 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 402612003587 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 402612003588 malate:quinone oxidoreductase; Validated; Region: PRK05257 402612003589 Predicted dehydrogenase [General function prediction only]; Region: COG0579 402612003590 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 402612003591 active site 402612003592 catalytic residues [active] 402612003593 metal binding site [ion binding]; metal-binding site 402612003594 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 402612003595 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 402612003596 homodimer interface [polypeptide binding]; other site 402612003597 metal binding site [ion binding]; metal-binding site 402612003598 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 402612003599 homodimer interface [polypeptide binding]; other site 402612003600 active site 402612003601 putative chemical substrate binding site [chemical binding]; other site 402612003602 metal binding site [ion binding]; metal-binding site 402612003603 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819 402612003604 Putative esterase; Region: Esterase; pfam00756 402612003605 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 402612003606 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 402612003607 Domain of unknown function (DUF336); Region: DUF336; pfam03928 402612003608 Uncharacterized proteins of the AP superfamily [General function prediction only]; Region: COG1524 402612003609 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 402612003610 putative enoyl-[acyl-carrier-protein] reductase II; Region: enACPred_II; TIGR03151 402612003611 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 402612003612 FMN binding site [chemical binding]; other site 402612003613 substrate binding site [chemical binding]; other site 402612003614 putative catalytic residue [active] 402612003615 Peptidase S8 family domain, uncharacterized subfamily 9; Region: Peptidases_S8_9; cd07493 402612003616 Subtilase family; Region: Peptidase_S8; pfam00082 402612003617 active site 402612003618 catalytic triad [active] 402612003619 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612003620 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 402612003621 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 402612003622 ABC transporter; Region: ABC_tran_2; pfam12848 402612003623 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 402612003624 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 402612003625 Clp amino terminal domain; Region: Clp_N; pfam02861 402612003626 Clp amino terminal domain; Region: Clp_N; pfam02861 402612003627 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 402612003628 Walker A motif; other site 402612003629 ATP binding site [chemical binding]; other site 402612003630 Walker B motif; other site 402612003631 arginine finger; other site 402612003632 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 402612003633 Walker A motif; other site 402612003634 ATP binding site [chemical binding]; other site 402612003635 Walker B motif; other site 402612003636 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 402612003637 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 402612003638 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 402612003639 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 402612003640 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 402612003641 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 402612003642 Thiamine pyrophosphokinase; Region: TPK; cd07995 402612003643 thiamine pyrophosphokinase; Region: thi_PPkinase; TIGR01378 402612003644 active site 402612003645 dimerization interface [polypeptide binding]; other site 402612003646 thiamine binding site [chemical binding]; other site 402612003647 23S rRNA mA1618 methyltransferase; Provisional; Region: PRK11727 402612003648 Shikimate 5-dehydrogenase [Amino acid transport and metabolism]; Region: AroE; COG0169 402612003649 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 402612003650 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 402612003651 shikimate binding site; other site 402612003652 NAD(P) binding site [chemical binding]; other site 402612003653 TPR repeat; Region: TPR_11; pfam13414 402612003654 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 402612003655 binding surface 402612003656 TPR motif; other site 402612003657 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 402612003658 binding surface 402612003659 TPR motif; other site 402612003660 TPR repeat; Region: TPR_11; pfam13414 402612003661 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 402612003662 binding surface 402612003663 TPR repeat; Region: TPR_11; pfam13414 402612003664 TPR motif; other site 402612003665 TPR repeat; Region: TPR_11; pfam13414 402612003666 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 402612003667 TPR motif; other site 402612003668 binding surface 402612003669 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 402612003670 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase [Coenzyme metabolism]; Region: BioA; COG0161 402612003671 inhibitor-cofactor binding pocket; inhibition site 402612003672 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612003673 OstA-like protein; Region: OstA; cl00844 402612003674 OstA-like protein; Region: OstA; cl00844 402612003675 putative voltage-gated ClC-type chloride channel ClcB; Provisional; Region: PRK01862 402612003676 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 402612003677 Cl- selectivity filter; other site 402612003678 Cl- binding residues [ion binding]; other site 402612003679 pore gating glutamate residue; other site 402612003680 dimer interface [polypeptide binding]; other site 402612003681 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC; Region: CBS_pair_SpoIVFB_EriC_assoc2; cd04613 402612003682 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 402612003683 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 402612003684 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 402612003685 Ligand Binding Site [chemical binding]; other site 402612003686 Protein of unknown function (DUF1003); Region: DUF1003; pfam06210 402612003687 Thermotoga maritima CorA_like subfamily; Region: TmCorA-like_1; cd12828 402612003688 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 402612003689 oligomer interface [polypeptide binding]; other site 402612003690 metal binding site [ion binding]; metal-binding site 402612003691 metal binding site [ion binding]; metal-binding site 402612003692 Cl binding site [ion binding]; other site 402612003693 aspartate ring; other site 402612003694 basic sphincter; other site 402612003695 putative hydrophobic gate; other site 402612003696 periplasmic entrance; other site 402612003697 imidazolonepropionase; Validated; Region: PRK09356 402612003698 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 402612003699 active site 402612003700 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:...; Region: TRX_Fd_family; cd02980 402612003701 dimer interface [polypeptide binding]; other site 402612003702 [2Fe-2S] cluster binding site [ion binding]; other site 402612003703 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 402612003704 Ferritin-like domain; Region: Ferritin; pfam00210 402612003705 ferroxidase diiron center [ion binding]; other site 402612003706 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 402612003707 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 402612003708 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 402612003709 N-terminal plug; other site 402612003710 ligand-binding site [chemical binding]; other site 402612003711 Phosphomannose isomerase [Carbohydrate transport and metabolism]; Region: ManA; COG1482 402612003712 Alpha-Mannosidase Binding Domain of Atg19/34; Region: ABD; cl19057 402612003713 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 402612003714 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 402612003715 catalytic triad [active] 402612003716 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 402612003717 active site 402612003718 Isopentenyldiphosphate isomerase [Lipid metabolism]; Region: Idi; COG1443 402612003719 Isopentenyl diphosphate (IPP) isomerase, a member of the Nudix hydrolase superfamily, is a key enzyme in the isoprenoid biosynthetic pathway. Isoprenoids comprise a large family of natural products including sterols, carotenoids, dolichols and prenylated...; Region: IPP_Isomerase; cd02885 402612003720 active site 402612003721 metal binding site [ion binding]; metal-binding site 402612003722 nudix motif; other site 402612003723 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 402612003724 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 402612003725 RNA binding site [nucleotide binding]; other site 402612003726 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 402612003727 RNA binding site [nucleotide binding]; other site 402612003728 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 402612003729 RNA binding site [nucleotide binding]; other site 402612003730 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 402612003731 RNA binding site [nucleotide binding]; other site 402612003732 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 402612003733 RNA binding site [nucleotide binding]; other site 402612003734 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 402612003735 RNA binding site [nucleotide binding]; other site 402612003736 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 402612003737 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 402612003738 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 402612003739 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 402612003740 active site 402612003741 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 402612003742 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 402612003743 Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]; Region: CrcB; COG0239 402612003744 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl19158 402612003745 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; pfam13557 402612003746 8-amino-7-oxononanoate synthase; Region: bioF; TIGR00858 402612003747 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; cl18945 402612003748 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 402612003749 catalytic residue [active] 402612003750 adenylosuccinate lyase; Provisional; Region: PRK09285 402612003751 Lyase class I_like superfamily: contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase, which catalyze similar beta-elimination reactions; Region: Lyase_I_like; cl00013 402612003752 tetramer interface [polypeptide binding]; other site 402612003753 SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which...; Region: SIRT5_Af1_CobB; cd01412 402612003754 NAD+ binding site [chemical binding]; other site 402612003755 substrate binding site [chemical binding]; other site 402612003756 Zn binding site [ion binding]; other site 402612003757 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 402612003758 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 402612003759 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 402612003760 MMPL family; Region: MMPL; cl14618 402612003761 MMPL family; Region: MMPL; cl14618 402612003762 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 402612003763 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 402612003764 HlyD family secretion protein; Region: HlyD_3; pfam13437 402612003765 Outer membrane efflux protein; Region: OEP; pfam02321 402612003766 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 402612003767 Outer membrane efflux protein; Region: OEP; pfam02321 402612003768 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 402612003769 catalytic residues [active] 402612003770 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 402612003771 active site residue [active] 402612003772 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 402612003773 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 402612003774 active site residue [active] 402612003775 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 402612003776 active site residue [active] 402612003777 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 402612003778 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612003779 helicase 45; Provisional; Region: PTZ00424 402612003780 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 402612003781 ATP binding site [chemical binding]; other site 402612003782 Mg++ binding site [ion binding]; other site 402612003783 motif III; other site 402612003784 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 402612003785 nucleotide binding region [chemical binding]; other site 402612003786 ATP-binding site [chemical binding]; other site 402612003787 Inner membrane complex protein; Region: IMCp; pfam12314 402612003788 RNA recognition motif in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases; Region: RRM_DbpA; cd12252 402612003789 RNA binding site [nucleotide binding]; other site 402612003790 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 402612003791 active site 402612003792 dimerization interface [polypeptide binding]; other site 402612003793 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 402612003794 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 402612003795 active site 402612003796 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 402612003797 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 402612003798 active site 402612003799 catalytic residues [active] 402612003800 metal binding site [ion binding]; metal-binding site 402612003801 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 402612003802 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 402612003803 quinone interaction residues [chemical binding]; other site 402612003804 active site 402612003805 catalytic residues [active] 402612003806 FMN binding site [chemical binding]; other site 402612003807 substrate binding site [chemical binding]; other site 402612003808 bacillithiol system protein YtxJ; Region: B_thiol_YtxJ; TIGR04019 402612003809 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 402612003810 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 402612003811 active site 402612003812 phosphorylation site [posttranslational modification] 402612003813 intermolecular recognition site; other site 402612003814 dimerization interface [polypeptide binding]; other site 402612003815 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 402612003816 DNA binding site [nucleotide binding] 402612003817 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 402612003818 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 402612003819 dimer interface [polypeptide binding]; other site 402612003820 phosphorylation site [posttranslational modification] 402612003821 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 402612003822 ATP binding site [chemical binding]; other site 402612003823 Mg2+ binding site [ion binding]; other site 402612003824 G-X-G motif; other site 402612003825 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 402612003826 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 402612003827 CoA-binding site [chemical binding]; other site 402612003828 ATP-binding [chemical binding]; other site 402612003829 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 402612003830 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 402612003831 active site 402612003832 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 402612003833 Interdomain contacts; other site 402612003834 Cytokine receptor motif; other site 402612003835 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612003836 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 402612003837 Escherichia coli UshA-like family, N-terminal metallophosphatase domain; Region: MPP_UshA_N_like; cd00845 402612003838 active site 402612003839 metal binding site [ion binding]; metal-binding site 402612003840 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 402612003841 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 402612003842 dimer interface [polypeptide binding]; other site 402612003843 active site 402612003844 catalytic residue [active] 402612003845 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 402612003846 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; pfam01192 402612003847 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 402612003848 Flavoprotein; Region: Flavoprotein; cl19190 402612003849 DNA / pantothenate metabolizm flavoprotein; Region: DFP; pfam04127 402612003850 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 402612003851 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 402612003852 Walker A/P-loop; other site 402612003853 ATP binding site [chemical binding]; other site 402612003854 Q-loop/lid; other site 402612003855 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 402612003856 Q-loop/lid; other site 402612003857 ABC transporter signature motif; other site 402612003858 Walker B; other site 402612003859 D-loop; other site 402612003860 H-loop/switch region; other site 402612003861 trans-2-enoyl-CoA reductase; Provisional; Region: PRK13656 402612003862 NAD(P)H binding domain of trans-2-enoyl-CoA reductase; Region: Eno-Rase_NADH_b; pfam12242 402612003863 Trans-2-enoyl-CoA reductase catalytic region; Region: Enoyl_reductase; pfam12241 402612003864 Enoyl reductase FAD binding domain; Region: Eno-Rase_FAD_bd; pfam07055 402612003865 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 402612003866 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 402612003867 nucleotide binding pocket [chemical binding]; other site 402612003868 K-X-D-G motif; other site 402612003869 catalytic site [active] 402612003870 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 402612003871 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 402612003872 Helix-hairpin-helix domain; Region: HHH_5; pfam14520 402612003873 Helix-hairpin-helix motif; Region: HHH_2; pfam12826 402612003874 DNA binding site [nucleotide binding] 402612003875 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 402612003876 Dimer interface [polypeptide binding]; other site 402612003877 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 402612003878 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 402612003879 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 402612003880 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 402612003881 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 402612003882 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 402612003883 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 402612003884 active site 402612003885 phosphorylation site [posttranslational modification] 402612003886 intermolecular recognition site; other site 402612003887 dimerization interface [polypeptide binding]; other site 402612003888 LytTr DNA-binding domain; Region: LytTR; smart00850 402612003889 primosome assembly protein PriA; Validated; Region: PRK05580 402612003890 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 402612003891 ATP binding site [chemical binding]; other site 402612003892 putative Mg++ binding site [ion binding]; other site 402612003893 helicase superfamily c-terminal domain; Region: HELICc; smart00490 402612003894 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 402612003895 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 402612003896 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 402612003897 Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]; Region: NadC; COG0157 402612003898 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 402612003899 dimerization interface [polypeptide binding]; other site 402612003900 active site 402612003901 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 402612003902 Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen...; Region: globin; cd01040 402612003903 heme-binding site [chemical binding]; other site 402612003904 FAD_NAD(P)H binding domain of flavohemoglobin. Flavohemoglobins have a globin domain containing a B-type heme fused with a ferredoxin reductase-like FAD/NAD-binding domain. Flavohemoglobins detoxify nitric oxide (NO) via an NO dioxygenase reaction. The...; Region: flavohem_like_fad_nad_binding; cd06184 402612003905 FAD binding pocket [chemical binding]; other site 402612003906 FAD binding motif [chemical binding]; other site 402612003907 phosphate binding motif [ion binding]; other site 402612003908 beta-alpha-beta structure motif; other site 402612003909 NAD binding pocket [chemical binding]; other site 402612003910 Heme binding pocket [chemical binding]; other site 402612003911 Transcriptional regulator; Region: Rrf2; cl17282 402612003912 Rrf2 family protein; Region: rrf2_super; TIGR00738 402612003913 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 402612003914 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 402612003915 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 402612003916 active site 402612003917 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 402612003918 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 402612003919 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 402612003920 active site 402612003921 WxcM-like, C-terminal; Region: FdtA; pfam05523 402612003922 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 402612003923 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 402612003924 putative ADP-binding pocket [chemical binding]; other site 402612003925 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 402612003926 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 402612003927 Glycosyl transferases group 1; Region: Glyco_trans_1_2; pfam13524 402612003928 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 402612003929 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 402612003930 Zn2+ binding site [ion binding]; other site 402612003931 Mg2+ binding site [ion binding]; other site 402612003932 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 402612003933 synthetase active site [active] 402612003934 NTP binding site [chemical binding]; other site 402612003935 metal binding site [ion binding]; metal-binding site 402612003936 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 402612003937 ACT domain; Region: ACT_4; pfam13291 402612003938 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 402612003939 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 402612003940 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 402612003941 Predicted membrane protein [Function unknown]; Region: COG2860 402612003942 UPF0126 domain; Region: UPF0126; pfam03458 402612003943 UPF0126 domain; Region: UPF0126; pfam03458 402612003944 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 402612003945 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 402612003946 inhibitor-cofactor binding pocket; inhibition site 402612003947 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612003948 catalytic residue [active] 402612003949 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 402612003950 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_10; cd13125 402612003951 isocitrate dehydrogenase; Validated; Region: PRK08299 402612003952 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 402612003953 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 402612003954 ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]; Region: SunT; COG2274 402612003955 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_C39B; cd02418 402612003956 putative active site [active] 402612003957 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 402612003958 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 402612003959 Walker A/P-loop; other site 402612003960 ATP binding site [chemical binding]; other site 402612003961 Q-loop/lid; other site 402612003962 ABC transporter signature motif; other site 402612003963 Walker B; other site 402612003964 D-loop; other site 402612003965 H-loop/switch region; other site 402612003966 radical SAM/SPASM domain Clo7bot peptide maturase; Region: rSAM_Clo7bot; TIGR04334 402612003967 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 402612003968 FeS/SAM binding site; other site 402612003969 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 402612003970 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612003971 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 402612003972 Outer membrane protein beta-barrel family; Region: OMP_b-brl_3; pfam14905 402612003973 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 402612003974 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 402612003975 active site 402612003976 Zn binding site [ion binding]; other site 402612003977 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 402612003978 SmpB-tmRNA interface; other site 402612003979 Uncharacterized conserved protein (DUF2132); Region: DUF2132; pfam09905 402612003980 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 402612003981 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 402612003982 Peptidase M1 family containing bacterial Aminopeptidase N; Region: M1_APN_5; cd09604 402612003983 Zn binding site [ion binding]; other site 402612003984 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 402612003985 active site 402612003986 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 402612003987 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 402612003988 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 402612003989 active site 402612003990 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 402612003991 peptidyl-prolyl isomerase, gliding motility-associated; Region: ppisom_GldI; TIGR03516 402612003992 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 402612003993 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 402612003994 DHH family; Region: DHH; pfam01368 402612003995 DHHA1 domain; Region: DHHA1; pfam02272 402612003996 GMP synthase; Reviewed; Region: guaA; PRK00074 402612003997 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 402612003998 AMP/PPi binding site [chemical binding]; other site 402612003999 candidate oxyanion hole; other site 402612004000 catalytic triad [active] 402612004001 potential glutamine specificity residues [chemical binding]; other site 402612004002 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 402612004003 ATP Binding subdomain [chemical binding]; other site 402612004004 Ligand Binding sites [chemical binding]; other site 402612004005 Dimerization subdomain; other site 402612004006 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 402612004007 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 402612004008 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 402612004009 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 402612004010 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 402612004011 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 402612004012 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 402612004013 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 402612004014 OsmC-like protein; Region: OsmC; pfam02566 402612004015 Protein of unknown function (DUF3820); Region: DUF3820; pfam12843 402612004016 CTP synthetase; Validated; Region: pyrG; PRK05380 402612004017 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 402612004018 Catalytic site [active] 402612004019 active site 402612004020 UTP binding site [chemical binding]; other site 402612004021 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 402612004022 active site 402612004023 putative oxyanion hole; other site 402612004024 catalytic triad [active] 402612004025 membrane protein insertase; Provisional; Region: PRK01318 402612004026 YidC periplasmic domain; Region: YidC_periplas; pfam14849 402612004027 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 402612004028 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 402612004029 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 402612004030 GDP-binding site [chemical binding]; other site 402612004031 ACT binding site; other site 402612004032 IMP binding site; other site 402612004033 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 402612004034 metal binding site 2 [ion binding]; metal-binding site 402612004035 putative DNA binding helix; other site 402612004036 metal binding site 1 [ion binding]; metal-binding site 402612004037 dimer interface [polypeptide binding]; other site 402612004038 structural Zn2+ binding site [ion binding]; other site 402612004039 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 402612004040 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 402612004041 active site 402612004042 oxyanion hole [active] 402612004043 catalytic triad [active] 402612004044 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 402612004045 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 402612004046 active site 402612004047 oxyanion hole [active] 402612004048 catalytic triad [active] 402612004049 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 402612004050 active site 402612004051 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 402612004052 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 402612004053 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 402612004054 S-adenosylmethionine binding site [chemical binding]; other site 402612004055 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 402612004056 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 402612004057 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 402612004058 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK05808 402612004059 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 402612004060 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 402612004061 Protein of unknown function (DUF1015); Region: DUF1015; pfam06245 402612004062 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 402612004063 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 402612004064 catalytic residue [active] 402612004065 23S rRNA-intervening sequence protein; Region: 23S_rRNA_IVP; cl05287 402612004066 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 402612004067 active site 402612004068 catalytic site [active] 402612004069 substrate binding site [chemical binding]; other site 402612004070 Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]; Region: UvrC; COG0322 402612004071 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 402612004072 GIY-YIG motif/motif A; other site 402612004073 active site 402612004074 catalytic site [active] 402612004075 putative DNA binding site [nucleotide binding]; other site 402612004076 metal binding site [ion binding]; metal-binding site 402612004077 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 402612004078 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 402612004079 peptidase T-like protein; Region: PepT-like; TIGR01883 402612004080 metal binding site [ion binding]; metal-binding site 402612004081 dimer interface [polypeptide binding]; other site 402612004082 Bacterial putative lipoprotein (DUF940); Region: DUF940; pfam06082 402612004083 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 402612004084 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 402612004085 ligand binding site [chemical binding]; other site 402612004086 peptide chain release factor 1; Validated; Region: prfA; PRK00591 402612004087 PCRF domain; Region: PCRF; pfam03462 402612004088 RF-1 domain; Region: RF-1; pfam00472 402612004089 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 402612004090 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 402612004091 N-terminal plug; other site 402612004092 ligand-binding site [chemical binding]; other site 402612004093 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 402612004094 Gram-negative bacterial TonB protein C-terminal; Region: TonB_C; cl10048 402612004095 Glu/Leu/Phe/Val dehydrogenase, dimerization domain; Region: ELFV_dehydrog_N; pfam02812 402612004096 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 402612004097 NAD(P) binding pocket [chemical binding]; other site 402612004098 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 402612004099 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 402612004100 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 402612004101 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 402612004102 active site 402612004103 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 402612004104 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 402612004105 metal binding site [ion binding]; metal-binding site 402612004106 dimer interface [polypeptide binding]; other site 402612004107 Protein of unknown function (DUF3810); Region: DUF3810; pfam12725 402612004108 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 402612004109 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 402612004110 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 402612004111 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 402612004112 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 402612004113 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 402612004114 DNA binding residues [nucleotide binding] 402612004115 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 402612004116 putative acyl-acceptor binding pocket; other site 402612004117 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 402612004118 putative active site [active] 402612004119 putative CoA binding site [chemical binding]; other site 402612004120 nudix motif; other site 402612004121 metal binding site [ion binding]; metal-binding site 402612004122 Domain of unknown function (DUF4268); Region: DUF4268; pfam14088 402612004123 Protein of unknown function (DUF4197); Region: DUF4197; pfam13852 402612004124 Plasmid stabilization system protein [General function prediction only]; Region: ParE; COG3668 402612004125 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 402612004126 B12 binding site [chemical binding]; other site 402612004127 cobalt ligand [ion binding]; other site 402612004128 Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]; Region: ArgK; COG1703 402612004129 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 402612004130 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM)-like family; contains proteins similar to MCM, and the large subunit of Streptomyces coenzyme B12-dependent isobutyryl-CoA mutase (ICM). MCM catalyzes the isomerization of...; Region: MM_CoA_mutase; cl00817 402612004131 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 402612004132 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 402612004133 motif 1; other site 402612004134 active site 402612004135 motif 2; other site 402612004136 motif 3; other site 402612004137 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 402612004138 DHHA1 domain; Region: DHHA1; pfam02272 402612004139 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 402612004140 Peptidase family M23; Region: Peptidase_M23; pfam01551 402612004141 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 402612004142 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 402612004143 DNA binding residues [nucleotide binding] 402612004144 LemA family; Region: LemA; cl00742 402612004145 TLP18.3, Psb32 and MOLO-1 founding proteins of phosphatase; Region: TPM; pfam04536 402612004146 TLP18.3, Psb32 and MOLO-1 founding proteins of phosphatase; Region: TPM; cl01535 402612004147 Predicted ATPase [General function prediction only]; Region: COG5293 402612004148 Mitochondrial import receptor subunit Tom22; Region: Tom22; cl11522 402612004149 Uncharacterized protein conserved in bacteria (DUF2326); Region: DUF2326; pfam10088 402612004150 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 402612004151 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 402612004152 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 402612004153 Walker A/P-loop; other site 402612004154 ATP binding site [chemical binding]; other site 402612004155 Q-loop/lid; other site 402612004156 ABC transporter signature motif; other site 402612004157 Walker B; other site 402612004158 D-loop; other site 402612004159 H-loop/switch region; other site 402612004160 GSCFA family; Region: GSCFA; pfam08885 402612004161 Protein of unknown function (DUF4230); Region: DUF4230; pfam14014 402612004162 Biopterin-dependent aromatic amino acid hydroxylase; a family of non-heme, iron(II)-dependent enzymes that includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH), eukaryotic tyrosine hydroxylase (TyrOH) and eukaryotic tryptophan...; Region: arom_aa_hydroxylase; cd00361 402612004163 cofactor binding site; other site 402612004164 metal binding site [ion binding]; metal-binding site 402612004165 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 402612004166 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 402612004167 urocanate hydratase; Provisional; Region: PRK05414 402612004168 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612004169 Domain of unknown function (DUF4494); Region: DUF4494; pfam14902 402612004170 GTP-binding protein Der; Reviewed; Region: PRK00093 402612004171 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 402612004172 G1 box; other site 402612004173 GTP/Mg2+ binding site [chemical binding]; other site 402612004174 Switch I region; other site 402612004175 G2 box; other site 402612004176 Switch II region; other site 402612004177 G3 box; other site 402612004178 G4 box; other site 402612004179 G5 box; other site 402612004180 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 402612004181 G1 box; other site 402612004182 GTP/Mg2+ binding site [chemical binding]; other site 402612004183 Switch I region; other site 402612004184 G2 box; other site 402612004185 G3 box; other site 402612004186 Switch II region; other site 402612004187 G4 box; other site 402612004188 G5 box; other site 402612004189 KH-domain-like of EngA bacterial GTPase enzymes, C-terminal; Region: KH_dom-like; pfam14714 402612004190 GTPase Era; Reviewed; Region: era; PRK00089 402612004191 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 402612004192 G1 box; other site 402612004193 GTP/Mg2+ binding site [chemical binding]; other site 402612004194 Switch I region; other site 402612004195 G2 box; other site 402612004196 Switch II region; other site 402612004197 G3 box; other site 402612004198 G4 box; other site 402612004199 G5 box; other site 402612004200 KH domain; Region: KH_2; pfam07650 402612004201 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 402612004202 HSP70 interaction site [polypeptide binding]; other site 402612004203 KTSC domain; Region: KTSC; pfam13619 402612004204 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 402612004205 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 402612004206 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 402612004207 ABC transporter; Region: ABC_tran_2; pfam12848 402612004208 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 402612004209 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 402612004210 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 402612004211 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 402612004212 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl19134 402612004213 gliding motility associated protien GldN; Region: GldN; TIGR03523 402612004214 gliding motility-associated protein GldM; Region: GldM_gliding; TIGR03517 402612004215 GldM N-terminal domain; Region: GldM_N; pfam12081 402612004216 GldM C-terminal domain; Region: GldM_C; pfam12080 402612004217 gliding motility-associated protein GldL; Region: GldL_gliding; TIGR03513 402612004218 Sulfatase-modifying factor enzyme 1; Region: FGE-sulfatase; cl19582 402612004219 gliding motility-associated lipoprotein GldK; Region: GldK_short; TIGR03529 402612004220 Formimidoylglutamase or HutE; Region: Formimidoylglutamase; cd09988 402612004221 putative active site [active] 402612004222 putative metal binding site [ion binding]; other site 402612004223 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 402612004224 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 402612004225 active site 402612004226 interdomain interaction site; other site 402612004227 putative metal-binding site [ion binding]; other site 402612004228 nucleotide binding site [chemical binding]; other site 402612004229 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 402612004230 domain I; other site 402612004231 DNA binding groove [nucleotide binding] 402612004232 phosphate binding site [ion binding]; other site 402612004233 domain II; other site 402612004234 domain III; other site 402612004235 nucleotide binding site [chemical binding]; other site 402612004236 catalytic site [active] 402612004237 domain IV; other site 402612004238 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 402612004239 Histone H1-like nucleoprotein HC2; Region: HC2; cl19298 402612004240 Protein of unknown function (DUF2490); Region: DUF2490; pfam10677 402612004241 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14329 402612004242 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 402612004243 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 402612004244 TRAM domain; Region: TRAM; pfam01938 402612004245 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 402612004246 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 402612004247 Walker A motif; other site 402612004248 ATP binding site [chemical binding]; other site 402612004249 Walker B motif; other site 402612004250 arginine finger; other site 402612004251 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 402612004252 Lipopolysaccharide-assembly; Region: LptE; pfam04390 402612004253 Tetratricopeptide repeat; Region: TPR_6; pfam13174 402612004254 Preprotein translocase SecG subunit; Region: SecG; pfam03840 402612004255 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 402612004256 oligomerisation interface [polypeptide binding]; other site 402612004257 mobile loop; other site 402612004258 roof hairpin; other site 402612004259 chaperonin GroEL; Reviewed; Region: groEL; PRK12850 402612004260 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 402612004261 ring oligomerisation interface [polypeptide binding]; other site 402612004262 ATP/Mg binding site [chemical binding]; other site 402612004263 stacking interactions; other site 402612004264 hinge regions; other site 402612004265 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 402612004266 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 402612004267 Carbamoylphosphate synthase large subunit (split gene in MJ) [Amino acid transport and metabolism / Nucleotide transport and metabolism]; Region: CarB; COG0458 402612004268 ATP-grasp domain; Region: ATP-grasp_4; cl17255 402612004269 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; smart01096 402612004270 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 402612004271 Carbamoylphosphate synthase large subunit (split gene in MJ) [Amino acid transport and metabolism / Nucleotide transport and metabolism]; Region: CarB; COG0458 402612004272 ATP-grasp domain; Region: ATP-grasp_4; cl17255 402612004273 Inward rectifier potassium channel; Region: IRK; pfam01007 402612004274 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 402612004275 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 402612004276 RmuC family; Region: RmuC; pfam02646 402612004277 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 402612004278 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 402612004279 active site 402612004280 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 402612004281 iron-dicitrate transporter ATP-binding subunit; Provisional; Region: fecE; PRK11231 402612004282 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 402612004283 Walker A/P-loop; other site 402612004284 ATP binding site [chemical binding]; other site 402612004285 Q-loop/lid; other site 402612004286 ABC transporter signature motif; other site 402612004287 Walker B; other site 402612004288 D-loop; other site 402612004289 H-loop/switch region; other site 402612004290 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 402612004291 FAD binding domain; Region: FAD_binding_4; cl19922 402612004292 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 402612004293 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 402612004294 active site 402612004295 asparagine synthase (glutamine-hydrolyzing); Region: asn_synth_AEB; TIGR01536 402612004296 dimer interface [polypeptide binding]; other site 402612004297 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 402612004298 Ligand Binding Site [chemical binding]; other site 402612004299 Molecular Tunnel; other site 402612004300 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 402612004301 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 402612004302 Conserved hypothetical protein (DUF2461); Region: DUF2461; pfam09365 402612004303 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 402612004304 active site residue [active] 402612004305 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 402612004306 catalytic residues [active] 402612004307 recombination protein F; Reviewed; Region: recF; PRK00064 402612004308 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 402612004309 Walker A/P-loop; other site 402612004310 ATP binding site [chemical binding]; other site 402612004311 Q-loop/lid; other site 402612004312 ABC transporter signature motif; other site 402612004313 Walker B; other site 402612004314 D-loop; other site 402612004315 H-loop/switch region; other site 402612004316 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 402612004317 homopentamer interface [polypeptide binding]; other site 402612004318 active site 402612004319 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 402612004320 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and...; Region: PLPDE_IV; cd00449 402612004321 homodimer interface [polypeptide binding]; other site 402612004322 substrate-cofactor binding pocket; other site 402612004323 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612004324 catalytic residue [active] 402612004325 Uncharacterized ACR, COG1678; Region: DUF179; pfam02622 402612004326 histone-like DNA-binding protein HU; Region: HU; cd13831 402612004327 dimer interface [polypeptide binding]; other site 402612004328 DNA binding site [nucleotide binding] 402612004329 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 402612004330 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 402612004331 putative active site [active] 402612004332 substrate binding site [chemical binding]; other site 402612004333 putative cosubstrate binding site; other site 402612004334 catalytic site [active] 402612004335 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 402612004336 substrate binding site [chemical binding]; other site 402612004337 DEAD-like helicases superfamily; Region: DEXDc; smart00487 402612004338 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 402612004339 ATP binding site [chemical binding]; other site 402612004340 putative Mg++ binding site [ion binding]; other site 402612004341 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 402612004342 nucleotide binding region [chemical binding]; other site 402612004343 ATP-binding site [chemical binding]; other site 402612004344 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 402612004345 AAA domain; Region: AAA_28; pfam13521 402612004346 Protein of unknown function (DUF493); Region: DUF493; pfam04359 402612004347 Domain of unknown function (DUF4290); Region: DUF4290; pfam14123 402612004348 EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase); Region: EPSP_synthase; pfam00275 402612004349 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 402612004350 hinge; other site 402612004351 active site 402612004352 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 402612004353 N-acetyl-D-glucosamine binding site [chemical binding]; other site 402612004354 catalytic residue [active] 402612004355 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 402612004356 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612004357 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 402612004358 trimer interface [polypeptide binding]; other site 402612004359 active site 402612004360 dimer interface [polypeptide binding]; other site 402612004361 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 402612004362 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 402612004363 active site 402612004364 Int/Topo IB signature motif; other site 402612004365 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 402612004366 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 402612004367 dimer interface [polypeptide binding]; other site 402612004368 motif 1; other site 402612004369 active site 402612004370 motif 2; other site 402612004371 motif 3; other site 402612004372 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 402612004373 anticodon binding site; other site 402612004374 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 402612004375 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 402612004376 FtsX-like permease family; Region: FtsX; pfam02687 402612004377 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 402612004378 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 402612004379 S-adenosylmethionine binding site [chemical binding]; other site 402612004380 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 402612004381 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 402612004382 Coenzyme A binding pocket [chemical binding]; other site 402612004383 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 402612004384 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 402612004385 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 402612004386 catalytic motif [active] 402612004387 Zn binding site [ion binding]; other site 402612004388 Pyrimidine reductase, riboflavin biosynthesis [Coenzyme metabolism]; Region: RibD; COG1985 402612004389 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 402612004390 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 402612004391 motif II; other site 402612004392 Uncharacterized conserved protein [Function unknown]; Region: COG1739 402612004393 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 402612004394 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 402612004395 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 402612004396 active site clefts [active] 402612004397 zinc binding site [ion binding]; other site 402612004398 dimer interface [polypeptide binding]; other site 402612004399 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 402612004400 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 402612004401 Sulfate transporter family; Region: Sulfate_transp; cl19250 402612004402 Heavy-metal-associated domain; Region: HMA; pfam00403 402612004403 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 402612004404 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 402612004405 exosortase F-associated protein; Region: flavo_near_exo; TIGR04127 402612004406 exosortase family protein XrtF; Region: exoso_Fjoh_1448; TIGR04128 402612004407 GAF domain-containing protein [Signal transduction mechanisms]; Region: COG1956 402612004408 Protein of unknown function (DUF2805); Region: DUF2805; pfam10985 402612004409 Protein of unknown function (DUF2452); Region: DUF2452; pfam10504 402612004410 Flavin Reductases; Region: FlaRed; cl00801 402612004411 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 402612004412 DNA photolyase; Region: DNA_photolyase; pfam00875 402612004413 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 402612004414 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 402612004415 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 402612004416 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 402612004417 cryptochrome, DASH family; Region: crypto_DASH; TIGR02765 402612004418 DNA photolyase; Region: DNA_photolyase; pfam00875 402612004419 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 402612004420 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 402612004421 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 402612004422 NAD(P) binding site [chemical binding]; other site 402612004423 active site 402612004424 Protein of unknown function (DUF2867); Region: DUF2867; pfam11066 402612004425 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 402612004426 16S/18S rRNA binding site [nucleotide binding]; other site 402612004427 S13e-L30e interaction site [polypeptide binding]; other site 402612004428 25S rRNA binding site [nucleotide binding]; other site 402612004429 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 402612004430 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 402612004431 oligomer interface [polypeptide binding]; other site 402612004432 RNA binding site [nucleotide binding]; other site 402612004433 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 402612004434 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 402612004435 RNase E interface [polypeptide binding]; other site 402612004436 trimer interface [polypeptide binding]; other site 402612004437 active site 402612004438 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl17245 402612004439 nucleic acid binding region [nucleotide binding]; other site 402612004440 G-X-X-G motif; other site 402612004441 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 402612004442 RNA binding site [nucleotide binding]; other site 402612004443 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 402612004444 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 402612004445 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 402612004446 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 402612004447 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 402612004448 DNA binding residues [nucleotide binding] 402612004449 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 402612004450 substrate binding site [chemical binding]; other site 402612004451 hexamer interface [polypeptide binding]; other site 402612004452 metal binding site [ion binding]; metal-binding site 402612004453 Glucose-regulated metallo-peptidase M90; Region: Peptidase_M90; cl01267 402612004454 Yqey-like protein; Region: YqeY; pfam09424 402612004455 Cell division GTPase [Cell division and chromosome partitioning]; Region: FtsZ; COG0206 402612004456 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 402612004457 nucleotide binding site [chemical binding]; other site 402612004458 SulA interaction site; other site 402612004459 Cell division ATPase FtsA [Cell division and chromosome partitioning]; Region: ftsA; COG0849 402612004460 Cell division protein FtsA; Region: FtsA; smart00842 402612004461 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 402612004462 nucleotide binding site [chemical binding]; other site 402612004463 Cell division protein FtsA; Region: FtsA; pfam14450 402612004464 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 402612004465 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 402612004466 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 402612004467 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 402612004468 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 402612004469 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 402612004470 active site 402612004471 homodimer interface [polypeptide binding]; other site 402612004472 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 402612004473 UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell envelope biogenesis, outer membrane]; Region: MurD; COG0771 402612004474 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 402612004475 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 402612004476 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 402612004477 Mg++ binding site [ion binding]; other site 402612004478 putative catalytic motif [active] 402612004479 putative substrate binding site [chemical binding]; other site 402612004480 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 402612004481 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 402612004482 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 402612004483 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 402612004484 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 402612004485 Penicillin-binding Protein dimerization domain; Region: PBP_dimer; pfam03717 402612004486 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 402612004487 PASTA domain of PBP2x-like proteins, second repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by...; Region: PASTA_Pbp2x-like_2; cd06575 402612004488 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 402612004489 cell division protein MraZ; Reviewed; Region: PRK00326 402612004490 MraZ protein; Region: MraZ; pfam02381 402612004491 MraZ protein; Region: MraZ; pfam02381 402612004492 Putative lysophospholipase; Region: Hydrolase_4; cl19140 402612004493 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 402612004494 Predicted GTPase [General function prediction only]; Region: COG0218 402612004495 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 402612004496 G1 box; other site 402612004497 GTP/Mg2+ binding site [chemical binding]; other site 402612004498 Switch I region; other site 402612004499 G2 box; other site 402612004500 G3 box; other site 402612004501 Switch II region; other site 402612004502 G4 box; other site 402612004503 G5 box; other site 402612004504 gliding motility-associated protein GldC; Region: GldC; TIGR03515 402612004505 gliding motility-associated lipoprotein GldB; Region: GldB_lipo; TIGR03514 402612004506 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 402612004507 homodimer interface [polypeptide binding]; other site 402612004508 NAD binding pocket [chemical binding]; other site 402612004509 ATP binding pocket [chemical binding]; other site 402612004510 Mg binding site [ion binding]; other site 402612004511 active-site loop [active] 402612004512 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 402612004513 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 402612004514 DNA binding residues [nucleotide binding] 402612004515 dimerization interface [polypeptide binding]; other site 402612004516 DNA primase; Validated; Region: dnaG; PRK05667 402612004517 CHC2 zinc finger; Region: zf-CHC2; cl17510 402612004518 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 402612004519 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 402612004520 active site 402612004521 metal binding site [ion binding]; metal-binding site 402612004522 interdomain interaction site; other site 402612004523 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 402612004524 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 402612004525 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 402612004526 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 402612004527 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 402612004528 DNA binding residues [nucleotide binding] 402612004529 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 402612004530 substrate binding pocket [chemical binding]; other site 402612004531 chain length determination region; other site 402612004532 substrate-Mg2+ binding site; other site 402612004533 catalytic residues [active] 402612004534 aspartate-rich region 1; other site 402612004535 active site lid residues [active] 402612004536 aspartate-rich region 2; other site 402612004537 Predicted Fe-S-cluster redox enzyme [General function prediction only]; Region: COG0820 402612004538 DRE-TIM metallolyase superfamily; Region: DRE_TIM_metallolyase; cl18962 402612004539 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 402612004540 FeS/SAM binding site; other site 402612004541 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 402612004542 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 402612004543 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 402612004544 active site 402612004545 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 402612004546 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 402612004547 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 402612004548 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 402612004549 Walker A motif; other site 402612004550 ATP binding site [chemical binding]; other site 402612004551 Walker B motif; other site 402612004552 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 402612004553 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 402612004554 oligomer interface [polypeptide binding]; other site 402612004555 active site residues [active] 402612004556 Bacterial trigger factor protein (TF); Region: Trigger_N; pfam05697 402612004557 trigger factor; Region: tig; TIGR00115 402612004558 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 402612004559 Membrane protein of unknown function; Region: DUF360; pfam04020 402612004560 Putative lysophospholipase; Region: Hydrolase_4; cl19140 402612004561 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 402612004562 phosphonate ABC transporter, ATP-binding protein; Region: ABC_phnC; TIGR02315 402612004563 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 402612004564 Walker A/P-loop; other site 402612004565 ATP binding site [chemical binding]; other site 402612004566 Q-loop/lid; other site 402612004567 ABC transporter signature motif; other site 402612004568 Walker B; other site 402612004569 D-loop; other site 402612004570 H-loop/switch region; other site 402612004571 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 402612004572 active site 402612004573 hydrophilic channel; other site 402612004574 dimerization interface [polypeptide binding]; other site 402612004575 catalytic residues [active] 402612004576 active site lid [active] 402612004577 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 402612004578 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK01911 402612004579 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 402612004580 Cis (Z)-Isoprenyl Diphosphate Synthases; Region: Cis_IPPS; cd00475 402612004581 active site 402612004582 dimer interface [polypeptide binding]; other site 402612004583 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 402612004584 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 402612004585 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 402612004586 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 402612004587 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 402612004588 Surface antigen; Region: Bac_surface_Ag; pfam01103 402612004589 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 402612004590 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 402612004591 glutamate racemase; Provisional; Region: PRK00865 402612004592 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 402612004593 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 402612004594 trimer interface [polypeptide binding]; other site 402612004595 putative metal binding site [ion binding]; other site 402612004596 Protein of unknown function (DUF3308); Region: DUF3308; pfam11751 402612004597 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; pfam08712 402612004598 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; pfam08712 402612004599 NifU-like domain; Region: NifU; pfam01106 402612004600 Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]; Region: COG1331 402612004601 TRX domain, SSP411 protein family; members of this family are highly conserved proteins present in eukaryotes, bacteria and archaea, about 600-800 amino acids in length, which contain a TRX domain with a redox active CXXC motif. The human/rat protein; Region: SSP411; cd02955 402612004602 catalytic residues [active] 402612004603 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; cl00183 402612004604 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 402612004605 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 402612004606 Glycoprotease family; Region: Peptidase_M22; pfam00814 402612004607 Protoheme IX farnesyltransferase; Region: PT_UbiA_Cox10; cd13957 402612004608 putative active site [active] 402612004609 Heme-copper oxidase subunit III. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The...; Region: Heme_Cu_Oxidase_III_like; cl00211 402612004610 Subunit I/III interface [polypeptide binding]; other site 402612004611 Heme-copper oxidase subunit III. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The...; Region: Heme_Cu_Oxidase_III_like; cl00211 402612004612 Subunit I/III interface [polypeptide binding]; other site 402612004613 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; pfam03626 402612004614 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 402612004615 Cu(I) binding site [ion binding]; other site 402612004616 Protein of unknown function (DUF420); Region: DUF420; pfam04238 402612004617 Domain of unknown function (DUF4403); Region: DUF4403; pfam14356 402612004618 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 402612004619 Outer membrane efflux protein; Region: OEP; pfam02321 402612004620 Outer membrane efflux protein; Region: OEP; pfam02321 402612004621 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 402612004622 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 402612004623 HlyD family secretion protein; Region: HlyD_3; pfam13437 402612004624 Capsule assembly protein Wzi; Region: Caps_assemb_Wzi; pfam14052 402612004625 Class I aldolases; Region: Aldolase_Class_I; cl17187 402612004626 catalytic residue [active] 402612004627 Predicted integral membrane protein [Function unknown]; Region: COG5652 402612004628 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 402612004629 lipoyl attachment site [posttranslational modification]; other site 402612004630 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 402612004631 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 402612004632 cell surface protein SprA; Region: surface_SprA; TIGR04189 402612004633 Motility related/secretion protein; Region: SprA_N; pfam14349 402612004634 Motility related/secretion protein; Region: SprA_N; pfam14349 402612004635 Motility related/secretion protein; Region: SprA_N; pfam14349 402612004636 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 402612004637 RuvA N terminal domain; Region: RuvA_N; pfam01330 402612004638 Helix-hairpin-helix domain; Region: HHH_5; pfam14520 402612004639 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 402612004640 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 402612004641 Malic enzyme, N-terminal domain; Region: malic; pfam00390 402612004642 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 402612004643 putative NAD(P) binding site [chemical binding]; other site 402612004644 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 402612004645 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 402612004646 4Fe-4S double cluster binding domain; Region: Fer4_16; pfam13484 402612004647 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 402612004648 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 402612004649 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 402612004650 Walker A motif; other site 402612004651 ATP binding site [chemical binding]; other site 402612004652 Walker B motif; other site 402612004653 arginine finger; other site 402612004654 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 402612004655 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 402612004656 Transmembrane amino acid transporter protein; Region: Aa_trans; cl17468 402612004657 Peptidase M1 family containing bacterial Aminopeptidase N; Region: M1_APN_5; cd09604 402612004658 Zn binding site [ion binding]; other site 402612004659 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612004660 Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E; Region: GAT1_Peptidase_E; cd03146 402612004661 active site pocket [active] 402612004662 oxyanion hole [active] 402612004663 catalytic triad [active] 402612004664 active site nucleophile [active] 402612004665 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 402612004666 Coenzyme A binding pocket [chemical binding]; other site 402612004667 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 402612004668 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 402612004669 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 402612004670 L,D-transpeptidase catalytic domain; Region: YkuD_2; pfam13645 402612004671 phosphoglyceromutase; Provisional; Region: PRK05434 402612004672 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 402612004673 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 402612004674 active site 402612004675 DNA binding site [nucleotide binding] 402612004676 Int/Topo IB signature motif; other site 402612004677 Methyltransferase domain; Region: Methyltransf_26; pfam13659 402612004678 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 402612004679 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 402612004680 Protein of unknown function (DUF2846); Region: DUF2846; pfam11008 402612004681 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 402612004682 Major Facilitator Superfamily; Region: MFS_1; pfam07690 402612004683 putative substrate translocation pore; other site 402612004684 Methyltransferase domain; Region: Methyltransf_26; pfam13659 402612004685 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 402612004686 EcoRII C terminal; Region: EcoRII-C; pfam09019 402612004687 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 402612004688 cofactor binding site; other site 402612004689 DNA binding site [nucleotide binding] 402612004690 substrate interaction site [chemical binding]; other site 402612004691 Transposase, Mutator family; Region: Transposase_mut; cl19537 402612004692 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3328 402612004693 radical SAM family uncharacterized protein; Region: rSAM_fuse_unch; TIGR03960 402612004694 Protein of unknown function (DUF2931); Region: DUF2931; pfam11153 402612004695 Gram-negative bacterial TonB protein C-terminal; Region: TonB_C; pfam03544 402612004696 Transposase, Mutator family; Region: Transposase_mut; cl19537 402612004697 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3328 402612004698 Fic family protein [Function unknown]; Region: COG3177 402612004699 Fic/DOC family N-terminal; Region: Fic_N; pfam13784 402612004700 Fic/DOC family; Region: Fic; pfam02661 402612004701 P-loop containing region of AAA domain; Region: AAA_29; cl17516 402612004702 AAA domain; Region: AAA_21; pfam13304 402612004703 Fungal Nap binding protein NBP1; Region: NBP1; pfam08537 402612004704 putative transposase OrfB; Reviewed; Region: PHA02517 402612004705 HTH-like domain; Region: HTH_21; pfam13276 402612004706 Integrase core domain; Region: rve; pfam00665 402612004707 Integrase core domain; Region: rve_3; pfam13683 402612004708 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 402612004709 Transposase; Region: HTH_Tnp_1; cl17663 402612004710 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 402612004711 active site 402612004712 phosphorylation site [posttranslational modification] 402612004713 intermolecular recognition site; other site 402612004714 dimerization interface [polypeptide binding]; other site 402612004715 LytTr DNA-binding domain; Region: LytTR; smart00850 402612004716 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 402612004717 active site 402612004718 AAA domain; Region: AAA_21; pfam13304 402612004719 ABC transporter signature motif; other site 402612004720 Walker B; other site 402612004721 D-loop; other site 402612004722 H-loop/switch region; other site 402612004723 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 402612004724 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 402612004725 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 402612004726 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 402612004727 DNA methylase; Region: N6_N4_Mtase; pfam01555 402612004728 Protein of unknown function DUF262; Region: DUF262; pfam03235 402612004729 Protein of unknown function DUF262; Region: DUF262; pfam03235 402612004730 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cl19048 402612004731 Zn binding sites [ion binding]; other site 402612004732 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cl19048 402612004733 Zn binding sites [ion binding]; other site 402612004734 tellurium resistance terB-like protein; Region: terB_like; cd07177 402612004735 metal binding site [ion binding]; metal-binding site 402612004736 VirE N-terminal domain; Region: VirE_N; pfam08800 402612004737 Virulence-associated protein E; Region: VirE; pfam05272 402612004738 Helix-turn-helix domain; Region: HTH_17; pfam12728 402612004739 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 402612004740 Transposase; Region: HTH_Tnp_1; cl17663 402612004741 putative transposase OrfB; Reviewed; Region: PHA02517 402612004742 HTH-like domain; Region: HTH_21; pfam13276 402612004743 Integrase core domain; Region: rve; pfam00665 402612004744 Integrase core domain; Region: rve_3; pfam13683 402612004745 ATPase-like protein; Region: PHA02244 402612004746 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 402612004747 Walker A motif; other site 402612004748 ATP binding site [chemical binding]; other site 402612004749 Walker B motif; other site 402612004750 Transposase, Mutator family; Region: Transposase_mut; cl19537 402612004751 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3328 402612004752 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3666 402612004753 Transposase domain (DUF772); Region: DUF772; pfam05598 402612004754 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 402612004755 Beta-lactamase; Region: Beta-lactamase; pfam00144 402612004756 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 402612004757 binding surface 402612004758 TPR repeat; Region: TPR_11; pfam13414 402612004759 TPR motif; other site 402612004760 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3666 402612004761 Transposase domain (DUF772); Region: DUF772; pfam05598 402612004762 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 402612004763 Divergent AAA domain; Region: AAA_4; pfam04326 402612004764 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 402612004765 Transposase; Region: HTH_Tnp_1; cl17663 402612004766 putative transposase OrfB; Reviewed; Region: PHA02517 402612004767 HTH-like domain; Region: HTH_21; pfam13276 402612004768 Integrase core domain; Region: rve; pfam00665 402612004769 Integrase core domain; Region: rve_3; pfam13683 402612004770 cell envelope integrity inner membrane protein TolA; Provisional; Region: tolA; PRK09510 402612004771 translation initiation factor IF-2; Validated; Region: infB; PRK05306 402612004772 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 402612004773 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 402612004774 G1 box; other site 402612004775 putative GEF interaction site [polypeptide binding]; other site 402612004776 GTP/Mg2+ binding site [chemical binding]; other site 402612004777 Switch I region; other site 402612004778 G2 box; other site 402612004779 G3 box; other site 402612004780 Switch II region; other site 402612004781 G4 box; other site 402612004782 G5 box; other site 402612004783 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 402612004784 Translation-initiation factor 2; Region: IF-2; pfam11987 402612004785 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 402612004786 transcription termination factor NusA; Region: NusA; TIGR01953 402612004787 NusA N-terminal domain; Region: NusA_N; pfam08529 402612004788 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 402612004789 RNA binding site [nucleotide binding]; other site 402612004790 homodimer interface [polypeptide binding]; other site 402612004791 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 402612004792 G-X-X-G motif; other site 402612004793 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 402612004794 G-X-X-G motif; other site 402612004795 hypothetical protein; Validated; Region: PRK02001 402612004796 heptamer interface [polypeptide binding]; other site 402612004797 Sm1 motif; other site 402612004798 hexamer interface [polypeptide binding]; other site 402612004799 RNA binding site [nucleotide binding]; other site 402612004800 Sm2 motif; other site 402612004801 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 402612004802 Ligand Binding Site [chemical binding]; other site 402612004803 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 402612004804 Ligand Binding Site [chemical binding]; other site 402612004805 tellurium resistance terB-like protein; Region: terB_like; cd07177 402612004806 metal binding site [ion binding]; metal-binding site 402612004807 HupE / UreJ protein; Region: HupE_UreJ_2; pfam13795 402612004808 Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the...; Region: deoxycytidylate_deaminase; cd01286 402612004809 catalytic motif [active] 402612004810 Zn binding site [ion binding]; other site 402612004811 C-terminal peptidase (prc); Region: prc; TIGR00225 402612004812 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 402612004813 protein binding site [polypeptide binding]; other site 402612004814 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 402612004815 Catalytic dyad [active] 402612004816 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl19134 402612004817 Multiple antibiotic transporter [Intracellular trafficking and secretion]; Region: MarC; COG2095 402612004818 Protein of unknown function (DUF3109); Region: DUF3109; pfam11307 402612004819 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 402612004820 dimer interface [polypeptide binding]; other site 402612004821 putative radical transfer pathway; other site 402612004822 diiron center [ion binding]; other site 402612004823 tyrosyl radical; other site 402612004824 ribonucleoside--diphosphate reductase large subunit; Region: PLN02437 402612004825 ATP cone domain; Region: ATP-cone; pfam03477 402612004826 Class I ribonucleotide reductase; Region: RNR_I; cd01679 402612004827 active site 402612004828 dimer interface [polypeptide binding]; other site 402612004829 catalytic residues [active] 402612004830 effector binding site; other site 402612004831 R2 peptide binding site; other site 402612004832 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 402612004833 23S rRNA interface [nucleotide binding]; other site 402612004834 L3 interface [polypeptide binding]; other site 402612004835 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 402612004836 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 402612004837 rRNA interaction site [nucleotide binding]; other site 402612004838 S8 interaction site; other site 402612004839 putative laminin-1 binding site; other site 402612004840 elongation factor Ts; Provisional; Region: tsf; PRK09377 402612004841 UBA/TS-N domain; Region: UBA; pfam00627 402612004842 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 402612004843 PAS fold; Region: PAS_3; pfam08447 402612004844 putative active site [active] 402612004845 heme pocket [chemical binding]; other site 402612004846 Transposase, Mutator family; Region: Transposase_mut; cl19537 402612004847 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3328 402612004848 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; cl01604 402612004849 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and...; Region: PLPDE_IV; cl00224 402612004850 homodimer interface [polypeptide binding]; other site 402612004851 substrate-cofactor binding pocket; other site 402612004852 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612004853 catalytic residue [active] 402612004854 dihydroxy-acid dehydratase; Provisional; Region: PRK00911 402612004855 acetolactate synthase, large subunit, biosynthetic type; Region: acolac_lg; TIGR00118 402612004856 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 402612004857 PYR/PP interface [polypeptide binding]; other site 402612004858 dimer interface [polypeptide binding]; other site 402612004859 TPP binding site [chemical binding]; other site 402612004860 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 402612004861 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 402612004862 TPP-binding site [chemical binding]; other site 402612004863 dimer interface [polypeptide binding]; other site 402612004864 acetolactate synthase, small subunit; Region: acolac_sm; TIGR00119 402612004865 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 402612004866 putative valine binding site [chemical binding]; other site 402612004867 dimer interface [polypeptide binding]; other site 402612004868 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 402612004869 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 402612004870 ketol-acid reductoisomerase; Region: ilvC; TIGR00465 402612004871 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 402612004872 threonine dehydratase; Validated; Region: PRK08639 402612004873 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 402612004874 tetramer interface [polypeptide binding]; other site 402612004875 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612004876 catalytic residue [active] 402612004877 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 402612004878 putative Ile/Val binding site [chemical binding]; other site 402612004879 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 402612004880 Major Facilitator Superfamily; Region: MFS_1; pfam07690 402612004881 putative substrate translocation pore; other site 402612004882 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 402612004883 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 402612004884 Coenzyme A binding pocket [chemical binding]; other site 402612004885 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 402612004886 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 402612004887 alanine--tRNA ligase; Region: alaS; TIGR00344 402612004888 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 402612004889 Major Facilitator Superfamily; Region: MFS_1; pfam07690 402612004890 putative substrate translocation pore; other site 402612004891 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl19483 402612004892 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 402612004893 hinge region; other site 402612004894 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 402612004895 putative nucleotide binding site [chemical binding]; other site 402612004896 uridine monophosphate binding site [chemical binding]; other site 402612004897 homohexameric interface [polypeptide binding]; other site 402612004898 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 402612004899 thiazole biosynthesis adenylyltransferase ThiF, E. coli subfamily; Region: adenyl_thiF; TIGR02356 402612004900 ATP binding site [chemical binding]; other site 402612004901 substrate interface [chemical binding]; other site 402612004902 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09240 402612004903 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 402612004904 FeS/SAM binding site; other site 402612004905 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 402612004906 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 402612004907 ThiS interaction site; other site 402612004908 putative active site [active] 402612004909 tetramer interface [polypeptide binding]; other site 402612004910 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 402612004911 thiamine phosphate binding site [chemical binding]; other site 402612004912 active site 402612004913 pyrophosphate binding site [ion binding]; other site 402612004914 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 402612004915 substrate binding site [chemical binding]; other site 402612004916 dimer interface [polypeptide binding]; other site 402612004917 ATP binding site [chemical binding]; other site 402612004918 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 402612004919 thiamine phosphate binding site [chemical binding]; other site 402612004920 active site 402612004921 pyrophosphate binding site [ion binding]; other site 402612004922 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 402612004923 ThiC-associated domain; Region: ThiC-associated; pfam13667 402612004924 ThiC family; Region: ThiC; pfam01964 402612004925 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 402612004926 thiS-thiF/thiG interaction site; other site 402612004927 heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase; Region: ATPase-IB2_Cd; TIGR01512 402612004928 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 402612004929 Soluble P-type ATPase [General function prediction only]; Region: COG4087 402612004930 Acetyl-CoA hydrolase [Energy production and conversion]; Region: ACH1; COG0427 402612004931 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 402612004932 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 402612004933 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 402612004934 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 402612004935 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 402612004936 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 402612004937 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 402612004938 Walker A/P-loop; other site 402612004939 ATP binding site [chemical binding]; other site 402612004940 Q-loop/lid; other site 402612004941 ABC transporter signature motif; other site 402612004942 Walker B; other site 402612004943 D-loop; other site 402612004944 H-loop/switch region; other site 402612004945 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 402612004946 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 402612004947 Biotin-lipoyl like; Region: Biotin_lipoyl_2; cl19169 402612004948 Outer membrane efflux protein; Region: OEP; pfam02321 402612004949 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 402612004950 Outer membrane efflux protein; Region: OEP; pfam02321 402612004951 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 402612004952 active site 402612004953 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 402612004954 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4627 402612004955 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 402612004956 Delta(1)-pyrroline-5-carboxylate dehydrogenase, ALDH families 4 and 17; Region: ALDH_F4-17_P5CDH; cd07123 402612004957 Glutamate binding site [chemical binding]; other site 402612004958 NAD binding site [chemical binding]; other site 402612004959 catalytic residues [active] 402612004960 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 402612004961 S-adenosylmethionine binding site [chemical binding]; other site 402612004962 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 402612004963 putative di-iron ligands [ion binding]; other site 402612004964 aspartate aminotransferase; Provisional; Region: PRK05764 402612004965 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 402612004966 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612004967 homodimer interface [polypeptide binding]; other site 402612004968 catalytic residue [active] 402612004969 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 402612004970 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 402612004971 ATP-grasp domain; Region: ATP-grasp; pfam02222 402612004972 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 402612004973 Polyketide synthase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3321 402612004974 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 402612004975 UDP-glucose 4-epimerase; Region: PLN02240 402612004976 NAD binding site [chemical binding]; other site 402612004977 homodimer interface [polypeptide binding]; other site 402612004978 active site 402612004979 substrate binding site [chemical binding]; other site 402612004980 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 402612004981 inhibitor-cofactor binding pocket; inhibition site 402612004982 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612004983 catalytic residue [active] 402612004984 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 402612004985 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 402612004986 GH3 auxin-responsive promoter; Region: GH3; pfam03321 402612004987 indole-3-acetic acid-amido synthetase; Region: PLN02249 402612004988 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 402612004989 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 402612004990 active site 402612004991 metal binding site [ion binding]; metal-binding site 402612004992 Protein of unknown function (DUF2797); Region: DUF2797; pfam10977 402612004993 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 402612004994 signal peptide peptidase SppA, 67K type; Region: SppA_67K; TIGR00705 402612004995 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 402612004996 tandem repeat interface [polypeptide binding]; other site 402612004997 oligomer interface [polypeptide binding]; other site 402612004998 active site residues [active] 402612004999 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 402612005000 tandem repeat interface [polypeptide binding]; other site 402612005001 oligomer interface [polypeptide binding]; other site 402612005002 active site residues [active] 402612005003 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 402612005004 catalytic center binding site [active] 402612005005 ATP binding site [chemical binding]; other site 402612005006 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 402612005007 Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1; Region: dNK; cd01673 402612005008 Substrate-binding site [chemical binding]; other site 402612005009 Substrate specificity [chemical binding]; other site 402612005010 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 402612005011 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 402612005012 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 402612005013 MutS domain I; Region: MutS_I; pfam01624 402612005014 MutS domain II; Region: MutS_II; pfam05188 402612005015 MutS domain III; Region: MutS_III; pfam05192 402612005016 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 402612005017 Walker A/P-loop; other site 402612005018 ATP binding site [chemical binding]; other site 402612005019 Q-loop/lid; other site 402612005020 ABC transporter signature motif; other site 402612005021 Walker B; other site 402612005022 D-loop; other site 402612005023 H-loop/switch region; other site 402612005024 Predicted NTPase (NACHT family) [Signal transduction mechanisms]; Region: COG5635 402612005025 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 402612005026 Catalytic site [active] 402612005027 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 402612005028 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 402612005029 active site 402612005030 DNA binding site [nucleotide binding] 402612005031 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 402612005032 Domain of unknown function (DUF1737); Region: DUF1737; cl10503 402612005033 D5 N terminal like; Region: D5_N; smart00885 402612005034 phage/plasmid primase, P4 family, C-terminal domain; Region: primase_Cterm; TIGR01613 402612005035 Helix-turn-helix domain; Region: HTH_17; pfam12728 402612005036 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 402612005037 active site 402612005038 Int/Topo IB signature motif; other site 402612005039 DNA binding site [nucleotide binding] 402612005040 Peptidase S46; Region: Peptidase_S46; pfam10459 402612005041 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 402612005042 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 402612005043 cytochrome c oxidase, subunit I; Region: CtaD_CoxA; TIGR02891 402612005044 cytochrome c oxidase, subunit II; Region: CoxB; TIGR02866 402612005045 Cupredoxin superfamily; Region: Cupredoxin; cl19115 402612005046 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 402612005047 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 402612005048 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 402612005049 Protein of unknown function (DUF3341); Region: DUF3341; pfam11821 402612005050 Polysulphide reductase [Energy production and conversion]; Region: COG5557; cl17901 402612005051 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 402612005052 molybdopterin cofactor binding site; other site 402612005053 Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum-...; Region: MopB_CT; cl09929 402612005054 molybdopterin cofactor binding site; other site 402612005055 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 402612005056 4Fe-4S binding domain; Region: Fer4; pfam00037 402612005057 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; cl19102 402612005058 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 402612005059 Cytochrome c; Region: Cytochrom_C; cl11414 402612005060 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cd08168 402612005061 heme-binding residues [chemical binding]; other site 402612005062 Sporulation related domain; Region: SPOR; pfam05036 402612005063 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 402612005064 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 402612005065 DNA binding site [nucleotide binding] 402612005066 active site 402612005067 LysE type translocator; Region: LysE; cl00565 402612005068 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 402612005069 S-adenosylmethionine binding site [chemical binding]; other site 402612005070 Predicted phosphohydrolases [General function prediction only]; Region: Icc; COG1409 402612005071 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 402612005072 putative active site [active] 402612005073 putative metal binding site [ion binding]; other site 402612005074 conserved hypothetical protein; Region: MJ1255; TIGR00661 402612005075 Glycosyltransferase family 28 C-terminal domain; Region: Glyco_tran_28_C; cl19139 402612005076 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 402612005077 PhoU domain; Region: PhoU; pfam01895 402612005078 PhoU domain; Region: PhoU; pfam01895 402612005079 ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: PstB; COG1117 402612005080 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 402612005081 Walker A/P-loop; other site 402612005082 ATP binding site [chemical binding]; other site 402612005083 Q-loop/lid; other site 402612005084 ABC transporter signature motif; other site 402612005085 Walker B; other site 402612005086 D-loop; other site 402612005087 H-loop/switch region; other site 402612005088 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 402612005089 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 402612005090 dimer interface [polypeptide binding]; other site 402612005091 conserved gate region; other site 402612005092 putative PBP binding loops; other site 402612005093 ABC-ATPase subunit interface; other site 402612005094 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstC; COG0573 402612005095 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 402612005096 dimer interface [polypeptide binding]; other site 402612005097 conserved gate region; other site 402612005098 putative PBP binding loops; other site 402612005099 ABC-ATPase subunit interface; other site 402612005100 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; cl19131 402612005101 Phosphate-selective porin O and P; Region: Porin_O_P; cl19535 402612005102 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 402612005103 dimer interface [polypeptide binding]; other site 402612005104 phosphorylation site [posttranslational modification] 402612005105 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 402612005106 ATP binding site [chemical binding]; other site 402612005107 Mg2+ binding site [ion binding]; other site 402612005108 G-X-G motif; other site 402612005109 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 402612005110 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 402612005111 active site 402612005112 phosphorylation site [posttranslational modification] 402612005113 intermolecular recognition site; other site 402612005114 dimerization interface [polypeptide binding]; other site 402612005115 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 402612005116 DNA binding site [nucleotide binding] 402612005117 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612005118 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 402612005119 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 402612005120 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 402612005121 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 402612005122 homodimer interface [polypeptide binding]; other site 402612005123 substrate-cofactor binding pocket; other site 402612005124 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612005125 catalytic residue [active] 402612005126 DinB superfamily; Region: DinB_2; pfam12867 402612005127 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 402612005128 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 402612005129 EamA-like transporter family; Region: EamA; pfam00892 402612005130 EamA-like transporter family; Region: EamA; pfam00892 402612005131 hypothetical protein; Provisional; Region: PRK11820 402612005132 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 402612005133 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 402612005134 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria and archaea; Region: GIY-YIG_unchar_2; cd10447 402612005135 GIY-YIG motif/motif A; other site 402612005136 putative active site [active] 402612005137 putative metal binding site [ion binding]; other site 402612005138 Domain of unknown function (DUF4357); Region: DUF4357; pfam14267 402612005139 Guanylate kinase; Region: Guanylate_kin; pfam00625 402612005140 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 402612005141 catalytic site [active] 402612005142 G-X2-G-X-G-K; other site 402612005143 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 402612005144 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 402612005145 active site 402612005146 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 402612005147 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 402612005148 S-adenosylmethionine binding site [chemical binding]; other site 402612005149 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 402612005150 RimM N-terminal domain; Region: RimM; pfam01782 402612005151 30S ribosomal protein S16; Provisional; Region: rpsP; PRK14520 402612005152 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 402612005153 long tail fiber, proximal subunit; Provisional; Region: 34; PHA02584 402612005154 RNA-binding proteins (RRM domain) [General function prediction only]; Region: COG0724 402612005155 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 402612005156 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 402612005157 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 402612005158 active site 402612005159 catalytic site [active] 402612005160 substrate binding site [chemical binding]; other site 402612005161 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 402612005162 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 402612005163 active site 402612005164 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 402612005165 Helix-hairpin-helix motif; Region: HHH_6; pfam14579 402612005166 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 402612005167 generic binding surface I; other site 402612005168 generic binding surface II; other site 402612005169 Microcin C7 self-immunity protein determines resistance to exogenous microcin C7; Region: Peptidase_S66_mccF_like; cd07062 402612005170 putative dimer interface [polypeptide binding]; other site 402612005171 catalytic triad [active] 402612005172 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 402612005173 dimer interface [polypeptide binding]; other site 402612005174 substrate binding site [chemical binding]; other site 402612005175 metal binding sites [ion binding]; metal-binding site 402612005176 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612005177 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 402612005178 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 402612005179 alpha subunit interface [polypeptide binding]; other site 402612005180 TPP binding site [chemical binding]; other site 402612005181 heterodimer interface [polypeptide binding]; other site 402612005182 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 402612005183 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 402612005184 Ligand binding site [chemical binding]; other site 402612005185 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 402612005186 Electron transfer flavoprotein domain; Region: ETF; pfam01012 402612005187 Ligand Binding Site [chemical binding]; other site 402612005188 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 402612005189 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 402612005190 Bifunctional nuclease; Region: DNase-RNase; pfam02577 402612005191 UvrB/uvrC motif; Region: UVR; pfam02151 402612005192 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 402612005193 dimerization interface [polypeptide binding]; other site 402612005194 active site 402612005195 GLPGLI family protein; Region: GLPGLI; TIGR01200 402612005196 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 402612005197 TonB dependent receptor; Region: TonB_dep_Rec; cl17754 402612005198 2TM domain; Region: 2TM; pfam13239 402612005199 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 402612005200 folate binding site [chemical binding]; other site 402612005201 NADP+ binding site [chemical binding]; other site 402612005202 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 402612005203 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 402612005204 S-adenosylmethionine binding site [chemical binding]; other site 402612005205 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 402612005206 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 402612005207 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 402612005208 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 402612005209 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 402612005210 Surface antigen; Region: Bac_surface_Ag; pfam01103 402612005211 Class II Type A, Fructose-1,6-bisphosphate (FBP) aldolases. The enzyme catalyses the zinc-dependent, reversible aldol condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to form fructose-1,6-bisphosphate. FBP aldolase is...; Region: FBP_aldolase_IIA; cd00946 402612005212 active site 402612005213 intersubunit interface [polypeptide binding]; other site 402612005214 zinc binding site [ion binding]; other site 402612005215 Na+ binding site [ion binding]; other site 402612005216 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl19172 402612005217 FOG: TPR repeat [General function prediction only]; Region: NrfG; COG0457 402612005218 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 402612005219 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 402612005220 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 402612005221 ligand binding site [chemical binding]; other site 402612005222 Protein of unknown function (DUF3308); Region: DUF3308; pfam11751 402612005223 Domain of unknown function DUF11; Region: DUF11; pfam01345 402612005224 C-terminal domain of CHU protein family; Region: CHU_C; pfam13585 402612005225 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 402612005226 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 402612005227 G1 box; other site 402612005228 putative GEF interaction site [polypeptide binding]; other site 402612005229 GTP/Mg2+ binding site [chemical binding]; other site 402612005230 Switch I region; other site 402612005231 G2 box; other site 402612005232 G3 box; other site 402612005233 Switch II region; other site 402612005234 G4 box; other site 402612005235 G5 box; other site 402612005236 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 402612005237 Protein of unknown function (DUF3467); Region: DUF3467; pfam11950 402612005238 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 402612005239 Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; Region: RNAP_beta'_N; cd01609 402612005240 beta and beta' interface [polypeptide binding]; other site 402612005241 beta' and sigma factor interface [polypeptide binding]; other site 402612005242 Zn-binding [ion binding]; other site 402612005243 active site region [active] 402612005244 catalytic site [active] 402612005245 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 402612005246 Rpb1 (beta') - Rpb6 (omega) interaction site [polypeptide binding]; other site 402612005247 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 402612005248 G-loop; other site 402612005249 DNA binding site [nucleotide binding] 402612005250 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 402612005251 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 402612005252 RPB12 interaction site [polypeptide binding]; other site 402612005253 RNA polymerase beta subunit; Region: RNA_pol_Rpb2_1; cl19478 402612005254 RPB1 interaction site [polypeptide binding]; other site 402612005255 RNA polymerase beta subunit external 1 domain; Region: RNA_pol_Rpb2_45; pfam10385 402612005256 RPB10 interaction site [polypeptide binding]; other site 402612005257 RPB11 interaction site [polypeptide binding]; other site 402612005258 RPB3 interaction site [polypeptide binding]; other site 402612005259 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 402612005260 core dimer interface [polypeptide binding]; other site 402612005261 peripheral dimer interface [polypeptide binding]; other site 402612005262 L10 interface [polypeptide binding]; other site 402612005263 L11 interface [polypeptide binding]; other site 402612005264 putative EF-Tu interaction site [polypeptide binding]; other site 402612005265 putative EF-G interaction site [polypeptide binding]; other site 402612005266 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 402612005267 23S rRNA interface [nucleotide binding]; other site 402612005268 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 402612005269 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 402612005270 mRNA/rRNA interface [nucleotide binding]; other site 402612005271 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 402612005272 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 402612005273 23S rRNA interface [nucleotide binding]; other site 402612005274 L7/L12 interface [polypeptide binding]; other site 402612005275 putative thiostrepton binding site; other site 402612005276 L25 interface [polypeptide binding]; other site 402612005277 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 402612005278 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 402612005279 putative homodimer interface [polypeptide binding]; other site 402612005280 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 402612005281 heterodimer interface [polypeptide binding]; other site 402612005282 homodimer interface [polypeptide binding]; other site 402612005283 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; pfam00584 402612005284 elongation factor Tu; Reviewed; Region: PRK12735 402612005285 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 402612005286 G1 box; other site 402612005287 GEF interaction site [polypeptide binding]; other site 402612005288 GTP/Mg2+ binding site [chemical binding]; other site 402612005289 Switch I region; other site 402612005290 G2 box; other site 402612005291 G3 box; other site 402612005292 Switch II region; other site 402612005293 G4 box; other site 402612005294 G5 box; other site 402612005295 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 402612005296 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 402612005297 Antibiotic Binding Site [chemical binding]; other site 402612005298 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 402612005299 30S subunit binding site; other site 402612005300 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 402612005301 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 402612005302 active site 402612005303 DNA binding site [nucleotide binding] 402612005304 Int/Topo IB signature motif; other site 402612005305 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 402612005306 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 402612005307 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 402612005308 active site 402612005309 DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]; Region: ComEA; COG1555 402612005310 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 402612005311 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 402612005312 PspC domain; Region: PspC; cl00864 402612005313 Protein of unknown function (DUF2851); Region: DUF2851; pfam11013 402612005314 an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III; Region: DNA_pol_III_epsilon_like; cd06130 402612005315 active site 402612005316 catalytic site [active] 402612005317 substrate binding site [chemical binding]; other site 402612005318 cystathionine beta-synthase; Region: cysta_beta; TIGR01137 402612005319 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 402612005320 dimer interface [polypeptide binding]; other site 402612005321 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612005322 catalytic residue [active] 402612005323 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 402612005324 Domain of unknown function (DUF4289); Region: DUF4289; pfam14121 402612005325 Susd and RagB outer membrane lipoprotein; Region: SusD-like; pfam12741 402612005326 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 402612005327 starch binding outer membrane protein SusD; Region: SusD; cd08977 402612005328 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 402612005329 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612005330 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 402612005331 Bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 402612005332 RNA/DNA hybrid binding site [nucleotide binding]; other site 402612005333 active site 402612005334 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 402612005335 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 402612005336 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 402612005337 dimer interface [polypeptide binding]; other site 402612005338 putative anticodon binding site; other site 402612005339 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 402612005340 motif 1; other site 402612005341 active site 402612005342 motif 2; other site 402612005343 motif 3; other site 402612005344 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 402612005345 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 402612005346 inhibitor-cofactor binding pocket; inhibition site 402612005347 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612005348 catalytic residue [active] 402612005349 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 402612005350 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 402612005351 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism]; Region: Acd; COG2515 402612005352 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 402612005353 catalytic residue [active] 402612005354 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 402612005355 active site 402612005356 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 402612005357 DnaA N-terminal domain; Region: DnaA_N; pfam11638 402612005358 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 402612005359 Walker A motif; other site 402612005360 ATP binding site [chemical binding]; other site 402612005361 Walker B motif; other site 402612005362 arginine finger; other site 402612005363 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 402612005364 DnaA box-binding interface [nucleotide binding]; other site 402612005365 Low molecular weight phosphatase family; Region: LMWPc; cd00115 402612005366 active site 402612005367 Uncharacterized subfamily of the tetrapyrrole methylase family similar to ribosomal RNA small subunit methyltransferase I (RsmI); Region: RsmI_like; cd11649 402612005368 putative SAM binding site [chemical binding]; other site 402612005369 homodimer interface [polypeptide binding]; other site 402612005370 Transglycosylase-like domain; Region: Transglycosylas; pfam06737 402612005371 YceG-like family; Region: YceG; pfam02618 402612005372 dimerization interface [polypeptide binding]; other site 402612005373 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 402612005374 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 402612005375 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 402612005376 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 402612005377 Diaminopimelate epimerase; Region: DAP_epimerase; cl19724 402612005378 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 402612005379 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 402612005380 PDZ domain of trypsin-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 402612005381 protein binding site [polypeptide binding]; other site 402612005382 glyceraldehyde-3-phosphate dehydrogenase; Reviewed; Region: PRK08289 402612005383 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 402612005384 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 402612005385 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 402612005386 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 402612005387 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 402612005388 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 402612005389 NlpC/P60 family; Region: NLPC_P60; pfam00877 402612005390 NIF3 (NGG1p interacting factor 3); Region: NIF3; pfam01784 402612005391 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3323 402612005392 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 402612005393 Putative zinc ribbon domain; Region: DUF164; pfam02591 402612005394 Putative lysophospholipase; Region: Hydrolase_4; cl19140 402612005395 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 402612005396 Putative lysophospholipase; Region: Hydrolase_4; cl19140 402612005397 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 402612005398 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 402612005399 RNA binding surface [nucleotide binding]; other site 402612005400 Pseudouridine synthase, Escherichia coli RluF like; Region: PseudoU_synth_RluF; cd02554 402612005401 probable active site [active] 402612005402 Ion channel; Region: Ion_trans_2; pfam07885 402612005403 Uncharacterized protein conserved in bacteria (DUF2136); Region: DUF2136; pfam09907 402612005404 Predicted transcription regulator containing HTH domain [Transcription]; Region: COG5499 402612005405 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 402612005406 non-specific DNA binding site [nucleotide binding]; other site 402612005407 salt bridge; other site 402612005408 sequence-specific DNA binding site [nucleotide binding]; other site 402612005409 mechanosensitive channel MscS; Provisional; Region: PRK10334 402612005410 Mechanosensitive ion channel; Region: MS_channel; pfam00924 402612005411 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl19134 402612005412 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl17483 402612005413 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 402612005414 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 402612005415 ATP binding site [chemical binding]; other site 402612005416 putative Mg++ binding site [ion binding]; other site 402612005417 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 402612005418 nucleotide binding region [chemical binding]; other site 402612005419 ATP-binding site [chemical binding]; other site 402612005420 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 402612005421 HRDC domain; Region: HRDC; pfam00570 402612005422 Helix-turn-helix domain; Region: HTH_40; pfam14493 402612005423 KpsF/GutQ family protein; Region: kpsF; TIGR00393 402612005424 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 402612005425 putative active site [active] 402612005426 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 402612005427 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 402612005428 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 402612005429 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 402612005430 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 402612005431 Walker A/P-loop; other site 402612005432 ATP binding site [chemical binding]; other site 402612005433 Q-loop/lid; other site 402612005434 ABC transporter signature motif; other site 402612005435 Walker B; other site 402612005436 D-loop; other site 402612005437 H-loop/switch region; other site 402612005438 YegX is an uncharacterized bacterial protein with a glycosyl hydrolase family 25 (GH25) catalytic domain that is similar in sequence to the CH-type (Chalaropsis-type) lysozymes of the GH25 family of endolysins; Region: GH25_YegX-like; cd06524 402612005439 Glycosyl hydrolases family 25; Region: Glyco_hydro_25; pfam01183 402612005440 active site 402612005441 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 402612005442 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 402612005443 Domain of unknown function (DUF4105); Region: DUF4105; pfam13387 402612005444 Domain of unknown function (DUF4184); Region: DUF4184; pfam13803 402612005445 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 402612005446 Prolyl oligopeptidase family; Region: Peptidase_S9; cl19144 402612005447 exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase; Region: EPS_sugtrans; TIGR03025 402612005448 Bacterial sugar transferase; Region: Bac_transf; pfam02397 402612005449 O-Antigen ligase; Region: Wzy_C; pfam04932 402612005450 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 402612005451 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 402612005452 putative ADP-binding pocket [chemical binding]; other site 402612005453 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 402612005454 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 402612005455 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 402612005456 trimer interface [polypeptide binding]; other site 402612005457 active site 402612005458 substrate binding site [chemical binding]; other site 402612005459 CoA binding site [chemical binding]; other site 402612005460 Methyltransferase domain; Region: Methyltransf_31; pfam13847 402612005461 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 402612005462 S-adenosylmethionine binding site [chemical binding]; other site 402612005463 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 402612005464 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 402612005465 active site 402612005466 N-terminal domain of galactosyltransferase; Region: Glyco_transf_7C; cl17476 402612005467 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 402612005468 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 402612005469 active site 402612005470 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 402612005471 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 402612005472 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 402612005473 trimer interface [polypeptide binding]; other site 402612005474 active site 402612005475 substrate binding site [chemical binding]; other site 402612005476 CoA binding site [chemical binding]; other site 402612005477 UDP-N-acetylglucosamine:LPS N-acetylglucosamine transferase [Cell envelope biogenesis, outer membrane]; Region: MurG; COG0707 402612005478 UDP-N-acetyl-D-glucosamine 2-epimerase, UDP-hydrolysing; Region: NeuC_NnaA; TIGR03568 402612005479 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 402612005480 active site 402612005481 homodimer interface [polypeptide binding]; other site 402612005482 N-acetylneuraminate synthase; Region: NeuB_NnaB; TIGR03569 402612005483 NeuB family; Region: NeuB; pfam03102 402612005484 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 402612005485 NeuB binding interface [polypeptide binding]; other site 402612005486 putative substrate binding site [chemical binding]; other site 402612005487 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 402612005488 ligand binding site; other site 402612005489 tetramer interface; other site 402612005490 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 402612005491 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 402612005492 active site 402612005493 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 402612005494 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 402612005495 active site 402612005496 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 402612005497 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 402612005498 Predicted O-acyltransferase [General function prediction only]; Region: COG3274 402612005499 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 402612005500 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 402612005501 active site 402612005502 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 402612005503 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 402612005504 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 402612005505 inhibitor-cofactor binding pocket; inhibition site 402612005506 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612005507 catalytic residue [active] 402612005508 Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing...; Region: LbH_AT_putative; cd03360 402612005509 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 402612005510 putative trimer interface [polypeptide binding]; other site 402612005511 putative CoA binding site [chemical binding]; other site 402612005512 WbqC-like protein family; Region: WbqC; pfam08889 402612005513 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 402612005514 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 402612005515 Walker A/P-loop; other site 402612005516 ATP binding site [chemical binding]; other site 402612005517 Q-loop/lid; other site 402612005518 ABC transporter signature motif; other site 402612005519 Walker B; other site 402612005520 D-loop; other site 402612005521 H-loop/switch region; other site 402612005522 C-Terminal domain of O-antigenic polysaccharide transporter protein Wzt and related proteins; Region: Wzt_C-like; cd10147 402612005523 putative carbohydrate binding site [chemical binding]; other site 402612005524 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 402612005525 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 402612005526 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612005527 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 402612005528 Capsular polysaccharide biosynthesis protein [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: CapC; COG4464 402612005529 Chain length determinant protein; Region: Wzz; pfam02706 402612005530 tyrosine kinase; Provisional; Region: PRK11519 402612005531 G-rich domain on putative tyrosine kinase; Region: GNVR; pfam13807 402612005532 AAA domain; Region: AAA_31; pfam13614 402612005533 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 402612005534 SLBB domain; Region: SLBB; pfam10531 402612005535 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 402612005536 CoA binding domain; Region: CoA_binding; cl17356 402612005537 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 402612005538 NAD(P) binding site [chemical binding]; other site 402612005539 homodimer interface [polypeptide binding]; other site 402612005540 substrate binding site [chemical binding]; other site 402612005541 active site 402612005542 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 402612005543 inhibitor-cofactor binding pocket; inhibition site 402612005544 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612005545 catalytic residue [active] 402612005546 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 402612005547 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 402612005548 active site 402612005549 metal binding site [ion binding]; metal-binding site 402612005550 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 402612005551 extended (e) SDRs; Region: SDR_e; cd08946 402612005552 NAD(P) binding site [chemical binding]; other site 402612005553 active site 402612005554 substrate binding site [chemical binding]; other site 402612005555 carbamoyl phosphate synthase-like protein; Provisional; Region: PRK12767 402612005556 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 402612005557 Bacterial sugar transferase; Region: Bac_transf; pfam02397 402612005558 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 402612005559 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 402612005560 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 402612005561 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 402612005562 active site 402612005563 homodimer interface [polypeptide binding]; other site 402612005564 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 402612005565 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 402612005566 NAD(P) binding site [chemical binding]; other site 402612005567 active site 402612005568 dTDP-4-dehydrorhamnose 3,5-epimerase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfbC; COG1898 402612005569 WxcM-like, C-terminal; Region: FdtA; pfam05523 402612005570 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 402612005571 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 402612005572 NAD(P) binding site [chemical binding]; other site 402612005573 homodimer interface [polypeptide binding]; other site 402612005574 substrate binding site [chemical binding]; other site 402612005575 active site 402612005576 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 402612005577 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 402612005578 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 402612005579 active site 402612005580 O-Antigen ligase; Region: Wzy_C; pfam04932 402612005581 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 402612005582 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 402612005583 EpsG family; Region: EpsG; pfam14897 402612005584 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 402612005585 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 402612005586 substrate binding site; other site 402612005587 tetramer interface; other site 402612005588 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 402612005589 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 402612005590 NAD binding site [chemical binding]; other site 402612005591 substrate binding site [chemical binding]; other site 402612005592 homodimer interface [polypeptide binding]; other site 402612005593 active site 402612005594 probable UDP-glucose 6-dehydrogenase; Region: PLN02353 402612005595 UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain; Region: UDPG_MGDP_dh_N; pfam03721 402612005596 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 402612005597 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 402612005598 Vi polysaccharide biosynthesis protein TviB; Provisional; Region: PRK15182 402612005599 UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain; Region: UDPG_MGDP_dh_N; pfam03721 402612005600 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 402612005601 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 402612005602 UDP-N-acetylglucosamine 4-epimerase, extended (e) SDRs; Region: UDP_AE_SDR_e; cd05256 402612005603 Vi polysaccharide biosynthesis protein TviC; Provisional; Region: PRK15181 402612005604 NAD binding site [chemical binding]; other site 402612005605 substrate binding site [chemical binding]; other site 402612005606 homodimer interface [polypeptide binding]; other site 402612005607 active site 402612005608 Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane]; Region: GumC; COG3206 402612005609 G-rich domain on putative tyrosine kinase; Region: GNVR; pfam13807 402612005610 capsular exopolysaccharide family; Region: eps_fam; TIGR01007 402612005611 AAA domain; Region: AAA_31; pfam13614 402612005612 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 402612005613 recombination protein RecR; Reviewed; Region: recR; PRK00076 402612005614 RecR protein; Region: RecR; pfam02132 402612005615 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 402612005616 putative active site [active] 402612005617 putative metal-binding site [ion binding]; other site 402612005618 tetramer interface [polypeptide binding]; other site 402612005619 Na(+)/iodide (NIS) and Na(+)/multivitamin (SMVT) cotransporters, and related proteins; solute binding domain; Region: SLC5sbd_NIS-like; cd10326 402612005620 Na binding site [ion binding]; other site 402612005621 CoA binding domain; Region: CoA_binding_2; pfam13380 402612005622 MarC family integral membrane protein; Region: MarC; cl00919 402612005623 Amidinotransferase; Region: Amidinotransf; cl19186 402612005624 23S rRNA-intervening sequence protein; Region: 23S_rRNA_IVP; cl05287 402612005625 Amidinotransferase; Region: Amidinotransf; cl19186 402612005626 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 402612005627 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 402612005628 dimer interface [polypeptide binding]; other site 402612005629 active site 402612005630 citrylCoA binding site [chemical binding]; other site 402612005631 NADH binding [chemical binding]; other site 402612005632 cationic pore residues; other site 402612005633 oxalacetate/citrate binding site [chemical binding]; other site 402612005634 coenzyme A binding site [chemical binding]; other site 402612005635 catalytic triad [active] 402612005636 enolase; Provisional; Region: eno; PRK00077 402612005637 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 402612005638 dimer interface [polypeptide binding]; other site 402612005639 metal binding site [ion binding]; metal-binding site 402612005640 substrate binding pocket [chemical binding]; other site 402612005641 Erythromycin esterase; Region: Erythro_esteras; cl17110 402612005642 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612005643 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 402612005644 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; pfam00988 402612005645 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 402612005646 catalytic site [active] 402612005647 subunit interface [polypeptide binding]; other site 402612005648 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 402612005649 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 402612005650 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 402612005651 alphaNTD homodimer interface [polypeptide binding]; other site 402612005652 alphaNTD - beta interaction site [polypeptide binding]; other site 402612005653 alphaNTD - beta' interaction site [polypeptide binding]; other site 402612005654 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 402612005655 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 402612005656 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 402612005657 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 402612005658 RNA binding surface [nucleotide binding]; other site 402612005659 30S ribosomal protein S11; Validated; Region: PRK05309 402612005660 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 402612005661 Ribosomal protein L36; Region: Ribosomal_L36; pfam00444 402612005662 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 402612005663 rRNA binding site [nucleotide binding]; other site 402612005664 predicted 30S ribosome binding site; other site 402612005665 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 402612005666 SecY translocase; Region: SecY; pfam00344 402612005667 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 402612005668 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 402612005669 23S rRNA binding site [nucleotide binding]; other site 402612005670 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 402612005671 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 402612005672 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 402612005673 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 402612005674 5S rRNA interface [nucleotide binding]; other site 402612005675 L27 interface [polypeptide binding]; other site 402612005676 23S rRNA interface [nucleotide binding]; other site 402612005677 L5 interface [polypeptide binding]; other site 402612005678 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 402612005679 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 402612005680 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 402612005681 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 402612005682 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 402612005683 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 402612005684 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 402612005685 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 402612005686 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 402612005687 RNA binding site [nucleotide binding]; other site 402612005688 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 402612005689 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 402612005690 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 402612005691 putative translocon interaction site; other site 402612005692 23S rRNA interface [nucleotide binding]; other site 402612005693 signal recognition particle (SRP54) interaction site; other site 402612005694 L23 interface [polypeptide binding]; other site 402612005695 trigger factor interaction site; other site 402612005696 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 402612005697 23S rRNA interface [nucleotide binding]; other site 402612005698 5S rRNA interface [nucleotide binding]; other site 402612005699 putative antibiotic binding site [chemical binding]; other site 402612005700 L25 interface [polypeptide binding]; other site 402612005701 L27 interface [polypeptide binding]; other site 402612005702 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 402612005703 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 402612005704 G-X-X-G motif; other site 402612005705 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 402612005706 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 402612005707 putative translocon binding site; other site 402612005708 protein-rRNA interface [nucleotide binding]; other site 402612005709 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 402612005710 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 402612005711 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 402612005712 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 402612005713 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 402612005714 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 402612005715 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 402612005716 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 402612005717 elongation factor G; Reviewed; Region: PRK12739 402612005718 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 402612005719 G1 box; other site 402612005720 putative GEF interaction site [polypeptide binding]; other site 402612005721 GTP/Mg2+ binding site [chemical binding]; other site 402612005722 Switch I region; other site 402612005723 G2 box; other site 402612005724 G3 box; other site 402612005725 Switch II region; other site 402612005726 G4 box; other site 402612005727 G5 box; other site 402612005728 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 402612005729 Elongation Factor G, domain II; Region: EFG_II; pfam14492 402612005730 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 402612005731 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 402612005732 30S ribosomal protein S7; Validated; Region: PRK05302 402612005733 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 402612005734 S17 interaction site [polypeptide binding]; other site 402612005735 S8 interaction site; other site 402612005736 16S rRNA interaction site [nucleotide binding]; other site 402612005737 streptomycin interaction site [chemical binding]; other site 402612005738 23S rRNA interaction site [nucleotide binding]; other site 402612005739 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 402612005740 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 402612005741 Surface antigen; Region: Bac_surface_Ag; pfam01103 402612005742 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 402612005743 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612005744 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 402612005745 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 402612005746 Susd and RagB outer membrane lipoprotein; Region: SusD-like; pfam12741 402612005747 starch binding outer membrane protein SusD; Region: SusD; cd08977 402612005748 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 402612005749 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 402612005750 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 402612005751 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 402612005752 recombination factor protein RarA; Reviewed; Region: PRK13342 402612005753 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 402612005754 Walker A motif; other site 402612005755 ATP binding site [chemical binding]; other site 402612005756 Walker B motif; other site 402612005757 arginine finger; other site 402612005758 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 402612005759 HAD superfamily (subfamily IA) hydrolase, TIGR02254; Region: YjjG/YfnB 402612005760 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 402612005761 motif II; other site 402612005762 hypothetical protein; Reviewed; Region: PRK00024 402612005763 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 402612005764 MPN+ (JAMM) motif; other site 402612005765 Zinc-binding site [ion binding]; other site 402612005766 UDP-N-acetylmuramate-alanine ligase [Cell envelope biogenesis, outer membrane]; Region: MurC; COG0773 402612005767 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 402612005768 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 402612005769 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 402612005770 binding surface 402612005771 Tetratricopeptide repeat; Region: TPR_16; pfam13432 402612005772 TPR motif; other site 402612005773 Peptidase S46; Region: Peptidase_S46; pfam10459 402612005774 LysM domain/BON superfamily protein; Provisional; Region: PRK11198 402612005775 BON domain; Region: BON; pfam04972 402612005776 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 402612005777 GTPase CgtA; Reviewed; Region: obgE; PRK12299 402612005778 GTP1/OBG; Region: GTP1_OBG; pfam01018 402612005779 Obg GTPase; Region: Obg; cd01898 402612005780 G1 box; other site 402612005781 GTP/Mg2+ binding site [chemical binding]; other site 402612005782 Switch I region; other site 402612005783 G2 box; other site 402612005784 G3 box; other site 402612005785 Switch II region; other site 402612005786 G4 box; other site 402612005787 G5 box; other site 402612005788 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 402612005789 Domain of unknown function DUF21; Region: DUF21; pfam01595 402612005790 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 402612005791 Transporter associated domain; Region: CorC_HlyC; smart01091 402612005792 adenylate kinase; Reviewed; Region: adk; PRK00279 402612005793 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 402612005794 AMP-binding site [chemical binding]; other site 402612005795 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 402612005796 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 402612005797 active site 402612005798 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 402612005799 ATP-grasp domain; Region: ATP-grasp_4; cl17255 402612005800 AIR carboxylase; Region: AIRC; pfam00731 402612005801 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 402612005802 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 402612005803 active site 402612005804 Zn binding site [ion binding]; other site 402612005805 UbiA family of prenyltransferases (PTases); Region: PT_UbiA; cl00337 402612005806 glycine dehydrogenase; Provisional; Region: PRK05367 402612005807 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 402612005808 tetramer interface [polypeptide binding]; other site 402612005809 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612005810 catalytic residue [active] 402612005811 Glycine cleavage system protein P (pyridoxal-binding), C-terminal domain [Amino acid transport and metabolism]; Region: GcvP; COG1003 402612005812 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 402612005813 catalytic residue [active] 402612005814 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 402612005815 heme-binding site [chemical binding]; other site 402612005816 3-oxoacyl-[acyl-carrier-protein]; Region: FabH; COG0332 402612005817 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 402612005818 dimer interface [polypeptide binding]; other site 402612005819 active site 402612005820 CoA binding pocket [chemical binding]; other site 402612005821 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 402612005822 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 402612005823 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 402612005824 Probable Catalytic site; other site 402612005825 metal-binding site 402612005826 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 402612005827 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 402612005828 active site 402612005829 Permease; Region: Permease; pfam02405 402612005830 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 402612005831 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 402612005832 Walker A/P-loop; other site 402612005833 ATP binding site [chemical binding]; other site 402612005834 Q-loop/lid; other site 402612005835 ABC transporter signature motif; other site 402612005836 Walker B; other site 402612005837 D-loop; other site 402612005838 H-loop/switch region; other site 402612005839 Domain of unknown function (DUF4145); Region: DUF4145; pfam13643 402612005840 Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]; Region: {ManC}; COG0836 402612005841 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 402612005842 Substrate binding site; other site 402612005843 SprT-like family; Region: SprT-like; cl19237 402612005844 short chain dehydrogenase; Region: adh_short; pfam00106 402612005845 classical (c) SDRs; Region: SDR_c; cd05233 402612005846 NAD(P) binding site [chemical binding]; other site 402612005847 active site 402612005848 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 402612005849 E3 interaction surface; other site 402612005850 lipoyl attachment site [posttranslational modification]; other site 402612005851 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 402612005852 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 402612005853 E3 interaction surface; other site 402612005854 lipoyl attachment site [posttranslational modification]; other site 402612005855 e3 binding domain; Region: E3_binding; pfam02817 402612005856 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 402612005857 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 402612005858 tetramer interface [polypeptide binding]; other site 402612005859 TPP-binding site [chemical binding]; other site 402612005860 heterodimer interface [polypeptide binding]; other site 402612005861 phosphorylation loop region [posttranslational modification] 402612005862 cytidine deaminase, homotetrameric; Region: cyt_deam_tetra; TIGR01354 402612005863 Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on...; Region: cytidine_deaminase; cd01283 402612005864 active site 402612005865 catalytic motif [active] 402612005866 Zn binding site [ion binding]; other site 402612005867 Peptidase C25 family N-terminal domain, found in Arg-gingipain (Rgp), Lys-gingipain (Kgp) and related proteins; Region: Peptidase_C25_N; cd02258 402612005868 active site 402612005869 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612005870 gliding motility-associated lipoprotein GldJ; Region: GldJ; TIGR03524 402612005871 Sulfatase-modifying factor enzyme 1; Region: FGE-sulfatase; cl19582 402612005872 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 402612005873 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 402612005874 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 402612005875 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 402612005876 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 402612005877 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 402612005878 FtsX-like permease family; Region: FtsX; pfam02687 402612005879 Protein of unknown function (DUF1343); Region: DUF1343; pfam07075 402612005880 Putative zinc- or iron-chelating domain; Region: CxxCxxCC; pfam03692 402612005881 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 402612005882 S-adenosylmethionine binding site [chemical binding]; other site 402612005883 Gram-negative bacterial TonB protein C-terminal; Region: TonB_C; pfam03544 402612005884 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 402612005885 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Region: rSAM_QueE_Ecoli; TIGR04322 402612005886 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612005887 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 402612005888 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 402612005889 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 402612005890 binding surface 402612005891 Tetratricopeptide repeat; Region: TPR_16; pfam13432 402612005892 TPR motif; other site 402612005893 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 402612005894 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 402612005895 TPR motif; other site 402612005896 binding surface 402612005897 PBP superfamily domain; Region: PBP_like_2; pfam12849 402612005898 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 402612005899 Gram-negative bacterial TonB protein C-terminal; Region: TonB_C; pfam03544 402612005900 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 402612005901 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 402612005902 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 402612005903 Domain of unknown function DUF87; Region: DUF87; cl19135 402612005904 AAA-like domain; Region: AAA_10; pfam12846 402612005905 Zonular occludens toxin (Zot); Region: Zot; cl17485 402612005906 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 402612005907 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl19134 402612005908 Penicillin amidase; Region: Penicil_amidase; pfam01804 402612005909 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 402612005910 active site 402612005911 Agmatinase and related proteins; Region: Agmatinase-like_2; cd11593 402612005912 putative active site [active] 402612005913 Mn binding site [ion binding]; other site 402612005914 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; cl18945 402612005915 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 402612005916 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 402612005917 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 402612005918 Domain of unknown function (DUF4332); Region: DUF4332; pfam14229 402612005919 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 402612005920 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 402612005921 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 402612005922 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 402612005923 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 402612005924 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 402612005925 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 402612005926 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 402612005927 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 402612005928 NADH-quinone oxidoreductase, chain I; Region: NuoI; TIGR01971 402612005929 4Fe-4S double cluster binding domain; Region: Fer4_16; pfam13484 402612005930 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 402612005931 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 402612005932 catalytic loop [active] 402612005933 iron binding site [ion binding]; other site 402612005934 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 402612005935 NADH-quinone oxidoreductase, F subunit; Region: nuoF_fam; TIGR01959 402612005936 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 402612005937 SLBB domain; Region: SLBB; pfam10531 402612005938 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 402612005939 Thioredoxin-like [2Fe-2S] ferredoxin; Region: 2Fe-2S_thioredx; pfam01257 402612005940 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 402612005941 putative dimer interface [polypeptide binding]; other site 402612005942 [2Fe-2S] cluster binding site [ion binding]; other site 402612005943 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 402612005944 Ni,Fe-hydrogenase III large subunit [Energy production and conversion]; Region: HycE; COG3261 402612005945 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl19197 402612005946 NADH dehydrogenase subunit B; Provisional; Region: PRK14820 402612005947 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 402612005948 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 402612005949 MG2 domain; Region: A2M_N; pfam01835 402612005950 Alpha-2-macroglobulin family N-terminal region; Region: A2M_N_2; pfam07703 402612005951 Alpha-2-macroglobulin family; Region: A2M; pfam00207 402612005952 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 402612005953 surface patch; other site 402612005954 thioester region; other site 402612005955 specificity defining residues; other site 402612005956 penicillin-binding protein 1C; Region: PBP_1c; TIGR02073 402612005957 Transglycosylase; Region: Transgly; pfam00912 402612005958 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 402612005959 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 402612005960 3-hydroxyanthranilate 3,4-dioxygenase; Provisional; Region: PRK13264 402612005961 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 402612005962 putative catalytic site [active] 402612005963 putative metal binding site [ion binding]; other site 402612005964 putative phosphate binding site [ion binding]; other site 402612005965 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612005966 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 402612005967 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 402612005968 GTP-binding protein LepA; Provisional; Region: PRK05433 402612005969 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 402612005970 G1 box; other site 402612005971 putative GEF interaction site [polypeptide binding]; other site 402612005972 GTP/Mg2+ binding site [chemical binding]; other site 402612005973 Switch I region; other site 402612005974 G2 box; other site 402612005975 G3 box; other site 402612005976 Switch II region; other site 402612005977 G4 box; other site 402612005978 G5 box; other site 402612005979 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 402612005980 Elongation Factor G, domain II; Region: EFG_II; pfam14492 402612005981 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 402612005982 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 402612005983 RecX family; Region: RecX; pfam02631 402612005984 Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor...; Region: IPT; cl15674 402612005985 Lamin Tail Domain; Region: LTD; pfam00932 402612005986 Transposase, Mutator family; Region: Transposase_mut; cl19537 402612005987 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3328 402612005988 recombinase A; Provisional; Region: recA; PRK09354 402612005989 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 402612005990 hexamer interface [polypeptide binding]; other site 402612005991 Walker A motif; other site 402612005992 ATP binding site [chemical binding]; other site 402612005993 Walker B motif; other site 402612005994 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 402612005995 putative acyl-acceptor binding pocket; other site 402612005996 tryptophanyl-tRNA synthetase; Reviewed; Region: PRK00927 402612005997 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 402612005998 active site 402612005999 HIGH motif; other site 402612006000 dimer interface [polypeptide binding]; other site 402612006001 KMSKS motif; other site 402612006002 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 402612006003 active site 402612006004 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 402612006005 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 402612006006 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 402612006007 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 402612006008 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 402612006009 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 402612006010 putative dimer interface [polypeptide binding]; other site 402612006011 putative anticodon binding site; other site 402612006012 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 402612006013 homodimer interface [polypeptide binding]; other site 402612006014 motif 1; other site 402612006015 motif 2; other site 402612006016 active site 402612006017 motif 3; other site 402612006018 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 402612006019 MMPL family; Region: MMPL; cl14618 402612006020 MMPL family; Region: MMPL; cl14618 402612006021 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 402612006022 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 402612006023 FMN binding site [chemical binding]; other site 402612006024 active site 402612006025 catalytic residues [active] 402612006026 substrate binding site [chemical binding]; other site 402612006027 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 402612006028 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 402612006029 acyl-activating enzyme (AAE) consensus motif; other site 402612006030 AMP binding site [chemical binding]; other site 402612006031 active site 402612006032 CoA binding site [chemical binding]; other site 402612006033 active site 402612006034 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 402612006035 Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG1233 402612006036 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl19134 402612006037 Predicted exporter [General function prediction only]; Region: COG4258 402612006038 MMPL family; Region: MMPL; cl14618 402612006039 MMPL family; Region: MMPL; cl14618 402612006040 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 402612006041 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 402612006042 putative acyl-acceptor binding pocket; other site 402612006043 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 402612006044 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 402612006045 Ligand binding site; other site 402612006046 Putative Catalytic site; other site 402612006047 DXD motif; other site 402612006048 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; pfam09835 402612006049 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 402612006050 active site 2 [active] 402612006051 active site 1 [active] 402612006052 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 402612006053 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl19192 402612006054 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 402612006055 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 402612006056 NodB motif; other site 402612006057 active site 402612006058 catalytic site [active] 402612006059 metal binding site [ion binding]; metal-binding site 402612006060 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 402612006061 active site 402612006062 3-oxoacyl-(acyl-carrier-protein) synthase [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: FabB; COG0304 402612006063 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 402612006064 dimer interface [polypeptide binding]; other site 402612006065 active site 402612006066 four helix bundle protein; Region: TIGR02436 402612006067 Phosphopantetheine attachment site; Region: PP-binding; cl09936 402612006068 3-oxoacyl-(acyl-carrier-protein) synthase [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: FabB; COG0304 402612006069 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 402612006070 active site 402612006071 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 402612006072 active site 402612006073 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 402612006074 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; cl19580 402612006075 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 402612006076 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 402612006077 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 402612006078 Walker A/P-loop; other site 402612006079 ATP binding site [chemical binding]; other site 402612006080 Q-loop/lid; other site 402612006081 ABC transporter signature motif; other site 402612006082 Walker B; other site 402612006083 D-loop; other site 402612006084 H-loop/switch region; other site 402612006085 HpaII restriction endonuclease; Region: RE_HpaII; pfam09561 402612006086 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 402612006087 cofactor binding site; other site 402612006088 DNA binding site [nucleotide binding] 402612006089 substrate interaction site [chemical binding]; other site 402612006090 NlpC/p60-like transpeptidase; Region: Transpep_BrtH; pfam14399 402612006091 putative active site [active] 402612006092 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 402612006093 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 402612006094 active site 2 [active] 402612006095 active site 1 [active] 402612006096 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK06816 402612006097 "initiating" condensing enzymes are a subclass of decarboxylating condensing enzymes, including beta-ketoacyl [ACP] synthase, type III and polyketide synthases, type III, which include chalcone synthase and related enzymes. They are...; Region: init_cond_enzymes; cd00827 402612006098 dimer interface [polypeptide binding]; other site 402612006099 active site 402612006100 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 402612006101 Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG1233 402612006102 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl19134 402612006103 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 402612006104 putative acyl-acceptor binding pocket; other site 402612006105 Phosphopantetheine attachment site; Region: PP-binding; cl09936 402612006106 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 402612006107 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 402612006108 dimer interface [polypeptide binding]; other site 402612006109 active site 402612006110 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 402612006111 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 402612006112 NAD(P) binding site [chemical binding]; other site 402612006113 active site 402612006114 WG containing repeat; Region: WG_beta_rep; pfam14903 402612006115 WG containing repeat; Region: WG_beta_rep; pfam14903 402612006116 WG containing repeat; Region: WG_beta_rep; pfam14903 402612006117 WG containing repeat; Region: WG_beta_rep; pfam14903 402612006118 WG containing repeat; Region: WG_beta_rep; pfam14903 402612006119 WG containing repeat; Region: WG_beta_rep; pfam14903 402612006120 WG containing repeat; Region: WG_beta_rep; pfam14903 402612006121 Aromatic amino acid lyase; Region: Lyase_aromatic; pfam00221 402612006122 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 402612006123 active sites [active] 402612006124 tetramer interface [polypeptide binding]; other site 402612006125 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl19134 402612006126 geranylgeranyl reductase family; Region: GG-red-SF; TIGR02032 402612006127 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 402612006128 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 402612006129 active site 402612006130 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 402612006131 putative acyl-acceptor binding pocket; other site 402612006132 cytoplasmic asparaginase I; Provisional; Region: ansA; PRK09461 402612006133 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 402612006134 active site 402612006135 homodimer interface [polypeptide binding]; other site 402612006136 Tn4399 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases, including cLV25, a Bacteroides fragilis chromosomal transfer factor integrase similar to the...; Region: INT_Tn4399; cd01185 402612006137 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 402612006138 Int/Topo IB signature motif; other site 402612006139 RteC protein; Region: RteC; pfam09357 402612006140 Helix-turn-helix domain; Region: HTH_17; pfam12728 402612006141 Helix-turn-helix domain; Region: HTH_36; pfam13730 402612006142 hypothetical protein; Validated; Region: PRK08116 402612006143 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; cl18944 402612006144 Walker A motif; other site 402612006145 ATP binding site [chemical binding]; other site 402612006146 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 402612006147 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 402612006148 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 402612006149 type II secretion system protein E; Region: type_II_gspE; TIGR02533 402612006150 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 402612006151 Walker A motif; other site 402612006152 ATP binding site [chemical binding]; other site 402612006153 Walker B motif; other site 402612006154 Type IV pilin PilA; Region: Pilin_PilA; pfam14245 402612006155 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 402612006156 TPR repeat; Region: TPR_11; pfam13414 402612006157 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 402612006158 binding surface 402612006159 TPR motif; other site 402612006160 Lamin Tail Domain; Region: LTD; pfam00932 402612006161 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 402612006162 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 402612006163 Domain of unknown function (DUF1768); Region: DUF1768; pfam08719 402612006164 Transposase IS200 like; Region: Y1_Tnp; cl00848 402612006165 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cd00146 402612006166 gliding motility-associated C-terminal domain; Region: Bac_Flav_CTERM; TIGR04131 402612006167 type II secretion system protein I; Region: gspI; TIGR01707 402612006168 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 402612006169 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 402612006170 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 402612006171 NAD+-dependent alpha-aminoadipic semialdehyde dehydrogenase, ALDH family members 7A1 and 7B; Region: ALDH_F7_AASADH; cd07130 402612006172 tetrameric interface [polypeptide binding]; other site 402612006173 NAD binding site [chemical binding]; other site 402612006174 catalytic residues [active] 402612006175 thiamine-monophosphate kinase; Region: thiL; TIGR01379 402612006176 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 402612006177 ATP binding site [chemical binding]; other site 402612006178 dimerization interface [polypeptide binding]; other site 402612006179 3-oxoacyl-(acyl-carrier-protein) synthase [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: FabB; COG0304 402612006180 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 402612006181 active site 402612006182 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase [Coenzyme metabolism]; Region: BioA; COG0161 402612006183 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 402612006184 inhibitor-cofactor binding pocket; inhibition site 402612006185 pyridoxal 5'-phosphate binding site [chemical binding]; other site 402612006186 catalytic residue [active] 402612006187 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 402612006188 AAA domain; Region: AAA_26; pfam13500 402612006189 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 402612006190 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 402612006191 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 402612006192 C-terminal peptidase (prc); Region: prc; TIGR00225 402612006193 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 402612006194 protein binding site [polypeptide binding]; other site 402612006195 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 402612006196 Catalytic dyad [active] 402612006197 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 402612006198 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 402612006199 Competence protein; Region: Competence; pfam03772 402612006200 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 402612006201 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 402612006202 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 402612006203 POT family; Region: PTR2; cl17359 402612006204 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 402612006205 putative substrate translocation pore; other site 402612006206 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 402612006207 POT family; Region: PTR2; cl17359 402612006208 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 402612006209 putative substrate translocation pore; other site 402612006210 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 402612006211 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 402612006212 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 402612006213 Class II hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR); Region: HMG-CoA_reductase_classII; cd00644 402612006214 homodimer interface [polypeptide binding]; other site 402612006215 catalytic residues [active] 402612006216 NAD binding site [chemical binding]; other site 402612006217 substrate binding pocket [chemical binding]; other site 402612006218 flexible flap; other site 402612006219 Mevalonate kinase [Lipid metabolism]; Region: ERG12; COG1577 402612006220 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 402612006221 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 402612006222 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 402612006223 protein binding site [polypeptide binding]; other site 402612006224 Catalytic dyad [active] 402612006225 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 402612006226 active site 402612006227 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 402612006228 Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane]; Region: MrcB; COG0744 402612006229 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 402612006230 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 402612006231 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 402612006232 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 402612006233 phosphorylation site [posttranslational modification] 402612006234 dimer interface [polypeptide binding]; other site 402612006235 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 402612006236 ATP binding site [chemical binding]; other site 402612006237 Mg2+ binding site [ion binding]; other site 402612006238 G-X-G motif; other site 402612006239 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 402612006240 Domain of unknown function (DUF3127); Region: DUF3127; pfam11325 402612006241 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 402612006242 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 402612006243 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 402612006244 Thioredoxin; Region: Thioredoxin_9; pfam14595 402612006245 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 402612006246 RNA binding site [nucleotide binding]; other site 402612006247 active site 402612006248 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 402612006249 Protein of unknown function (DUF3098); Region: DUF3098; pfam11297 402612006250 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 402612006251 FtsX-like permease family; Region: FtsX; pfam02687 402612006252 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cd01610 402612006253 active site 402612006254 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 402612006255 PAP2_like_5 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_5; cd03394 402612006256 active site 402612006257 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 402612006258 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 402612006259 active site 402612006260 HIGH motif; other site 402612006261 nucleotide binding site [chemical binding]; other site 402612006262 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 402612006263 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 402612006264 active site 402612006265 KMSKS motif; other site 402612006266 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 402612006267 tRNA binding surface [nucleotide binding]; other site 402612006268 Putative neutral zinc metallopeptidase; Region: Zn_peptidase_2; pfam04298 402612006269 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 402612006270 iron-sulfur cluster [ion binding]; other site 402612006271 [2Fe-2S] cluster binding site [ion binding]; other site 402612006272 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 402612006273 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 402612006274 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 402612006275 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 402612006276 nucleotide binding site/active site [active] 402612006277 HIT family signature motif; other site 402612006278 catalytic residue [active] 402612006279 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 402612006280 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 402612006281 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some...; Region: Peptidase_C1; cl00298 402612006282 active site 402612006283 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 402612006284 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 402612006285 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 402612006286 putative active site [active] 402612006287 putative metal binding site [ion binding]; other site 402612006288 DNA-binding transcriptional regulator AsnC; Provisional; Region: PRK11179 402612006289 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 402612006290 putative DNA binding site [nucleotide binding]; other site 402612006291 putative Zn2+ binding site [ion binding]; other site 402612006292 AsnC family; Region: AsnC_trans_reg; pfam01037 402612006293 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; cl19130 402612006294 Saccharopine dehydrogenase; Region: Saccharop_dh; pfam03435 402612006295 Protein of unknown function (DUF423); Region: DUF423; pfam04241 402612006296 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_ATP; cd00484 402612006297 active site 402612006298 substrate-binding site [chemical binding]; other site 402612006299 metal-binding site [ion binding] 402612006300 ATP binding site [chemical binding]; other site 402612006301 ribonuclease P; Reviewed; Region: rnpA; PRK01903 402612006302 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 402612006303 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 402612006304 ATP-grasp domain; Region: ATP-grasp_4; cl17255 402612006305 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 402612006306 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 402612006307 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 402612006308 carboxyltransferase (CT) interaction site; other site 402612006309 biotinylation site [posttranslational modification]; other site 402612006310 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 402612006311 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 402612006312 dimer interface [polypeptide binding]; other site 402612006313 active site 402612006314 CoA binding pocket [chemical binding]; other site 402612006315 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 402612006316 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 402612006317 4-hydroxythreonine-4-phosphate dehydrogenase; Region: pdxA; TIGR00557 402612006318 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 402612006319 Lumazine binding domain; Region: Lum_binding; pfam00677 402612006320 Lumazine binding domain; Region: Lum_binding; pfam00677 402612006321 Protein of unknown function (DUF3078); Region: DUF3078; pfam11276 402612006322 Protein of unknown function (DUF2480); Region: DUF2480; pfam10652 402612006323 FeS assembly SUF system protein; Region: SUF_assoc; TIGR02945 402612006324 Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones]; Region: sufE; COG2166 402612006325 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 402612006326 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 402612006327 catalytic residue [active] 402612006328 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 402612006329 Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]; Region: SufB; COG0719 402612006330 Uncharacterized protein family (UPF0051); Region: UPF0051; pfam01458 402612006331 FeS assembly ATPase SufC; Region: sufC; TIGR01978 402612006332 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 402612006333 Walker A/P-loop; other site 402612006334 ATP binding site [chemical binding]; other site 402612006335 Q-loop/lid; other site 402612006336 ABC transporter signature motif; other site 402612006337 Walker B; other site 402612006338 D-loop; other site 402612006339 H-loop/switch region; other site 402612006340 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814 402612006341 Uncharacterized protein family (UPF0051); Region: UPF0051; pfam01458 402612006342 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 402612006343 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 402612006344 Peptidase S8 family domain in Subtilisin_Novo-like proteins; Region: Peptidases_S8_Subtilisin_Novo-like; cd07483 402612006345 catalytic triad [active] 402612006346 Subtilase family; Region: Peptidase_S8; pfam00082 402612006347 active site 402612006348 Peptidase M1 family containing bacterial Aminopeptidase N; Region: M1_APN_5; cd09604 402612006349 Zn binding site [ion binding]; other site 402612006350 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 402612006351 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 402612006352 MMPL family; Region: MMPL; cl14618 402612006353 UbiA family of prenyltransferases (PTases); Region: PT_UbiA; cl00337 402612006354 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 402612006355 Biotin-lipoyl like; Region: Biotin_lipoyl_2; cl19169 402612006356 HlyD family secretion protein; Region: HlyD_3; pfam13437 402612006357 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 402612006358 Outer membrane efflux protein; Region: OEP; pfam02321 402612006359 Outer membrane efflux protein; Region: OEP; pfam02321 402612006360 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 402612006361 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 402612006362 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 402612006363 substrate binding pocket [chemical binding]; other site 402612006364 chain length determination region; other site 402612006365 substrate-Mg2+ binding site; other site 402612006366 catalytic residues [active] 402612006367 aspartate-rich region 1; other site 402612006368 active site lid residues [active] 402612006369 aspartate-rich region 2; other site 402612006370 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 402612006371 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 402612006372 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 402612006373 TPP-binding site [chemical binding]; other site 402612006374 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 402612006375 dimer interface [polypeptide binding]; other site 402612006376 PYR/PP interface [polypeptide binding]; other site 402612006377 TPP binding site [chemical binding]; other site 402612006378 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 402612006379 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 402612006380 E3 interaction surface; other site 402612006381 lipoyl attachment site [posttranslational modification]; other site 402612006382 e3 binding domain; Region: E3_binding; pfam02817 402612006383 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 402612006384 Major Facilitator Superfamily; Region: MFS_1; pfam07690 402612006385 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 402612006386 putative substrate translocation pore; other site 402612006387 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 402612006388 binding surface 402612006389 TPR motif; other site 402612006390 TPR repeat; Region: TPR_11; pfam13414 402612006391 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 402612006392 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 402612006393 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 402612006394 ligand binding site [chemical binding]; other site 402612006395 Protein of unknown function (DUF3308); Region: DUF3308; pfam11751 402612006396 Fibronectin type III domain; Region: fn3; pfam00041 402612006397 Fibronectin type III domain; Region: fn3; pfam00041 402612006398 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 402612006399 Interdomain contacts; other site 402612006400 Cytokine receptor motif; other site 402612006401 CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast; Region: CUB; cd00041 402612006402 heterodimerization interface [polypeptide binding]; other site 402612006403 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 402612006404 Interdomain contacts; other site 402612006405 Cytokine receptor motif; other site 402612006406 C-terminal domain of CHU protein family; Region: CHU_C; pfam13585 402612006407 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 402612006408 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 402612006409 HflX GTPase family; Region: HflX; cd01878 402612006410 G1 box; other site 402612006411 GTP/Mg2+ binding site [chemical binding]; other site 402612006412 Switch I region; other site 402612006413 G2 box; other site 402612006414 G3 box; other site 402612006415 Switch II region; other site 402612006416 G4 box; other site 402612006417 G5 box; other site 402612006418 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 402612006419 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 402612006420 FtsX-like permease family; Region: FtsX; pfam02687 402612006421 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 402612006422 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 402612006423 purine monophosphate binding site [chemical binding]; other site 402612006424 dimer interface [polypeptide binding]; other site 402612006425 putative catalytic residues [active] 402612006426 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 402612006427 rod shape-determining protein MreB; Provisional; Region: PRK13927 402612006428 MreB and similar proteins; Region: MreB_like; cd10225 402612006429 nucleotide binding site [chemical binding]; other site 402612006430 Mg binding site [ion binding]; other site 402612006431 putative protofilament interaction site [polypeptide binding]; other site 402612006432 RodZ interaction site [polypeptide binding]; other site 402612006433 rod shape-determining protein MreC; Provisional; Region: PRK13922 402612006434 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 402612006435 Penicillin-binding Protein dimerization domain; Region: PBP_dimer; pfam03717 402612006436 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 402612006437 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 402612006438 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; cd00091 402612006439 active site 402612006440 substrate binding site [chemical binding]; other site 402612006441 Mg2+ binding site [ion binding]; other site 402612006442 Bacterial Ig-like domain; Region: Big_5; pfam13205 402612006443 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 402612006444 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 402612006445 active site 402612006446 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 402612006447 glycyl-tRNA synthetase; Provisional; Region: PRK04173 402612006448 Glycyl-tRNA synthetase (GlyRS)-like class II core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes. It is responsible for the attachment of glycine to the 3...; Region: GlyRS-like_core; cd00774 402612006449 dimer interface [polypeptide binding]; other site 402612006450 motif 1; other site 402612006451 active site 402612006452 motif 2; other site 402612006453 motif 3; other site 402612006454 GlyRS Glycyl-anticodon binding domain. GlyRS 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: GlyRS_anticodon; cd00858 402612006455 anticodon binding site; other site 402612006456 SurA N-terminal domain; Region: SurA_N_3; cl07813 402612006457 PPIC-type PPIASE domain; Region: Rotamase_3; pfam13616 402612006458 Lipopolysaccharide-assembly, LptC-related; Region: LptC; cl01200 402612006459 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 402612006460 pantothenate kinase; Reviewed; Region: PRK13320 402612006461 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 402612006462 Helix-hairpin-helix domain; Region: HHH_5; pfam14520 402612006463 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 402612006464 Sporulation related domain; Region: SPOR; pfam05036 402612006465 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 402612006466 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 402612006467 Peptidase family M23; Region: Peptidase_M23; pfam01551 402612006468 Domain of unknown function (DUF4292); Region: DUF4292; pfam14125 402612006469 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 402612006470 binding surface 402612006471 TPR motif; other site 402612006472 TPR repeat; Region: TPR_11; pfam13414 402612006473 Putative lysophospholipase; Region: Hydrolase_4; cl19140 402612006474 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 402612006475 Plasmid encoded toxin Txe; Region: Plasmid_Txe; cl17389 402612006476 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 402612006477 glucose-1-phosphate thymidylylransferase, long form; Region: rmlA_long; TIGR01208 402612006478 NTP_transferases catalyze the transfer of nucleotides onto phosphosugars; Region: NTP_transferase; cd04181 402612006479 active site 402612006480 Substrate binding site; other site 402612006481 Mg++ binding site; other site 402612006482 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 402612006483 putative trimer interface [polypeptide binding]; other site 402612006484 putative CoA binding site [chemical binding]; other site 402612006485 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 402612006486 trimer interface [polypeptide binding]; other site 402612006487 active site 402612006488 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 402612006489 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 402612006490 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 402612006491 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 402612006492 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 402612006493 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 402612006494 putative substrate translocation pore; other site 402612006495 IucA / IucC family; Region: IucA_IucC; pfam04183 402612006496 Ferric iron reductase FhuF-like transporter; Region: FhuF; pfam06276 402612006497 cyanophycin synthetase; Provisional; Region: PRK14016 402612006498 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612006499 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 402612006500 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 402612006501 N-terminal plug; other site 402612006502 ligand-binding site [chemical binding]; other site 402612006503 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 402612006504 core domain interface [polypeptide binding]; other site 402612006505 delta subunit interface [polypeptide binding]; other site 402612006506 epsilon subunit interface [polypeptide binding]; other site 402612006507 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 402612006508 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 402612006509 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 402612006510 beta subunit interaction interface [polypeptide binding]; other site 402612006511 Walker A motif; other site 402612006512 ATP binding site [chemical binding]; other site 402612006513 Walker B motif; other site 402612006514 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 402612006515 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 402612006516 F0F1 ATP synthase subunit B; Provisional; Region: PRK14471 402612006517 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 402612006518 ATP synthase subunit C; Region: ATP-synt_C; cl00466 402612006519 ATP synthase A chain; Region: ATP-synt_A; cl00413 402612006520 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 402612006521 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 402612006522 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 402612006523 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 402612006524 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 402612006525 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 402612006526 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 402612006527 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 402612006528 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 402612006529 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 402612006530 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 402612006531 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 402612006532 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 402612006533 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 402612006534 binding surface 402612006535 TPR motif; other site 402612006536 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 402612006537 TPR motif; other site 402612006538 Tetratricopeptide repeat; Region: TPR_12; pfam13424 402612006539 binding surface 402612006540 phenylacetate-CoA oxygenase/reductase, PaaK subunit; Region: PA_CoA_Oxy5; TIGR02160 402612006541 NAD(P) binding domain of ferredoxin reductase like phenylacetic acid (PA) degradation oxidoreductase. PA oxidoreductases of E. coli hydroxylate PA-CoA in the second step of PA degradation. Members of this group typically fuse a ferredoxin reductase-like...; Region: PA_degradation_oxidoreductase_like; cd06214 402612006542 FAD binding pocket [chemical binding]; other site 402612006543 FAD binding motif [chemical binding]; other site 402612006544 phosphate binding motif [ion binding]; other site 402612006545 beta-alpha-beta structure motif; other site 402612006546 NAD(p) ribose binding residues [chemical binding]; other site 402612006547 NAD binding pocket [chemical binding]; other site 402612006548 NAD(P)-pyrophosphate-nicotinamide binding residues [chemical binding]; other site 402612006549 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 402612006550 catalytic loop [active] 402612006551 iron binding site [ion binding]; other site 402612006552 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 402612006553 putative active site [active] 402612006554 Protein of unknown function (DUF4254); Region: DUF4254; pfam14063 402612006555 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 402612006556 active site 402612006557 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 402612006558 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 402612006559 ATP-grasp domain; Region: ATP-grasp_4; cl17255 402612006560 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 402612006561 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 402612006562 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 402612006563 active site 402612006564 AMP binding site [chemical binding]; other site 402612006565 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 402612006566 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 402612006567 active site 402612006568 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 402612006569 CoA binding domain; Region: CoA_binding; cl17356 402612006570 Bacterial sugar transferase; Region: Bac_transf; pfam02397 402612006571 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 402612006572 UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs; Region: UGD_SDR_e; cd05230 402612006573 NAD binding site [chemical binding]; other site 402612006574 putative substrate binding site 2 [chemical binding]; other site 402612006575 putative substrate binding site 1 [chemical binding]; other site 402612006576 active site 402612006577 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 402612006578 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 402612006579 NADP binding site [chemical binding]; other site 402612006580 active site 402612006581 putative substrate binding site [chemical binding]; other site 402612006582 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; pfam00908 402612006583 Domain of unknown function (DUF4480); Region: DUF4480; pfam13715 402612006584 GH3 auxin-responsive promoter; Region: GH3; pfam03321 402612006585 indole-3-acetic acid-amido synthetase; Region: PLN02620 402612006586 Sec-independent protein secretion pathway components [Intracellular trafficking and secretion]; Region: TatA; COG1826 402612006587 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 402612006588 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 402612006589 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 402612006590 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 402612006591 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 402612006592 RNA binding site [nucleotide binding]; other site 402612006593 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 402612006594 Ribose/Galactose Isomerase; Region: LacAB_rpiB; pfam02502