-- dump date 20120504_155000 -- class Genbank::misc_feature -- table misc_feature_note -- id note 553174000001 Carbohydrate Binding Module 6 (CBM6) domains; many are found in association with discoidin domain(s); Region: CBM6_discoidin-like; cd04083 553174000002 Right handed beta helix region; Region: Beta_helix; pfam13229 553174000003 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 553174000004 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 553174000005 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 553174000006 dimerization interface [polypeptide binding]; other site 553174000007 active site 553174000008 metal binding site [ion binding]; metal-binding site 553174000009 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 553174000010 dsRNA binding site [nucleotide binding]; other site 553174000011 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 553174000012 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 553174000013 dimer interface [polypeptide binding]; other site 553174000014 active site 553174000015 Phosphopantetheine attachment site; Region: PP-binding; cl09936 553174000016 Protein of unknown function (DUF4254); Region: DUF4254; pfam14063 553174000017 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 553174000018 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 553174000019 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 553174000020 putative active site [active] 553174000021 ribonucleotide-diphosphate reductase subunit alpha; Provisional; Region: PRK12364 553174000022 ATP cone domain; Region: ATP-cone; pfam03477 553174000023 Class I ribonucleotide reductase; Region: RNR_I; cd01679 553174000024 active site 553174000025 dimer interface [polypeptide binding]; other site 553174000026 catalytic residues [active] 553174000027 effector binding site; other site 553174000028 R2 peptide binding site; other site 553174000029 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 553174000030 dimer interface [polypeptide binding]; other site 553174000031 putative radical transfer pathway; other site 553174000032 diiron center [ion binding]; other site 553174000033 tyrosyl radical; other site 553174000034 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 553174000035 GTP-binding protein YchF; Reviewed; Region: PRK09601 553174000036 YchF GTPase; Region: YchF; cd01900 553174000037 G1 box; other site 553174000038 GTP/Mg2+ binding site [chemical binding]; other site 553174000039 Switch I region; other site 553174000040 G2 box; other site 553174000041 Switch II region; other site 553174000042 G3 box; other site 553174000043 G4 box; other site 553174000044 G5 box; other site 553174000045 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 553174000046 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 553174000047 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 553174000048 MutS domain I; Region: MutS_I; pfam01624 553174000049 MutS domain II; Region: MutS_II; pfam05188 553174000050 MutS family domain IV; Region: MutS_IV; pfam05190 553174000051 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal...; Region: ABC_MutS1; cd03284 553174000052 Walker A/P-loop; other site 553174000053 ATP binding site [chemical binding]; other site 553174000054 Q-loop/lid; other site 553174000055 ABC transporter signature motif; other site 553174000056 Walker B; other site 553174000057 D-loop; other site 553174000058 H-loop/switch region; other site 553174000059 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 553174000060 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 553174000061 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 553174000062 DNA binding residues [nucleotide binding] 553174000063 RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA...; Region: RT_Bac_retron_II; cd03487 553174000064 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 553174000065 putative active site [active] 553174000066 putative NTP binding site [chemical binding]; other site 553174000067 putative nucleic acid binding site [nucleotide binding]; other site 553174000068 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 4-amino-4-deoxychorismate...; Region: PLPDE_IV; cl00224 553174000069 substrate-cofactor binding pocket; other site 553174000070 pyridoxal 5'-phosphate binding site [chemical binding]; other site 553174000071 catalytic residue [active] 553174000072 chorismate binding enzyme; Region: Chorismate_bind; cl10555 553174000073 CC3(TIP30)-like, atypical (a) SDRs; Region: CC3_like_SDR_a; cd05250 553174000074 NAD binding site [chemical binding]; other site 553174000075 active site 553174000076 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 553174000077 Histidine kinase; Region: His_kinase; pfam06580 553174000078 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Provisional; Region: PRK02048 553174000079 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 553174000080 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 553174000081 AIR carboxylase; Region: AIRC; cl00310 553174000082 RNA polymerase sigma-54 factor; Region: rpoN_sigma; TIGR02395 553174000083 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 553174000084 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 553174000085 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 553174000086 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 553174000087 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; cl01155 553174000088 leucyl-tRNA synthetase, eubacterial and mitochondrial family; Region: leuS_bact; TIGR00396 553174000089 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 553174000090 active site 553174000091 HIGH motif; other site 553174000092 nucleotide binding site [chemical binding]; other site 553174000093 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 553174000094 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 553174000095 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 553174000096 active site 553174000097 KMSKS motif; other site 553174000098 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 553174000099 tRNA binding surface [nucleotide binding]; other site 553174000100 Uncharacterized conserved protein [Function unknown]; Region: COG1284 553174000101 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 553174000102 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 553174000103 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; cl10498 553174000104 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 553174000105 active site 553174000106 dimerization interface [polypeptide binding]; other site 553174000107 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 553174000108 FlgD Ig-like domain; Region: FlgD_ig; cl15790 553174000109 Bacterial Ig-like domain; Region: Big_5; cl01012 553174000110 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174000111 GH3 auxin-responsive promoter; Region: GH3; cl04006 553174000112 DNA polymerase I; Provisional; Region: PRK05755 553174000113 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 553174000114 active site 553174000115 metal binding site 1 [ion binding]; metal-binding site 553174000116 putative 5' ssDNA interaction site; other site 553174000117 metal binding site 3; metal-binding site 553174000118 metal binding site 2 [ion binding]; metal-binding site 553174000119 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 553174000120 putative DNA binding site [nucleotide binding]; other site 553174000121 putative metal binding site [ion binding]; other site 553174000122 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 553174000123 active site 553174000124 catalytic site [active] 553174000125 substrate binding site [chemical binding]; other site 553174000126 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 553174000127 active site 553174000128 DNA binding site [nucleotide binding] 553174000129 catalytic site [active] 553174000130 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 553174000131 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 553174000132 substrate binding pocket [chemical binding]; other site 553174000133 chain length determination region; other site 553174000134 substrate-Mg2+ binding site; other site 553174000135 catalytic residues [active] 553174000136 aspartate-rich region 1; other site 553174000137 active site lid residues [active] 553174000138 aspartate-rich region 2; other site 553174000139 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 553174000140 intersubunit interface [polypeptide binding]; other site 553174000141 active site 553174000142 catalytic residue [active] 553174000143 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 553174000144 homodimer interface [polypeptide binding]; other site 553174000145 metal binding site [ion binding]; metal-binding site 553174000146 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 553174000147 putative active site [active] 553174000148 dimerization interface [polypeptide binding]; other site 553174000149 putative tRNAtyr binding site [nucleotide binding]; other site 553174000150 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 553174000151 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 553174000152 GIY-YIG motif/motif A; other site 553174000153 active site 553174000154 catalytic site [active] 553174000155 putative DNA binding site [nucleotide binding]; other site 553174000156 metal binding site [ion binding]; metal-binding site 553174000157 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 553174000158 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 553174000159 active site 553174000160 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 553174000161 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174000162 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 553174000163 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; cl01768 553174000164 Major Facilitator Superfamily; Region: MFS_1; pfam07690 553174000165 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 553174000166 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 553174000167 beta-N-acetylglucosaminidase; Region: NAGidase; pfam07555 553174000168 Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes; Region: FA58C; cl12042 553174000169 succinate dehydrogenase (or fumarate reductase) cytochrome b subunit, b558 family; Region: sdhC_b558_fam; TIGR02046 553174000170 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 553174000171 putative Iron-sulfur protein interface [polypeptide binding]; other site 553174000172 proximal heme binding site [chemical binding]; other site 553174000173 distal heme binding site [chemical binding]; other site 553174000174 putative dimer interface [polypeptide binding]; other site 553174000175 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07573 553174000176 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174000177 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 553174000178 succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Validated; Region: PRK07570 553174000179 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 553174000180 Catalytic domain of Protein Kinases; Region: PKc; cd00180 553174000181 active site 553174000182 substrate binding site [chemical binding]; other site 553174000183 ATP binding site [chemical binding]; other site 553174000184 Protein kinase domain; Region: Pkinase; pfam00069 553174000185 activation loop (A-loop); other site 553174000186 D-alanyl-D-alanine carboxypeptidase; Region: VanY; cl00813 553174000187 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; cl16911 553174000188 Endonuclease I; Region: Endonuclease_1; cl01003 553174000189 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 553174000190 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 553174000191 ATP binding site [chemical binding]; other site 553174000192 Mg2+ binding site [ion binding]; other site 553174000193 G-X-G motif; other site 553174000194 MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second...; Region: TopoII_MutL_Trans; cl02783 553174000195 ATP binding site [chemical binding]; other site 553174000196 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 553174000197 active site 553174000198 putative metal-binding site [ion binding]; other site 553174000199 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 553174000200 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 553174000201 C-terminal peptidase (prc); Region: prc; TIGR00225 553174000202 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 553174000203 protein binding site [polypeptide binding]; other site 553174000204 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 553174000205 Catalytic dyad [active] 553174000206 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 553174000207 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 553174000208 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 553174000209 active site 553174000210 nucleotide binding site [chemical binding]; other site 553174000211 HIGH motif; other site 553174000212 KMSKS motif; other site 553174000213 Domain of unknown function (DUF4252); Region: DUF4252; pfam14060 553174000214 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 553174000215 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 553174000216 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 553174000217 DNA binding residues [nucleotide binding] 553174000218 Domain of unknown function (DUF4252); Region: DUF4252; pfam14060 553174000219 Domain of unknown function (DUF4252); Region: DUF4252; pfam14060 553174000220 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 553174000221 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 553174000222 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 553174000223 active site 553174000224 Protein of unknown function (DUF2851); Region: DUF2851; pfam11013 553174000225 dihydrodipicolinate reductase; Provisional; Region: PRK00048 553174000226 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174000227 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 553174000228 signal peptidase I; Provisional; Region: PRK10861 553174000229 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 553174000230 Catalytic site [active] 553174000231 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 553174000232 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 553174000233 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 553174000234 WbqC-like protein family; Region: WbqC; pfam08889 553174000235 Domain of unknown function (DUF4294); Region: DUF4294; pfam14127 553174000236 Phosphate-selective porin O and P; Region: Porin_O_P; cl01524 553174000237 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 553174000238 Aspartase; Region: Aspartase; cd01357 553174000239 active sites [active] 553174000240 tetramer interface [polypeptide binding]; other site 553174000241 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174000242 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174000243 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174000244 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174000245 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; cl01155 553174000246 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; cl01155 553174000247 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 553174000248 active site 553174000249 metal binding site [ion binding]; metal-binding site 553174000250 homotetramer interface [polypeptide binding]; other site 553174000251 Acyltransferase family; Region: Acyl_transf_3; pfam01757 553174000252 OpgC protein; Region: OpgC_C; cl00792 553174000253 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 553174000254 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 553174000255 Walker A motif; other site 553174000256 ATP binding site [chemical binding]; other site 553174000257 Walker B motif; other site 553174000258 arginine finger; other site 553174000259 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 553174000260 Uncharacterized conserved protein [Function unknown]; Region: COG1284 553174000261 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 553174000262 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; cl10498 553174000263 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 553174000264 catalytic residues [active] 553174000265 dimer interface [polypeptide binding]; other site 553174000266 NAD-dependent deacetylase; Provisional; Region: PRK00481 553174000267 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 553174000268 NAD+ binding site [chemical binding]; other site 553174000269 substrate binding site [chemical binding]; other site 553174000270 Zn binding site [ion binding]; other site 553174000271 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 553174000272 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 553174000273 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 553174000274 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 553174000275 peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK11570 553174000276 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 553174000277 peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK11570 553174000278 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 553174000279 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 553174000280 DNA-binding transcriptional regulator AsnC; Provisional; Region: PRK11179 553174000281 Helix-turn-helix domains; Region: HTH; cl00088 553174000282 AsnC family; Region: AsnC_trans_reg; pfam01037 553174000283 Peptidase C26; Region: Peptidase_C26; pfam07722 553174000284 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 553174000285 catalytic triad [active] 553174000286 renal dipeptidase (rDP), best studied in mammals and also called membrane or microsomal dipeptidase, is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics; Region: rDP_like; cd01301 553174000287 active site 553174000288 dimer interface [polypeptide binding]; other site 553174000289 M28 Zn-Peptidases; Region: M28_like_6; cd08656 553174000290 metal binding site [ion binding]; metal-binding site 553174000291 Domain of unknown function (DUF4299); Region: DUF4299; pfam14132 553174000292 Nucleoside recognition; Region: Gate; cl00486 553174000293 Nucleoside recognition; Region: Gate; cl00486 553174000294 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 553174000295 Peptidase S46; Region: Peptidase_S46; pfam10459 553174000296 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 553174000297 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 553174000298 DEAD-like helicases superfamily; Region: DEXDc; smart00487 553174000299 ATP binding site [chemical binding]; other site 553174000300 Mg++ binding site [ion binding]; other site 553174000301 motif III; other site 553174000302 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 553174000303 nucleotide binding region [chemical binding]; other site 553174000304 ATP-binding site [chemical binding]; other site 553174000305 DbpA RNA binding domain; Region: DbpA; pfam03880 553174000306 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 553174000307 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 553174000308 RNase E interface [polypeptide binding]; other site 553174000309 trimer interface [polypeptide binding]; other site 553174000310 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 553174000311 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 553174000312 RNase E interface [polypeptide binding]; other site 553174000313 trimer interface [polypeptide binding]; other site 553174000314 active site 553174000315 Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to...; Region: PNPase_KH; cd02393 553174000316 putative nucleic acid binding region [nucleotide binding]; other site 553174000317 G-X-X-G motif; other site 553174000318 S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA; Region: S1_PNPase; cd04472 553174000319 RNA binding site [nucleotide binding]; other site 553174000320 domain interface; other site 553174000321 Lamin Tail Domain; Region: LTD; pfam00932 553174000322 Domain of unknown function (DUF3332); Region: DUF3332; pfam11810 553174000323 Glycoside hydrolase 97; Region: Glyco_hydro_97; pfam10566 553174000324 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 553174000325 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 553174000326 Glycosyl hydrolase family 66; Region: Glyco_hydro_66; pfam13199 553174000327 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 553174000328 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 553174000329 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 553174000330 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 553174000331 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 553174000332 Fructokinases (FRKs) mainly from bacteria and plants are enzymes with high specificity for fructose, as are all FRKs, but they catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into...; Region: bac_FRK; cd01167 553174000333 putative substrate binding site [chemical binding]; other site 553174000334 putative ATP binding site [chemical binding]; other site 553174000335 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 553174000336 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 553174000337 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 553174000338 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 553174000339 glycosyl hydrolase family 16; Region: Glyco_hydrolase_16; cl00218 553174000340 active site 553174000341 catalytic residues [active] 553174000342 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 553174000343 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 553174000344 catalytic residues [active] 553174000345 MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis; Region: MECDP_synthase; cd00554 553174000346 homotrimer interaction site [polypeptide binding]; other site 553174000347 zinc binding site [ion binding]; other site 553174000348 CDP-binding sites; other site 553174000349 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; cl01155 553174000350 Peptidase C25 family N-terminal domain, found in Arg-gingipain (Rgp), Lys-gingipain (Kgp) and related proteins; Region: Peptidase_C25_N; cd02258 553174000351 active site 553174000352 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 553174000353 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 553174000354 elongation factor Ts; Provisional; Region: tsf; PRK09377 553174000355 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 553174000356 Elongation factor TS; Region: EF_TS; pfam00889 553174000357 Elongation factor TS; Region: EF_TS; pfam00889 553174000358 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 553174000359 rRNA interaction site [nucleotide binding]; other site 553174000360 S8 interaction site; other site 553174000361 putative laminin-1 binding site; other site 553174000362 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 553174000363 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 553174000364 23S rRNA interface [nucleotide binding]; other site 553174000365 L3 interface [polypeptide binding]; other site 553174000366 Lactonase, 7-bladed beta-propeller; Region: Lactonase; pfam10282 553174000367 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 553174000368 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 553174000369 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 553174000370 dimer interface [polypeptide binding]; other site 553174000371 phosphorylation site [posttranslational modification] 553174000372 sensory histidine kinase UhpB; Provisional; Region: PRK11644 553174000373 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 553174000374 ATP binding site [chemical binding]; other site 553174000375 Mg2+ binding site [ion binding]; other site 553174000376 G-X-G motif; other site 553174000377 Response regulator receiver domain; Region: Response_reg; pfam00072 553174000378 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 553174000379 active site 553174000380 phosphorylation site [posttranslational modification] 553174000381 intermolecular recognition site; other site 553174000382 dimerization interface [polypeptide binding]; other site 553174000383 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 553174000384 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 553174000385 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174000386 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174000387 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; cl01155 553174000388 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; cl01155 553174000389 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174000390 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174000391 Glycosyl hydrolases family 32; Region: Glyco_32; smart00640 553174000392 Glycosyl hydrolase family 32, beta-fructosidases; Region: GH32_B_Fructosidase; cd08996 553174000393 substrate binding [chemical binding]; other site 553174000394 active site 553174000395 Glycosyl hydrolases family 32 C terminal; Region: Glyco_hydro_32C; pfam08244 553174000396 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 553174000397 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 553174000398 putative substrate translocation pore; other site 553174000399 Fructokinases (FRKs) mainly from bacteria and plants are enzymes with high specificity for fructose, as are all FRKs, but they catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into...; Region: bac_FRK; cd01167 553174000400 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 553174000401 putative substrate binding site [chemical binding]; other site 553174000402 putative ATP binding site [chemical binding]; other site 553174000403 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 553174000404 non-specific DNA binding site [nucleotide binding]; other site 553174000405 salt bridge; other site 553174000406 sequence-specific DNA binding site [nucleotide binding]; other site 553174000407 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 553174000408 Sulfatase; Region: Sulfatase; cl10460 553174000409 Sulfatase; Region: Sulfatase; cl10460 553174000410 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 553174000411 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 553174000412 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 553174000413 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 553174000414 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_22; cd04681 553174000415 nudix motif; other site 553174000416 DNA topoisomerase I; Provisional; Region: PRK08780 553174000417 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 553174000418 active site 553174000419 interdomain interaction site; other site 553174000420 putative metal-binding site [ion binding]; other site 553174000421 nucleotide binding site [chemical binding]; other site 553174000422 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 553174000423 domain I; other site 553174000424 DNA binding groove [nucleotide binding] 553174000425 phosphate binding site [ion binding]; other site 553174000426 domain II; other site 553174000427 domain III; other site 553174000428 nucleotide binding site [chemical binding]; other site 553174000429 catalytic site [active] 553174000430 domain IV; other site 553174000431 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 553174000432 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 553174000433 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 553174000434 Shikimate kinase [Amino acid transport and metabolism]; Region: AroK; COG0703 553174000435 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 553174000436 ADP binding site [chemical binding]; other site 553174000437 magnesium binding site [ion binding]; other site 553174000438 putative shikimate binding site; other site 553174000439 arginine decarboxylase; Provisional; Region: PRK05354 553174000440 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 553174000441 dimer interface [polypeptide binding]; other site 553174000442 active site 553174000443 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 553174000444 catalytic residues [active] 553174000445 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 553174000446 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 553174000447 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 553174000448 generic binding surface II; other site 553174000449 ssDNA binding site; other site 553174000450 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 553174000451 ATP binding site [chemical binding]; other site 553174000452 putative Mg++ binding site [ion binding]; other site 553174000453 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 553174000454 nucleotide binding region [chemical binding]; other site 553174000455 ATP-binding site [chemical binding]; other site 553174000456 Peptidase family M23; Region: Peptidase_M23; pfam01551 553174000457 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 553174000458 anaerobic sulfatase-maturase; Provisional; Region: PRK13745 553174000459 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 553174000460 FeS/SAM binding site; other site 553174000461 Domain of unknown function (DUF4008); Region: DUF4008; cl14869 553174000462 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 553174000463 metal-binding site 553174000464 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 553174000465 This family is most closely related to the GT1 family of glycosyltransferases. wcfI in Bacteroides fragilis has been shown to be involved in the capsular polysaccharide biosynthesis; Region: GT1_wcfI_like; cd03825 553174000466 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 553174000467 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 553174000468 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 553174000469 DNA binding residues [nucleotide binding] 553174000470 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 553174000471 substrate binding site; other site 553174000472 dimer interface; other site 553174000473 DJ-1 family protein; Region: not_thiJ; TIGR01383 553174000474 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Region: GATase1_DJ-1; cd03135 553174000475 conserved cys residue [active] 553174000476 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 553174000477 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK03708 553174000478 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 553174000479 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 553174000480 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174000481 Walker A/P-loop; other site 553174000482 ATP binding site [chemical binding]; other site 553174000483 Q-loop/lid; other site 553174000484 ABC transporter signature motif; other site 553174000485 Walker B; other site 553174000486 D-loop; other site 553174000487 H-loop/switch region; other site 553174000488 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 553174000489 catalytic residues [active] 553174000490 Gram-negative bacterial tonB protein; Region: TonB; cl10048 553174000491 Cyclomaltodextrinase, N-terminal; Region: Cyc-maltodext_N; pfam09087 553174000492 Alpha amylase catalytic domain found in bacterial cyclomaltodextrinases and related proteins; Region: AmyAc_bac_CMD_like_3; cd11340 553174000493 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 553174000494 Ca binding site [ion binding]; other site 553174000495 active site 553174000496 homodimer interface [polypeptide binding]; other site 553174000497 catalytic site [active] 553174000498 Cyclo-malto-dextrinase C-terminal domain; Region: Cyc-maltodext_C; pfam10438 553174000499 Early set domain associated with the catalytic domain of pullulanase (also called dextrinase and alpha-dextrin endo-1,6-alpha glucosidase); Region: E_set_Pullulanase; cd02860 553174000500 pullulanase, type I; Region: pulA_typeI; TIGR02104 553174000501 Alpha amylase catalytic domain found in Pullulanase (also called dextrinase; alpha-dextrin endo-1,6-alpha glucosidase), limit dextrinase, and related proteins; Region: AmyAc_Pullulanase_LD-like; cd11341 553174000502 Ca binding site [ion binding]; other site 553174000503 active site 553174000504 catalytic site [active] 553174000505 4-alpha-glucanotransferase; Region: PLN02950 553174000506 The family 20 carbohydrate-binding module (CBM20), also known as the starch-binding domain, is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is...; Region: CBM20; cl15347 553174000507 starch-binding site 2 [chemical binding]; other site 553174000508 starch-binding site 1 [chemical binding]; other site 553174000509 The family 20 carbohydrate-binding module (CBM20), also known as the starch-binding domain, is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is...; Region: CBM20; cl15347 553174000510 starch-binding site 2 [chemical binding]; other site 553174000511 starch-binding site 1 [chemical binding]; other site 553174000512 4-alpha-glucanotransferase; Region: Glyco_hydro_77; cl00711 553174000513 Major Facilitator Superfamily; Region: MFS_1; pfam07690 553174000514 GPH family sucrose/H+ symporter; Region: GPH_sucrose; TIGR01301 553174000515 Transcriptional regulators [Transcription]; Region: PurR; COG1609 553174000516 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 553174000517 DNA binding site [nucleotide binding] 553174000518 domain linker motif; other site 553174000519 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 553174000520 dimerization interface [polypeptide binding]; other site 553174000521 ligand binding site [chemical binding]; other site 553174000522 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174000523 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174000524 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; cl01155 553174000525 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; cl01155 553174000526 starch binding outer membrane protein SusD; Region: SusD; cd08977 553174000527 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174000528 SusE outer membrane protein; Region: SusE; pfam14292 553174000529 Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; Region: E_set; cl09101 553174000530 alpha-amylase; Region: PLN02361 553174000531 Alpha amylase catalytic domain found in archaeal, bacterial, and plant Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase); Region: AmyAc_arch_bac_plant_AmyA; cd11314 553174000532 active site 553174000533 Ca binding site [ion binding]; other site 553174000534 catalytic site [active] 553174000535 desulfoferrodoxin; Region: dfx_rbo; TIGR00320 553174000536 Superoxide reductase-like (SORL) domain; present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin. Superoxide reductase-like proteins scavenge superoxide anion radicals as a defense mechanism...; Region: SORL; cl00014 553174000537 non-heme iron binding site [ion binding]; other site 553174000538 Transposase; Region: DDE_Tnp_ISL3; pfam01610 553174000539 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 553174000540 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 553174000541 protein binding site [polypeptide binding]; other site 553174000542 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 553174000543 Catalytic dyad [active] 553174000544 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 553174000545 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 553174000546 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 553174000547 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 553174000548 Sm1 motif; other site 553174000549 RNA binding pocket [nucleotide binding]; other site 553174000550 transcription termination factor NusA; Region: NusA; TIGR01953 553174000551 NusA N-terminal domain; Region: NusA_N; pfam08529 553174000552 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 553174000553 RNA binding site [nucleotide binding]; other site 553174000554 homodimer interface [polypeptide binding]; other site 553174000555 KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional...; Region: KH-II; cl00098 553174000556 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 553174000557 G-X-X-G motif; other site 553174000558 translation initiation factor IF-2; Region: IF-2; TIGR00487 553174000559 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 553174000560 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 553174000561 G1 box; other site 553174000562 putative GEF interaction site [polypeptide binding]; other site 553174000563 GTP/Mg2+ binding site [chemical binding]; other site 553174000564 Switch I region; other site 553174000565 G2 box; other site 553174000566 G3 box; other site 553174000567 Switch II region; other site 553174000568 G4 box; other site 553174000569 G5 box; other site 553174000570 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 553174000571 Translation-initiation factor 2; Region: IF-2; pfam11987 553174000572 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 553174000573 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 553174000574 putative ABC transporter; Region: ycf24; CHL00085 553174000575 FeS assembly ATPase SufC; Region: sufC; TIGR01978 553174000576 ABC-type transport system involved in Fe-S cluster assembly, ATPase component. Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under...; Region: ABC_FeS_Assembly; cd03217 553174000577 Walker A/P-loop; other site 553174000578 ATP binding site [chemical binding]; other site 553174000579 Q-loop/lid; other site 553174000580 ABC transporter signature motif; other site 553174000581 Walker B; other site 553174000582 D-loop; other site 553174000583 H-loop/switch region; other site 553174000584 Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]; Region: SufB; COG0719 553174000585 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 553174000586 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 553174000587 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 553174000588 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 553174000589 catalytic residue [active] 553174000590 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 553174000591 RNA/DNA hybrid binding site [nucleotide binding]; other site 553174000592 active site 553174000593 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174000594 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174000595 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; cl01155 553174000596 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; cl01155 553174000597 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174000598 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174000599 Predicted transcriptional regulator [Transcription]; Region: COG2378 553174000600 WYL domain; Region: WYL; cl14852 553174000601 SGNH_hydrolase subfamily, similar to the putative arylesterase/acylhydrolase from the rumen anaerobe Prevotella bryantii XynE. The P. bryantii XynE gene is located in a xylanase gene cluster. SGNH hydrolases are a diverse family of lipases and esterases; Region: XynE_like; cd01830 553174000602 active site 553174000603 catalytic triad [active] 553174000604 oxyanion hole [active] 553174000605 Domain of unknown function (DUF1910); Region: DUF1910; pfam08928 553174000606 Domain of unknown function (DUF1911); Region: DUF1911; pfam08929 553174000607 Gram-negative bacterial tonB protein; Region: TonB; cl10048 553174000608 Gram-negative bacterial tonB protein; Region: TonB; cl10048 553174000609 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 553174000610 Sulfatase; Region: Sulfatase; cl10460 553174000611 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 553174000612 ligand binding site [chemical binding]; other site 553174000613 active site 553174000614 UGI interface [polypeptide binding]; other site 553174000615 catalytic site [active] 553174000616 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 553174000617 ligand binding site [chemical binding]; other site 553174000618 active site 553174000619 UGI interface [polypeptide binding]; other site 553174000620 catalytic site [active] 553174000621 Protein of unknown function (DUF3109); Region: DUF3109; pfam11307 553174000622 Helix-turn-helix domain; Region: HTH_18; pfam12833 553174000623 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 553174000624 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 553174000625 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 553174000626 ATP binding site [chemical binding]; other site 553174000627 Mg2+ binding site [ion binding]; other site 553174000628 G-X-G motif; other site 553174000629 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 553174000630 anchoring element; other site 553174000631 dimer interface [polypeptide binding]; other site 553174000632 ATP binding site [chemical binding]; other site 553174000633 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 553174000634 active site 553174000635 metal binding site [ion binding]; metal-binding site 553174000636 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 553174000637 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 553174000638 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 553174000639 N-terminal plug; other site 553174000640 ligand-binding site [chemical binding]; other site 553174000641 siderophore transporter, RhtX/FptX family; Region: sider_RhtX_FptX; TIGR02718 553174000642 muropeptide transporter; Validated; Region: ampG; PRK11010 553174000643 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 553174000644 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 553174000645 FeS/SAM binding site; other site 553174000646 HemN C-terminal domain; Region: HemN_C; pfam06969 553174000647 protoporphyrinogen oxidase; Region: PLN02576 553174000648 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174000649 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 553174000650 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 553174000651 Recombination protein O N terminal; Region: RecO_N; cl15812 553174000652 Recombination protein O C terminal; Region: RecO_C; pfam02565 553174000653 Conserved hypothetical protein 698; Region: Cons_hypoth698; cl01075 553174000654 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 553174000655 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 553174000656 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 553174000657 nucleotide binding site [chemical binding]; other site 553174000658 SulA interaction site; other site 553174000659 Cell division protein FtsA; Region: FtsA; cl11496 553174000660 Cell division protein FtsA; Region: FtsA; cl11496 553174000661 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 553174000662 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 553174000663 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 553174000664 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 553174000665 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 553174000666 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 553174000667 homodimer interface [polypeptide binding]; other site 553174000668 active site 553174000669 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 553174000670 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK02472 553174000671 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174000672 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 553174000673 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 553174000674 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 553174000675 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 553174000676 Mg++ binding site [ion binding]; other site 553174000677 putative catalytic motif [active] 553174000678 putative substrate binding site [chemical binding]; other site 553174000679 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 553174000680 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 553174000681 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 553174000682 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 553174000683 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 553174000684 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 553174000685 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 553174000686 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 553174000687 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 553174000688 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; cl16911 553174000689 cell division protein MraZ; Reviewed; Region: PRK00326 553174000690 MraZ protein; Region: MraZ; pfam02381 553174000691 MraZ protein; Region: MraZ; pfam02381 553174000692 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 553174000693 putative acyl-acceptor binding pocket; other site 553174000694 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 553174000695 Uncharacterized protein related to glutamine synthetase [General function prediction only]; Region: COG3968 553174000696 Glutamine synthetase type III N terminal; Region: GSIII_N; pfam12437 553174000697 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 553174000698 Helix-turn-helix domain; Region: HTH_18; pfam12833 553174000699 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 553174000700 AAA domain; Region: AAA_22; pfam13401 553174000701 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174000702 Family description; Region: UvrD_C_2; cl15862 553174000703 Protein of unknown function (DUF2400); Region: DUF2400; cl09884 553174000704 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 553174000705 catalytic triad [active] 553174000706 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 553174000707 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 553174000708 active site 553174000709 Zn binding site [ion binding]; other site 553174000710 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 553174000711 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174000712 Surface protein; Region: DUF3664; pfam12406 553174000713 Predicted membrane protein (DUF2339); Region: DUF2339; pfam10101 553174000714 Predicted membrane protein [Function unknown]; Region: COG5373 553174000715 hypothetical protein; Provisional; Region: PRK10649 553174000716 Sulfatase; Region: Sulfatase; cl10460 553174000717 Acyltransferase family; Region: Acyl_transf_3; pfam01757 553174000718 OpgC protein; Region: OpgC_C; cl00792 553174000719 OpgC protein; Region: OpgC_C; cl00792 553174000720 Acyltransferase family; Region: Acyl_transf_3; pfam01757 553174000721 UbiA prenyltransferase family; Region: UbiA; cl00337 553174000722 arginine/ornithine antiporter; Region: arg_ornith_anti; TIGR03810 553174000723 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 553174000724 active site 553174000725 MatE; Region: MatE; cl10513 553174000726 LicD family; Region: LicD; cl01378 553174000727 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 553174000728 substrate binding site; other site 553174000729 dimer interface; other site 553174000730 bifunctional sterol desaturase/short chain dehydrogenase; Validated; Region: PRK07424 553174000731 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174000732 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 553174000733 NAD(P) binding site [chemical binding]; other site 553174000734 active site 553174000735 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 553174000736 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 553174000737 active site 553174000738 (T/H)XGH motif; other site 553174000739 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 553174000740 putative active site [active] 553174000741 Guanylate kinase; Region: Guanylate_kin; pfam00625 553174000742 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 553174000743 catalytic site [active] 553174000744 G-X2-G-X-G-K; other site 553174000745 hypothetical protein; Provisional; Region: PRK11820 553174000746 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 553174000747 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 553174000748 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 553174000749 Domain of unknown function (DUF4290); Region: DUF4290; pfam14123 553174000750 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 553174000751 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 553174000752 hinge; other site 553174000753 active site 553174000754 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 553174000755 RimM N-terminal domain; Region: RimM; pfam01782 553174000756 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 553174000757 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 553174000758 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 553174000759 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 553174000760 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 553174000761 RIP metalloprotease RseP; Region: TIGR00054 553174000762 active site 553174000763 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 553174000764 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 553174000765 putative substrate binding region [chemical binding]; other site 553174000766 Chromate transporter; Region: Chromate_transp; pfam02417 553174000767 Chromate transporter; Region: Chromate_transp; pfam02417 553174000768 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 553174000769 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), first repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP; Region: PurL_repeat1; cd02203 553174000770 dimerization interface [polypeptide binding]; other site 553174000771 ATP binding site [chemical binding]; other site 553174000772 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 553174000773 dimerization interface [polypeptide binding]; other site 553174000774 ATP binding site [chemical binding]; other site 553174000775 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 553174000776 putative active site [active] 553174000777 catalytic triad [active] 553174000778 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 553174000779 flagellar motor protein MotB; Reviewed; Region: motB; PRK07734 553174000780 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 553174000781 ligand binding site [chemical binding]; other site 553174000782 Protein of unknown function (DUF1304); Region: DUF1304; cl01533 553174000783 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; cl00920 553174000784 Protein of unknown function (DUF2795); Region: DUF2795; pfam11387 553174000785 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; cl15394 553174000786 gliding motility-associated protein GldL; Region: GldL_gliding; TIGR03513 553174000787 gliding motility-associated protein GldM; Region: GldM_gliding; TIGR03517 553174000788 GldM N-terminal domain; Region: GldM_N; pfam12081 553174000789 GldM C-terminal domain; Region: GldM_C; pfam12080 553174000790 gliding motility associated protien GldN; Region: GldN; TIGR03523 553174000791 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; cl01155 553174000792 primosome assembly protein PriA; Validated; Region: PRK05580 553174000793 primosome assembly protein PriA; Validated; Region: PRK05580 553174000794 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 553174000795 ATP binding site [chemical binding]; other site 553174000796 putative Mg++ binding site [ion binding]; other site 553174000797 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174000798 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; cl01155 553174000799 7TM-HD extracellular; Region: 7TMR-HDED; pfam07697 553174000800 7TM receptor with intracellular HD hydrolase; Region: 7TM-7TMR_HD; pfam07698 553174000801 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 553174000802 Zn2+ binding site [ion binding]; other site 553174000803 Mg2+ binding site [ion binding]; other site 553174000804 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 553174000805 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 553174000806 HIGH motif; other site 553174000807 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 553174000808 active site 553174000809 KMSKS motif; other site 553174000810 Mpr1p, Pad1p N-terminal (MPN) domains; Region: MPN; cl13996 553174000811 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 553174000812 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 553174000813 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 553174000814 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 553174000815 active site 553174000816 HIGH motif; other site 553174000817 dimer interface [polypeptide binding]; other site 553174000818 KMSKS motif; other site 553174000819 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174000820 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174000821 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; cl01155 553174000822 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; cl01155 553174000823 starch binding outer membrane protein SusD; Region: SusD; cd08977 553174000824 Malate/lactate dehydrogenases [Energy production and conversion]; Region: Mdh; COG0039 553174000825 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174000826 NAD(P) binding site [chemical binding]; other site 553174000827 LDH/MDH dimer interface [polypeptide binding]; other site 553174000828 substrate binding site [chemical binding]; other site 553174000829 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 553174000830 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 553174000831 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP; cd01085 553174000832 active site 553174000833 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 553174000834 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 553174000835 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 553174000836 active site 553174000837 DNA binding site [nucleotide binding] 553174000838 Int/Topo IB signature motif; other site 553174000839 RaiA ('ribosome-associated inhibitor A', also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site; Region: RaiA; cd00552 553174000840 30S subunit binding site; other site 553174000841 elongation factor Tu; Reviewed; Region: PRK12735 553174000842 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 553174000843 G1 box; other site 553174000844 GEF interaction site [polypeptide binding]; other site 553174000845 GTP/Mg2+ binding site [chemical binding]; other site 553174000846 Switch I region; other site 553174000847 G2 box; other site 553174000848 G3 box; other site 553174000849 Switch II region; other site 553174000850 G4 box; other site 553174000851 G5 box; other site 553174000852 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 553174000853 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 553174000854 Antibiotic Binding Site [chemical binding]; other site 553174000855 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 553174000856 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 553174000857 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 553174000858 putative homodimer interface [polypeptide binding]; other site 553174000859 KOW motif; Region: KOW; cl00354 553174000860 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 553174000861 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 553174000862 23S rRNA interface [nucleotide binding]; other site 553174000863 L7/L12 interface [polypeptide binding]; other site 553174000864 putative thiostrepton binding site; other site 553174000865 L25 interface [polypeptide binding]; other site 553174000866 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 553174000867 mRNA/rRNA interface [nucleotide binding]; other site 553174000868 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 553174000869 23S rRNA interface [nucleotide binding]; other site 553174000870 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 553174000871 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 553174000872 core dimer interface [polypeptide binding]; other site 553174000873 peripheral dimer interface [polypeptide binding]; other site 553174000874 L10 interface [polypeptide binding]; other site 553174000875 L11 interface [polypeptide binding]; other site 553174000876 putative EF-Tu interaction site [polypeptide binding]; other site 553174000877 putative EF-G interaction site [polypeptide binding]; other site 553174000878 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 553174000879 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 553174000880 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 553174000881 RPB11 interaction site [polypeptide binding]; other site 553174000882 RPB12 interaction site [polypeptide binding]; other site 553174000883 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 553174000884 RPB3 interaction site [polypeptide binding]; other site 553174000885 RPB1 interaction site [polypeptide binding]; other site 553174000886 RPB11 interaction site [polypeptide binding]; other site 553174000887 RPB10 interaction site [polypeptide binding]; other site 553174000888 DNA-directed RNA polymerase subunit gamma; Provisional; Region: rpoC1; PRK02625 553174000889 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 553174000890 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 553174000891 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 553174000892 DNA-directed RNA polymerase subunit beta'; Provisional; Region: rpoC2; PRK02597 553174000893 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 553174000894 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 553174000895 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 553174000896 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 553174000897 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 553174000898 DNA binding site [nucleotide binding] 553174000899 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 553174000900 Gram-negative bacterial tonB protein; Region: TonB; cl10048 553174000901 Protein of unknown function (DUF3467); Region: DUF3467; pfam11950 553174000902 Sulfatase; Region: Sulfatase; cl10460 553174000903 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174000904 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174000905 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 553174000906 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; cl01155 553174000907 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 553174000908 S17 interaction site [polypeptide binding]; other site 553174000909 S8 interaction site; other site 553174000910 16S rRNA interaction site [nucleotide binding]; other site 553174000911 streptomycin interaction site [chemical binding]; other site 553174000912 23S rRNA interaction site [nucleotide binding]; other site 553174000913 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 553174000914 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 553174000915 elongation factor G; Reviewed; Region: PRK12739 553174000916 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 553174000917 G1 box; other site 553174000918 putative GEF interaction site [polypeptide binding]; other site 553174000919 GTP/Mg2+ binding site [chemical binding]; other site 553174000920 Switch I region; other site 553174000921 G2 box; other site 553174000922 G3 box; other site 553174000923 Switch II region; other site 553174000924 G4 box; other site 553174000925 G5 box; other site 553174000926 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 553174000927 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 553174000928 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 553174000929 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 553174000930 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 553174000931 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 553174000932 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 553174000933 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 553174000934 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 553174000935 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 553174000936 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 553174000937 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 553174000938 putative translocon binding site; other site 553174000939 protein-rRNA interface [nucleotide binding]; other site 553174000940 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 553174000941 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 553174000942 G-X-X-G motif; other site 553174000943 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 553174000944 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 553174000945 23S rRNA interface [nucleotide binding]; other site 553174000946 5S rRNA interface [nucleotide binding]; other site 553174000947 putative antibiotic binding site [chemical binding]; other site 553174000948 L25 interface [polypeptide binding]; other site 553174000949 L27 interface [polypeptide binding]; other site 553174000950 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 553174000951 23S rRNA interface [nucleotide binding]; other site 553174000952 putative translocon interaction site; other site 553174000953 signal recognition particle (SRP54) interaction site; other site 553174000954 L23 interface [polypeptide binding]; other site 553174000955 trigger factor interaction site; other site 553174000956 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 553174000957 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 553174000958 KOW motif; Region: KOW; cl00354 553174000959 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 553174000960 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 553174000961 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 553174000962 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 553174000963 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 553174000964 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 553174000965 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 553174000966 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 553174000967 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 553174000968 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 553174000969 5S rRNA interface [nucleotide binding]; other site 553174000970 23S rRNA interface [nucleotide binding]; other site 553174000971 L5 interface [polypeptide binding]; other site 553174000972 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 553174000973 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 553174000974 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 553174000975 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 553174000976 23S rRNA binding site [nucleotide binding]; other site 553174000977 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 553174000978 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 553174000979 SecY translocase; Region: SecY; pfam00344 553174000980 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 553174000981 active site 553174000982 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 553174000983 rRNA binding site [nucleotide binding]; other site 553174000984 predicted 30S ribosome binding site; other site 553174000985 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 553174000986 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 553174000987 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 553174000988 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 553174000989 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 553174000990 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 553174000991 RNA binding surface [nucleotide binding]; other site 553174000992 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 553174000993 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 553174000994 alphaNTD - beta interaction site [polypeptide binding]; other site 553174000995 alphaNTD homodimer interface [polypeptide binding]; other site 553174000996 alphaNTD - beta' interaction site [polypeptide binding]; other site 553174000997 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 553174000998 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 553174000999 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174001000 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174001001 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174001002 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 553174001003 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; cl01155 553174001004 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 553174001005 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 553174001006 Leucine rich repeat; Region: LRR_8; pfam13855 553174001007 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 553174001008 Substrate binding site [chemical binding]; other site 553174001009 stage V sporulation protein K; Region: spore_V_K; TIGR02881 553174001010 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 553174001011 Walker A motif; other site 553174001012 ATP binding site [chemical binding]; other site 553174001013 Walker B motif; other site 553174001014 arginine finger; other site 553174001015 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 553174001016 Predicted permease; Region: DUF318; pfam03773 553174001017 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 553174001018 glutamate dehydrogenase; Provisional; Region: PRK14030 553174001019 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 553174001020 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 553174001021 NAD(P) binding site [chemical binding]; other site 553174001022 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 553174001023 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 553174001024 non-specific DNA binding site [nucleotide binding]; other site 553174001025 salt bridge; other site 553174001026 sequence-specific DNA binding site [nucleotide binding]; other site 553174001027 HipA N-terminal domain; Region: Couple_hipA; cl11853 553174001028 HipA-like N-terminal domain; Region: HipA_N; pfam07805 553174001029 HipA-like C-terminal domain; Region: HipA_C; pfam07804 553174001030 acyl-CoA synthetase; Provisional; Region: PRK13383 553174001031 AMP-binding enzyme; Region: AMP-binding; cl15778 553174001032 AMP-binding enzyme; Region: AMP-binding; cl15778 553174001033 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 553174001034 classical (c) SDRs; Region: SDR_c; cd05233 553174001035 NAD(P) binding site [chemical binding]; other site 553174001036 active site 553174001037 RDD family; Region: RDD; cl00746 553174001038 Integral membrane protein DUF95; Region: DUF95; cl00572 553174001039 Domain of unknown function (DUF4350); Region: DUF4350; pfam14258 553174001040 MoxR-like ATPases [General function prediction only]; Region: COG0714 553174001041 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 553174001042 Walker A motif; other site 553174001043 ATP binding site [chemical binding]; other site 553174001044 Walker B motif; other site 553174001045 arginine finger; other site 553174001046 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 553174001047 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 553174001048 Lipocalin-like domain; Region: Lipocalin_6; pfam13944 553174001049 Bacterial proteins similar to Porphyromonas gingivalis HmuY; Region: HmuY_like; cd07472 553174001050 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 553174001051 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 553174001052 N-terminal plug; other site 553174001053 ligand-binding site [chemical binding]; other site 553174001054 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 553174001055 catalytic residues [active] 553174001056 Outer membrane protein Omp28; Region: Omp28; pfam11551 553174001057 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174001058 Walker A/P-loop; other site 553174001059 ATP binding site [chemical binding]; other site 553174001060 Q-loop/lid; other site 553174001061 ABC transporter signature motif; other site 553174001062 Walker B; other site 553174001063 D-loop; other site 553174001064 H-loop/switch region; other site 553174001065 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 553174001066 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 553174001067 active site 553174001068 motif I; other site 553174001069 motif II; other site 553174001070 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 553174001071 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal...; Region: MIP; cd00333 553174001072 amphipathic channel; other site 553174001073 Asn-Pro-Ala signature motifs; other site 553174001074 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 553174001075 hypothetical protein; Provisional; Region: PRK08185 553174001076 intersubunit interface [polypeptide binding]; other site 553174001077 active site 553174001078 zinc binding site [ion binding]; other site 553174001079 Na+ binding site [ion binding]; other site 553174001080 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 553174001081 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 553174001082 putative substrate binding site [chemical binding]; other site 553174001083 putative ATP binding site [chemical binding]; other site 553174001084 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 553174001085 active site 553174001086 adenylate kinase; Reviewed; Region: adk; PRK00279 553174001087 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 553174001088 AMP-binding site [chemical binding]; other site 553174001089 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 553174001090 S23 ribosomal protein; Region: Ribosomal_S23p; cl05287 553174001091 GTPase CgtA; Reviewed; Region: obgE; PRK12298 553174001092 GTP1/OBG; Region: GTP1_OBG; pfam01018 553174001093 Obg GTPase; Region: Obg; cd01898 553174001094 G1 box; other site 553174001095 GTP/Mg2+ binding site [chemical binding]; other site 553174001096 Switch I region; other site 553174001097 G2 box; other site 553174001098 G3 box; other site 553174001099 Switch II region; other site 553174001100 G4 box; other site 553174001101 G5 box; other site 553174001102 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 553174001103 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 553174001104 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 553174001105 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 553174001106 homotrimer interaction site [polypeptide binding]; other site 553174001107 putative active site [active] 553174001108 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 553174001109 PAP2, bacterial acid phosphatase or class A non-specific acid phosphatases. These enzymes catalyze phosphomonoester hydrolysis, with optimal activity in low pH conditions. They are secreted into the periplasmic space, and their physiological role remains...; Region: PAP2_acid_phosphatase; cd03397 553174001110 active site 553174001111 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 553174001112 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 553174001113 N-terminal plug; other site 553174001114 ligand-binding site [chemical binding]; other site 553174001115 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 553174001116 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein; Reviewed; Region: cpdB; PRK09420 553174001117 Escherichia coli UshA-like family, N-terminal metallophosphatase domain; Region: MPP_UshA_N_like; cd00845 553174001118 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 553174001119 active site 553174001120 metal binding site [ion binding]; metal-binding site 553174001121 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174001122 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; cl01155 553174001123 Uncharacterized Fe-S center protein [General function prediction only]; Region: COG2768 553174001124 4Fe-4S binding domain; Region: Fer4; cl02805 553174001125 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 553174001126 hydrophobic ligand binding site; other site 553174001127 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 553174001128 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 553174001129 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 553174001130 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 553174001131 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cd00641 553174001132 dimerization interface [polypeptide binding]; other site 553174001133 active site 553174001134 aspartate aminotransferase; Provisional; Region: PRK05764 553174001135 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 553174001136 pyridoxal 5'-phosphate binding site [chemical binding]; other site 553174001137 homodimer interface [polypeptide binding]; other site 553174001138 catalytic residue [active] 553174001139 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 553174001140 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 553174001141 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 553174001142 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 553174001143 Gram-negative bacterial tonB protein; Region: TonB; cl10048 553174001144 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 553174001145 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 553174001146 muropeptide transporter; Validated; Region: ampG; PRK11010 553174001147 AmpG-like permease; Region: 2A0125; TIGR00901 553174001148 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 553174001149 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 553174001150 minor groove reading motif; other site 553174001151 helix-hairpin-helix signature motif; other site 553174001152 substrate binding pocket [chemical binding]; other site 553174001153 active site 553174001154 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 553174001155 DNA binding and oxoG recognition site [nucleotide binding] 553174001156 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 553174001157 purine monophosphate binding site [chemical binding]; other site 553174001158 dimer interface [polypeptide binding]; other site 553174001159 putative catalytic residues [active] 553174001160 rod shape-determining protein MreB; Provisional; Region: PRK13927 553174001161 Actin; An ubiquitous protein involved in the formation of filaments that are a major component of the cytoskeleton. Interaction with myosin provides the basis of muscular contraction and many aspects of cell motility. Each actin protomer binds one...; Region: ACTIN; cl11528 553174001162 ATP binding site [chemical binding]; other site 553174001163 profilin binding site; other site 553174001164 rod shape-determining protein MreC; Provisional; Region: PRK13922 553174001165 rod shape-determining protein MreC; Region: MreC; pfam04085 553174001166 rod shape-determining protein MreD; Region: MreD; cl01087 553174001167 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 553174001168 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 553174001169 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 553174001170 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 553174001171 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 553174001172 GldH lipoprotein; Region: GldH_lipo; cl11905 553174001173 PSP1 C-terminal conserved region; Region: PSP1; cl00770 553174001174 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174001175 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 553174001176 Walker A motif; other site 553174001177 ATP binding site [chemical binding]; other site 553174001178 DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]; Region: DnaX; COG2812 553174001179 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174001180 Methylenetetrahydrofolate reductase; Region: MTHFR; pfam02219 553174001181 Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase...; Region: MTHFR; cd00537 553174001182 FAD binding site [chemical binding]; other site 553174001183 Endo-beta-mannanase [Carbohydrate transport and metabolism]; Region: COG3934 553174001184 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; cl15381 553174001185 Phosphomannose isomerase [Carbohydrate transport and metabolism]; Region: ManA; COG1482 553174001186 Phosphomannose isomerase type I; Region: PMI_typeI; cl15429 553174001187 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 553174001188 thymidine kinase; Provisional; Region: PRK04296 553174001189 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 553174001190 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 553174001191 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 553174001192 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 553174001193 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 553174001194 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 553174001195 DNA binding residues [nucleotide binding] 553174001196 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 553174001197 nucleoside/Zn binding site; other site 553174001198 dimer interface [polypeptide binding]; other site 553174001199 catalytic motif [active] 553174001200 Restriction endonuclease; Region: Mrr_cat; cl00516 553174001201 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 553174001202 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 553174001203 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 553174001204 putative nucleotide binding site [chemical binding]; other site 553174001205 uridine monophosphate binding site [chemical binding]; other site 553174001206 homohexameric interface [polypeptide binding]; other site 553174001207 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 553174001208 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 553174001209 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 553174001210 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 553174001211 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174001212 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174001213 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 553174001214 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; cl01155 553174001215 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174001216 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin; Region: ZnMc_MMP_like_2; cd04276 553174001217 active site 553174001218 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin; Region: ZnMc_MMP_like_2; cd04276 553174001219 active site 553174001220 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174001221 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; cl01155 553174001222 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 553174001223 catalytic residues [active] 553174001224 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 553174001225 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 553174001226 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 553174001227 generic binding surface II; other site 553174001228 generic binding surface I; other site 553174001229 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 553174001230 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 553174001231 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 553174001232 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 553174001233 Response regulator receiver domain; Region: Response_reg; pfam00072 553174001234 active site 553174001235 phosphorylation site [posttranslational modification] 553174001236 intermolecular recognition site; other site 553174001237 dimerization interface [polypeptide binding]; other site 553174001238 PglZ domain; Region: PglZ; pfam08665 553174001239 Tetratricopeptide repeat; Region: TPR_12; pfam13424 553174001240 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 553174001241 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 553174001242 3-phosphoshikimate 1-carboxyvinyltransferase; Region: aroA; TIGR01356 553174001243 hinge; other site 553174001244 active site 553174001245 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 553174001246 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 553174001247 The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i)...; Region: GH20_chitobiase-like; cd06563 553174001248 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 553174001249 active site 553174001250 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 553174001251 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 553174001252 N-terminal plug; other site 553174001253 ligand-binding site [chemical binding]; other site 553174001254 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 553174001255 active site 553174001256 xanthine permease; Region: pbuX; TIGR03173 553174001257 Domain of unknown function (DUF4251); Region: DUF4251; pfam14059 553174001258 Gram-negative bacterial tonB protein; Region: TonB; cl10048 553174001259 MBOAT, membrane-bound O-acyltransferase family; Region: MBOAT; cl00738 553174001260 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 553174001261 active site 553174001262 oxyanion hole [active] 553174001263 Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Ape1-like_AP-endo; cd09087 553174001264 active site 553174001265 putative catalytic site [active] 553174001266 DNA binding site [nucleotide binding] 553174001267 putative phosphate binding site [ion binding]; other site 553174001268 metal binding site A [ion binding]; metal-binding site 553174001269 AP binding site [nucleotide binding]; other site 553174001270 metal binding site B [ion binding]; metal-binding site 553174001271 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In...; Region: GTP_cyclohydro1; cd00642 553174001272 homodecamer interface [polypeptide binding]; other site 553174001273 GTP cyclohydrolase I; Provisional; Region: PLN03044 553174001274 active site 553174001275 putative catalytic site residues [active] 553174001276 zinc binding site [ion binding]; other site 553174001277 GTP-CH-I/GFRP interaction surface; other site 553174001278 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 553174001279 substrate binding site [chemical binding]; other site 553174001280 dimer interface [polypeptide binding]; other site 553174001281 catalytic triad [active] 553174001282 Domain of Unknown Function (DUF1599); Region: DUF1599; pfam07659 553174001283 Domain of Unknown Function (DUF1599); Region: DUF1599; pfam07659 553174001284 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 553174001285 tRNA adenylyltransferase; Region: tRNA_CCA_actino; TIGR02692 553174001286 active site 553174001287 NTP binding site [chemical binding]; other site 553174001288 metal binding triad [ion binding]; metal-binding site 553174001289 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 553174001290 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 553174001291 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 553174001292 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 553174001293 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 553174001294 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 553174001295 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 553174001296 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK12461 553174001297 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 553174001298 putative trimer interface [polypeptide binding]; other site 553174001299 putative CoA binding site [chemical binding]; other site 553174001300 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 553174001301 Radical SAM superfamily; Region: Radical_SAM; pfam04055 553174001302 FeS/SAM binding site; other site 553174001303 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 553174001304 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 553174001305 G1 box; other site 553174001306 putative GEF interaction site [polypeptide binding]; other site 553174001307 GTP/Mg2+ binding site [chemical binding]; other site 553174001308 Switch I region; other site 553174001309 G2 box; other site 553174001310 G3 box; other site 553174001311 Switch II region; other site 553174001312 G4 box; other site 553174001313 G5 box; other site 553174001314 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 553174001315 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 553174001316 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 553174001317 16S/18S rRNA binding site [nucleotide binding]; other site 553174001318 S13e-L30e interaction site [polypeptide binding]; other site 553174001319 25S rRNA binding site [nucleotide binding]; other site 553174001320 Peptidase C10 family; Region: Peptidase_C10; pfam01640 553174001321 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 553174001322 catalytic center binding site [active] 553174001323 ATP binding site [chemical binding]; other site 553174001324 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 553174001325 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 553174001326 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 553174001327 RNA binding site [nucleotide binding]; other site 553174001328 active site 553174001329 Bacitracin resistance protein BacA; Region: BacA; cl00858 553174001330 Protein of unknown function (DUF3098); Region: DUF3098; pfam11297 553174001331 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 553174001332 FtsX-like permease family; Region: FtsX; cl15850 553174001333 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; cl01155 553174001334 Protein of unknown function (DUF3078); Region: DUF3078; pfam11276 553174001335 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174001336 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174001337 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; cl01155 553174001338 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; cl01155 553174001339 starch binding outer membrane protein SusD; Region: SusD; cd08977 553174001340 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 553174001341 Tetratricopeptide repeat; Region: TPR_12; pfam13424 553174001342 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 553174001343 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 553174001344 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 553174001345 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 553174001346 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 553174001347 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 553174001348 Cation efflux family; Region: Cation_efflux; cl00316 553174001349 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 553174001350 active site 553174001351 GDP-L-galactose-hexose-1-phosphate guanyltransferase; Provisional; Region: PLN03103 553174001352 Stage II sporulation protein; Region: SpoIID; pfam08486 553174001353 SpoIID/LytB domain; Region: SpoIID_LytB; TIGR02669 553174001354 siderophore transporter, RhtX/FptX family; Region: sider_RhtX_FptX; TIGR02718 553174001355 Peptidase family M48; Region: Peptidase_M48; cl12018 553174001356 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 553174001357 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 553174001358 Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form...; Region: Band_7_stomatin_like; cd03403 553174001359 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 553174001360 active site 553174001361 UDP-N-acetylglucosamine 2-epimerase; Region: Epimerase_2; pfam02350 553174001362 homodimer interface [polypeptide binding]; other site 553174001363 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 553174001364 MatE; Region: MatE; cl10513 553174001365 MatE; Region: MatE; cl10513 553174001366 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; cl00207 553174001367 Helix-turn-helix domain; Region: HTH_18; pfam12833 553174001368 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 553174001369 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 553174001370 metal-binding site [ion binding] 553174001371 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 553174001372 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 553174001373 active site 553174001374 motif I; other site 553174001375 motif II; other site 553174001376 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 553174001377 aldose 1-epimerase superfamily; Region: Aldose_epim; cl14648 553174001378 active site 553174001379 catalytic residues [active] 553174001380 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 553174001381 NeuB family; Region: NeuB; cl00496 553174001382 Chorismate mutase type II; Region: CM_2; cl00693 553174001383 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 553174001384 putative catalytic site [active] 553174001385 putative metal binding site [ion binding]; other site 553174001386 putative phosphate binding site [ion binding]; other site 553174001387 Protein of unknown function, DUF481; Region: DUF481; cl01213 553174001388 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 553174001389 Domain of unknown function (DUF4339); Region: DUF4339; pfam14237 553174001390 Domain of unknown function (DUF4359); Region: DUF4359; pfam14271 553174001391 Protein of unknown function (DUF421); Region: DUF421; cl00990 553174001392 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cl00220 553174001393 catalytic triad [active] 553174001394 conserved cis-peptide bond; other site 553174001395 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 553174001396 Tetramer interface [polypeptide binding]; other site 553174001397 active site 553174001398 FMN-binding site [chemical binding]; other site 553174001399 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 553174001400 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 553174001401 active site 553174001402 catalytic residues [active] 553174001403 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 553174001404 catalytic residues [active] 553174001405 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 553174001406 Protein of unknown function (DUF2023); Region: DUF2023; pfam09633 553174001407 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 553174001408 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174001409 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 553174001410 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174001411 Nitroreductase-like family 1. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_1; cd02137 553174001412 dimer interface [polypeptide binding]; other site 553174001413 FMN binding site [chemical binding]; other site 553174001414 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 553174001415 dimer interface [polypeptide binding]; other site 553174001416 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 553174001417 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 553174001418 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 553174001419 putative Mg(2+) transport ATPase; Provisional; Region: PRK09977 553174001420 MgtC family; Region: MgtC; pfam02308 553174001421 maltose O-acetyltransferase; Provisional; Region: PRK10092 553174001422 Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively at the C6...; Region: LbH_MAT_GAT; cd03357 553174001423 active site 553174001424 substrate binding site [chemical binding]; other site 553174001425 trimer interface [polypeptide binding]; other site 553174001426 CoA binding site [chemical binding]; other site 553174001427 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174001428 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174001429 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; cl01155 553174001430 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174001431 SusD family; Region: SusD; pfam07980 553174001432 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 553174001433 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 553174001434 N-terminal plug; other site 553174001435 ligand-binding site [chemical binding]; other site 553174001436 Protein of unknown function (DUF805); Region: DUF805; cl01224 553174001437 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 553174001438 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 553174001439 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; cl03295 553174001440 nucleotide binding pocket [chemical binding]; other site 553174001441 K-X-D-G motif; other site 553174001442 catalytic site [active] 553174001443 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 553174001444 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 553174001445 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 553174001446 Dimer interface [polypeptide binding]; other site 553174001447 BRCT sequence motif; other site 553174001448 The MutT pyrophosphohydrolase is a prototypical Nudix hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic...; Region: MutT_pyrophosphohydrolase; cd03425 553174001449 active site 553174001450 8-oxo-dGMP binding site [chemical binding]; other site 553174001451 nudix motif; other site 553174001452 metal binding site [ion binding]; metal-binding site 553174001453 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 553174001454 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 553174001455 transmembrane helices; other site 553174001456 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 553174001457 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; cl01155 553174001458 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 553174001459 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174001460 Family description; Region: UvrD_C_2; cl15862 553174001461 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 553174001462 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 553174001463 active site 553174001464 substrate binding site [chemical binding]; other site 553174001465 Mg2+ binding site [ion binding]; other site 553174001466 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 553174001467 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 553174001468 Walker A/P-loop; other site 553174001469 ATP binding site [chemical binding]; other site 553174001470 Q-loop/lid; other site 553174001471 ABC transporter signature motif; other site 553174001472 Walker B; other site 553174001473 D-loop; other site 553174001474 H-loop/switch region; other site 553174001475 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 553174001476 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 553174001477 DNA-binding site [nucleotide binding]; DNA binding site 553174001478 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 553174001479 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 553174001480 ATP binding site [chemical binding]; other site 553174001481 putative Mg++ binding site [ion binding]; other site 553174001482 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 553174001483 nucleotide binding region [chemical binding]; other site 553174001484 ATP-binding site [chemical binding]; other site 553174001485 recombinase A; Provisional; Region: recA; PRK09354 553174001486 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 553174001487 hexamer interface [polypeptide binding]; other site 553174001488 Walker A motif; other site 553174001489 ATP binding site [chemical binding]; other site 553174001490 Walker B motif; other site 553174001491 TfoX N-terminal domain; Region: TfoX_N; cl01167 553174001492 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 553174001493 Protein of unknown function (DUF1648); Region: DUF1648; pfam07853 553174001494 malate dehydrogenase; Provisional; Region: PRK13529 553174001495 Malic enzyme, N-terminal domain; Region: malic; pfam00390 553174001496 NAD(P) binding domain of malic enzyme (ME), subgroup 1; Region: NAD_bind_1_malic_enz; cd05312 553174001497 NAD(P) binding site [chemical binding]; other site 553174001498 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 553174001499 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 553174001500 dimer interface [polypeptide binding]; other site 553174001501 PYR/PP interface [polypeptide binding]; other site 553174001502 TPP binding site [chemical binding]; other site 553174001503 substrate binding site [chemical binding]; other site 553174001504 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 553174001505 Domain of unknown function; Region: EKR; cl11037 553174001506 4Fe-4S binding domain; Region: Fer4; cl02805 553174001507 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 553174001508 Thiamine pyrophosphate (TPP family), PFOR_PNO subfamily, TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This...; Region: TPP_PFOR_PNO; cd03377 553174001509 TPP-binding site [chemical binding]; other site 553174001510 dimer interface [polypeptide binding]; other site 553174001511 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 553174001512 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174001513 Helix-turn-helix domains; Region: HTH; cl00088 553174001514 ATP-grasp domain; Region: ATP-grasp_4; cl03087 553174001515 Phosphate-selective porin O and P; Region: Porin_O_P; cl01524 553174001516 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 553174001517 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 553174001518 S-adenosylmethionine binding site [chemical binding]; other site 553174001519 pyruvate phosphate dikinase; Provisional; Region: PRK09279 553174001520 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 553174001521 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 553174001522 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; cl09155 553174001523 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 553174001524 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 553174001525 Clp amino terminal domain; Region: Clp_N; pfam02861 553174001526 Clp amino terminal domain; Region: Clp_N; pfam02861 553174001527 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 553174001528 Walker A motif; other site 553174001529 ATP binding site [chemical binding]; other site 553174001530 Walker B motif; other site 553174001531 arginine finger; other site 553174001532 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 553174001533 Walker A motif; other site 553174001534 ATP binding site [chemical binding]; other site 553174001535 Walker B motif; other site 553174001536 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 553174001537 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 553174001538 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 553174001539 FeS/SAM binding site; other site 553174001540 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 553174001541 Acetyl xylan esterase (AXE1); Region: AXE1; pfam05448 553174001542 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 553174001543 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 553174001544 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the...; Region: Peptidase_S24_S26; cl10465 553174001545 Catalytic site [active] 553174001546 ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: PstB; COG1117 553174001547 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 553174001548 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 553174001549 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 553174001550 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 553174001551 DNA binding residues [nucleotide binding] 553174001552 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 553174001553 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 553174001554 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 553174001555 protein binding site [polypeptide binding]; other site 553174001556 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 553174001557 protein binding site [polypeptide binding]; other site 553174001558 Protein of unknown function (DUF1232); Region: DUF1232; cl01318 553174001559 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174001560 BlaR1 peptidase M56; Region: Peptidase_M56; cl15829 553174001561 copper transport repressor, CopY/TcrY family; Region: CopY_TcrY; TIGR02698 553174001562 Helix-turn-helix domains; Region: HTH; cl00088 553174001563 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 553174001564 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 553174001565 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 553174001566 NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for...; Region: NADH_pyrophosphatase; cd03429 553174001567 putative NADH binding site [chemical binding]; other site 553174001568 putative active site [active] 553174001569 nudix motif; other site 553174001570 putative metal binding site [ion binding]; other site 553174001571 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 553174001572 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 553174001573 active site 553174001574 metal binding site [ion binding]; metal-binding site 553174001575 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 553174001576 glutamate dehydrogenase; Provisional; Region: PRK14031 553174001577 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 553174001578 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 553174001579 NAD(P) binding site [chemical binding]; other site 553174001580 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 553174001581 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 553174001582 ATP binding site [chemical binding]; other site 553174001583 Mg++ binding site [ion binding]; other site 553174001584 motif III; other site 553174001585 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 553174001586 nucleotide binding region [chemical binding]; other site 553174001587 ATP-binding site [chemical binding]; other site 553174001588 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 553174001589 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 553174001590 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 553174001591 tRNA-guanine transglycosylases, various specificities; Region: tgt_general; TIGR00449 553174001592 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 553174001593 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 553174001594 Walker A motif; other site 553174001595 ATP binding site [chemical binding]; other site 553174001596 Walker B motif; other site 553174001597 arginine finger; other site 553174001598 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 553174001599 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 553174001600 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 553174001601 S-adenosylmethionine binding site [chemical binding]; other site 553174001602 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 553174001603 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 553174001604 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 553174001605 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 553174001606 substrate-cofactor binding pocket; other site 553174001607 pyridoxal 5'-phosphate binding site [chemical binding]; other site 553174001608 catalytic residue [active] 553174001609 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 553174001610 dimer interface [polypeptide binding]; other site 553174001611 ssDNA binding site [nucleotide binding]; other site 553174001612 tetramer (dimer of dimers) interface [polypeptide binding]; other site 553174001613 gliding motility-associated protein GldE; Region: GldE; TIGR03520 553174001614 Domain of unknown function DUF21; Region: DUF21; pfam01595 553174001615 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 553174001616 Transporter associated domain; Region: CorC_HlyC; cl08393 553174001617 Phosphopantetheinyl transferase [Coenzyme metabolism]; Region: Sfp; COG2091 553174001618 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 553174001619 CT domains found N-terminal of phosphoserine phosphatase (PSP, SerB); Region: ACT_PSP_1; cd04870 553174001620 ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB); Region: ACT_PSP_2; cd04871 553174001621 phosphoserine phosphatase SerB; Region: serB; TIGR00338 553174001622 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 553174001623 motif II; other site 553174001624 Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane]; Region: GumC; COG3206 553174001625 Chain length determinant protein; Region: Wzz; cl15801 553174001626 capsular exopolysaccharide family; Region: eps_fam; TIGR01007 553174001627 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174001628 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 553174001629 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 553174001630 substrate binding site; other site 553174001631 tetramer interface; other site 553174001632 Cell division protein ZapA; Region: ZapA; cl01146 553174001633 phosphodiesterase; Provisional; Region: PRK12704 553174001634 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 553174001635 Zn2+ binding site [ion binding]; other site 553174001636 Mg2+ binding site [ion binding]; other site 553174001637 Transposase; Region: DDE_Tnp_ISL3; pfam01610 553174001638 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 553174001639 Protein of unknown function (DUF2492); Region: DUF2492; cl11278 553174001640 IgA Peptidase M64; Region: Peptidase_M64; pfam09471 553174001641 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 553174001642 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 553174001643 dimer interface [polypeptide binding]; other site 553174001644 active site 553174001645 glycine-pyridoxal phosphate binding site [chemical binding]; other site 553174001646 folate binding site [chemical binding]; other site 553174001647 Cupin domain; Region: Cupin_2; cl09118 553174001648 Uncharacterized Fe-S protein [Energy production and conversion]; Region: COG1600 553174001649 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 553174001650 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 553174001651 NodB motif; other site 553174001652 active site 553174001653 catalytic site [active] 553174001654 metal binding site [ion binding]; metal-binding site 553174001655 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 553174001656 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 553174001657 The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance. Bacitracin is a dodecapeptide antibiotic produced by B. licheniformis and B. subtilis. The synthesis of bacitracin is non-ribosomally catalyzed by a multienzyme...; Region: ABC_BcrA_bacitracin_resist; cd03268 553174001658 Walker A/P-loop; other site 553174001659 ATP binding site [chemical binding]; other site 553174001660 Q-loop/lid; other site 553174001661 ABC transporter signature motif; other site 553174001662 Walker B; other site 553174001663 D-loop; other site 553174001664 H-loop/switch region; other site 553174001665 ABC-2 type transporter; Region: ABC2_membrane; cl11417 553174001666 ATP cone domain; Region: ATP-cone; pfam03477 553174001667 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK08271 553174001668 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 553174001669 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 553174001670 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 553174001671 motif II; other site 553174001672 Protein of unknown function (DUF4199); Region: DUF4199; pfam13858 553174001673 dolichyl-phosphate beta-D-mannosyltransferase; Region: PLN02726 553174001674 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 553174001675 Ligand binding site; other site 553174001676 Putative Catalytic site; other site 553174001677 DXD motif; other site 553174001678 ApbE family; Region: ApbE; cl00643 553174001679 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 553174001680 ligand binding site [chemical binding]; other site 553174001681 flexible hinge region; other site 553174001682 Helix-turn-helix domains; Region: HTH; cl00088 553174001683 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 553174001684 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 553174001685 active site 553174001686 Zn binding site [ion binding]; other site 553174001687 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 553174001688 catalytic motif [active] 553174001689 Zn binding site [ion binding]; other site 553174001690 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 553174001691 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 553174001692 protein binding site [polypeptide binding]; other site 553174001693 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 553174001694 Catalytic dyad [active] 553174001695 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 553174001696 Initiator Replication protein; Region: Rep_3; cl03080 553174001697 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 553174001698 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 553174001699 DNA binding residues [nucleotide binding] 553174001700 dimerization interface [polypeptide binding]; other site 553174001701 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 553174001702 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 553174001703 DNA binding residues [nucleotide binding] 553174001704 dimerization interface [polypeptide binding]; other site 553174001705 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 553174001706 putative active site [active] 553174001707 catalytic site [active] 553174001708 catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_2; cd09112 553174001709 PLD-like domain; Region: PLDc_2; pfam13091 553174001710 putative active site [active] 553174001711 catalytic site [active] 553174001712 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 553174001713 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 553174001714 putative active site [active] 553174001715 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 553174001716 NeuB family; Region: NeuB; cl00496 553174001717 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; cl01155 553174001718 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 553174001719 Mechanosensitive ion channel; Region: MS_channel; pfam00924 553174001720 Predicted N-acetylglucosamine kinase [Carbohydrate transport and metabolism]; Region: COG2971 553174001721 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 553174001722 NADH dehydrogenase subunit B; Provisional; Region: PRK14816 553174001723 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl15792 553174001724 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl16917 553174001725 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 553174001726 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; pfam00346 553174001727 NADH dehydrogenase; Region: NADHdh; cl00469 553174001728 NADH-quinone oxidoreductase, chain I; Region: NuoI; TIGR01971 553174001729 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 553174001730 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 553174001731 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 553174001732 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 553174001733 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 553174001734 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 553174001735 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 553174001736 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 553174001737 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 553174001738 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 553174001739 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 553174001740 Domain of unknown function (DUF3127); Region: DUF3127; pfam11325 553174001741 DNA polymerase III subunit beta; Validated; Region: PRK05643 553174001742 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 553174001743 putative DNA binding surface [nucleotide binding]; other site 553174001744 dimer interface [polypeptide binding]; other site 553174001745 beta-clamp/clamp loader binding surface; other site 553174001746 beta-clamp/translesion DNA polymerase binding surface; other site 553174001747 exodeoxyribonuclease X; Provisional; Region: PRK07983 553174001748 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 553174001749 active site 553174001750 catalytic site [active] 553174001751 substrate binding site [chemical binding]; other site 553174001752 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 553174001753 Flavoprotein; Region: Flavoprotein; cl08021 553174001754 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 553174001755 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 553174001756 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 553174001757 Walker A/P-loop; other site 553174001758 ATP binding site [chemical binding]; other site 553174001759 Q-loop/lid; other site 553174001760 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 553174001761 ABC transporter signature motif; other site 553174001762 Walker B; other site 553174001763 D-loop; other site 553174001764 H-loop/switch region; other site 553174001765 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 553174001766 TPR motif; other site 553174001767 binding surface 553174001768 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 553174001769 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 553174001770 active site 553174001771 DNA binding site [nucleotide binding] 553174001772 Int/Topo IB signature motif; other site 553174001773 Relaxase/Mobilisation nuclease domain; Region: Relaxase; cl01584 553174001774 Restriction endonuclease; Region: Mrr_cat; cl00516 553174001775 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 553174001776 ATP binding site [chemical binding]; other site 553174001777 Mg2+ binding site [ion binding]; other site 553174001778 G-X-G motif; other site 553174001779 WYL domain; Region: WYL; cl14852 553174001780 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 553174001781 Protein of unknown function (DUF3373); Region: DUF3373; pfam11853 553174001782 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 553174001783 AAA domain; Region: AAA_31; pfam13614 553174001784 P-loop; other site 553174001785 Magnesium ion binding site [ion binding]; other site 553174001786 Helix-turn-helix domains; Region: HTH; cl00088 553174001787 O-Antigen ligase; Region: Wzy_C; cl04850 553174001788 Bacteroides conjugation system ATPase, TraG family; Region: Bac_Flav_CT_G; TIGR03783 553174001789 Bacteroides conjugation system ATPase, TraG family; Region: Bac_Flav_CT_G; TIGR03783 553174001790 Bacteroides conjugative transposon TraJ protein; Region: Bac_Flav_CT_J; TIGR03782 553174001791 Bacteroides conjugative transposon TraK protein; Region: Bac_Flav_CT_K; TIGR03781 553174001792 Bacteroides conjugative transposon TraM protein; Region: Bac_Flav_CT_M; TIGR03779 553174001793 Protein of unknown function (DUF3714); Region: DUF3714; pfam12508 553174001794 Domain of unknown function (DUF4138); Region: DUF4138; pfam13595 553174001795 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174001796 Walker B motif; other site 553174001797 TraX protein; Region: TraX; cl05434 553174001798 Predicted P-loop ATPase [General function prediction only]; Region: COG4928 553174001799 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 553174001800 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4487 553174001801 Uncharacterized protein conserved in bacteria (DUF2130); Region: DUF2130; pfam09903 553174001802 WYL domain; Region: WYL; cl14852 553174001803 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 553174001804 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 553174001805 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 553174001806 ATP binding site [chemical binding]; other site 553174001807 putative Mg++ binding site [ion binding]; other site 553174001808 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 553174001809 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 553174001810 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 553174001811 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 553174001812 Fic/DOC family; Region: Fic; cl00960 553174001813 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 553174001814 non-specific DNA binding site [nucleotide binding]; other site 553174001815 salt bridge; other site 553174001816 sequence-specific DNA binding site [nucleotide binding]; other site 553174001817 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174001818 Family description; Region: UvrD_C_2; cl15862 553174001819 Peptidase family M23; Region: Peptidase_M23; pfam01551 553174001820 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 553174001821 Protein of unknown function (DUF4099); Region: DUF4099; pfam13351 553174001822 Protein of unknown function (DUF3945); Region: DUF3945; pfam13101 553174001823 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 553174001824 active site 553174001825 MutS domain I; Region: MutS_I; pfam01624 553174001826 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 553174001827 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 553174001828 Protein of unknown function (DUF3991); Region: DUF3991; pfam13154 553174001829 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 553174001830 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 553174001831 DNA topoisomerase I; Validated; Region: PRK05582 553174001832 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 553174001833 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 553174001834 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 553174001835 salt bridge; other site 553174001836 non-specific DNA binding site [nucleotide binding]; other site 553174001837 sequence-specific DNA binding site [nucleotide binding]; other site 553174001838 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like_2; cd04847 553174001839 active site 553174001840 catalytic triad [active] 553174001841 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 553174001842 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 553174001843 Walker A motif; other site 553174001844 ATP binding site [chemical binding]; other site 553174001845 Walker B motif; other site 553174001846 arginine finger; other site 553174001847 DNA primase, catalytic core; Region: dnaG; TIGR01391 553174001848 CHC2 zinc finger; Region: zf-CHC2; cl15369 553174001849 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 553174001850 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 553174001851 active site 553174001852 metal binding site [ion binding]; metal-binding site 553174001853 interdomain interaction site; other site 553174001854 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174001855 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 553174001856 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 553174001857 Sulfatase; Region: Sulfatase; cl10460 553174001858 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 553174001859 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 553174001860 motif II; other site 553174001861 OsmC-like protein; Region: OsmC; cl00767 553174001862 N-terminal Early set domain associated with the catalytic domain of putative esterases; Region: E_set_Esterase_like_N; cd11294 553174001863 Enterochelin esterase and related enzymes [Inorganic ion transport and metabolism]; Region: Fes; COG2382 553174001864 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 553174001865 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 553174001866 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174001867 CoA-ligase; Region: Ligase_CoA; cl02894 553174001868 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 553174001869 ATP-grasp domain; Region: ATP-grasp_4; cl03087 553174001870 CoA-ligase; Region: Ligase_CoA; cl02894 553174001871 Acetokinase family; Region: Acetate_kinase; cl01029 553174001872 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 553174001873 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 553174001874 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 553174001875 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 553174001876 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 553174001877 NAD(P) binding site [chemical binding]; other site 553174001878 homodimer interface [polypeptide binding]; other site 553174001879 substrate binding site [chemical binding]; other site 553174001880 active site 553174001881 multidrug efflux protein; Reviewed; Region: PRK01766 553174001882 MatE; Region: MatE; cl10513 553174001883 MatE; Region: MatE; cl10513 553174001884 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 553174001885 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 553174001886 active site 553174001887 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 553174001888 ResB-like family; Region: ResB; pfam05140 553174001889 ResB-like family; Region: ResB; pfam05140 553174001890 cytochrome c nitrite reductase subunit c552; Provisional; Region: nrfA; PRK11125 553174001891 cytochrome c nitrate reductase, small subunit; Region: cytochr_NrfH; TIGR03153 553174001892 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 553174001893 metal binding site 2 [ion binding]; metal-binding site 553174001894 putative DNA binding helix; other site 553174001895 metal binding site 1 [ion binding]; metal-binding site 553174001896 dimer interface [polypeptide binding]; other site 553174001897 structural Zn2+ binding site [ion binding]; other site 553174001898 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 553174001899 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 553174001900 GDP-binding site [chemical binding]; other site 553174001901 ACT binding site; other site 553174001902 IMP binding site; other site 553174001903 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 553174001904 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: HisRS-like_core; cd00773 553174001905 dimer interface [polypeptide binding]; other site 553174001906 motif 1; other site 553174001907 active site 553174001908 motif 2; other site 553174001909 motif 3; other site 553174001910 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 553174001911 anticodon binding site; other site 553174001912 Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; Region: EEP-1; cd09083 553174001913 putative catalytic site [active] 553174001914 putative metal binding site [ion binding]; other site 553174001915 putative phosphate binding site [ion binding]; other site 553174001916 enolase; Provisional; Region: eno; PRK00077 553174001917 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 553174001918 dimer interface [polypeptide binding]; other site 553174001919 metal binding site [ion binding]; metal-binding site 553174001920 substrate binding pocket [chemical binding]; other site 553174001921 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; cl00674 553174001922 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 553174001923 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; cl00674 553174001924 Cysteine-rich domain; Region: CCG; pfam02754 553174001925 CoB--CoM heterodisulfide reductase, subunit B; Region: CoB_CoM_SS_B; TIGR03288 553174001926 Cysteine-rich domain; Region: CCG; pfam02754 553174001927 DNA topoisomerase III; Provisional; Region: PRK07726 553174001928 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 553174001929 active site 553174001930 putative interdomain interaction site [polypeptide binding]; other site 553174001931 putative metal-binding site [ion binding]; other site 553174001932 putative nucleotide binding site [chemical binding]; other site 553174001933 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 553174001934 domain I; other site 553174001935 DNA binding groove [nucleotide binding] 553174001936 phosphate binding site [ion binding]; other site 553174001937 domain II; other site 553174001938 domain III; other site 553174001939 nucleotide binding site [chemical binding]; other site 553174001940 catalytic site [active] 553174001941 domain IV; other site 553174001942 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 553174001943 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 553174001944 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 553174001945 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 553174001946 Outer membrane efflux protein; Region: OEP; pfam02321 553174001947 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 553174001948 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 553174001949 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 553174001950 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 553174001951 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 553174001952 ABC-2 type transporter; Region: ABC2_membrane; cl11417 553174001953 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 553174001954 ABC-2 type transporter; Region: ABC2_membrane; cl11417 553174001955 classical (c) SDR, subgroup 5; Region: SDR_c5; cd05346 553174001956 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 553174001957 putative NAD(P) binding site [chemical binding]; other site 553174001958 homodimer interface [polypeptide binding]; other site 553174001959 homotetramer interface [polypeptide binding]; other site 553174001960 active site 553174001961 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 553174001962 EamA-like transporter family; Region: EamA; cl01037 553174001963 EamA-like transporter family; Region: EamA; cl01037 553174001964 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 553174001965 EamA-like transporter family; Region: EamA; cl01037 553174001966 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 553174001967 dimer interface [polypeptide binding]; other site 553174001968 substrate binding site [chemical binding]; other site 553174001969 ATP binding site [chemical binding]; other site 553174001970 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 553174001971 active site 553174001972 thiamine phosphate binding site [chemical binding]; other site 553174001973 pyrophosphate binding site [ion binding]; other site 553174001974 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 553174001975 ThiC-associated domain; Region: ThiC-associated; pfam13667 553174001976 ThiC family; Region: ThiC; cl08031 553174001977 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174001978 Ribulose 1,5-bisphosphate synthetase, converts PRPP to RuBP, flavoprotein [Carbohydrate transport and metabolism]; Region: THI4; COG1635 553174001979 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 553174001980 thiamine phosphate binding site [chemical binding]; other site 553174001981 active site 553174001982 pyrophosphate binding site [ion binding]; other site 553174001983 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 553174001984 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174001985 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174001986 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; cl01155 553174001987 conserved hypothetical protein YmdA/YtgF; Region: YmdA_YtgF; TIGR03319 553174001988 Uncharacterized protein conserved in bacteria (DUF2130); Region: DUF2130; pfam09903 553174001989 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 553174001990 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 553174001991 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 553174001992 Protein of unknown function (DUF4230); Region: DUF4230; pfam14014 553174001993 Protein of unknown function (DUF4230); Region: DUF4230; pfam14014 553174001994 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 553174001995 MatE; Region: MatE; cl10513 553174001996 MatE; Region: MatE; cl10513 553174001997 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+; Region: ADPRase_NUDT5; cd03424 553174001998 dimer interface [polypeptide binding]; other site 553174001999 ADP-ribose binding site [chemical binding]; other site 553174002000 active site 553174002001 nudix motif; other site 553174002002 metal binding site [ion binding]; metal-binding site 553174002003 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 553174002004 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 553174002005 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 553174002006 catalytic residues [active] 553174002007 Helix-turn-helix domains; Region: HTH; cl00088 553174002008 Phosphotransferase enzyme family; Region: APH; pfam01636 553174002009 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 553174002010 P-loop ATPase protein family; Region: ATP_bind_2; cl15794 553174002011 HD superfamily phosphohydrolases [General function prediction only]; Region: COG1078 553174002012 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 553174002013 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 553174002014 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 553174002015 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 553174002016 trimer interface [polypeptide binding]; other site 553174002017 active site 553174002018 UDP-GlcNAc binding site [chemical binding]; other site 553174002019 lipid binding site [chemical binding]; lipid-binding site 553174002020 bifunctional UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase/(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase; Reviewed; Region: PRK13188 553174002021 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 553174002022 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 553174002023 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 553174002024 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 553174002025 active site 553174002026 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174002027 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 553174002028 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 553174002029 Transglycosylase; Region: Transgly; cl07896 553174002030 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 553174002031 PIF1-like helicase; Region: PIF1; pfam05970 553174002032 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174002033 Family description; Region: UvrD_C_2; cl15862 553174002034 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 553174002035 Ferritin-like domain; Region: Ferritin; pfam00210 553174002036 ferroxidase diiron center [ion binding]; other site 553174002037 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 553174002038 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and...; Region: BCAT_beta_family; cd01557 553174002039 homodimer interface [polypeptide binding]; other site 553174002040 substrate-cofactor binding pocket; other site 553174002041 catalytic residue [active] 553174002042 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 553174002043 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 553174002044 ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a...; Region: ExoVII_LU_OBF; cd04489 553174002045 generic binding surface II; other site 553174002046 generic binding surface I; other site 553174002047 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 553174002048 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 553174002049 Peptidase S8 family domain, uncharacterized subfamily 9; Region: Peptidases_S8_9; cd07493 553174002050 active site 553174002051 catalytic triad [active] 553174002052 Uncharacterized conserved protein [Function unknown]; Region: COG2966 553174002053 Protein of unknown function (DUF1212); Region: DUF1212; cl01118 553174002054 Protein of unknown function (DUF1212); Region: DUF1212; cl01118 553174002055 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 553174002056 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 553174002057 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 553174002058 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174002059 ATP binding site [chemical binding]; other site 553174002060 putative Mg++ binding site [ion binding]; other site 553174002061 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; cl16911 553174002062 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; cl16911 553174002063 Domain of unknown function (DUF4372); Region: DUF4372; pfam14294 553174002064 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 553174002065 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 553174002066 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 553174002067 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 553174002068 active site 553174002069 DNA binding site [nucleotide binding] 553174002070 Int/Topo IB signature motif; other site 553174002071 Glycerate kinase family; Region: Gly_kinase; cl00841 553174002072 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 553174002073 tandem repeat interface [polypeptide binding]; other site 553174002074 oligomer interface [polypeptide binding]; other site 553174002075 active site residues [active] 553174002076 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 553174002077 tandem repeat interface [polypeptide binding]; other site 553174002078 oligomer interface [polypeptide binding]; other site 553174002079 active site residues [active] 553174002080 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 553174002081 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 553174002082 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 553174002083 thiamine-monophosphate kinase; Region: thiL; TIGR01379 553174002084 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 553174002085 ATP binding site [chemical binding]; other site 553174002086 dimerization interface [polypeptide binding]; other site 553174002087 Transposase; Region: DDE_Tnp_ISL3; pfam01610 553174002088 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 553174002089 active site 553174002090 catalytic triad [active] 553174002091 oxyanion hole [active] 553174002092 Domain of unknown function (DUF303); Region: DUF303; pfam03629 553174002093 Sulfatase; Region: Sulfatase; cl10460 553174002094 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 553174002095 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 553174002096 Sulfatase; Region: Sulfatase; cl10460 553174002097 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 553174002098 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 553174002099 Transposase; Region: DDE_Tnp_ISL3; pfam01610 553174002100 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 553174002101 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 553174002102 ring oligomerisation interface [polypeptide binding]; other site 553174002103 ATP/Mg binding site [chemical binding]; other site 553174002104 stacking interactions; other site 553174002105 hinge regions; other site 553174002106 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 553174002107 oligomerisation interface [polypeptide binding]; other site 553174002108 mobile loop; other site 553174002109 roof hairpin; other site 553174002110 DNA alkylation repair enzyme; Region: DNA_alkylation; pfam08713 553174002111 A new structural DNA glycosylase; Region: AlkD_like; cd06561 553174002112 active site 553174002113 Transposase, Mutator family; Region: Transposase_mut; pfam00872 553174002114 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 553174002115 active site 553174002116 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 553174002117 DHH family; Region: DHH; pfam01368 553174002118 Nitroreductase-like family 3. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_3; cd02139 553174002119 putative FMN binding site [chemical binding]; other site 553174002120 hypothetical protein; Provisional; Region: PRK11770 553174002121 Domain of unknown function (DUF307); Region: DUF307; pfam03733 553174002122 Domain of unknown function (DUF307); Region: DUF307; pfam03733 553174002123 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 553174002124 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 553174002125 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 553174002126 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 553174002127 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 553174002128 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl11420 553174002129 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; cl01155 553174002130 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 553174002131 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 553174002132 Family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases such as the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domain of the ionotropic glutamate recep; Region: PBP1_glutamate_receptors_like; cd06269 553174002133 dimerization interface [polypeptide binding]; other site 553174002134 FlgD Ig-like domain; Region: FlgD_ig; cl15790 553174002135 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 553174002136 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 553174002137 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 553174002138 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 553174002139 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 553174002140 N-acyl-D-glucosamine 2-epimerase [Carbohydrate transport and metabolism]; Region: COG2942 553174002141 dimerization interface [polypeptide binding]; other site 553174002142 putative active cleft [active] 553174002143 Low molecular weight phosphatase family; Region: LMWPc; cd00115 553174002144 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 553174002145 active site 553174002146 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 553174002147 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 553174002148 active site 553174002149 nucleophile elbow; other site 553174002150 carbamoyl-phosphate synthase, large subunit; Region: CPSaseII_lrg; TIGR01369 553174002151 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 553174002152 ATP-grasp domain; Region: ATP-grasp_4; cl03087 553174002153 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 553174002154 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 553174002155 ATP-grasp domain; Region: ATP-grasp_4; cl03087 553174002156 Methylglyoxal synthase-like domain found in pyr1 and URA1-like carbamoyl phosphate synthetases (CPS), including ammonia-dependent CPS Type I, and glutamine-dependent CPS Type III. These are multidomain proteins, in which MGS is the C-terminal domain; Region: MGS_CPS_I_III; cd01423 553174002157 probable substrate binding site [chemical binding]; other site 553174002158 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 553174002159 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 553174002160 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 553174002161 catalytic site [active] 553174002162 subunit interface [polypeptide binding]; other site 553174002163 Glutamine phosphoribosylpyrophosphate amidotransferase [Nucleotide transport and metabolism]; Region: PurF; COG0034 553174002164 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 553174002165 active site 553174002166 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 553174002167 active site 553174002168 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 553174002169 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 553174002170 glutaminase active site [active] 553174002171 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 553174002172 dimer interface [polypeptide binding]; other site 553174002173 active site 553174002174 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 553174002175 dimer interface [polypeptide binding]; other site 553174002176 active site 553174002177 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 553174002178 SLBB domain; Region: SLBB; pfam10531 553174002179 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 553174002180 Predicted phosphohydrolases [General function prediction only]; Region: COG1408 553174002181 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 553174002182 putative active site [active] 553174002183 putative metal binding site [ion binding]; other site 553174002184 DNA-damage-inducible SOS response protein; Provisional; Region: PRK10367 553174002185 MatE; Region: MatE; cl10513 553174002186 MatE; Region: MatE; cl10513 553174002187 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 553174002188 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 553174002189 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 553174002190 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174002191 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 553174002192 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 553174002193 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 553174002194 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 553174002195 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; cl00233 553174002196 catalytic center binding site [active] 553174002197 ATP binding site [chemical binding]; other site 553174002198 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 553174002199 binding surface 553174002200 TPR motif; other site 553174002201 Anaphase-promoting complex, cyclosome, subunit 3; Region: Apc3; pfam12895 553174002202 aminotransferase, LLPSF_NHT_00031 family; Region: NHT_00031; TIGR04181 553174002203 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 553174002204 inhibitor-cofactor binding pocket; inhibition site 553174002205 pyridoxal 5'-phosphate binding site [chemical binding]; other site 553174002206 catalytic residue [active] 553174002207 carbamoyl phosphate synthase-like protein; Provisional; Region: PRK12767 553174002208 ATP-grasp domain; Region: ATP-grasp_4; cl03087 553174002209 diaminopimelate decarboxylase; Region: PLN02537 553174002210 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 553174002211 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 553174002212 catalytic residue [active] 553174002213 Bacterial sugar transferase; Region: Bac_transf; cl00939 553174002214 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 553174002215 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174002216 NAD(P) binding site [chemical binding]; other site 553174002217 active site 553174002218 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 553174002219 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 553174002220 active site 553174002221 catalytic tetrad [active] 553174002222 Sugar-transfer associated ATP-grasp; Region: ATPgrasp_ST; pfam14397 553174002223 ATP-grasp domain; Region: ATP-grasp_4; cl03087 553174002224 ATP-grasp domain; Region: ATP-grasp_4; cl03087 553174002225 This family is most closely related to the GT1 family of glycosyltransferases. cap1E in Streptococcus pneumoniae is required for the synthesis of type 1 capsular polysaccharides; Region: GT1_cap1E_like; cd03808 553174002226 putative ADP-binding pocket [chemical binding]; other site 553174002227 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 553174002228 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 553174002229 putative ADP-binding pocket [chemical binding]; other site 553174002230 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 553174002231 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 553174002232 active site 553174002233 Bacterial membrane protein YfhO; Region: YfhO; pfam09586 553174002234 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 553174002235 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 553174002236 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 553174002237 active site 553174002238 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 553174002239 trimer interface [polypeptide binding]; other site 553174002240 active site 553174002241 substrate binding site [chemical binding]; other site 553174002242 CoA binding site [chemical binding]; other site 553174002243 putative glycosyl transferase; Provisional; Region: PRK10073 553174002244 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 553174002245 active site 553174002246 Vi polysaccharide biosynthesis protein TviB; Provisional; Region: PRK15182 553174002247 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174002248 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 553174002249 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174002250 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 553174002251 MatE; Region: MatE; cl10513 553174002252 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; cl01155 553174002253 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 553174002254 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 553174002255 putative active site [active] 553174002256 substrate binding site [chemical binding]; other site 553174002257 putative cosubstrate binding site; other site 553174002258 catalytic site [active] 553174002259 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 553174002260 substrate binding site [chemical binding]; other site 553174002261 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 553174002262 Voltage gated chloride channel; Region: Voltage_CLC; pfam00654 553174002263 Cl- selectivity filter; other site 553174002264 Cl- binding residues [ion binding]; other site 553174002265 pore gating glutamate residue; other site 553174002266 dimer interface [polypeptide binding]; other site 553174002267 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 553174002268 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 553174002269 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 553174002270 LysE type translocator; Region: LysE; cl00565 553174002271 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 553174002272 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 553174002273 NADP binding site [chemical binding]; other site 553174002274 active site 553174002275 putative substrate binding site [chemical binding]; other site 553174002276 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 553174002277 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 553174002278 G1 box; other site 553174002279 putative GEF interaction site [polypeptide binding]; other site 553174002280 GTP/Mg2+ binding site [chemical binding]; other site 553174002281 Switch I region; other site 553174002282 G2 box; other site 553174002283 G3 box; other site 553174002284 Switch II region; other site 553174002285 G4 box; other site 553174002286 G5 box; other site 553174002287 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 553174002288 RNA polymerase sigma factor; Provisional; Region: PRK12513 553174002289 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 553174002290 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 553174002291 DNA binding residues [nucleotide binding] 553174002292 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 553174002293 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 553174002294 substrate binding site [chemical binding]; other site 553174002295 hexamer interface [polypeptide binding]; other site 553174002296 metal binding site [ion binding]; metal-binding site 553174002297 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are monomeric; Region: PRAI; cd00405 553174002298 active site 553174002299 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 553174002300 Glutamine amidotransferase class-I; Region: GATase; pfam00117 553174002301 glutamine binding [chemical binding]; other site 553174002302 catalytic triad [active] 553174002303 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; Region: NGN_SP_UpxY; cd09895 553174002304 N-terminal catalytic domain of a thermoactive alpha-amylase from Methanococcus jannaschii and similar proteins; glycoside hydrolase family 57 (GH57); Region: GH57N_MJA1_like; cd10795 553174002305 Glycosyl hydrolase family 57; Region: Glyco_hydro_57; pfam03065 553174002306 putative active site [active] 553174002307 catalytic site [active] 553174002308 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 553174002309 Glycogen debranching enzyme N terminal; Region: GDE_N; pfam12439 553174002310 glycogen debranching enzyme, archaeal type, putative; Region: gde_arch; TIGR01561 553174002311 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; cl01801 553174002312 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 553174002313 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 553174002314 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174002315 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 553174002316 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174002317 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 553174002318 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 553174002319 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 553174002320 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 553174002321 GMP synthase; Reviewed; Region: guaA; PRK00074 553174002322 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 553174002323 AMP/PPi binding site [chemical binding]; other site 553174002324 candidate oxyanion hole; other site 553174002325 catalytic triad [active] 553174002326 potential glutamine specificity residues [chemical binding]; other site 553174002327 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 553174002328 ATP Binding subdomain [chemical binding]; other site 553174002329 Ligand Binding sites [chemical binding]; other site 553174002330 Dimerization subdomain; other site 553174002331 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 553174002332 Substrate binding site; other site 553174002333 metal-binding site 553174002334 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 553174002335 DNA binding site [nucleotide binding] 553174002336 active site 553174002337 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 553174002338 catalytic residues [active] 553174002339 dimer interface [polypeptide binding]; other site 553174002340 Predicted membrane protein [Function unknown]; Region: COG4270 553174002341 Protein of unknown function DUF262; Region: DUF262; cl14890 553174002342 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 553174002343 active site 553174002344 Adenine-specific methyltransferase EcoRI; Region: EcoRI_methylase; pfam13651 553174002345 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14466 553174002346 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 553174002347 FeS/SAM binding site; other site 553174002348 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 553174002349 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 553174002350 Uncharacterized protein family (UPF0104); Region: UPF0104; cl04219 553174002351 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 553174002352 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 553174002353 Walker A motif; other site 553174002354 ATP binding site [chemical binding]; other site 553174002355 Walker B motif; other site 553174002356 arginine finger; other site 553174002357 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 553174002358 Helix-turn-helix domains; Region: HTH; cl00088 553174002359 Lipopolysaccharide-assembly; Region: LptE; cl01125 553174002360 Domain of unknown function (DUF4132); Region: DUF4132; pfam13569 553174002361 phosphoglucosamine mutase; Region: Arch_GlmM; TIGR03990 553174002362 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 553174002363 active site 553174002364 substrate binding site [chemical binding]; other site 553174002365 metal binding site [ion binding]; metal-binding site 553174002366 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 553174002367 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 553174002368 active site 553174002369 nucleophile elbow; other site 553174002370 Aminopeptidase P, N-terminal domain; Region: AMP_N; cl08433 553174002371 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 553174002372 active site 553174002373 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 553174002374 active site 553174002375 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 553174002376 DHH family; Region: DHH; pfam01368 553174002377 DHHA1 domain; Region: DHHA1; pfam02272 553174002378 DEAD-like helicases superfamily; Region: DEXDc; smart00487 553174002379 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 553174002380 ATP binding site [chemical binding]; other site 553174002381 putative Mg++ binding site [ion binding]; other site 553174002382 ski2-like helicase; Provisional; Region: PRK01172 553174002383 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 553174002384 nucleotide binding region [chemical binding]; other site 553174002385 ATP-binding site [chemical binding]; other site 553174002386 Superfamily II DNA helicase [DNA replication, recombination, and repair]; Region: RecQ; COG0514 553174002387 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 553174002388 Acyl-ACP thioesterase; Region: Acyl-ACP_TE; pfam01643 553174002389 active site 553174002390 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 553174002391 ligand binding site [chemical binding]; other site 553174002392 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 553174002393 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 553174002394 Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR...; Region: TPP_OGFOR; cd03375 553174002395 TPP-binding site [chemical binding]; other site 553174002396 2-ketoisovalerate ferredoxin reductase; Validated; Region: PRK07119 553174002397 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 553174002398 dimer interface [polypeptide binding]; other site 553174002399 PYR/PP interface [polypeptide binding]; other site 553174002400 TPP binding site [chemical binding]; other site 553174002401 substrate binding site [chemical binding]; other site 553174002402 Ferredoxin [Energy production and conversion]; Region: COG1146 553174002403 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 553174002404 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 553174002405 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14185 553174002406 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 553174002407 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 553174002408 homodimer interface [polypeptide binding]; other site 553174002409 NADP binding site [chemical binding]; other site 553174002410 substrate binding site [chemical binding]; other site 553174002411 signal recognition particle protein; Provisional; Region: PRK10867 553174002412 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 553174002413 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 553174002414 P loop; other site 553174002415 GTP binding site [chemical binding]; other site 553174002416 Signal peptide binding domain; Region: SRP_SPB; pfam02978 553174002417 dihydroorotate dehydrogenase (subfamily 1) family protein; Region: pyrD_sub1_fam; TIGR01037 553174002418 Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. 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...; Region: DHOD_1B_like; cd04740 553174002419 heterodimer interface [polypeptide binding]; other site 553174002420 active site 553174002421 FMN binding site [chemical binding]; other site 553174002422 homodimer interface [polypeptide binding]; other site 553174002423 substrate binding site [chemical binding]; other site 553174002424 2-polyprenylphenol hydroxylase and related flavodoxin oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiB; COG0543 553174002425 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to...; Region: DHOD_e_trans; cd06218 553174002426 FAD binding pocket [chemical binding]; other site 553174002427 FAD binding motif [chemical binding]; other site 553174002428 phosphate binding motif [ion binding]; other site 553174002429 beta-alpha-beta structure motif; other site 553174002430 NAD binding pocket [chemical binding]; other site 553174002431 Iron coordination center [ion binding]; other site 553174002432 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 553174002433 non-specific DNA binding site [nucleotide binding]; other site 553174002434 salt bridge; other site 553174002435 sequence-specific DNA binding site [nucleotide binding]; other site 553174002436 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 553174002437 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 553174002438 Dna-J like membrane chaperone protein; Provisional; Region: djlA; PRK09430 553174002439 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 553174002440 putative metal binding site [ion binding]; other site 553174002441 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 553174002442 HSP70 interaction site [polypeptide binding]; other site 553174002443 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 553174002444 active site 553174002445 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cl00197 553174002446 TM2 domain; Region: TM2; cl00984 553174002447 agmatine deiminase; Region: agmatine_aguA; TIGR03380 553174002448 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; cl01113 553174002449 N-carbamolyputrescine amidase; Region: PLN02747 553174002450 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 553174002451 putative active site; other site 553174002452 catalytic triad [active] 553174002453 putative dimer interface [polypeptide binding]; other site 553174002454 Asparagine synthetase (aspartate-ammonia ligase) (AsnA) catalyses the conversion of L-aspartate to L-asparagine in the presence of ATP and ammonia. AsnA is a homodimeric enzyme which is structurally similiar to the catalytic core domain of class II...; Region: AsnA; cd00645 553174002455 dimer interface [polypeptide binding]; other site 553174002456 active site 553174002457 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 553174002458 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 553174002459 peptidase T; Region: peptidase-T; TIGR01882 553174002460 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 553174002461 metal binding site [ion binding]; metal-binding site 553174002462 dimer interface [polypeptide binding]; other site 553174002463 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 553174002464 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 553174002465 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 553174002466 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 553174002467 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174002468 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174002469 Family description; Region: UvrD_C_2; cl15862 553174002470 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 553174002471 Uncharacterized conserved protein [Function unknown]; Region: COG0327 553174002472 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 553174002473 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 553174002474 Putative zinc ribbon domain; Region: DUF164; pfam02591 553174002475 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; cd02062 553174002476 FMN binding site [chemical binding]; other site 553174002477 dimer interface [polypeptide binding]; other site 553174002478 Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]; Region: MalY; COG1168 553174002479 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 553174002480 pyridoxal 5'-phosphate binding site [chemical binding]; other site 553174002481 homodimer interface [polypeptide binding]; other site 553174002482 catalytic residue [active] 553174002483 Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism]; Region: MetC; COG0626 553174002484 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 553174002485 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 553174002486 catalytic residue [active] 553174002487 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 553174002488 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14971 553174002489 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 553174002490 Walker A motif; other site 553174002491 ATP binding site [chemical binding]; other site 553174002492 Walker B motif; other site 553174002493 arginine finger; other site 553174002494 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 553174002495 Septum formation initiator; Region: DivIC; cl11433 553174002496 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 553174002497 dihydroorotase; Reviewed; Region: PRK09236 553174002498 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 553174002499 active site 553174002500 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 553174002501 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 553174002502 Predicted phosphohydrolases [General function prediction only]; Region: COG1408 553174002503 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 553174002504 putative active site [active] 553174002505 putative metal binding site [ion binding]; other site 553174002506 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 553174002507 putative acyl-acceptor binding pocket; other site 553174002508 DPM1_like represents putative enzymes similar to eukaryotic DPM1; Region: DPM1_like; cd06442 553174002509 dolichyl-phosphate beta-D-mannosyltransferase; Region: PLN02726 553174002510 Ligand binding site; other site 553174002511 Putative Catalytic site; other site 553174002512 DXD motif; other site 553174002513 hypothetical protein; Provisional; Region: PRK08201 553174002514 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_3; cd05680 553174002515 metal binding site [ion binding]; metal-binding site 553174002516 putative dimer interface [polypeptide binding]; other site 553174002517 HEPN domain; Region: HEPN; cl00824 553174002518 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 553174002519 active site 553174002520 NTP binding site [chemical binding]; other site 553174002521 metal binding triad [ion binding]; metal-binding site 553174002522 antibiotic binding site [chemical binding]; other site 553174002523 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 553174002524 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 553174002525 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 553174002526 ATP binding site [chemical binding]; other site 553174002527 putative Mg++ binding site [ion binding]; other site 553174002528 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 553174002529 nucleotide binding region [chemical binding]; other site 553174002530 ATP-binding site [chemical binding]; other site 553174002531 TRCF domain; Region: TRCF; cl04088 553174002532 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 553174002533 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 553174002534 conserved cys residue [active] 553174002535 Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction; Region: HP_HAP_like; cd07061 553174002536 catalytic core [active] 553174002537 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 553174002538 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 553174002539 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 553174002540 catalytic residues [active] 553174002541 K+-dependent Na+/Ca+ exchanger related-protein; Region: TIGR00367 553174002542 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 553174002543 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 553174002544 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 553174002545 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; cl00047 553174002546 ligand binding site [chemical binding]; other site 553174002547 flexible hinge region; other site 553174002548 Helix-turn-helix domains; Region: HTH; cl00088 553174002549 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 553174002550 Protein of unknown function, DUF488; Region: DUF488; cl01246 553174002551 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 553174002552 putative dimer interface [polypeptide binding]; other site 553174002553 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 553174002554 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 553174002555 CoA-binding site [chemical binding]; other site 553174002556 ATP-binding [chemical binding]; other site 553174002557 YbbR-like protein; Region: YbbR; pfam07949 553174002558 Preprotein translocase subunit; Region: YajC; cl00806 553174002559 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 553174002560 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 553174002561 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 553174002562 5S rRNA interface [nucleotide binding]; other site 553174002563 CTC domain interface [polypeptide binding]; other site 553174002564 L16 interface [polypeptide binding]; other site 553174002565 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 553174002566 putative active site [active] 553174002567 catalytic residue [active] 553174002568 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 553174002569 RNA binding surface [nucleotide binding]; other site 553174002570 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 553174002571 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 553174002572 metal binding site [ion binding]; metal-binding site 553174002573 dimer interface [polypeptide binding]; other site 553174002574 Uncharacterized protein family (UPF0104); Region: UPF0104; cl04219 553174002575 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; cl16911 553174002576 GAF domain; Region: GAF; cl15785 553174002577 GAF domain; Region: GAF_2; pfam13185 553174002578 ribosome recycling factor; Reviewed; Region: frr; PRK00083 553174002579 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are 'recycled' and ready for another round of...; Region: RRF; cd00520 553174002580 hinge region; other site 553174002581 GTPase RsgA; Reviewed; Region: PRK00098 553174002582 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 553174002583 RNA binding site [nucleotide binding]; other site 553174002584 homodimer interface [polypeptide binding]; other site 553174002585 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 553174002586 GTPase/Zn-binding domain interface [polypeptide binding]; other site 553174002587 GTP/Mg2+ binding site [chemical binding]; other site 553174002588 G4 box; other site 553174002589 G5 box; other site 553174002590 G1 box; other site 553174002591 Switch I region; other site 553174002592 G2 box; other site 553174002593 G3 box; other site 553174002594 Switch II region; other site 553174002595 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 553174002596 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 553174002597 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 553174002598 motif II; other site 553174002599 glucose-6-phosphate isomerase; Provisional; Region: pgi; PRK14097 553174002600 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 553174002601 active site 553174002602 dimer interface [polypeptide binding]; other site 553174002603 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 553174002604 dimer interface [polypeptide binding]; other site 553174002605 active site 553174002606 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GpsA; COG0240 553174002607 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174002608 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 553174002609 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 553174002610 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 553174002611 dimer interface [polypeptide binding]; other site 553174002612 putative anticodon binding site; other site 553174002613 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 553174002614 motif 1; other site 553174002615 active site 553174002616 motif 2; other site 553174002617 Domain of unknown function (DUF4332); Region: DUF4332; pfam14229 553174002618 motif 3; other site 553174002619 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 553174002620 CoenzymeA binding site [chemical binding]; other site 553174002621 subunit interaction site [polypeptide binding]; other site 553174002622 PHB binding site; other site 553174002623 chorismate binding enzyme; Region: Chorismate_bind; cl10555 553174002624 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylic-acid synthase; Region: menD; TIGR00173 553174002625 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 553174002626 dimer interface [polypeptide binding]; other site 553174002627 tetramer interface [polypeptide binding]; other site 553174002628 PYR/PP interface [polypeptide binding]; other site 553174002629 TPP binding site [chemical binding]; other site 553174002630 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 553174002631 TPP-binding site [chemical binding]; other site 553174002632 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 553174002633 Enoyl-CoA hydratase/isomerase family; Region: ECH; pfam00378 553174002634 substrate binding site [chemical binding]; other site 553174002635 oxyanion hole (OAH) forming residues; other site 553174002636 trimer interface [polypeptide binding]; other site 553174002637 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_3; cl16254 553174002638 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 553174002639 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 553174002640 active site 553174002641 AMP-binding enzyme; Region: AMP-binding; cl15778 553174002642 acyl-CoA synthetase; Validated; Region: PRK07798 553174002643 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 553174002644 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 553174002645 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 553174002646 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 553174002647 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 553174002648 seryl-tRNA synthetase; Provisional; Region: PRK05431 553174002649 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 553174002650 active site residue [active] 553174002651 Oligomerisation domain; Region: Oligomerisation; cl00519 553174002652 FtsH Extracellular; Region: FtsH_ext; pfam06480 553174002653 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 553174002654 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 553174002655 Walker A motif; other site 553174002656 ATP binding site [chemical binding]; other site 553174002657 Walker B motif; other site 553174002658 arginine finger; other site 553174002659 Peptidase family M41; Region: Peptidase_M41; pfam01434 553174002660 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 553174002661 SprT homologues; Region: SprT; cl01182 553174002662 beta-D-galactosidase; Reviewed; Region: lacZ; PRK09525 553174002663 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; cl08371 553174002664 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 553174002665 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; cl15381 553174002666 Beta galactosidase small chain; Region: Bgal_small_N; cl03787 553174002667 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174002668 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 553174002669 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; cl01155 553174002670 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; cl01155 553174002671 starch binding outer membrane protein SusD; Region: SusD; cd08977 553174002672 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174002673 Peptidase C1B subfamily (MEROPS database nomenclature); composed of eukaryotic bleomycin hydrolases (BH) and bacterial aminopeptidases C (pepC). The proteins of this subfamily contain a large insert relative to the C1A peptidase (papain) subfamily. BH is...; Region: Peptidase_C1B; cd00585 553174002674 trimer interface [polypeptide binding]; other site 553174002675 active site 553174002676 G bulge; other site 553174002677 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 553174002678 CutC family; Region: CutC; cl01218 553174002679 Abi-like protein; Region: Abi_2; cl01988 553174002680 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 553174002681 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 553174002682 DNA binding residues [nucleotide binding] 553174002683 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 553174002684 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of...; Region: AlaRS_core; cd00673 553174002685 motif 1; other site 553174002686 active site 553174002687 motif 2; other site 553174002688 motif 3; other site 553174002689 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 553174002690 DHHA1 domain; Region: DHHA1; pfam02272 553174002691 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 553174002692 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 553174002693 Survival protein SurE; Region: SurE; cl00448 553174002694 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 553174002695 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 553174002696 P-loop; other site 553174002697 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174002698 Magnesium ion binding site [ion binding]; other site 553174002699 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 553174002700 Magnesium ion binding site [ion binding]; other site 553174002701 ParB-like partition proteins; Region: parB_part; TIGR00180 553174002702 ParB-like nuclease domain; Region: ParBc; cl02129 553174002703 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 553174002704 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 553174002705 N-acetyl-D-glucosamine binding site [chemical binding]; other site 553174002706 catalytic residue [active] 553174002707 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 553174002708 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 553174002709 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 553174002710 synthetase active site [active] 553174002711 NTP binding site [chemical binding]; other site 553174002712 metal binding site [ion binding]; metal-binding site 553174002713 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 553174002714 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 553174002715 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174002716 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; cl01155 553174002717 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; cl01155 553174002718 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 553174002719 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 553174002720 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 553174002721 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 553174002722 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 553174002723 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 553174002724 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174002725 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 553174002726 DNA binding residues [nucleotide binding] 553174002727 dimerization interface [polypeptide binding]; other site 553174002728 LrgB-like family; Region: LrgB; cl00596 553174002729 LrgA family; Region: LrgA; cl00608 553174002730 Protein of unknown function (DUF3822); Region: DUF3822; pfam12864 553174002731 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 553174002732 S-adenosylmethionine binding site [chemical binding]; other site 553174002733 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cl00257 553174002734 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 553174002735 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 553174002736 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 553174002737 putative active site [active] 553174002738 catalytic site [active] 553174002739 catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_2; cd09112 553174002740 putative active site [active] 553174002741 catalytic site [active] 553174002742 transcriptional regulator MalT; Provisional; Region: PRK04841 553174002743 DNA primase, catalytic core; Region: dnaG; TIGR01391 553174002744 CHC2 zinc finger; Region: zf-CHC2; cl15369 553174002745 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 553174002746 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 553174002747 active site 553174002748 metal binding site [ion binding]; metal-binding site 553174002749 interdomain interaction site; other site 553174002750 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 553174002751 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174002752 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 553174002753 Ligand binding site [chemical binding]; other site 553174002754 Electron transfer flavoprotein domain; Region: ETF; pfam01012 553174002755 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 553174002756 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 553174002757 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 553174002758 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 553174002759 putative active site [active] 553174002760 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 553174002761 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 553174002762 active site 553174002763 Acyl-CoA dehydrogenase C terminal; Region: AcylCoA_dehyd_C; pfam12186 553174002764 Mechanosensitive ion channel; Region: MS_channel; pfam00924 553174002765 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 553174002766 D-alanyl-D-alanine carboxypeptidase, serine-type, PBP4 family; Region: PBP4; TIGR00666 553174002767 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 553174002768 Domain of unknown function (DUF1200); Region: DUF1200; pfam06713 553174002769 diaminopimelate dehydrogenase; Region: DAP-DH; TIGR01921 553174002770 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174002771 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 553174002772 RuvA N terminal domain; Region: RuvA_N; pfam01330 553174002773 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 553174002774 cell surface protein SprA; Region: surface_SprA; TIGR04189 553174002775 Motility related/secretion protein; Region: SprA_N; pfam14349 553174002776 Motility related/secretion protein; Region: SprA_N; pfam14349 553174002777 Motility related/secretion protein; Region: SprA_N; pfam14349 553174002778 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 553174002779 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 553174002780 dimer interface [polypeptide binding]; other site 553174002781 pyridoxal 5'-phosphate binding site [chemical binding]; other site 553174002782 catalytic residue [active] 553174002783 AAA domain; Region: AAA_21; pfam13304 553174002784 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174002785 ABC transporter signature motif; other site 553174002786 Walker B; other site 553174002787 D-loop; other site 553174002788 H-loop/switch region; other site 553174002789 Alpha-L-fucosidase; Region: Alpha_L_fucos; cl12119 553174002790 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 553174002791 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 553174002792 active site 553174002793 metal binding site [ion binding]; metal-binding site 553174002794 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 553174002795 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 553174002796 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 553174002797 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 553174002798 ATP binding site [chemical binding]; other site 553174002799 putative Mg++ binding site [ion binding]; other site 553174002800 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 553174002801 Abortive infection C-terminus; Region: Abi_C; pfam14355 553174002802 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 553174002803 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 553174002804 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 553174002805 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 553174002806 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 553174002807 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 553174002808 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 553174002809 active site 553174002810 DNA binding site [nucleotide binding] 553174002811 Int/Topo IB signature motif; other site 553174002812 HsdM N-terminal domain; Region: HsdM_N; pfam12161 553174002813 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 553174002814 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; cl16911 553174002815 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 553174002816 non-specific DNA binding site [nucleotide binding]; other site 553174002817 salt bridge; other site 553174002818 sequence-specific DNA binding site [nucleotide binding]; other site 553174002819 Relaxase/Mobilisation nuclease domain; Region: Relaxase; cl01584 553174002820 Bacterial mobilisation protein (MobC); Region: MobC; pfam05713 553174002821 DNA primase (bacterial type) [DNA replication, recombination, and repair]; Region: DnaG; COG0358 553174002822 CHC2 zinc finger; Region: zf-CHC2; cl15369 553174002823 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 553174002824 Virulence-associated protein E; Region: VirE; pfam05272 553174002825 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 553174002826 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 553174002827 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 553174002828 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 553174002829 Int/Topo IB signature motif; other site 553174002830 Bacteriophage Lambda NinG protein; Region: NinG; pfam05766 553174002831 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 553174002832 Helix-turn-helix domains; Region: HTH; cl00088 553174002833 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 553174002834 Cell division protein FtsA; Region: FtsA; cl11496 553174002835 Cation transport protein; Region: TrkH; cl10514 553174002836 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 553174002837 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 553174002838 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174002839 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 553174002840 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174002841 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 553174002842 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 553174002843 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 553174002844 TPP-binding site; other site 553174002845 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 553174002846 PYR/PP interface [polypeptide binding]; other site 553174002847 dimer interface [polypeptide binding]; other site 553174002848 TPP binding site [chemical binding]; other site 553174002849 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 553174002850 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 553174002851 ligand binding site [chemical binding]; other site 553174002852 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 553174002853 MatE; Region: MatE; cl10513 553174002854 MatE; Region: MatE; cl10513 553174002855 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 553174002856 glycyl-tRNA synthetase; Provisional; Region: PRK04173 553174002857 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 attaches...; Region: class_II_aaRS-like_core; cl00268 553174002858 motif 1; other site 553174002859 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 553174002860 active site 553174002861 motif 2; other site 553174002862 motif 3; other site 553174002863 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 553174002864 anticodon binding site; other site 553174002865 DNA topoisomerase IV subunit A; Provisional; Region: PRK12758 553174002866 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA...; Region: TOP4c; cl00148 553174002867 CAP-like domain; other site 553174002868 active site 553174002869 primary dimer interface [polypeptide binding]; other site 553174002870 Protein of unknown function (DUF3316); Region: DUF3316; pfam11777 553174002871 Interphotoreceptor retinoid-binding protein; serine protease family S41; Region: Peptidase_S41_IRBP; cd07563 553174002872 active site triad [active] 553174002873 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; cl01155 553174002874 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cl00257 553174002875 IHF dimer interface [polypeptide binding]; other site 553174002876 adenylosuccinate lyase; Provisional; Region: PRK09285 553174002877 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 553174002878 tetramer interface [polypeptide binding]; other site 553174002879 active site 553174002880 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 553174002881 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 553174002882 RNA binding surface [nucleotide binding]; other site 553174002883 Pseudouridine synthases, RsuA subfamily; Region: PseudoU_synth_RsuA_like; cd02870 553174002884 active site 553174002885 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 553174002886 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 553174002887 putative dimer interface [polypeptide binding]; other site 553174002888 putative anticodon binding site; other site 553174002889 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 553174002890 homodimer interface [polypeptide binding]; other site 553174002891 motif 1; other site 553174002892 motif 2; other site 553174002893 active site 553174002894 motif 3; other site 553174002895 Orthopoxvirus protein of unknown function (DUF830); Region: DUF830; cl13998 553174002896 hypothetical protein; Provisional; Region: PRK14851 553174002897 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 553174002898 dimer interface [polypeptide binding]; other site 553174002899 Helix-turn-helix domains; Region: HTH; cl00088 553174002900 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 553174002901 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 553174002902 putative ATP binding site [chemical binding]; other site 553174002903 putative substrate interface [chemical binding]; other site 553174002904 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 553174002905 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 553174002906 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 553174002907 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 553174002908 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 553174002909 Walker A/P-loop; other site 553174002910 ATP binding site [chemical binding]; other site 553174002911 Q-loop/lid; other site 553174002912 ABC transporter signature motif; other site 553174002913 Walker B; other site 553174002914 D-loop; other site 553174002915 H-loop/switch region; other site 553174002916 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 553174002917 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 553174002918 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 553174002919 Ligand Binding Site [chemical binding]; other site 553174002920 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 553174002921 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174002922 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 553174002923 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 553174002924 FMN-binding domain; Region: FMN_bind; cl01081 553174002925 lipoyltransferase and lipoate-protein ligase; Region: lipoyltrans; TIGR00545 553174002926 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 553174002927 Bacterial lipoate protein ligase C-terminus; Region: Lip_prot_lig_C; pfam10437 553174002928 lipoyl synthase; Provisional; Region: PRK05481 553174002929 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 553174002930 FeS/SAM binding site; other site 553174002931 HAP1 N-terminal conserved region; Region: HAP1_N; pfam04849 553174002932 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 553174002933 ligand binding site [chemical binding]; other site 553174002934 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 553174002935 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 553174002936 ATP binding site [chemical binding]; other site 553174002937 Mg2+ binding site [ion binding]; other site 553174002938 G-X-G motif; other site 553174002939 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 553174002940 ATP binding site [chemical binding]; other site 553174002941 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 553174002942 OstA-like protein; Region: OstA_2; pfam13100 553174002943 OstA-like protein; Region: OstA; cl00844 553174002944 OstA-like protein; Region: OstA; cl00844 553174002945 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 553174002946 PPIC-type PPIASE domain; Region: Rotamase; cl08278 553174002947 PPIC-type PPIASE domain; Region: Rotamase; cl08278 553174002948 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 553174002949 PPIC-type PPIASE domain; Region: Rotamase; cl08278 553174002950 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 553174002951 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 553174002952 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key...; Region: CBS_pair_IMPDH; cd04601 553174002953 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the guanine...; Region: IMPDH; cd00381 553174002954 active site 553174002955 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 553174002956 dimerization interface [polypeptide binding]; other site 553174002957 DPS ferroxidase diiron center [ion binding]; other site 553174002958 ion pore; other site 553174002959 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 553174002960 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 553174002961 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 553174002962 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 553174002963 ATP binding site [chemical binding]; other site 553174002964 putative Mg++ binding site [ion binding]; other site 553174002965 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 553174002966 nucleotide binding region [chemical binding]; other site 553174002967 ATP-binding site [chemical binding]; other site 553174002968 RQC domain; Region: RQC; cl09632 553174002969 HRDC domain; Region: HRDC; cl02578 553174002970 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 553174002971 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 553174002972 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 553174002973 Walker A motif; other site 553174002974 ATP binding site [chemical binding]; other site 553174002975 Walker B motif; other site 553174002976 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 553174002977 Clp protease; Region: CLP_protease; pfam00574 553174002978 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 553174002979 oligomer interface [polypeptide binding]; other site 553174002980 active site residues [active] 553174002981 trigger factor; Region: tig; TIGR00115 553174002982 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 553174002983 The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in...; Region: ABC_YhbG; cd03218 553174002984 Walker A/P-loop; other site 553174002985 ATP binding site [chemical binding]; other site 553174002986 Q-loop/lid; other site 553174002987 ABC transporter signature motif; other site 553174002988 Walker B; other site 553174002989 D-loop; other site 553174002990 H-loop/switch region; other site 553174002991 Transposase IS200 like; Region: Y1_Tnp; cl00848 553174002992 Permease; Region: Permease; cl00510 553174002993 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 553174002994 ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex...; Region: ABC_Org_Solvent_Resistant; cd03261 553174002995 Walker A/P-loop; other site 553174002996 ATP binding site [chemical binding]; other site 553174002997 Q-loop/lid; other site 553174002998 ABC transporter signature motif; other site 553174002999 Walker B; other site 553174003000 D-loop; other site 553174003001 H-loop/switch region; other site 553174003002 Lumazine-binding domain; Region: Lumazine_bd; pfam12870 553174003003 GTP-binding protein Der; Reviewed; Region: PRK00093 553174003004 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 553174003005 G1 box; other site 553174003006 GTP/Mg2+ binding site [chemical binding]; other site 553174003007 Switch I region; other site 553174003008 G2 box; other site 553174003009 Switch II region; other site 553174003010 G3 box; other site 553174003011 G4 box; other site 553174003012 G5 box; other site 553174003013 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 553174003014 G1 box; other site 553174003015 GTP/Mg2+ binding site [chemical binding]; other site 553174003016 Switch I region; other site 553174003017 G2 box; other site 553174003018 G3 box; other site 553174003019 Switch II region; other site 553174003020 G4 box; other site 553174003021 G5 box; other site 553174003022 GTPase Era; Reviewed; Region: era; PRK00089 553174003023 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 553174003024 G1 box; other site 553174003025 GTP/Mg2+ binding site [chemical binding]; other site 553174003026 Switch I region; other site 553174003027 G2 box; other site 553174003028 Switch II region; other site 553174003029 G3 box; other site 553174003030 G4 box; other site 553174003031 G5 box; other site 553174003032 KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional...; Region: KH-II; cl00098 553174003033 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 553174003034 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 553174003035 dimer interface [polypeptide binding]; other site 553174003036 active site 553174003037 CoA binding pocket [chemical binding]; other site 553174003038 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 553174003039 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 553174003040 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 553174003041 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 553174003042 ATP binding site [chemical binding]; other site 553174003043 Mg2+ binding site [ion binding]; other site 553174003044 G-X-G motif; other site 553174003045 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 553174003046 AMP-binding enzyme; Region: AMP-binding; cl15778 553174003047 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 553174003048 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 553174003049 non-specific DNA binding site [nucleotide binding]; other site 553174003050 salt bridge; other site 553174003051 sequence-specific DNA binding site [nucleotide binding]; other site 553174003052 Cupin domain; Region: Cupin_2; cl09118 553174003053 Arginine repressor [Transcription]; Region: ArgR; COG1438 553174003054 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 553174003055 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 553174003056 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 553174003057 Peptidase family M48; Region: Peptidase_M48; cl12018 553174003058 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 553174003059 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 553174003060 ATP-grasp domain; Region: ATP-grasp_4; cl03087 553174003061 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 553174003062 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 553174003063 RNA binding surface [nucleotide binding]; other site 553174003064 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 553174003065 active site 553174003066 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2815 553174003067 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 553174003068 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 553174003069 elongation factor P; Validated; Region: PRK00529 553174003070 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 553174003071 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 553174003072 RNA binding site [nucleotide binding]; other site 553174003073 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 553174003074 RNA binding site [nucleotide binding]; other site 553174003075 Competence protein CoiA-like family; Region: CoiA; cl11541 553174003076 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 553174003077 dihydropteroate synthase; Region: DHPS; TIGR01496 553174003078 substrate binding pocket [chemical binding]; other site 553174003079 dimer interface [polypeptide binding]; other site 553174003080 inhibitor binding site; inhibition site 553174003081 Uncharacterized conserved protein [Function unknown]; Region: COG1624 553174003082 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 553174003083 Uncharacterized conserved protein (DUF2156); Region: DUF2156; cl12090 553174003084 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 553174003085 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 553174003086 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 553174003087 Acetokinase family; Region: Acetate_kinase; cl01029 553174003088 acetate kinase; Region: ackA; TIGR00016 553174003089 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 553174003090 putative active site [active] 553174003091 putative metal binding site [ion binding]; other site 553174003092 Domain of unknown function DUF59; Region: DUF59; cl00941 553174003093 hypothetical protein; Provisional; Region: PRK06771 553174003094 hypothetical protein; Reviewed; Region: PRK00024 553174003095 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 553174003096 MPN+ (JAMM) motif; other site 553174003097 Zinc-binding site [ion binding]; other site 553174003098 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 553174003099 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 553174003100 active site 553174003101 methionine gamma-lyase; Provisional; Region: PRK06767 553174003102 NigD-like protein; Region: NigD; pfam12667 553174003103 Peptidase C10 family; Region: Peptidase_C10; pfam01640 553174003104 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 553174003105 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 553174003106 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 553174003107 substrate-cofactor binding pocket; other site 553174003108 pyridoxal 5'-phosphate binding site [chemical binding]; other site 553174003109 catalytic residue [active] 553174003110 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 553174003111 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174003112 NAD(P) binding site [chemical binding]; other site 553174003113 active site 553174003114 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 553174003115 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 553174003116 Helix-turn-helix domains; Region: HTH; cl00088 553174003117 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 553174003118 dimerization interface [polypeptide binding]; other site 553174003119 peroxiredoxin; Region: AhpC; TIGR03137 553174003120 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 553174003121 dimer interface [polypeptide binding]; other site 553174003122 decamer (pentamer of dimers) interface [polypeptide binding]; other site 553174003123 catalytic triad [active] 553174003124 peroxidatic and resolving cysteines [active] 553174003125 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 553174003126 Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the reduction...; Region: AhpF_NTD_N; cd02974 553174003127 catalytic residue [active] 553174003128 TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then...; Region: AhpF_NTD_C; cd03026 553174003129 catalytic residues [active] 553174003130 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174003131 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 553174003132 heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase; Region: ATPase-IB2_Cd; TIGR01512 553174003133 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 553174003134 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 553174003135 Protein of unknown function (DUF3990); Region: DUF3990; pfam13151 553174003136 Protein of unknown function (DUF3791); Region: DUF3791; pfam12668 553174003137 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 553174003138 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 553174003139 FMN binding site [chemical binding]; other site 553174003140 active site 553174003141 catalytic residues [active] 553174003142 substrate binding site [chemical binding]; other site 553174003143 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 553174003144 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 553174003145 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 553174003146 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 553174003147 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 553174003148 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 553174003149 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 553174003150 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 553174003151 Na2 binding site [ion binding]; other site 553174003152 putative substrate binding site 1 [chemical binding]; other site 553174003153 Na binding site 1 [ion binding]; other site 553174003154 putative substrate binding site 2 [chemical binding]; other site 553174003155 CYTH-like Clostridium thermocellum TTM-like subgroup 1; Region: CYTH-like_CthTTM-like_1; cd07891 553174003156 putative active site [active] 553174003157 putative metal binding residues [ion binding]; other site 553174003158 signature motif; other site 553174003159 putative dimer interface [polypeptide binding]; other site 553174003160 putative phosphate binding site [ion binding]; other site 553174003161 peptide chain release factor 2; Validated; Region: prfB; PRK00578 553174003162 RF-1 domain; Region: RF-1; cl02875 553174003163 RF-1 domain; Region: RF-1; cl02875 553174003164 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 553174003165 AMP-binding enzyme; Region: AMP-binding; cl15778 553174003166 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3883 553174003167 Peptidase family M23; Region: Peptidase_M23; pfam01551 553174003168 Domain of unknown function (DUF4292); Region: DUF4292; pfam14125 553174003169 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 553174003170 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 553174003171 binding surface 553174003172 TPR motif; other site 553174003173 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70); Region: 3a0801s09; TIGR00990 553174003174 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 553174003175 binding surface 553174003176 TPR motif; other site 553174003177 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 553174003178 TPR motif; other site 553174003179 binding surface 553174003180 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 553174003181 trimer interface [polypeptide binding]; other site 553174003182 active site 553174003183 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01096 553174003184 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 553174003185 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 553174003186 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 553174003187 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 553174003188 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174003189 Family description; Region: UvrD_C_2; cl15862 553174003190 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 553174003191 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 553174003192 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 553174003193 active site 553174003194 HIGH motif; other site 553174003195 nucleotide binding site [chemical binding]; other site 553174003196 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 553174003197 KMSK motif region; other site 553174003198 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 553174003199 tRNA binding surface [nucleotide binding]; other site 553174003200 anticodon binding site; other site 553174003201 RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; Region: RNase_H; cd06222 553174003202 active site 553174003203 RNA/DNA hybrid binding site [nucleotide binding]; other site 553174003204 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 553174003205 Enoyl-(Acyl carrier protein) reductase; Region: adh_short_C2; pfam13561 553174003206 NAD binding site [chemical binding]; other site 553174003207 homotetramer interface [polypeptide binding]; other site 553174003208 homodimer interface [polypeptide binding]; other site 553174003209 substrate binding site [chemical binding]; other site 553174003210 active site 553174003211 Predicted membrane protein (DUF2238); Region: DUF2238; cl01464 553174003212 N-terminal putative catalytic domain of uncharacterized HKD family nucleases fused to putative helicases from the Snf2-like family; Region: PLDc_N_Snf2_like; cd09178 553174003213 putative homodimer interface [polypeptide binding]; other site 553174003214 putative active site [active] 553174003215 catalytic site [active] 553174003216 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 553174003217 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 553174003218 ATP binding site [chemical binding]; other site 553174003219 putative Mg++ binding site [ion binding]; other site 553174003220 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 553174003221 nucleotide binding region [chemical binding]; other site 553174003222 ATP-binding site [chemical binding]; other site 553174003223 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; cl16911 553174003224 Domain of unknown function (DUF4145); Region: DUF4145; pfam13643 553174003225 Divergent AAA domain; Region: AAA_4; pfam04326 553174003226 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]; Region: COG2865 553174003227 ATP-dependent DNA helicase recG C-terminal; Region: HATPase_c_4; pfam13749 553174003228 Virulence protein [General function prediction only]; Region: COG3943 553174003229 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 553174003230 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 553174003231 Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]; Region: {ManC}; COG0836 553174003232 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 553174003233 Substrate binding site; other site 553174003234 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 553174003235 nucleotide binding site/active site [active] 553174003236 HIT family signature motif; other site 553174003237 catalytic residue [active] 553174003238 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 553174003239 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 553174003240 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 553174003241 Glutamine Amidotransferase (GATase_I) involved in pyridoxine biosynthesis; Region: GATase1_PB; cd01749 553174003242 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13181 553174003243 predicted active site [active] 553174003244 catalytic triad [active] 553174003245 PdxS is a subunit of the pyridoxal 5'-phosphate (PLP) synthase, an important enzyme in deoxyxylulose 5-phosphate (DXP)-independent pathway for de novo biosynthesis of PLP, present in some eubacteria, in archaea, fungi, plants, plasmodia, and some...; Region: pdxS; cd04727 553174003246 active site 553174003247 multimer interface [polypeptide binding]; other site 553174003248 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 553174003249 dimer interface [polypeptide binding]; other site 553174003250 substrate binding site [chemical binding]; other site 553174003251 ATP binding site [chemical binding]; other site 553174003252 Helix-turn-helix domain; Region: HTH_18; pfam12833 553174003253 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 553174003254 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174003255 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 553174003256 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 553174003257 N-terminal plug; other site 553174003258 ligand-binding site [chemical binding]; other site 553174003259 The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase; Region: GH31; cl11402 553174003260 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174003261 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174003262 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174003263 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174003264 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; cl01155 553174003265 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 553174003266 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 553174003267 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174003268 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 553174003269 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 553174003270 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 553174003271 catalytic residues [active] 553174003272 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 553174003273 active site 553174003274 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 553174003275 Endo-beta-N-acetylglucosaminidases are bacterial chitinases that hydrolyze the chitin core of various asparagine (N)-linked glycans and glycoproteins. The endo-beta-N-acetylglucosaminidases have a glycosyl hydrolase family 18 (GH18) catalytic domain; Region: GH18_EndoS-like; cd06542 553174003276 active site 553174003277 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 553174003278 Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of...; Region: LamG; cl00102 553174003279 Susd and RagB outer membrane lipoprotein; Region: SusD-like; pfam12741 553174003280 starch binding outer membrane protein SusD; Region: SusD; cd08977 553174003281 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174003282 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174003283 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; cl01155 553174003284 comF family protein; Region: comF; TIGR00201 553174003285 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 553174003286 active site 553174003287 RecX family; Region: RecX; cl00936 553174003288 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 553174003289 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 553174003290 S-adenosylmethionine binding site [chemical binding]; other site 553174003291 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 553174003292 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 553174003293 catalytic motif [active] 553174003294 Zn binding site [ion binding]; other site 553174003295 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; cl00161 553174003296 L-cysteine desulfidase [Amino acid transport and metabolism]; Region: COG3681 553174003297 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 553174003298 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 553174003299 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174003300 Family description; Region: UvrD_C_2; cl15862 553174003301 Fic family protein [Function unknown]; Region: COG3177 553174003302 Fic/DOC family; Region: Fic; cl00960 553174003303 Dipeptidase [Amino acid transport and metabolism]; Region: PepD; COG4690 553174003304 Peptidase family C69; Region: Peptidase_C69; pfam03577 553174003305 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; cl00614 553174003306 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 553174003307 nucleophile elbow; other site 553174003308 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 553174003309 active site 553174003310 K+ potassium transporter; Region: K_trans; cl15781 553174003311 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 553174003312 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 553174003313 active site 553174003314 HIGH motif; other site 553174003315 KMSKS motif; other site 553174003316 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 553174003317 tRNA binding surface [nucleotide binding]; other site 553174003318 anticodon binding site; other site 553174003319 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 553174003320 dimer interface [polypeptide binding]; other site 553174003321 putative tRNA-binding site [nucleotide binding]; other site 553174003322 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 553174003323 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 553174003324 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 553174003325 Walker A/P-loop; other site 553174003326 ATP binding site [chemical binding]; other site 553174003327 Q-loop/lid; other site 553174003328 ABC transporter signature motif; other site 553174003329 Walker B; other site 553174003330 D-loop; other site 553174003331 H-loop/switch region; other site 553174003332 putative transporter; Validated; Region: PRK03818 553174003333 Predicted Permease Membrane Region; Region: Asp-Al_Ex; cl06061 553174003334 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 553174003335 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 553174003336 Predicted Permease Membrane Region; Region: Asp-Al_Ex; cl06061 553174003337 Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and...; Region: pyridoxal_pyridoxamine_kinase; cd01173 553174003338 pyridoxal binding site [chemical binding]; other site 553174003339 dimer interface [polypeptide binding]; other site 553174003340 ATP binding site [chemical binding]; other site 553174003341 bifunctional preprotein translocase subunit SecD/SecF; Reviewed; Region: PRK13024 553174003342 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 553174003343 bifunctional preprotein translocase subunit SecD/SecF; Reviewed; Region: PRK13024 553174003344 bifunctional preprotein translocase subunit SecD/SecF; Reviewed; Region: PRK13024 553174003345 Protein export membrane protein; Region: SecD_SecF; cl14618 553174003346 Protein export membrane protein; Region: SecD_SecF; cl14618 553174003347 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; Region: EEP-2; cd09084 553174003348 putative catalytic site [active] 553174003349 putative metal binding site [ion binding]; other site 553174003350 putative phosphate binding site [ion binding]; other site 553174003351 Rhomboid family; Region: Rhomboid; cl11446 553174003352 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 553174003353 IHF - DNA interface [nucleotide binding]; other site 553174003354 IHF dimer interface [polypeptide binding]; other site 553174003355 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; cl01155 553174003356 Helix-turn-helix domains; Region: HTH; cl00088 553174003357 DNA binding site [nucleotide binding] 553174003358 The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase; Region: GH31; cl11402 553174003359 Membrane transport protein; Region: Mem_trans; cl09117 553174003360 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 553174003361 FMN-dependent dehydrogenase; Region: FMN_dh; pfam01070 553174003362 phosphate binding site [ion binding]; other site 553174003363 Clostripain family; Region: Peptidase_C11; cl04055 553174003364 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 553174003365 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 553174003366 active site 553174003367 HIGH motif; other site 553174003368 dimer interface [polypeptide binding]; other site 553174003369 KMSKS motif; other site 553174003370 Haemolytic domain; Region: Haemolytic; cl00506 553174003371 Ribonuclease P; Region: Ribonuclease_P; cl00457 553174003372 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 553174003373 active site 553174003374 Uroporphyrinogen-III synthase HemD; Region: HEM4; pfam02602 553174003375 Domain of unknown function (DUF4271); Region: DUF4271; pfam14093 553174003376 S-adenosylmethionine synthetase; Validated; Region: PRK05250 553174003377 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 553174003378 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 553174003379 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 553174003380 Fic family protein [Function unknown]; Region: COG3177 553174003381 Domain of unknown function (DUF4172); Region: DUF4172; pfam13776 553174003382 Fic/DOC family; Region: Fic; cl00960 553174003383 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 553174003384 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 553174003385 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 553174003386 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 553174003387 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 553174003388 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 553174003389 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 553174003390 active site 553174003391 Int/Topo IB signature motif; other site 553174003392 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 553174003393 trimer interface [polypeptide binding]; other site 553174003394 active site 553174003395 dimer interface [polypeptide binding]; other site 553174003396 O-methyltransferase; Region: Methyltransf_3; pfam01596 553174003397 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 553174003398 S-adenosylmethionine binding site [chemical binding]; other site 553174003399 Ribosome-binding factor A; Region: RBFA; cl00542 553174003400 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 553174003401 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 553174003402 FtsX-like permease family; Region: FtsX; cl15850 553174003403 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 553174003404 Fic/DOC family; Region: Fic; cl00960 553174003405 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cl00257 553174003406 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 553174003407 This family is most closely related to the oligosaccharide phosphorylase domain family and other unidentified sequences. Oligosaccharide phosphorylase catalyzes the breakdown of oligosaccharides into glucose-1-phosphate units. They are important...; Region: GT1_Glycogen_Phosphorylase_like; cd04299 553174003408 putative homodimer interface [polypeptide binding]; other site 553174003409 putative active site pocket [active] 553174003410 alpha-glucan phosphorylases; Region: more_P_ylases; TIGR02094 553174003411 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 553174003412 Glycogen synthase; Region: Glycogen_syn; pfam05693 553174003413 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 553174003414 Domain of unknown function (DUF4112); Region: DUF4112; pfam13430 553174003415 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 553174003416 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 553174003417 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 553174003418 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174003419 OAH/OAS sulfhydrylase; Region: OAH_OAS_sulfhy; TIGR01326 553174003420 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 553174003421 homodimer interface [polypeptide binding]; other site 553174003422 substrate-cofactor binding pocket; other site 553174003423 pyridoxal 5'-phosphate binding site [chemical binding]; other site 553174003424 catalytic residue [active] 553174003425 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 553174003426 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 553174003427 putative DNA binding site [nucleotide binding]; other site 553174003428 putative Zn2+ binding site [ion binding]; other site 553174003429 AsnC family; Region: AsnC_trans_reg; pfam01037 553174003430 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 553174003431 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 553174003432 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 553174003433 PhoU domain; Region: PhoU; pfam01895 553174003434 threonyl-tRNA synthetase; Reviewed; Region: PRK12444 553174003435 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 553174003436 Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK); Region: UMPK_like; cd02028 553174003437 active site 553174003438 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 553174003439 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 553174003440 active site 553174003441 HIGH motif; other site 553174003442 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 553174003443 active site 553174003444 KMSKS motif; other site 553174003445 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 553174003446 tRNA binding surface [nucleotide binding]; other site 553174003447 anticodon binding site; other site 553174003448 Domain of unknown function (DUF4250); Region: DUF4250; pfam14056 553174003449 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 553174003450 active site 553174003451 catalytic motif [active] 553174003452 Zn binding site [ion binding]; other site 553174003453 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 553174003454 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 553174003455 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 553174003456 periplasmic chaperone; Provisional; Region: PRK10780 553174003457 periplasmic chaperone; Provisional; Region: PRK10780 553174003458 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 553174003459 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 553174003460 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 553174003461 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 553174003462 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 553174003463 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 553174003464 Surface antigen; Region: Bac_surface_Ag; cl03097 553174003465 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cd00475 553174003466 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 553174003467 catalytic residue [active] 553174003468 putative FPP diphosphate binding site; other site 553174003469 putative FPP binding hydrophobic cleft; other site 553174003470 dimer interface [polypeptide binding]; other site 553174003471 putative IPP diphosphate binding site; other site 553174003472 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; cl01155 553174003473 KilA-N domain; Region: KilA-N; pfam04383 553174003474 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 553174003475 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 553174003476 active site 553174003477 substrate-binding site [chemical binding]; other site 553174003478 metal-binding site [ion binding] 553174003479 ATP binding site [chemical binding]; other site 553174003480 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 553174003481 active site 553174003482 zinc metallopeptidase RseP; Provisional; Region: PRK10779 553174003483 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 553174003484 Active site serine [active] 553174003485 LemA family; Region: LemA; cl00742 553174003486 Methyltransferase domain; Region: Methyltransf_31; pfam13847 553174003487 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 553174003488 S-adenosylmethionine binding site [chemical binding]; other site 553174003489 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 553174003490 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 553174003491 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 553174003492 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; cl01155 553174003493 LytTr DNA-binding domain; Region: LytTR; cl04498 553174003494 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Reviewed; Region: PRK11867 553174003495 Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR...; Region: TPP_OGFOR; cd03375 553174003496 TPP-binding site [chemical binding]; other site 553174003497 2-oxoacid:acceptor oxidoreductase, alpha subunit; Region: OAFO_sf; TIGR03710 553174003498 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 553174003499 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 553174003500 dimer interface [polypeptide binding]; other site 553174003501 PYR/PP interface [polypeptide binding]; other site 553174003502 TPP binding site [chemical binding]; other site 553174003503 substrate binding site [chemical binding]; other site 553174003504 Laminarinase, member of the glycosyl hydrolase family 16; Region: GH16_laminarinase_like; cd08023 553174003505 active site 553174003506 catalytic residues [active] 553174003507 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 553174003508 putative active site [active] 553174003509 putative catalytic site [active] 553174003510 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 553174003511 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 553174003512 Ligand binding site; other site 553174003513 Putative Catalytic site; other site 553174003514 DXD motif; other site 553174003515 GtrA-like protein; Region: GtrA; cl00971 553174003516 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 553174003517 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 553174003518 Protein of unknown function (DUF2029); Region: DUF2029; cl09812 553174003519 Glycosyltransferase sugar-binding region containing DXD motif; Region: Gly_transf_sug; pfam04488 553174003520 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 553174003521 metal-binding site 553174003522 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 553174003523 putative metal binding site; other site 553174003524 Sulfatase; Region: Sulfatase; cl10460 553174003525 GDP-fucose protein O-fucosyltransferase and related proteins; Region: O-FucT_like; cl16914 553174003526 GDP-Fucose binding site [chemical binding]; other site 553174003527 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 553174003528 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 553174003529 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 553174003530 putative acyl-acceptor binding pocket; other site 553174003531 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 553174003532 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 553174003533 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 553174003534 Walker A/P-loop; other site 553174003535 ATP binding site [chemical binding]; other site 553174003536 Q-loop/lid; other site 553174003537 ABC transporter signature motif; other site 553174003538 Walker B; other site 553174003539 D-loop; other site 553174003540 H-loop/switch region; other site 553174003541 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14329 553174003542 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 553174003543 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 553174003544 FeS/SAM binding site; other site 553174003545 TRAM domain; Region: TRAM; cl01282 553174003546 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 553174003547 Peptidase family U32; Region: Peptidase_U32; cl03113 553174003548 Fe-S metabolism associated domain; Region: SufE; cl00951 553174003549 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 553174003550 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 553174003551 active site 553174003552 Haemolysin-III related; Region: HlyIII; cl03831 553174003553 ribonuclease R; Region: RNase_R; TIGR02063 553174003554 RNB domain; Region: RNB; pfam00773 553174003555 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important...; Region: S1_RNase_R; cd04471 553174003556 RNA binding site [nucleotide binding]; other site 553174003557 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 553174003558 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174003559 NAD(P) binding site [chemical binding]; other site 553174003560 active site 553174003561 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 553174003562 active site 553174003563 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1672 553174003564 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174003565 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; cl01155 553174003566 Glycoside hydrolase 97; Region: Glyco_hydro_97; pfam10566 553174003567 Uncharacterized glycoside hydrolase family 99-like domain; Region: GH99_GH71_like_3; cd11575 553174003568 putative ligand binding site [chemical binding]; other site 553174003569 putative catalytic site [active] 553174003570 starch binding outer membrane protein SusD; Region: SusD; cd08977 553174003571 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174003572 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174003573 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174003574 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; cl01155 553174003575 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 553174003576 DnaA N-terminal domain; Region: DnaA_N; pfam11638 553174003577 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 553174003578 Walker A motif; other site 553174003579 ATP binding site [chemical binding]; other site 553174003580 Walker B motif; other site 553174003581 arginine finger; other site 553174003582 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 553174003583 DnaA box-binding interface [nucleotide binding]; other site 553174003584 Na+/H+ antiporter, bacterial form; Region: a_cpa1; TIGR00831 553174003585 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 553174003586 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 553174003587 dimer interface [polypeptide binding]; other site 553174003588 active site 553174003589 metal binding site [ion binding]; metal-binding site 553174003590 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 553174003591 Cupin domain; Region: Cupin_2; cl09118 553174003592 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 553174003593 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 553174003594 The family 20 carbohydrate-binding module (CBM20), also known as the starch-binding domain, is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is...; Region: CBM20; cl15347 553174003595 starch-binding site 2 [chemical binding]; other site 553174003596 Thiamine pyrophosphokinase; Region: TPK; cd07995 553174003597 thiamine pyrophosphokinase; Region: thi_PPkinase; TIGR01378 553174003598 active site 553174003599 dimerization interface [polypeptide binding]; other site 553174003600 thiamine binding site [chemical binding]; other site 553174003601 Nicotinamide mononucleotide transporter; Region: NMN_transporter; cl01256 553174003602 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 553174003603 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; cl01155 553174003604 Nucleoside 2-deoxyribosyltransferase; Region: Nuc_deoxyrib_tr; cl16918 553174003605 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174003606 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 553174003607 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; cl01155 553174003608 Protein of unknown function (Porph_ging); Region: Porph_ging; cl09903 553174003609 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 553174003610 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 553174003611 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 553174003612 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 553174003613 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 553174003614 Predicted phosphoesterases, related to the Icc protein [General function prediction only]; Region: COG2129 553174003615 Homo sapiens 239FB and related proteins, metallophosphatase domain; Region: MPP_239FB; cd07379 553174003616 putative active site [active] 553174003617 putative metal binding site [ion binding]; other site 553174003618 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 553174003619 oligomeric interface; other site 553174003620 putative active site [active] 553174003621 homodimer interface [polypeptide binding]; other site 553174003622 Domain of unknown function (DUF377); Region: DUF377; pfam04041 553174003623 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 553174003624 active site 553174003625 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 553174003626 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; cl15460 553174003627 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 553174003628 The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i)...; Region: GH20_chitobiase-like; cd06563 553174003629 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 553174003630 active site 553174003631 Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes; Region: FA58C; cl12042 553174003632 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 553174003633 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; cl15460 553174003634 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 553174003635 DOMON-like type 9 carbohydrate binding module; Region: CBM9_like_3; cd09620 553174003636 putative ligand binding site [chemical binding]; other site 553174003637 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 553174003638 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 553174003639 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 553174003640 DNA binding site [nucleotide binding] 553174003641 active site 553174003642 Short repeat of unknown function (DUF308); Region: DUF308; cl15828 553174003643 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 553174003644 catalytic core [active] 553174003645 HipA-like N-terminal domain; Region: HipA_N; pfam07805 553174003646 HipA-like C-terminal domain; Region: HipA_C; pfam07804 553174003647 HipA N-terminal domain; Region: Couple_hipA; cl11853 553174003648 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 553174003649 non-specific DNA binding site [nucleotide binding]; other site 553174003650 salt bridge; other site 553174003651 sequence-specific DNA binding site [nucleotide binding]; other site 553174003652 Capsule assembly protein Wzi; Region: Caps_assemb_Wzi; pfam14052 553174003653 This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins. WecA is an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate (Und-P) GlcNAc-1-phosphate transferase that catalyzes the formation of a phosphodiester bond...; Region: GT_WecA_like; cd06853 553174003654 Mg++ binding site [ion binding]; other site 553174003655 putative catalytic motif [active] 553174003656 substrate binding site [chemical binding]; other site 553174003657 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 553174003658 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 553174003659 active site 553174003660 The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; Region: BAR; cl12013 553174003661 polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Region: pepcterm_ChnLen; TIGR03007 553174003662 MatE; Region: MatE; cl10513 553174003663 O-Antigen ligase; Region: Wzy_C; cl04850 553174003664 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 553174003665 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 553174003666 active site 553174003667 Alpha-1,2-fucosyltransferase; Region: Fut1_Fut2_like; cd11301 553174003668 GDP-Fucose binding site [chemical binding]; other site 553174003669 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 553174003670 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 553174003671 SLBB domain; Region: SLBB; pfam10531 553174003672 SLBB domain; Region: SLBB; pfam10531 553174003673 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 553174003674 SLBB domain; Region: SLBB; pfam10531 553174003675 Bacterial sugar transferase; Region: Bac_transf; cl00939 553174003676 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 553174003677 active site 553174003678 DNA polymerase IV; Validated; Region: PRK02406 553174003679 DNA binding site [nucleotide binding] 553174003680 pyruvate kinase; Provisional; Region: PRK05826 553174003681 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; cl09155 553174003682 domain interfaces; other site 553174003683 active site 553174003684 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 553174003685 transketolase; Reviewed; Region: PRK05899 553174003686 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 553174003687 TPP-binding site [chemical binding]; other site 553174003688 dimer interface [polypeptide binding]; other site 553174003689 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 553174003690 PYR/PP interface [polypeptide binding]; other site 553174003691 dimer interface [polypeptide binding]; other site 553174003692 TPP binding site [chemical binding]; other site 553174003693 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 553174003694 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 553174003695 nudix motif; other site 553174003696 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 553174003697 galactokinase; Provisional; Region: PRK05322 553174003698 Galactokinase galactose-binding signature; Region: GalKase_gal_bdg; pfam10509 553174003699 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 553174003700 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 553174003701 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl11420 553174003702 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 553174003703 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 553174003704 active site 553174003705 catalytic residues [active] 553174003706 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 553174003707 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; cl01155 553174003708 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to PFK family that includes ATP- and pyrophosphate (PPi)- dependent phosphofructokinases; Region: PFK; cl00204 553174003709 active site 553174003710 ADP/pyrophosphate binding site [chemical binding]; other site 553174003711 dimerization interface [polypeptide binding]; other site 553174003712 allosteric effector site; other site 553174003713 fructose-1,6-bisphosphate binding site; other site 553174003714 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 553174003715 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 553174003716 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 553174003717 alpha subunit interaction interface [polypeptide binding]; other site 553174003718 Walker A motif; other site 553174003719 ATP binding site [chemical binding]; other site 553174003720 Walker B motif; other site 553174003721 inhibitor binding site; inhibition site 553174003722 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 553174003723 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 553174003724 ATP synthase A chain; Region: ATP-synt_A; cl00413 553174003725 ATP synthase subunit C; Region: ATP-synt_C; cl00466 553174003726 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 553174003727 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 553174003728 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 553174003729 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 553174003730 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 553174003731 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 553174003732 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 553174003733 beta subunit interaction interface [polypeptide binding]; other site 553174003734 Walker A motif; other site 553174003735 ATP binding site [chemical binding]; other site 553174003736 Walker B motif; other site 553174003737 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 553174003738 ATP synthase; Region: ATP-synt; cl00365 553174003739 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 553174003740 Domain of unknown function (DUF389); Region: DUF389; cl00781 553174003741 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 553174003742 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 consists...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 553174003743 RNA binding site [nucleotide binding]; other site 553174003744 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 consists...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 553174003745 RNA binding site [nucleotide binding]; other site 553174003746 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 553174003747 RNA binding site [nucleotide binding]; other site 553174003748 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 553174003749 RNA binding site [nucleotide binding]; other site 553174003750 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec5; cd05690 553174003751 RNA binding site [nucleotide binding]; other site 553174003752 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 553174003753 Family of unknown function (DUF490); Region: DUF490; pfam04357 553174003754 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 553174003755 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 553174003756 E3 interaction surface; other site 553174003757 lipoyl attachment site [posttranslational modification]; other site 553174003758 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 553174003759 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 553174003760 FMN-binding domain; Region: FMN_bind; cl01081 553174003761 NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit; Region: nqrC; TIGR01938 553174003762 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 553174003763 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 553174003764 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 553174003765 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 553174003766 catalytic loop [active] 553174003767 iron binding site [ion binding]; other site 553174003768 Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+ oxidoreductase; Region: NADH_quinone_reductase; cd06188 553174003769 FAD binding pocket [chemical binding]; other site 553174003770 FAD binding motif [chemical binding]; other site 553174003771 phosphate binding motif [ion binding]; other site 553174003772 beta-alpha-beta structure motif; other site 553174003773 NAD binding pocket [chemical binding]; other site 553174003774 TolB amino-terminal domain; Region: TolB_N; cl00639 553174003775 Abi-like protein; Region: Abi_2; cl01988 553174003776 Firmicute fructose-1,6-bisphosphatase; Region: FBPase_2; pfam06874 553174003777 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 553174003778 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 553174003779 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 553174003780 active site 553174003781 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 553174003782 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 553174003783 active site 553174003784 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 553174003785 substrate binding site [chemical binding]; other site 553174003786 catalytic residues [active] 553174003787 dimer interface [polypeptide binding]; other site 553174003788 aspartate kinase III; Validated; Region: PRK09084 553174003789 AAK_AK-HSDH-like: Amino Acid Kinase Superfamily (AAK), AK-HSDH-like; this family includes the N-terminal catalytic domain of aspartokinase (AK) of the bifunctional enzyme AK- homoserine dehydrogenase (HSDH). These aspartokinases are found in such...; Region: AAK_AK-HSDH-like; cd04243 553174003790 putative catalytic residues [active] 553174003791 nucleotide binding site [chemical binding]; other site 553174003792 aspartate binding site [chemical binding]; other site 553174003793 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC-like_1; cd04912 553174003794 dimer interface [polypeptide binding]; other site 553174003795 allosteric regulatory binding pocket; other site 553174003796 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 553174003797 cell division ATP-binding protein FtsE; Region: FtsE; TIGR02673 553174003798 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174003799 Walker A/P-loop; other site 553174003800 ATP binding site [chemical binding]; other site 553174003801 Q-loop/lid; other site 553174003802 ABC transporter signature motif; other site 553174003803 Walker B; other site 553174003804 D-loop; other site 553174003805 H-loop/switch region; other site 553174003806 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; cl01747 553174003807 fumarate hydratase; Provisional; Region: PRK15389 553174003808 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 553174003809 Fumarase C-terminus; Region: Fumerase_C; cl00795 553174003810 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 553174003811 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 553174003812 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 553174003813 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 553174003814 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 553174003815 UDP-3-O-[3-hydroxymyristoyl]; Region: LpxD; COG1044 553174003816 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 553174003817 putative trimer interface [polypeptide binding]; other site 553174003818 putative CoA binding site [chemical binding]; other site 553174003819 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 553174003820 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 553174003821 HflX GTPase family; Region: HflX; cd01878 553174003822 G1 box; other site 553174003823 GTP/Mg2+ binding site [chemical binding]; other site 553174003824 Switch I region; other site 553174003825 G2 box; other site 553174003826 G3 box; other site 553174003827 Switch II region; other site 553174003828 G4 box; other site 553174003829 G5 box; other site 553174003830 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 553174003831 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 553174003832 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 553174003833 FAD binding domain; Region: FAD_binding_4; pfam01565 553174003834 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 553174003835 Domain of unknown function (DUF4348); Region: DUF4348; pfam14254 553174003836 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 553174003837 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 553174003838 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 553174003839 dimer interface [polypeptide binding]; other site 553174003840 motif 1; other site 553174003841 active site 553174003842 motif 2; other site 553174003843 motif 3; other site 553174003844 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 553174003845 active site 553174003846 catalytic site [active] 553174003847 substrate binding site [chemical binding]; other site 553174003848 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 553174003849 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174003850 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 553174003851 active site 553174003852 catalytic site [active] 553174003853 substrate binding site [chemical binding]; other site 553174003854 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 553174003855 Family description; Region: UvrD_C_2; cl15862 553174003856 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 553174003857 MiaB-like tRNA modifying enzyme; Region: MiaB-like-C; TIGR01579 553174003858 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 553174003859 FeS/SAM binding site; other site 553174003860 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 553174003861 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 553174003862 Probable Catalytic site; other site 553174003863 metal-binding site 553174003864 gliding motility-associated lipoprotein GldB; Region: GldB_lipo; TIGR03514 553174003865 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174003866 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174003867 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174003868 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174003869 Radical SAM superfamily; Region: Radical_SAM; pfam04055 553174003870 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 553174003871 FeS/SAM binding site; other site 553174003872 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 553174003873 MG2 domain; Region: A2M_N; pfam01835 553174003874 Alpha-2-macroglobulin family; Region: A2M; pfam00207 553174003875 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cl08267 553174003876 LytB protein; Region: LYTB; cl00507 553174003877 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 553174003878 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl11420 553174003879 glucose/galactose transporter; Region: gluP; TIGR01272 553174003880 Secretin and TonB N terminus short domain; Region: STN; cl06624 553174003881 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174003882 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174003883 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 553174003884 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; cl01155 553174003885 starch binding outer membrane protein SusD; Region: SusD; cd08977 553174003886 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin; Region: ZnMc_MMP_like_2; cd04276 553174003887 active site 553174003888 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin; Region: ZnMc_MMP_like_2; cd04276 553174003889 active site 553174003890 YtxH-like protein; Region: YtxH; cl02079 553174003891 Sporulation related domain; Region: SPOR; cl10051 553174003892 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 553174003893 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 553174003894 active site 553174003895 catalytic residues [active] 553174003896 metal binding site [ion binding]; metal-binding site 553174003897 TPR repeat; Region: TPR_11; pfam13414 553174003898 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 553174003899 binding surface 553174003900 TPR motif; other site 553174003901 TPR repeat; Region: TPR_11; pfam13414 553174003902 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 553174003903 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 553174003904 Fibronectin type III-like domain; Region: Fn3-like; cl15273 553174003905 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174003906 Starch-binding associating with outer membrane; Region: SusD-like_2; pfam12771 553174003907 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174003908 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174003909 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174003910 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; cl01155 553174003911 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; cl01155 553174003912 Endoglucanase [Carbohydrate transport and metabolism]; Region: BglC; COG2730 553174003913 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; cl15381 553174003914 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 553174003915 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 553174003916 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 553174003917 dimer interface [polypeptide binding]; other site 553174003918 phosphorylation site [posttranslational modification] 553174003919 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 553174003920 ATP binding site [chemical binding]; other site 553174003921 Mg2+ binding site [ion binding]; other site 553174003922 G-X-G motif; other site 553174003923 Response regulator receiver domain; Region: Response_reg; pfam00072 553174003924 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 553174003925 active site 553174003926 phosphorylation site [posttranslational modification] 553174003927 intermolecular recognition site; other site 553174003928 dimerization interface [polypeptide binding]; other site 553174003929 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 553174003930 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 553174003931 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 553174003932 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 553174003933 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 553174003934 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 553174003935 active site 553174003936 dimer interface [polypeptide binding]; other site 553174003937 motif 1; other site 553174003938 motif 2; other site 553174003939 motif 3; other site 553174003940 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 553174003941 anticodon binding site; other site 553174003942 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 553174003943 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 553174003944 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 553174003945 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 553174003946 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 553174003947 23S rRNA binding site [nucleotide binding]; other site 553174003948 L21 binding site [polypeptide binding]; other site 553174003949 L13 binding site [polypeptide binding]; other site 553174003950 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 553174003951 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 553174003952 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 553174003953 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 553174003954 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 553174003955 RNA binding site [nucleotide binding]; other site 553174003956 L,D-transpeptidase catalytic domain; Region: YkuD_2; pfam13645 553174003957 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 553174003958 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 553174003959 active site 553174003960 Zn binding site [ion binding]; other site 553174003961 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 553174003962 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 553174003963 ABC-ATPase subunit interface; other site 553174003964 dimer interface [polypeptide binding]; other site 553174003965 putative PBP binding regions; other site 553174003966 Periplasmic binding protein TroA_d. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a...; Region: TroA_d; cd01141 553174003967 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 553174003968 putative ligand binding site [chemical binding]; other site 553174003969 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 553174003970 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 553174003971 transmembrane helices; other site 553174003972 Domain of unknown function (DUF386); Region: DUF386; cl01047 553174003973 Thiol-activated cytolysin; Region: Thiol_cytolysin; pfam01289 553174003974 Peptidase C10 family; Region: Peptidase_C10; pfam01640 553174003975 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 553174003976 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 553174003977 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; cl01155 553174003978 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 553174003979 DRE-TIM metallolyase superfamily; Region: DRE_TIM_metallolyase; cl07974 553174003980 Peptidase family U32; Region: Peptidase_U32; cl03113 553174003981 metal binding site [ion binding]; metal-binding site 553174003982 Collagenase; Region: DUF3656; pfam12392 553174003983 Homoserine O-succinyltransferase; Region: HTS; pfam04204 553174003984 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 553174003985 proposed active site lysine [active] 553174003986 conserved cys residue [active] 553174003987 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 553174003988 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 553174003989 active site 553174003990 Zn binding site [ion binding]; other site 553174003991 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 553174003992 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 553174003993 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 553174003994 ABC transporter; Region: ABC_tran_2; pfam12848 553174003995 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 553174003996 Myosin tail; Region: Myosin_tail_1; pfam01576 553174003997 SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate...; Region: SERPIN; cd00172 553174003998 reactive center loop; other site 553174003999 uracil transporter; Provisional; Region: PRK10720 553174004000 Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]; Region: HemN; COG0635 553174004001 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 553174004002 HemN C-terminal domain; Region: HemN_C; pfam06969 553174004003 Elongation factor G (EF-G) family; Region: EF-G_bact; cd04170 553174004004 elongation factor G; Reviewed; Region: PRK12740 553174004005 G1 box; other site 553174004006 putative GEF interaction site [polypeptide binding]; other site 553174004007 GTP/Mg2+ binding site [chemical binding]; other site 553174004008 Switch I region; other site 553174004009 G2 box; other site 553174004010 G3 box; other site 553174004011 Switch II region; other site 553174004012 G4 box; other site 553174004013 G5 box; other site 553174004014 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 553174004015 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 553174004016 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 553174004017 Domain of unknown function (DUF4372); Region: DUF4372; pfam14294 553174004018 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 553174004019 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 553174004020 Dipeptidase [Amino acid transport and metabolism]; Region: PepD; COG4690 553174004021 Peptidase family C69; Region: Peptidase_C69; pfam03577 553174004022 Peptidase family M23; Region: Peptidase_M23; pfam01551 553174004023 Domain of unknown function (DUF4296); Region: DUF4296; pfam14129 553174004024 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 553174004025 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 553174004026 isoleucyl-tRNA synthetase; Region: ileS; TIGR00392 553174004027 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 553174004028 active site 553174004029 HIGH motif; other site 553174004030 nucleotide binding site [chemical binding]; other site 553174004031 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 553174004032 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 553174004033 active site 553174004034 KMSKS motif; other site 553174004035 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 553174004036 tRNA binding surface [nucleotide binding]; other site 553174004037 anticodon binding site; other site 553174004038 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 553174004039 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 553174004040 metal binding site 2 [ion binding]; metal-binding site 553174004041 putative DNA binding helix; other site 553174004042 metal binding site 1 [ion binding]; metal-binding site 553174004043 dimer interface [polypeptide binding]; other site 553174004044 structural Zn2+ binding site [ion binding]; other site 553174004045 Flavin Reductases; Region: FlaRed; cl00801 553174004046 glucose-1-phosphatase/inositol phosphatase; Provisional; Region: PRK10173 553174004047 Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction; Region: HP_HAP_like; cd07061 553174004048 catalytic core [active] 553174004049 Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction; Region: HP_HAP_like; cd07061 553174004050 Phosphate-selective porin O and P; Region: Porin_O_P; cl01524 553174004051 PAP2, bacterial acid phosphatase or class A non-specific acid phosphatases. These enzymes catalyze phosphomonoester hydrolysis, with optimal activity in low pH conditions. They are secreted into the periplasmic space, and their physiological role remains...; Region: PAP2_acid_phosphatase; cd03397 553174004052 active site 553174004053 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 553174004054 Protein of unknown function, DUF417; Region: DUF417; cl01162 553174004055 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 553174004056 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 553174004057 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; cl15460 553174004058 copper transport repressor, CopY/TcrY family; Region: CopY_TcrY; TIGR02698 553174004059 Helix-turn-helix domains; Region: HTH; cl00088 553174004060 BlaR1 peptidase M56; Region: Peptidase_M56; cl15829 553174004061 Gram-negative bacterial tonB protein; Region: TonB; cl10048 553174004062 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_cladeD; cd03379 553174004063 active site clefts [active] 553174004064 zinc binding site [ion binding]; other site 553174004065 dimer interface [polypeptide binding]; other site 553174004066 DKNYY family; Region: DKNYY; pfam13644 553174004067 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 553174004068 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 553174004069 ABC transporter; Region: ABC_tran_2; pfam12848 553174004070 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 553174004071 Predicted GTPase [General function prediction only]; Region: COG0218 553174004072 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 553174004073 G1 box; other site 553174004074 GTP/Mg2+ binding site [chemical binding]; other site 553174004075 Switch I region; other site 553174004076 G2 box; other site 553174004077 G3 box; other site 553174004078 Switch II region; other site 553174004079 G4 box; other site 553174004080 G5 box; other site 553174004081 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 553174004082 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174004083 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 553174004084 Domain of unknown function (DUF4421); Region: DUF4421; pfam14391 553174004085 methionine sulfoxide reductase B; Provisional; Region: PRK00222; cl15841 553174004086 bifunctional methionine sulfoxide reductase B/A protein; Provisional; Region: PRK05550 553174004087 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 553174004088 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 553174004089 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 553174004090 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 553174004091 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 553174004092 Substrate-binding site [chemical binding]; other site 553174004093 Substrate specificity [chemical binding]; other site 553174004094 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 553174004095 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 553174004096 Substrate-binding site [chemical binding]; other site 553174004097 Substrate specificity [chemical binding]; other site 553174004098 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 553174004099 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 553174004100 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 553174004101 DNA binding residues [nucleotide binding] 553174004102 dimerization interface [polypeptide binding]; other site 553174004103 oligopeptide transporters, OPT superfamily; Region: OPT_sfam; TIGR00728 553174004104 OPT oligopeptide transporter protein; Region: OPT; cl14607 553174004105 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 553174004106 homodimer interaction site [polypeptide binding]; other site 553174004107 cofactor binding site; other site 553174004108 zinc-ribbon domain; Region: zf-ribbon_3; cl11198 553174004109 Protein of unknown function (DUF3256); Region: DUF3256; pfam11644 553174004110 nucleoside transporter; Region: 2A0110; TIGR00889 553174004111 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385; cl00611 553174004112 RNA methyltransferase; Region: Methyltrans_RNA; pfam04452 553174004113 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174004114 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 553174004115 outer membrane receptor FepA; Provisional; Region: PRK13528 553174004116 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; cl01155 553174004117 Cupin domain; Region: Cupin_2; cl09118 553174004118 cyclically-permuted mutarotase family protein; Region: mutarot_permut; TIGR03548 553174004119 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 553174004120 D-galactonate transporter; Region: 2A0114; TIGR00893 553174004121 putative substrate translocation pore; other site 553174004122 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 553174004123 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 553174004124 catalytic residue [active] 553174004125 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 553174004126 active site 553174004127 homodimer interface [polypeptide binding]; other site 553174004128 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 553174004129 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 553174004130 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 553174004131 putative catalytic site [active] 553174004132 putative metal binding site [ion binding]; other site 553174004133 putative phosphate binding site [ion binding]; other site 553174004134 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 553174004135 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 553174004136 trmE is a tRNA modification GTPase; Region: trmE; cd04164 553174004137 G1 box; other site 553174004138 GTP/Mg2+ binding site [chemical binding]; other site 553174004139 Switch I region; other site 553174004140 G2 box; other site 553174004141 Switch II region; other site 553174004142 G3 box; other site 553174004143 G4 box; other site 553174004144 G5 box; other site 553174004145 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 553174004146 Protein of unknown function (DUF3584); Region: DUF3584; pfam12128 553174004147 Cupin domain; Region: Cupin_2; cl09118 553174004148 Sporulation related domain; Region: SPOR; cl10051 553174004149 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cl00062 553174004150 phosphopeptide binding site; other site 553174004151 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 553174004152 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 553174004153 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 553174004154 dimer interface [polypeptide binding]; other site 553174004155 anticodon binding site; other site 553174004156 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the...; Region: AspRS_core; cd00777 553174004157 homodimer interface [polypeptide binding]; other site 553174004158 motif 1; other site 553174004159 active site 553174004160 motif 2; other site 553174004161 GAD domain; Region: GAD; pfam02938 553174004162 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the...; Region: AspRS_core; cd00777 553174004163 motif 3; other site 553174004164 Protein of unknown function (DUF2582); Region: DUF2582; pfam10771 553174004165 Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]; Region: {ManC}; COG0836 553174004166 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 553174004167 Substrate binding site; other site 553174004168 Esterase-like activity of phytase; Region: Phytase-like; pfam13449 553174004169 SdiA-regulated; Region: SdiA-regulated; cd09971 553174004170 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 553174004171 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 553174004172 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 553174004173 DNA binding residues [nucleotide binding] 553174004174 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 553174004175 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 553174004176 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 553174004177 TPR motif; other site 553174004178 binding surface 553174004179 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 553174004180 binding surface 553174004181 TPR motif; other site 553174004182 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 553174004183 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 553174004184 active site 553174004185 HIGH motif; other site 553174004186 nucleotide binding site [chemical binding]; other site 553174004187 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 553174004188 KMSKS motif; other site 553174004189 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 553174004190 manganese transport protein MntH; Reviewed; Region: PRK00701; cl15845 553174004191 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 553174004192 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 553174004193 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 553174004194 minor groove reading motif; other site 553174004195 helix-hairpin-helix signature motif; other site 553174004196 substrate binding pocket [chemical binding]; other site 553174004197 active site 553174004198 Conserved hypothetical protein (DUF2461); Region: DUF2461; cl02374 553174004199 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 553174004200 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 553174004201 active site 553174004202 HIGH motif; other site 553174004203 nucleotide binding site [chemical binding]; other site 553174004204 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 553174004205 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 553174004206 active site 553174004207 KMSKS motif; other site 553174004208 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 553174004209 tRNA binding surface [nucleotide binding]; other site 553174004210 anticodon binding site; other site 553174004211 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 553174004212 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 553174004213 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 553174004214 homodimer interface [polypeptide binding]; other site 553174004215 metal binding site [ion binding]; metal-binding site 553174004216 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 553174004217 homodimer interface [polypeptide binding]; other site 553174004218 active site 553174004219 putative chemical substrate binding site [chemical binding]; other site 553174004220 metal binding site [ion binding]; metal-binding site 553174004221 Lipocalin-like; Region: Lipocalin_3; pfam12702 553174004222 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 553174004223 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 553174004224 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 553174004225 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 553174004226 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 553174004227 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 553174004228 AAA domain; Region: AAA_28; pfam13521 553174004229 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174004230 CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) Phosphatases; Region: CYTH-like_Pase; cl11964 553174004231 putative active site; other site 553174004232 putative metal binding residues [ion binding]; other site 553174004233 signature motif; other site 553174004234 putative triphosphate binding site [ion binding]; other site 553174004235 DDE superfamily endonuclease; Region: DDE_4; cl15789 553174004236 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 553174004237 DDE superfamily endonuclease; Region: DDE_4; cl15789 553174004238 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 553174004239 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174004240 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 553174004241 HSP70 interaction site [polypeptide binding]; other site 553174004242 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 553174004243 dimer interface [polypeptide binding]; other site 553174004244 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 553174004245 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 553174004246 active site 553174004247 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 553174004248 dimer interface [polypeptide binding]; other site 553174004249 catalytic residues [active] 553174004250 substrate binding site [chemical binding]; other site 553174004251 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 553174004252 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 553174004253 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 553174004254 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 553174004255 active site 553174004256 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4642 553174004257 phosphatidylinositol phosphate kinase; Provisional; Region: PLN03185 553174004258 MORN repeat; Region: MORN; cl14787 553174004259 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4642 553174004260 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]; Region: GlgB; COG0296 553174004261 N-terminal Early set domain associated with the catalytic domain of eukaryotic glycogen branching enzyme (also called 1,4 alpha glucan branching enzyme); Region: E_set_GBE_euk_N; cd02854 553174004262 Alpha amylase catalytic domain found in bacterial and eukaryotic branching enzymes; Region: AmyAc_bac_euk_BE; cd11321 553174004263 active site 553174004264 catalytic site [active] 553174004265 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; cl02706 553174004266 Imelysin; Region: Peptidase_M75; cl09159 553174004267 Predicted thiol oxidoreductase [Energy production and conversion]; Region: COG3488 553174004268 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 553174004269 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 553174004270 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 553174004271 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 553174004272 Walker A/P-loop; other site 553174004273 ATP binding site [chemical binding]; other site 553174004274 Q-loop/lid; other site 553174004275 ABC transporter signature motif; other site 553174004276 Walker B; other site 553174004277 D-loop; other site 553174004278 H-loop/switch region; other site 553174004279 preprotein translocase subunit SecA; Reviewed; Region: secA; PRK12901 553174004280 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 553174004281 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 553174004282 nucleotide binding region [chemical binding]; other site 553174004283 ATP-binding site [chemical binding]; other site 553174004284 SEC-C motif; Region: SEC-C; pfam02810 553174004285 Domain of unknown function (DUF4105); Region: DUF4105; pfam13387 553174004286 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; cl01155 553174004287 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 553174004288 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 553174004289 Domain of unknown function DUF21; Region: DUF21; pfam01595 553174004290 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 553174004291 Transporter associated domain; Region: CorC_HlyC; cl08393 553174004292 SurA N-terminal domain; Region: SurA_N_3; cl07813 553174004293 PPIC-type PPIASE domain; Region: Rotamase; cl08278 553174004294 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 553174004295 AMP-binding enzyme; Region: AMP-binding; cl15778 553174004296 Cation efflux family; Region: Cation_efflux; cl00316 553174004297 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 553174004298 Cof subfamily of IIB subfamily of haloacid dehalogenase superfamily; Region: Cof-subfamily; TIGR00099 553174004299 active site 553174004300 motif I; other site 553174004301 motif II; other site 553174004302 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 553174004303 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; cl16911 553174004304 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 553174004305 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 553174004306 active site 553174004307 phosphorylation site [posttranslational modification] 553174004308 intermolecular recognition site; other site 553174004309 dimerization interface [polypeptide binding]; other site 553174004310 LytTr DNA-binding domain; Region: LytTR; cl04498 553174004311 Histidine kinase; Region: His_kinase; pfam06580 553174004312 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 553174004313 ATP binding site [chemical binding]; other site 553174004314 Mg2+ binding site [ion binding]; other site 553174004315 G-X-G motif; other site 553174004316 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 553174004317 Lumazine binding domain; Region: Lum_binding; pfam00677 553174004318 Lumazine binding domain; Region: Lum_binding; pfam00677 553174004319 dihydrolipoamide dehydrogenase; Region: lipoamide_DH; TIGR01350 553174004320 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174004321 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 553174004322 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 553174004323 Glycine cleavage system protein P (pyridoxal-binding), C-terminal domain [Amino acid transport and metabolism]; Region: GcvP; COG1003 553174004324 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 553174004325 tetramer interface [polypeptide binding]; other site 553174004326 pyridoxal 5'-phosphate binding site [chemical binding]; other site 553174004327 catalytic residue [active] 553174004328 glycine dehydrogenase subunit 1; Validated; Region: PRK00451 553174004329 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 553174004330 tetramer interface [polypeptide binding]; other site 553174004331 pyridoxal 5'-phosphate binding site [chemical binding]; other site 553174004332 catalytic residue [active] 553174004333 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 553174004334 lipoyl attachment site [posttranslational modification]; other site 553174004335 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 553174004336 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 553174004337 FMN-binding domain; Region: FMN_bind; cl01081 553174004338 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 553174004339 4Fe-4S binding domain; Region: Fer4_5; pfam12801 553174004340 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 553174004341 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 553174004342 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 553174004343 shikimate binding site; other site 553174004344 NAD(P) binding site [chemical binding]; other site 553174004345 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 553174004346 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 553174004347 S-adenosylmethionine binding site [chemical binding]; other site 553174004348 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 553174004349 ATP binding site [chemical binding]; other site 553174004350 active site 553174004351 substrate binding site [chemical binding]; other site 553174004352 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 553174004353 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174004354 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 553174004355 imidazolonepropionase; Validated; Region: PRK09356 553174004356 Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria; Region: Imidazolone-5PH; cd01296 553174004357 active site 553174004358 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 553174004359 active sites [active] 553174004360 tetramer interface [polypeptide binding]; other site 553174004361 urocanate hydratase; Provisional; Region: PRK05414 553174004362 glutamate formiminotransferase; Region: FtcD; TIGR02024 553174004363 Formiminotransferase domain, N-terminal subdomain; Region: FTCD_N; pfam07837 553174004364 Formiminotransferase domain; Region: FTCD; pfam02971 553174004365 Formiminotransferase-cyclodeaminase; Region: FTCD_C; cl01350 553174004366 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174004367 NAD(P) binding site [chemical binding]; other site 553174004368 active site 553174004369 Putative glycoside hydrolase xylanase; Region: Xylanase; pfam13201 553174004370 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; cl01155 553174004371 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase contains two...; Region: OMP_decarboxylase_like; cd04725 553174004372 active site 553174004373 dimer interface [polypeptide binding]; other site 553174004374 peptide chain release factor 1; Validated; Region: prfA; PRK00591 553174004375 RF-1 domain; Region: RF-1; cl02875 553174004376 RF-1 domain; Region: RF-1; cl02875 553174004377 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 553174004378 dimerization interface [polypeptide binding]; other site 553174004379 ATP binding site [chemical binding]; other site 553174004380 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 553174004381 Ligand binding site; other site 553174004382 oligomer interface; other site 553174004383 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174004384 Domain of unknown function (DUF2520); Region: DUF2520; pfam10728 553174004385 Low specificity phosphatase (HAD superfamily) [General function prediction only]; Region: COG1778 553174004386 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 553174004387 Maf-like protein; Region: Maf; pfam02545 553174004388 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 553174004389 active site 553174004390 dimer interface [polypeptide binding]; other site 553174004391 Uncharacterized conserved protein [Function unknown]; Region: COG1576; cl00679 553174004392 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; pfam02590 553174004393 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 553174004394 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 553174004395 motif II; other site 553174004396 YceG-like family; Region: YceG; pfam02618 553174004397 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 553174004398 dimerization interface [polypeptide binding]; other site 553174004399 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 553174004400 active site 553174004401 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 553174004402 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 553174004403 NAD(P) binding site [chemical binding]; other site 553174004404 homotetramer interface [polypeptide binding]; other site 553174004405 homodimer interface [polypeptide binding]; other site 553174004406 active site 553174004407 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 553174004408 Helix-turn-helix domains; Region: HTH; cl00088 553174004409 UDP-glucose 4-epimerase; Region: PLN02240 553174004410 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 553174004411 NAD binding site [chemical binding]; other site 553174004412 homodimer interface [polypeptide binding]; other site 553174004413 active site 553174004414 substrate binding site [chemical binding]; other site 553174004415 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 553174004416 transcription termination factor Rho; Provisional; Region: PRK12608 553174004417 RNA binding site [nucleotide binding]; other site 553174004418 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 553174004419 multimer interface [polypeptide binding]; other site 553174004420 Walker A motif; other site 553174004421 ATP binding site [chemical binding]; other site 553174004422 Walker B motif; other site 553174004423 Domain of unknown function (DUF4301); Region: DUF4301; pfam14134 553174004424 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 553174004425 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 553174004426 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 553174004427 synthetase active site [active] 553174004428 NTP binding site [chemical binding]; other site 553174004429 metal binding site [ion binding]; metal-binding site 553174004430 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 553174004431 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 553174004432 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 553174004433 Endo-N-acetylmuramidases (muramidases) are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues; Region: GH25_muramidase; cl10448 553174004434 Glycosyl hydrolases family 25; Region: Glyco_hydro_25; pfam01183 553174004435 active site 553174004436 serine O-acetyltransferase; Region: cysE; TIGR01172 553174004437 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 553174004438 trimer interface [polypeptide binding]; other site 553174004439 active site 553174004440 substrate binding site [chemical binding]; other site 553174004441 CoA binding site [chemical binding]; other site 553174004442 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 553174004443 THUMP domain; Region: THUMP; cl12076 553174004444 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; cl16911 553174004445 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 553174004446 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 553174004447 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 553174004448 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 553174004449 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 553174004450 ATP-grasp domain; Region: ATP-grasp_4; cl03087 553174004451 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 553174004452 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 553174004453 formate--tetrahydrofolate ligase; Provisional; Region: PRK13505 553174004454 Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2...; Region: FTHFS; cd00477 553174004455 Potassium binding sites [ion binding]; other site 553174004456 Cesium cation binding sites [ion binding]; other site 553174004457 Endo-N-acetylmuramidases (muramidases) are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues; Region: GH25_muramidase; cl10448 553174004458 active site 553174004459 Glycosyl hydrolases family 25; Region: Glyco_hydro_25; pfam01183 553174004460 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 553174004461 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 553174004462 active site 553174004463 catalytic triad [active] 553174004464 oxyanion hole [active] 553174004465 replicative DNA helicase; Region: DnaB; TIGR00665 553174004466 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 553174004467 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 553174004468 Walker A motif; other site 553174004469 ATP binding site [chemical binding]; other site 553174004470 Walker B motif; other site 553174004471 DNA binding loops [nucleotide binding] 553174004472 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK14609 553174004473 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 553174004474 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 553174004475 Family description; Region: UvrD_C_2; cl15862 553174004476 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 553174004477 Inactivated superfamily I helicase [DNA replication, recombination, and repair]; Region: COG3893 553174004478 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 553174004479 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 553174004480 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174004481 Family description; Region: UvrD_C_2; cl15862 553174004482 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 553174004483 Transglycosylase; Region: Transgly; cl07896 553174004484 heat shock protein 90; Provisional; Region: PRK05218 553174004485 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 553174004486 ATP binding site [chemical binding]; other site 553174004487 Mg2+ binding site [ion binding]; other site 553174004488 G-X-G motif; other site 553174004489 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 553174004490 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 553174004491 metal binding site [ion binding]; metal-binding site 553174004492 dimer interface [polypeptide binding]; other site 553174004493 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 553174004494 Predicted peptidase [General function prediction only]; Region: COG4099 553174004495 Fe-S oxidoreductase [Energy production and conversion]; Region: COG1032 553174004496 B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the...; Region: radical_SAM_B12_BD; cd02068 553174004497 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 553174004498 FeS/SAM binding site; other site 553174004499 Domain of unknown function (DUF4372); Region: DUF4372; pfam14294 553174004500 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 553174004501 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 553174004502 Domain of unknown function (DUF4295); Region: DUF4295; pfam14128 553174004503 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 553174004504 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 553174004505 Competence-damaged protein; Region: CinA; cl00666 553174004506 UGMP family protein; Validated; Region: PRK09604 553174004507 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 553174004508 methionine aminopeptidase; Provisional; Region: PRK12318 553174004509 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 553174004510 active site 553174004511 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 553174004512 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 553174004513 MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent...; Region: MeTr; cd00740 553174004514 substrate binding pocket [chemical binding]; other site 553174004515 B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy); Region: methionine_synthase_B12_BD; cd02069 553174004516 B12 binding site [chemical binding]; other site 553174004517 cobalt ligand [ion binding]; other site 553174004518 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 553174004519 SmpB-tmRNA interface; other site 553174004520 Domain of unknown function (DUF4375); Region: DUF4375; pfam14300 553174004521 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 553174004522 Rubredoxin; Region: Rubredoxin; pfam00301 553174004523 iron binding site [ion binding]; other site 553174004524 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 553174004525 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 553174004526 Surface antigen; Region: Bac_surface_Ag; cl03097 553174004527 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 553174004528 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 553174004529 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 553174004530 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 553174004531 pyridoxal 5'-phosphate binding site [chemical binding]; other site 553174004532 homodimer interface [polypeptide binding]; other site 553174004533 catalytic residue [active] 553174004534 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 553174004535 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 553174004536 catalytic residue [active] 553174004537 aspartate aminotransferase; Provisional; Region: PRK07568 553174004538 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 553174004539 pyridoxal 5'-phosphate binding site [chemical binding]; other site 553174004540 homodimer interface [polypeptide binding]; other site 553174004541 catalytic residue [active] 553174004542 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 553174004543 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 553174004544 FtsX-like permease family; Region: FtsX; cl15850 553174004545 YolD-like protein; Region: YolD; pfam08863 553174004546 DNA polymerase IV; Reviewed; Region: PRK03103 553174004547 Y-family of DNA polymerases; Region: PolY; cl12025 553174004548 active site 553174004549 DNA binding site [nucleotide binding] 553174004550 GTP-binding protein LepA; Provisional; Region: PRK05433 553174004551 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 553174004552 G1 box; other site 553174004553 putative GEF interaction site [polypeptide binding]; other site 553174004554 GTP/Mg2+ binding site [chemical binding]; other site 553174004555 Switch I region; other site 553174004556 G2 box; other site 553174004557 G3 box; other site 553174004558 Switch II region; other site 553174004559 G4 box; other site 553174004560 G5 box; other site 553174004561 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 553174004562 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 553174004563 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 553174004564 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 553174004565 ligand binding site [chemical binding]; other site 553174004566 flexible hinge region; other site 553174004567 MG2 domain; Region: A2M_N; pfam01835 553174004568 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; cl01155 553174004569 Domain of unknown function (DUF4372); Region: DUF4372; pfam14294 553174004570 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 553174004571 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 553174004572 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 553174004573 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174004574 Walker A/P-loop; other site 553174004575 ATP binding site [chemical binding]; other site 553174004576 Q-loop/lid; other site 553174004577 ABC transporter signature motif; other site 553174004578 Walker B; other site 553174004579 D-loop; other site 553174004580 H-loop/switch region; other site 553174004581 Smr domain; Region: Smr; cl02619 553174004582 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 553174004583 TPR motif; other site 553174004584 binding surface 553174004585 Tetratricopeptide repeat; Region: TPR_16; pfam13432 553174004586 Periplasmic component of the Tol biopolymer transport system [Intracellular trafficking and secretion]; Region: TolB; COG0823 553174004587 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 553174004588 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 553174004589 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 553174004590 ligand binding site [chemical binding]; other site 553174004591 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; cl16911 553174004592 pre-rRNA processing and ribosome biogenesis; Region: Nol1_Nop2_Fmu_2; cl01283 553174004593 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 553174004594 dimerization interface [polypeptide binding]; other site 553174004595 active site 553174004596 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 553174004597 folate binding site [chemical binding]; other site 553174004598 NADP+ binding site [chemical binding]; other site 553174004599 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 553174004600 Surface antigen; Region: Bac_surface_Ag; cl03097 553174004601 TIGR03545 family protein; Region: TIGR03545 553174004602 Family of unknown function (DUF490); Region: DUF490; pfam04357 553174004603 Uncharacterized conserved protein [Function unknown]; Region: COG1739 553174004604 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 553174004605 Protein of unknown function (DUF1015); Region: DUF1015; cl01715 553174004606 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK13581 553174004607 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174004608 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 553174004609 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 553174004610 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 553174004611 catalytic residue [active] 553174004612 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 553174004613 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174004614 ATP binding site [chemical binding]; other site 553174004615 putative Mg++ binding site [ion binding]; other site 553174004616 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 553174004617 nucleotide binding region [chemical binding]; other site 553174004618 ATP-binding site [chemical binding]; other site 553174004619 DbpA RNA binding domain; Region: DbpA; pfam03880 553174004620 Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilF; COG3063 553174004621 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 553174004622 binding surface 553174004623 TPR motif; other site 553174004624 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 553174004625 TPR motif; other site 553174004626 binding surface 553174004627 DNA gyrase subunit A; Validated; Region: PRK05560 553174004628 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA...; Region: TOP4c; cd00187 553174004629 CAP-like domain; other site 553174004630 active site 553174004631 primary dimer interface [polypeptide binding]; other site 553174004632 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 553174004633 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 553174004634 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 553174004635 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 553174004636 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 553174004637 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 553174004638 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174004639 NAD synthetase; Reviewed; Region: nadE; PRK02628 553174004640 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 553174004641 multimer interface [polypeptide binding]; other site 553174004642 active site 553174004643 catalytic triad [active] 553174004644 protein interface 1 [polypeptide binding]; other site 553174004645 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 553174004646 homodimer interface [polypeptide binding]; other site 553174004647 NAD binding pocket [chemical binding]; other site 553174004648 ATP binding pocket [chemical binding]; other site 553174004649 Mg binding site [ion binding]; other site 553174004650 active-site loop [active] 553174004651 Domain of unknown function (DUF2027); Region: DUF2027; pfam09640 553174004652 Smr domain; Region: Smr; cl02619 553174004653 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 553174004654 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 553174004655 PAP2_like_4 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_4; cd03395 553174004656 active site 553174004657 Oxygen tolerance; Region: BatD; pfam13584 553174004658 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 553174004659 binding surface 553174004660 TPR motif; other site 553174004661 Bacterial SH3 domain; Region: SH3_3; cl02551 553174004662 TPR repeat; Region: TPR_11; pfam13414 553174004663 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 553174004664 binding surface 553174004665 TPR motif; other site 553174004666 TPR repeat; Region: TPR_11; pfam13414 553174004667 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 553174004668 metal ion-dependent adhesion site (MIDAS); other site 553174004669 Aerotolerance regulator N-terminal; Region: BatA; cl06567 553174004670 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 553174004671 metal ion-dependent adhesion site (MIDAS); other site 553174004672 Oxygen tolerance; Region: BatD; pfam13584 553174004673 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 553174004674 metal ion-dependent adhesion site (MIDAS); other site 553174004675 MoxR-like ATPases [General function prediction only]; Region: COG0714 553174004676 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174004677 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 553174004678 IHF dimer interface [polypeptide binding]; other site 553174004679 IHF - DNA interface [nucleotide binding]; other site 553174004680 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 553174004681 IHF - DNA interface [nucleotide binding]; other site 553174004682 IHF dimer interface [polypeptide binding]; other site 553174004683 ribosomal protein S12 methylthiotransferase RimO; Region: TIGR01125 553174004684 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 553174004685 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 553174004686 FeS/SAM binding site; other site 553174004687 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 553174004688 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 553174004689 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174004690 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 553174004691 putative substrate translocation pore; other site 553174004692 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 553174004693 oligomerization interface [polypeptide binding]; other site 553174004694 active site 553174004695 metal binding site [ion binding]; metal-binding site 553174004696 beta-phosphoglucomutase family hydrolase; Region: PGMB-YQAB-SF; TIGR02009 553174004697 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 553174004698 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 553174004699 motif II; other site 553174004700 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 553174004701 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; cl16911 553174004702 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 553174004703 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cd00529 553174004704 active site 553174004705 putative DNA-binding cleft [nucleotide binding]; other site 553174004706 dimer interface [polypeptide binding]; other site 553174004707 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 553174004708 Transglycosylase; Region: Transgly; cl07896 553174004709 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 553174004710 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 553174004711 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 553174004712 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174004713 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 553174004714 aspartate carbamoyltransferase regulatory subunit; Reviewed; Region: PRK00893 553174004715 Aspartate carbamoyltransferase regulatory chain, allosteric domain; Region: PyrI; pfam01948 553174004716 Aspartate carbamoyltransferase regulatory chain, metal binding domain; Region: PyrI_C; pfam02748 553174004717 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 553174004718 MatE; Region: MatE; cl10513 553174004719 MatE; Region: MatE; cl10513 553174004720 Cytidylate kinase-like family; Region: Cytidylate_kin2; pfam13189 553174004721 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174004722 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 553174004723 active site 553174004724 metal binding site [ion binding]; metal-binding site 553174004725 homotetramer interface [polypeptide binding]; other site 553174004726 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 553174004727 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 553174004728 NAD binding site [chemical binding]; other site 553174004729 substrate binding site [chemical binding]; other site 553174004730 homodimer interface [polypeptide binding]; other site 553174004731 active site 553174004732 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 553174004733 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 553174004734 ATP-grasp domain; Region: ATP-grasp_4; cl03087 553174004735 Cupin domain; Region: Cupin_2; cl09118 553174004736 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 553174004737 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 553174004738 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 553174004739 inhibitor-cofactor binding pocket; inhibition site 553174004740 pyridoxal 5'-phosphate binding site [chemical binding]; other site 553174004741 catalytic residue [active] 553174004742 Protein of unknown function (DUF1237); Region: DUF1237; cl15402 553174004743 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 553174004744 MBOAT, membrane-bound O-acyltransferase family; Region: MBOAT; cl00738 553174004745 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 553174004746 active site 553174004747 oxyanion hole [active] 553174004748 catalytic triad [active] 553174004749 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 553174004750 Helix-turn-helix domains; Region: HTH; cl00088 553174004751 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 553174004752 Malic enzyme, N-terminal domain; Region: malic; pfam00390 553174004753 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 553174004754 putative NAD(P) binding site [chemical binding]; other site 553174004755 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 553174004756 Peptidase family M49; Region: Peptidase_M49; pfam03571 553174004757 Helix-turn-helix domain; Region: HTH_18; pfam12833 553174004758 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 553174004759 hybrid cluster protein; Provisional; Region: PRK05290 553174004760 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 553174004761 ACS interaction site; other site 553174004762 CODH interaction site; other site 553174004763 Hybrid cluster protein (HCP), formerly known as prismane, is thought to play a role in nitrogen metabolism but its specific function is unknown. HCP has three structural domains, an N-terminal alpha-helical domain, and two similar domains comprising a...; Region: HCP; cd01914 553174004764 hybrid metal cluster; other site 553174004765 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 553174004766 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 553174004767 NADP-binding site; other site 553174004768 homotetramer interface [polypeptide binding]; other site 553174004769 substrate binding site [chemical binding]; other site 553174004770 homodimer interface [polypeptide binding]; other site 553174004771 active site 553174004772 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 553174004773 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 553174004774 NADP binding site [chemical binding]; other site 553174004775 active site 553174004776 putative substrate binding site [chemical binding]; other site 553174004777 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 553174004778 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 553174004779 Protein of unknown function (DUF328); Region: DUF328; cl01143 553174004780 acyl-CoA synthetase; Validated; Region: PRK06145 553174004781 ribosomal protein L11 methyltransferase; Reviewed; Region: prmA; PRK00517 553174004782 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 553174004783 S-adenosylmethionine binding site [chemical binding]; other site 553174004784 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to PFK family that includes ATP- and pyrophosphate (PPi)- dependent phosphofructokinases; Region: PFK; cl00204 553174004785 active site 553174004786 ADP/pyrophosphate binding site [chemical binding]; other site 553174004787 dimerization interface [polypeptide binding]; other site 553174004788 allosteric effector site; other site 553174004789 fructose-1,6-bisphosphate binding site; other site 553174004790 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ABO13168; Region: LPLAT_ABO13168-like; cd07988 553174004791 putative acyl-acceptor binding pocket; other site 553174004792 Carbohydrate Binding Module 6 (CBM6); appended to several carbohydrate binding enzymes, including several glycoside hydrolase (GH) family 26 mannanase domains; Region: CBM6_mannanase-like; cd04086 553174004793 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; cl02713 553174004794 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 553174004795 Interdomain contacts; other site 553174004796 Cytokine receptor motif; other site 553174004797 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 553174004798 hypothetical protein; Provisional; Region: PRK00955 553174004799 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 553174004800 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 553174004801 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 553174004802 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 553174004803 pyruvate carboxylase subunit B; Validated; Region: PRK09282 553174004804 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 553174004805 carboxyltransferase (CT) interaction site; other site 553174004806 biotinylation site [posttranslational modification]; other site 553174004807 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 553174004808 tetramerization interface [polypeptide binding]; other site 553174004809 active site 553174004810 Pantoate-beta-alanine ligase; Region: PanC; cd00560 553174004811 pantoate--beta-alanine ligase; Region: panC; TIGR00018 553174004812 active site 553174004813 ATP-binding site [chemical binding]; other site 553174004814 pantoate-binding site; other site 553174004815 HXXH motif; other site 553174004816 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 553174004817 Domain of unknown function (DUF4270); Region: DUF4270; pfam14092 553174004818 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 553174004819 Clp amino terminal domain; Region: Clp_N; pfam02861 553174004820 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 553174004821 Walker A motif; other site 553174004822 ATP binding site [chemical binding]; other site 553174004823 Walker B motif; other site 553174004824 arginine finger; other site 553174004825 UvrB/uvrC motif; Region: UVR; pfam02151 553174004826 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 553174004827 Walker A motif; other site 553174004828 ATP binding site [chemical binding]; other site 553174004829 Walker B motif; other site 553174004830 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 553174004831 phosphoglucomutase-2-like protein; Provisional; Region: PTZ00150 553174004832 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 553174004833 active site 553174004834 substrate binding site [chemical binding]; other site 553174004835 metal binding site [ion binding]; metal-binding site 553174004836 conjugal transfer coupling protein TraG; Provisional; Region: PRK13822 553174004837 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174004838 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; cl01155 553174004839 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin; Region: ZnMc_MMP_like_2; cd04276 553174004840 active site 553174004841 peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional; Region: PRK10791 553174004842 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 553174004843 active site 553174004844 EamA-like transporter family; Region: EamA; cl01037 553174004845 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 553174004846 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; cd00229 553174004847 active site 553174004848 catalytic triad [active] 553174004849 oxyanion hole [active] 553174004850 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 553174004851 Membrane transport protein; Region: Mem_trans; cl09117 553174004852 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 553174004853 catalytic residues [active] 553174004854 dimer interface [polypeptide binding]; other site 553174004855 Na(+)/iodide (NIS) and Na(+)/multivitamin (SMVT) cotransporters, and related proteins; solute binding domain; Region: SLC5sbd_NIS-like; cd10326 553174004856 Na binding site [ion binding]; other site 553174004857 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 553174004858 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 553174004859 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 553174004860 catalytic residue [active] 553174004861 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 553174004862 pantothenate kinase, eukaryotic/staphyloccocal type; Region: panK_eukar; TIGR00555 553174004863 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 553174004864 IHF - DNA interface [nucleotide binding]; other site 553174004865 IHF dimer interface [polypeptide binding]; other site 553174004866 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 553174004867 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 553174004868 homodimer interface [polypeptide binding]; other site 553174004869 oligonucleotide binding site [chemical binding]; other site 553174004870 Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]; Region: COG2872 553174004871 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 553174004872 Alpha amylase catalytic domain found in an uncharacterized protein family; Region: AmyAc_3; cd11349 553174004873 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 553174004874 active site 553174004875 catalytic site [active] 553174004876 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; cl02706 553174004877 Acyl transferase domain; Region: Acyl_transf_1; cl08282 553174004878 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 553174004879 CrcB-like protein; Region: CRCB; cl09114 553174004880 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174004881 Myo-inositol-1-phosphate synthase; Region: NAD_binding_5; cl00554 553174004882 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 553174004883 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 553174004884 motif II; other site 553174004885 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 553174004886 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 553174004887 active site 553174004888 YARHG domain; Region: YARHG; pfam13308 553174004889 Protein of unknown function (DUF3160); Region: DUF3160; pfam11369 553174004890 Bacterial capsule synthesis protein PGA_cap; Region: PGA_cap; smart00854 553174004891 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 553174004892 putative active site [active] 553174004893 putative metal binding site [ion binding]; other site 553174004894 A new structural DNA glycosylase; Region: AlkD_like; cd06561 553174004895 active site 553174004896 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 553174004897 binding surface 553174004898 TPR motif; other site 553174004899 TPR repeat; Region: TPR_11; pfam13414 553174004900 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 553174004901 binding surface 553174004902 Tetratricopeptide repeat; Region: TPR_16; pfam13432 553174004903 TPR motif; other site 553174004904 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 553174004905 DNA repair protein RadA; Provisional; Region: PRK11823 553174004906 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 553174004907 Walker A motif/ATP binding site; other site 553174004908 ATP binding site [chemical binding]; other site 553174004909 Walker B motif; other site 553174004910 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 553174004911 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 553174004912 homopentamer interface [polypeptide binding]; other site 553174004913 active site 553174004914 Tetratricopeptide repeat; Region: TPR_12; pfam13424 553174004915 recombination protein F; Reviewed; Region: recF; PRK00064 553174004916 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174004917 Walker A/P-loop; other site 553174004918 ATP binding site [chemical binding]; other site 553174004919 Q-loop/lid; other site 553174004920 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174004921 ABC transporter signature motif; other site 553174004922 Walker B; other site 553174004923 D-loop; other site 553174004924 H-loop/switch region; other site 553174004925 Protein of unknown function (DUF721); Region: DUF721; cl02324 553174004926 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 553174004927 dihydrodipicolinate synthase; Region: dapA; TIGR00674 553174004928 dimer interface [polypeptide binding]; other site 553174004929 active site 553174004930 catalytic residue [active] 553174004931 EamA-like transporter family; Region: EamA; cl01037 553174004932 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 553174004933 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 553174004934 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 553174004935 dimerization interface 3.5A [polypeptide binding]; other site 553174004936 active site 553174004937 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 553174004938 Competence protein; Region: Competence; cl00471 553174004939 Ferredoxin [Energy production and conversion]; Region: COG1146 553174004940 4Fe-4S binding domain; Region: Fer4; cl02805 553174004941 Immune inhibitor A peptidase M6; Region: Peptidase_M6; cl11525 553174004942 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 553174004943 AMP-binding enzyme; Region: AMP-binding; cl15778 553174004944 Transcriptional regulator; Region: Transcrip_reg; cl00361 553174004945 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 553174004946 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 553174004947 putative tRNA-binding site [nucleotide binding]; other site 553174004948 B3/4 domain; Region: B3_4; cl11458 553174004949 tRNA synthetase B5 domain; Region: B5; cl08394 553174004950 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 553174004951 dimer interface [polypeptide binding]; other site 553174004952 motif 1; other site 553174004953 motif 3; other site 553174004954 motif 2; other site 553174004955 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 553174004956 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; cl00988 553174004957 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 553174004958 bifunctional aspartokinase I/homoserine dehydrogenase I; Provisional; Region: thrA; PRK09436 553174004959 AAK_AK-HSDH: Amino Acid Kinase Superfamily (AAK), AK-HSDH; this CD includes the N-terminal catalytic domain of aspartokinase (AK) of the bifunctional enzyme AK - homoserine dehydrogenase (HSDH). These aspartokinases are found in bacteria (E. coli...; Region: AAK_AK-HSDH; cd04257 553174004960 putative catalytic residues [active] 553174004961 putative nucleotide binding site [chemical binding]; other site 553174004962 putative aspartate binding site [chemical binding]; other site 553174004963 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA-like_1; cd04921 553174004964 dimer interface [polypeptide binding]; other site 553174004965 putative threonine allosteric regulatory site; other site 553174004966 ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase); Region: ACT_AK-like_2; cd04892 553174004967 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174004968 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 553174004969 Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]; Region: NadC; COG0157 553174004970 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 553174004971 dimerization interface [polypeptide binding]; other site 553174004972 active site 553174004973 Quinolinate synthetase A protein; Region: NadA; cl00420 553174004974 L-aspartate oxidase; Provisional; Region: PRK09077 553174004975 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174004976 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 553174004977 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 553174004978 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 553174004979 active site 553174004980 phosphorylation site [posttranslational modification] 553174004981 intermolecular recognition site; other site 553174004982 dimerization interface [polypeptide binding]; other site 553174004983 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 553174004984 DNA binding site [nucleotide binding] 553174004985 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 553174004986 dimer interface [polypeptide binding]; other site 553174004987 phosphorylation site [posttranslational modification] 553174004988 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 553174004989 ATP binding site [chemical binding]; other site 553174004990 Mg2+ binding site [ion binding]; other site 553174004991 G-X-G motif; other site 553174004992 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174004993 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; cl01155 553174004994 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 553174004995 Ligand Binding Site [chemical binding]; other site 553174004996 B3/4 domain; Region: B3_4; cl11458 553174004997 PUA domain; Region: PUA; cl00607 553174004998 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 553174004999 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 553174005000 putative RNA binding site [nucleotide binding]; other site 553174005001 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 553174005002 S-adenosylmethionine binding site [chemical binding]; other site 553174005003 DEDDy 3'-5' exonuclease domain of WRN and similar proteins; Region: WRN_exo; cd06141 553174005004 catalytic site [active] 553174005005 putative active site [active] 553174005006 putative substrate binding site [chemical binding]; other site 553174005007 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 553174005008 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174005009 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 553174005010 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 553174005011 seryl-tRNA synthetase; Provisional; Region: PRK05431 553174005012 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 553174005013 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme bound...; Region: SerRS_core; cd00770 553174005014 dimer interface [polypeptide binding]; other site 553174005015 active site 553174005016 motif 1; other site 553174005017 motif 2; other site 553174005018 motif 3; other site 553174005019 putative bifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta; Provisional; Region: PRK12778 553174005020 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)...; Region: DHOD_e_trans_like1; cd06219 553174005021 FAD binding pocket [chemical binding]; other site 553174005022 FAD binding motif [chemical binding]; other site 553174005023 phosphate binding motif [ion binding]; other site 553174005024 beta-alpha-beta structure motif; other site 553174005025 NAD binding pocket [chemical binding]; other site 553174005026 Iron coordination center [ion binding]; other site 553174005027 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 553174005028 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174005029 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 553174005030 ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In...; Region: ExsB; cd01995 553174005031 Ligand Binding Site [chemical binding]; other site 553174005032 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; cl00198 553174005033 Phosphoglycerate kinase; Region: PGK; pfam00162 553174005034 substrate binding site [chemical binding]; other site 553174005035 hinge regions; other site 553174005036 ADP binding site [chemical binding]; other site 553174005037 catalytic site [active] 553174005038 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 553174005039 putative active site [active] 553174005040 LytTr DNA-binding domain; Region: LytTR; cl04498 553174005041 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 553174005042 Alpha-L-fucosidase [Carbohydrate transport and metabolism]; Region: COG3669 553174005043 Alpha-L-fucosidase; Region: Alpha_L_fucos; cl12119 553174005044 Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes; Region: FA58C; cl12042 553174005045 muropeptide transporter; Reviewed; Region: ampG; PRK11902 553174005046 muropeptide transporter; Validated; Region: ampG; PRK11010 553174005047 GlcN6P_deaminase: Glucosamine-6-phosphate (GlcN6P) deaminase subfamily; GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium. The reaction is an aldo-keto isomerization coupled with an amination or...; Region: GlcN6P_deaminase; cd01399 553174005048 active site 553174005049 trimer interface [polypeptide binding]; other site 553174005050 allosteric site; other site 553174005051 active site lid [active] 553174005052 hexamer (dimer of trimers) interface [polypeptide binding]; other site 553174005053 glucosamine-6-phosphate deaminase-like protein; Validated; Region: PRK02122 553174005054 GlcN6P_deaminase: Glucosamine-6-phosphate (GlcN6P) deaminase subfamily; GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium. The reaction is an aldo-keto isomerization coupled with an amination or...; Region: GlcN6P_deaminase; cd01399 553174005055 active site 553174005056 trimer interface [polypeptide binding]; other site 553174005057 allosteric site; other site 553174005058 active site lid [active] 553174005059 hexamer (dimer of trimers) interface [polypeptide binding]; other site 553174005060 GlcNAc-PI de-N-acetylase; Region: PIG-L; cl00929 553174005061 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 553174005062 catalytic site [active] 553174005063 BNR repeat-like domain; Region: BNR_2; pfam13088 553174005064 Asp-box motif; other site 553174005065 Domain of unknown function (DUF4091); Region: DUF4091; pfam13320 553174005066 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; cl01113 553174005067 Susd and RagB outer membrane lipoprotein; Region: SusD-like; pfam12741 553174005068 starch binding outer membrane protein SusD; Region: SusD; cd08977 553174005069 Secretin and TonB N terminus short domain; Region: STN; cl06624 553174005070 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174005071 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174005072 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 553174005073 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; cl01155 553174005074 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 553174005075 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 553174005076 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 553174005077 DNA binding residues [nucleotide binding] 553174005078 Transposase; Region: DDE_Tnp_ISL3; pfam01610 553174005079 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 553174005080 FecR protein; Region: FecR; pfam04773 553174005081 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 553174005082 cryptic beta-D-galactosidase subunit alpha; Reviewed; Region: ebgA; PRK10340 553174005083 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; cl08371 553174005084 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 553174005085 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; cl15381 553174005086 Beta galactosidase small chain; Region: Bgal_small_N; cl03787 553174005087 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 553174005088 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 553174005089 RNA binding surface [nucleotide binding]; other site 553174005090 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 553174005091 active site 553174005092 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 553174005093 Zn2+ binding site [ion binding]; other site 553174005094 Mg2+ binding site [ion binding]; other site 553174005095 Pyruvate/oxaloacetate carboxyltransferase [Energy production and conversion]; Region: COG5016 553174005096 DRE-TIM metallolyase superfamily; Region: DRE_TIM_metallolyase; cl07974 553174005097 active site 553174005098 metal binding site [ion binding]; metal-binding site 553174005099 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 553174005100 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 553174005101 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 553174005102 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 553174005103 helix_turn_helix ASNC type; Region: HTH_ASNC; smart00344 553174005104 Helix-turn-helix domains; Region: HTH; cl00088 553174005105 AsnC family; Region: AsnC_trans_reg; pfam01037 553174005106 Major Facilitator Superfamily; Region: MFS_1; pfam07690 553174005107 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 553174005108 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 553174005109 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 553174005110 membrane protein insertase; Provisional; Region: PRK01318 553174005111 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 553174005112 CTP synthetase; Validated; Region: pyrG; PRK05380 553174005113 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 553174005114 Catalytic site [active] 553174005115 active site 553174005116 UTP binding site [chemical binding]; other site 553174005117 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 553174005118 active site 553174005119 putative oxyanion hole; other site 553174005120 catalytic triad [active] 553174005121 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 553174005122 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174005123 NAD(P) binding site [chemical binding]; other site 553174005124 active site 553174005125 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 553174005126 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 553174005127 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 553174005128 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 553174005129 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 553174005130 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 553174005131 active site 553174005132 catalytic residues [active] 553174005133 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 553174005134 HsdM N-terminal domain; Region: HsdM_N; pfam12161 553174005135 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 553174005136 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; cl16911 553174005137 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 553174005138 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 553174005139 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 553174005140 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 553174005141 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 553174005142 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 553174005143 ATP binding site [chemical binding]; other site 553174005144 putative Mg++ binding site [ion binding]; other site 553174005145 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 553174005146 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 553174005147 Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of...; Region: LamG; cl00102 553174005148 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 553174005149 active site 553174005150 Susd and RagB outer membrane lipoprotein; Region: SusD-like; pfam12741 553174005151 starch binding outer membrane protein SusD; Region: SusD; cd08977 553174005152 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174005153 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174005154 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; cl01155 553174005155 Domain of unknown function DUF59; Region: DUF59; cl00941 553174005156 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 553174005157 Walker A motif; other site 553174005158 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 553174005159 Transposase; Region: DDE_Tnp_ISL3; pfam01610 553174005160 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 553174005161 Helix-turn-helix domain of transposase family ISL3; Region: HTH_Tnp_ISL3; pfam13542 553174005162 DDE superfamily endonuclease; Region: DDE_4; cl15789 553174005163 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 553174005164 DDE superfamily endonuclease; Region: DDE_4; cl15789 553174005165 Putative catalytic domain of uncharacterized hypothetical proteins closely related to Nuc, , an endonuclease from Salmonella typhimurium; Region: PLDc_Nuc_like_unchar2; cd09174 553174005166 PLD-like domain; Region: PLDc_2; pfam13091 553174005167 putative active site [active] 553174005168 catalytic site [active] 553174005169 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 553174005170 DNA primase (bacterial type) [DNA replication, recombination, and repair]; Region: DnaG; COG0358 553174005171 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 553174005172 active site 553174005173 metal binding site [ion binding]; metal-binding site 553174005174 interdomain interaction site; other site 553174005175 AAA domain; Region: AAA_25; pfam13481 553174005176 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 553174005177 Abi-like protein; Region: Abi_2; cl01988 553174005178 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174005179 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 553174005180 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 553174005181 active site 553174005182 DNA binding site [nucleotide binding] 553174005183 Int/Topo IB signature motif; other site 553174005184 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 553174005185 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 553174005186 active site 553174005187 DNA binding site [nucleotide binding] 553174005188 Int/Topo IB signature motif; other site 553174005189 Domain of unknown function (DUF1896); Region: DUF1896; pfam08989 553174005190 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 553174005191 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 553174005192 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 553174005193 Salmonella virulence plasmid 65kDa B protein; Region: SpvB; pfam03534 553174005194 Family description; Region: VCBS; pfam13517 553174005195 Family description; Region: VCBS; pfam13517 553174005196 Family description; Region: VCBS; pfam13517 553174005197 Family description; Region: VCBS; pfam13517 553174005198 Insecticide toxin TcdB middle/N-terminal region; Region: TcdB_toxin_midN; pfam12256 553174005199 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 553174005200 RHS Repeat; Region: RHS_repeat; cl11982 553174005201 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 553174005202 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 553174005203 Domain of unknown function (DUF4285); Region: DUF4285; pfam14113 553174005204 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 553174005205 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; cl01155 553174005206 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 553174005207 Salmonella virulence plasmid 65kDa B protein; Region: SpvB; pfam03534 553174005208 Insecticide toxin TcdB middle/N-terminal region; Region: TcdB_toxin_midN; pfam12256 553174005209 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 553174005210 RHS Repeat; Region: RHS_repeat; cl11982 553174005211 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 553174005212 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 553174005213 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 553174005214 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 553174005215 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 553174005216 RHS Repeat; Region: RHS_repeat; cl11982 553174005217 RHS Repeat; Region: RHS_repeat; cl11982 553174005218 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 553174005219 Domain of unknown function (DUF4372); Region: DUF4372; pfam14294 553174005220 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 553174005221 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 553174005222 putative peroxiredoxin; Provisional; Region: PRK13190 553174005223 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 553174005224 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 553174005225 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 553174005226 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 553174005227 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 553174005228 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 553174005229 Domain of unknown function (DUF1896); Region: DUF1896; pfam08989 553174005230 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 553174005231 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 553174005232 active site 553174005233 DNA binding site [nucleotide binding] 553174005234 Int/Topo IB signature motif; other site 553174005235 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 553174005236 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 553174005237 active site 553174005238 DNA binding site [nucleotide binding] 553174005239 Int/Topo IB signature motif; other site 553174005240 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; cl16911 553174005241 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 553174005242 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 553174005243 DNA translocase FtsK; Provisional; Region: PRK10263 553174005244 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174005245 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174005246 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 553174005247 DNA topoisomerase III; Provisional; Region: PRK07726 553174005248 active site 553174005249 putative interdomain interaction site [polypeptide binding]; other site 553174005250 putative metal-binding site [ion binding]; other site 553174005251 putative nucleotide binding site [chemical binding]; other site 553174005252 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 553174005253 domain I; other site 553174005254 DNA binding groove [nucleotide binding] 553174005255 phosphate binding site [ion binding]; other site 553174005256 domain II; other site 553174005257 domain III; other site 553174005258 nucleotide binding site [chemical binding]; other site 553174005259 catalytic site [active] 553174005260 domain IV; other site 553174005261 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 553174005262 Protein of unknown function (DUF4099); Region: DUF4099; pfam13351 553174005263 Protein of unknown function (DUF3945); Region: DUF3945; pfam13101 553174005264 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 553174005265 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 553174005266 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 553174005267 Aminotransferase class I and II; Region: Aminotran_1_2; pfam00155 553174005268 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 553174005269 catalytic residue [active] 553174005270 Carbohydrate Binding Module 6 (CBM6) and CBM35_like superfamily; Region: CBM6-CBM35-CBM36_like; cl14880 553174005271 Peptidase C10 family; Region: Peptidase_C10; pfam01640 553174005272 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 553174005273 B12 binding site [chemical binding]; other site 553174005274 B12-binding domain/radical SAM domain protein, MJ_1487 family; Region: B12_SAM_MJ_1487; TIGR04013 553174005275 Radical SAM superfamily; Region: Radical_SAM; pfam04055 553174005276 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 553174005277 FeS/SAM binding site; other site 553174005278 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; cl01155 553174005279 YWFCY protein; Region: YWFCY; pfam14293 553174005280 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174005281 AAA-like domain; Region: AAA_10; pfam12846 553174005282 Walker A motif; other site 553174005283 ATP binding site [chemical binding]; other site 553174005284 Walker B motif; other site 553174005285 Relaxase/Mobilisation nuclease domain; Region: Relaxase; cl01584 553174005286 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 553174005287 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 553174005288 Domain of unknown function (DUF4134); Region: DUF4134; pfam13572 553174005289 Bacteroides conjugation system ATPase, TraG family; Region: Bac_Flav_CT_G; TIGR03783 553174005290 Domain of unknown function, B. Theta Gene description (DUF3875); Region: DUF3875; pfam12991 553174005291 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174005292 Walker A/P-loop; other site 553174005293 ATP binding site [chemical binding]; other site 553174005294 Domain of unknown function (DUF4141); Region: DUF4141; pfam13605 553174005295 Bacteroides conjugative transposon TraJ protein; Region: Bac_Flav_CT_J; TIGR03782 553174005296 Bacteroides conjugative transposon TraK protein; Region: Bac_Flav_CT_K; TIGR03781 553174005297 Bacteroides conjugative transposon TraM protein; Region: Bac_Flav_CT_M; TIGR03779 553174005298 Protein of unknown function (DUF3714); Region: DUF3714; pfam12508 553174005299 Bacteroides conjugative transposon TraN protein; Region: Bac_Flav_CT_N; TIGR03780 553174005300 Domain of unknown function (DUF4138); Region: DUF4138; pfam13595 553174005301 Conjugative transposon protein TraO; Region: TraO; pfam10626 553174005302 Domain of unknown function, B. Theta Gene description (DUF3872); Region: DUF3872; pfam12988 553174005303 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 553174005304 catalytic residue [active] 553174005305 Peptidase U49; Region: Peptidase_U49; cl15458 553174005306 PcfJ-like protein; Region: PcfJ; pfam14284 553174005307 PcfK-like protein; Region: PcfK; pfam14058 553174005308 Protein of unknown function (DUF3260); Region: DUF3260; cl11881 553174005309 Domain of unknown function (DUF1896); Region: DUF1896; pfam08989 553174005310 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 553174005311 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 553174005312 Int/Topo IB signature motif; other site 553174005313 flavoprotein, HI0933 family; Region: TIGR00275 553174005314 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174005315 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 553174005316 pyruvate formate-lyase 1-activating enzyme; Region: PFLA; TIGR02493 553174005317 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 553174005318 FeS/SAM binding site; other site 553174005319 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 553174005320 Pyruvate formate lyase 1; Region: PFL1; cd01678 553174005321 coenzyme A binding site [chemical binding]; other site 553174005322 active site 553174005323 catalytic residues [active] 553174005324 glycine loop; other site 553174005325 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 553174005326 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174005327 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 553174005328 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 553174005329 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 553174005330 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 553174005331 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 553174005332 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174005333 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174005334 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174005335 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174005336 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 553174005337 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 553174005338 nucleoside/Zn binding site; other site 553174005339 dimer interface [polypeptide binding]; other site 553174005340 catalytic motif [active] 553174005341 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 553174005342 UbiA prenyltransferase family; Region: UbiA; cl00337 553174005343 Domain of unknown function (DUF4289); Region: DUF4289; pfam14121 553174005344 Domain of unknown function (DUF4289); Region: DUF4289; pfam14121 553174005345 excinuclease ABC subunit B; Provisional; Region: PRK05298 553174005346 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 553174005347 ATP binding site [chemical binding]; other site 553174005348 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 553174005349 nucleotide binding region [chemical binding]; other site 553174005350 ATP-binding site [chemical binding]; other site 553174005351 Ultra-violet resistance protein B; Region: UvrB; pfam12344 553174005352 UvrB/uvrC motif; Region: UVR; pfam02151 553174005353 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 553174005354 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 553174005355 Domain of unknown function (DUF4293); Region: DUF4293; pfam14126 553174005356 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 553174005357 Sugar specificity; other site 553174005358 Pyrimidine base specificity; other site 553174005359 ATP-binding site [chemical binding]; other site 553174005360 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 553174005361 putative active site [active] 553174005362 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 553174005363 putative catalytic site [active] 553174005364 putative metal binding site [ion binding]; other site 553174005365 putative phosphate binding site [ion binding]; other site 553174005366 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 553174005367 Zn binding site [ion binding]; other site 553174005368 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 553174005369 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 553174005370 DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases. They exists as monomers and homodimers; Region: NUC; cl00089 553174005371 active site 553174005372 substrate binding site [chemical binding]; other site 553174005373 Mg2+ binding site [ion binding]; other site 553174005374 Protein of unknown function with HXXEE motif; Region: HXXEE; pfam13787 553174005375 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 553174005376 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 553174005377 Uncharacterized conserved protein [Function unknown]; Region: COG2461 553174005378 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 553174005379 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 553174005380 active site 553174005381 dimer interface [polypeptide binding]; other site 553174005382 metal binding site [ion binding]; metal-binding site 553174005383 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174005384 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; cl01155 553174005385 Predicted peptidase [General function prediction only]; Region: COG4099 553174005386 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 553174005387 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 553174005388 Domain of unknown function (DUF4302); Region: DUF4302; pfam14135 553174005389 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 553174005390 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174005391 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174005392 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174005393 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174005394 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 553174005395 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; cl01155 553174005396 putative transporter; Validated; Region: PRK03818 553174005397 Predicted Permease Membrane Region; Region: Asp-Al_Ex; cl06061 553174005398 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 553174005399 Predicted Permease Membrane Region; Region: Asp-Al_Ex; cl06061 553174005400 Leucine rich repeat; Region: LRR_8; pfam13855 553174005401 Leucine rich repeat; Region: LRR_8; pfam13855 553174005402 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 553174005403 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 553174005404 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 553174005405 active site 553174005406 catalytic residues [active] 553174005407 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 553174005408 type VII secretion-associated serine protease mycosin; Region: T7SS_mycosin; TIGR03921 553174005409 catalytic residues [active] 553174005410 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 553174005411 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 553174005412 Uncharacterized conserved protein [Function unknown]; Region: COG1284 553174005413 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 553174005414 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; cl10498 553174005415 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 553174005416 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 553174005417 DoxX; Region: DoxX; cl00976 553174005418 FeoA domain; Region: FeoA; cl00838 553174005419 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 553174005420 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 553174005421 G1 box; other site 553174005422 GTP/Mg2+ binding site [chemical binding]; other site 553174005423 Switch I region; other site 553174005424 G2 box; other site 553174005425 G3 box; other site 553174005426 Switch II region; other site 553174005427 G4 box; other site 553174005428 G5 box; other site 553174005429 Nucleoside recognition; Region: Gate; cl00486 553174005430 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 553174005431 Nucleoside recognition; Region: Gate; cl00486 553174005432 Gram-negative bacterial tonB protein; Region: TonB; cl10048 553174005433 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 553174005434 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 553174005435 substrate binding pocket [chemical binding]; other site 553174005436 chain length determination region; other site 553174005437 substrate-Mg2+ binding site; other site 553174005438 catalytic residues [active] 553174005439 aspartate-rich region 1; other site 553174005440 active site lid residues [active] 553174005441 aspartate-rich region 2; other site 553174005442 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 553174005443 active site 553174005444 cytidylate kinase; Provisional; Region: cmk; PRK00023 553174005445 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174005446 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 553174005447 CMP-binding site; other site 553174005448 The sites determining sugar specificity; other site 553174005449 Endo-N-acetylmuramidases (muramidases) are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues; Region: GH25_muramidase; cl10448 553174005450 active site 553174005451 Glycosyl hydrolases family 25; Region: Glyco_hydro_25; pfam01183 553174005452 zinc-ribbon domain; Region: zf-ribbon_3; cl11198 553174005453 Double zinc ribbon; Region: DZR; pfam12773 553174005454 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 553174005455 Helix-turn-helix domains; Region: HTH; cl00088 553174005456 NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their...; Region: NodN; cd03450 553174005457 putative active site [active] 553174005458 putative catalytic site [active] 553174005459 threonine synthase; Validated; Region: PRK06260 553174005460 DNA directed RNA polymerase, 7 kDa subunit; Region: DNA_RNApol_7kD; cl00874 553174005461 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174005462 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174005463 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; cl01155 553174005464 starch binding outer membrane protein SusD; Region: SusD; cd08977 553174005465 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174005466 Helix-turn-helix domains; Region: HTH; cl00088 553174005467 Cupin domain; Region: Cupin_2; cl09118 553174005468 cryptic beta-D-galactosidase subunit alpha; Reviewed; Region: ebgA; PRK10340 553174005469 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; cl08371 553174005470 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 553174005471 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; cl15381 553174005472 Beta galactosidase small chain; Region: Bgal_small_N; cl03787 553174005473 Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; Region: E_set; cl09101 553174005474 Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes; Region: FA58C; cl12042 553174005475 sugar binding site [chemical binding]; other site 553174005476 Orthopoxvirus protein of unknown function (DUF830); Region: DUF830; cl13998 553174005477 anaerobic ribonucleotide reductase-activating protein; Provisional; Region: nrdG; cl15804 553174005478 4Fe-4S single cluster domain; Region: Fer4_14; pfam13394 553174005479 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 553174005480 RmuC family; Region: RmuC; pfam02646 553174005481 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 553174005482 DNA binding site [nucleotide binding] 553174005483 domain linker motif; other site 553174005484 Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_sugar_binding_like; cd01536 553174005485 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 553174005486 ligand binding site [chemical binding]; other site 553174005487 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 553174005488 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 553174005489 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 553174005490 The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i)...; Region: GH20_chitobiase-like; cd06563 553174005491 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 553174005492 active site 553174005493 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; cl14891 553174005494 Integrase core domain; Region: rve; cl01316 553174005495 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 553174005496 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 553174005497 motif II; other site 553174005498 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 553174005499 Transposase; Region: DDE_Tnp_ISL3; pfam01610 553174005500 phosphatidylinositol phosphate kinase; Provisional; Region: PLN03185 553174005501 Endo-N-acetylmuramidases (muramidases) are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues; Region: GH25_muramidase; cl10448 553174005502 Glycosyl hydrolases family 25; Region: Glyco_hydro_25; pfam01183 553174005503 active site 553174005504 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 553174005505 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; cl01155 553174005506 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 553174005507 metal-binding site [ion binding] 553174005508 alcohol dehydrogenase and quinone reductase-like medium chain degydrogenases/reductases; Region: MDR_like_2; cd05289 553174005509 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 553174005510 putative NAD(P) binding site [chemical binding]; other site 553174005511 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 553174005512 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 553174005513 Helix-turn-helix domains; Region: HTH; cl00088 553174005514 CAAX protease self-immunity; Region: Abi; cl00558 553174005515 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 553174005516 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 553174005517 active site 553174005518 Riboflavin kinase; Region: Flavokinase; cl03312 553174005519 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 553174005520 active site 553174005521 DNA binding site [nucleotide binding] 553174005522 Int/Topo IB signature motif; other site 553174005523 Domain of unknown function, B. Theta Gene description (DUF3871); Region: DUF3871; pfam12987 553174005524 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 553174005525 MPN+ (JAMM) motif; other site 553174005526 Zinc-binding site [ion binding]; other site 553174005527 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 553174005528 active site 553174005529 DNA binding site [nucleotide binding] 553174005530 Int/Topo IB signature motif; other site 553174005531 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 553174005532 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 553174005533 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]; Region: COG5540 553174005534 HNH endonuclease; Region: HNH_3; pfam13392 553174005535 Double zinc ribbon; Region: DZR; pfam12773 553174005536 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 553174005537 Int/Topo IB signature motif; other site 553174005538 Domain of unknown function (DUF1896); Region: DUF1896; pfam08989 553174005539 PcfK-like protein; Region: PcfK; pfam14058 553174005540 The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases, as well as cobalamine (B12) independent methionine synthases; Region: URO-D_CIMS_like; cl00464 553174005541 PcfJ-like protein; Region: PcfJ; pfam14284 553174005542 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 553174005543 catalytic residue [active] 553174005544 Domain of unknown function, B. Theta Gene description (DUF3872); Region: DUF3872; pfam12988 553174005545 Conjugative transposon protein TraO; Region: TraO; pfam10626 553174005546 Domain of unknown function (DUF4372); Region: DUF4372; pfam14294 553174005547 AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis...; Region: AE_Prim_S_like; cl01287 553174005548 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 553174005549 ATP binding site [chemical binding]; other site 553174005550 putative Mg++ binding site [ion binding]; other site 553174005551 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174005552 C-terminal putative phospholipase D-like domain of uncharacterized prokaryotic HKD family nucleases fused to DEAD/DEAH box helicases; Region: PLDc_C_DEXD_like; cd09126 553174005553 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 553174005554 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl09944 553174005555 active site 553174005556 phosphorylation site [posttranslational modification] 553174005557 intermolecular recognition site; other site 553174005558 Tetratricopeptide repeat; Region: TPR_12; pfam13424 553174005559 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 553174005560 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 553174005561 ATP binding site [chemical binding]; other site 553174005562 Mg2+ binding site [ion binding]; other site 553174005563 G-X-G motif; other site 553174005564 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 553174005565 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174005566 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 553174005567 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 553174005568 N-terminal plug; other site 553174005569 ligand-binding site [chemical binding]; other site 553174005570 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 553174005571 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 553174005572 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 553174005573 Leucine rich repeat; Region: LRR_8; pfam13855 553174005574 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 553174005575 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 553174005576 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; cl00973 553174005577 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 553174005578 folylpolyglutamate synthase/dihydrofolate synthase; Region: folC; TIGR01499 553174005579 chaperone protein DnaJ; Provisional; Region: PRK14289 553174005580 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 553174005581 HSP70 interaction site [polypeptide binding]; other site 553174005582 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 553174005583 substrate binding site [polypeptide binding]; other site 553174005584 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 553174005585 Zn binding sites [ion binding]; other site 553174005586 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 553174005587 dimer interface [polypeptide binding]; other site 553174005588 heat shock protein GrpE; Provisional; Region: PRK14140 553174005589 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 553174005590 dimer interface [polypeptide binding]; other site 553174005591 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 553174005592 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 553174005593 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174005594 Walker A/P-loop; other site 553174005595 ATP binding site [chemical binding]; other site 553174005596 Q-loop/lid; other site 553174005597 ABC transporter signature motif; other site 553174005598 Walker B; other site 553174005599 D-loop; other site 553174005600 H-loop/switch region; other site 553174005601 ABC transporter; Region: ABC_tran_2; pfam12848 553174005602 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 553174005603 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 553174005604 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl11420 553174005605 cryptic beta-D-galactosidase subunit alpha; Reviewed; Region: ebgA; PRK10340 553174005606 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; cl08371 553174005607 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 553174005608 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; cl15381 553174005609 Beta galactosidase small chain; Region: Bgal_small_N; cl03787 553174005610 Uncharacterized BCR, COG1649; Region: DUF187; cl15398 553174005611 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_15; cd04673 553174005612 nudix motif; other site 553174005613 GSCFA family; Region: GSCFA; pfam08885 553174005614 Helix-turn-helix domains; Region: HTH; cl00088 553174005615 metal binding site 2 [ion binding]; metal-binding site 553174005616 putative DNA binding helix; other site 553174005617 metal binding site 1 [ion binding]; metal-binding site 553174005618 dimer interface [polypeptide binding]; other site 553174005619 structural Zn2+ binding site [ion binding]; other site 553174005620 putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional; Region: PRK11930 553174005621 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 553174005622 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 553174005623 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 553174005624 active site 553174005625 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 553174005626 dimer interface [polypeptide binding]; other site 553174005627 substrate binding site [chemical binding]; other site 553174005628 catalytic residues [active] 553174005629 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 553174005630 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 553174005631 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 553174005632 active site 553174005633 ambiguous bases; PCR confirmed polymorphic indel with 454 reads supporting both presence and absence of T 553174005634 MatE; Region: MatE; cl10513 553174005635 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 553174005636 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 553174005637 active site 553174005638 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 553174005639 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 553174005640 Uncharacterized BCR, COG1649; Region: DUF187; cl15398 553174005641 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 553174005642 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 553174005643 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 553174005644 DNA binding residues [nucleotide binding] 553174005645 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 553174005646 HutD; Region: HutD; cl01532 553174005647 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 553174005648 active site 553174005649 Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of...; Region: LamG; cl00102 553174005650 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 553174005651 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 553174005652 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 553174005653 active site 553174005654 Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of...; Region: LamG; cl00102 553174005655 Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; Region: E_set; cl09101 553174005656 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 553174005657 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 553174005658 active site 553174005659 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 553174005660 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174005661 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174005662 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174005663 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; cl01155 553174005664 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; cl01155 553174005665 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]; Region: COG2865 553174005666 ATP-dependent DNA helicase recG C-terminal; Region: HATPase_c_4; pfam13749 553174005667 Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes; Region: FA58C; cl12042 553174005668 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 553174005669 Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of...; Region: LamG; cl00102 553174005670 Endo-beta-N-acetylglucosaminidases are bacterial chitinases that hydrolyze the chitin core of various asparagine (N)-linked glycans and glycoproteins. The endo-beta-N-acetylglucosaminidases have a glycosyl hydrolase family 18 (GH18) catalytic domain; Region: GH18_EndoS-like; cd06542 553174005671 active site 553174005672 Susd and RagB outer membrane lipoprotein; Region: SusD-like; pfam12741 553174005673 starch binding outer membrane protein SusD; Region: SusD; cd08977 553174005674 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174005675 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174005676 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; cl01155 553174005677 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 553174005678 active site 553174005679 delta-lactam-biosynthetic de-N-acetylase; Region: spore_pdaA; TIGR02884 553174005680 Catalytic NodB homology domain of uncharacterized bacterial glycosyl transferase, group 2-like family proteins; Region: CE4_GT2-like; cd10962 553174005681 NodB motif; other site 553174005682 putative active site [active] 553174005683 putative catalytic site [active] 553174005684 putative Zn binding site [ion binding]; other site 553174005685 Glycosyltransferases, probably involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG1215 553174005686 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 553174005687 DXD motif; other site 553174005688 Uncharacterized conserved protein [Function unknown]; Region: COG4938 553174005689 Predicted membrane protein [Function unknown]; Region: COG2860 553174005690 UPF0126 domain; Region: UPF0126; pfam03458 553174005691 UPF0126 domain; Region: UPF0126; pfam03458 553174005692 glycerate dehydrogenase; Provisional; Region: PRK06487 553174005693 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 553174005694 recombination factor protein RarA; Reviewed; Region: PRK13342 553174005695 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 553174005696 Walker A motif; other site 553174005697 ATP binding site [chemical binding]; other site 553174005698 Walker B motif; other site 553174005699 arginine finger; other site 553174005700 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 553174005701 Sulfatase; Region: Sulfatase; cl10460 553174005702 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 553174005703 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174005704 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174005705 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174005706 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174005707 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 553174005708 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; cl01155 553174005709 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 553174005710 non-specific DNA binding site [nucleotide binding]; other site 553174005711 salt bridge; other site 553174005712 sequence-specific DNA binding site [nucleotide binding]; other site 553174005713 HipA N-terminal domain; Region: Couple_hipA; cl11853 553174005714 HipA-like N-terminal domain; Region: HipA_N; pfam07805 553174005715 HipA-like C-terminal domain; Region: HipA_C; pfam07804 553174005716 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 553174005717 AAA domain; Region: AAA_31; pfam13614 553174005718 P-loop; other site 553174005719 Magnesium ion binding site [ion binding]; other site 553174005720 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 553174005721 non-specific DNA binding site [nucleotide binding]; other site 553174005722 salt bridge; other site 553174005723 sequence-specific DNA binding site [nucleotide binding]; other site 553174005724 Domain of unknown function (DUF955); Region: DUF955; cl01076 553174005725 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 553174005726 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 553174005727 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 553174005728 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 553174005729 ATP binding site [chemical binding]; other site 553174005730 putative Mg++ binding site [ion binding]; other site 553174005731 type I restriction system adenine methylase (hsdM); Region: hsdM; TIGR00497 553174005732 HsdM N-terminal domain; Region: HsdM_N; pfam12161 553174005733 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 553174005734 S-adenosylmethionine binding site [chemical binding]; other site 553174005735 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; cl16911 553174005736 Protein of unknown function DUF262; Region: DUF262; cl14890 553174005737 Protein of unknown function DUF262; Region: DUF262; cl14890 553174005738 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]; Region: COG2865 553174005739 Divergent AAA domain; Region: AAA_4; pfam04326 553174005740 ATP-dependent DNA helicase recG C-terminal; Region: HATPase_c_4; pfam13749 553174005741 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 553174005742 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 553174005743 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 553174005744 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 553174005745 phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus...; Region: INT_phiLC3_C; cd01189 553174005746 Int/Topo IB signature motif; other site 553174005747 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional; Region: PRK11331 553174005748 Domain of unknown function (DUF4268); Region: DUF4268; pfam14088 553174005749 LlaJI restriction endonuclease; Region: RE_LlaJI; pfam09563 553174005750 Domain of unknown function (DUF4420); Region: DUF4420; pfam14390 553174005751 Z1 domain; Region: Z1; pfam10593 553174005752 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 553174005753 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 553174005754 cofactor binding site; other site 553174005755 DNA binding site [nucleotide binding] 553174005756 substrate interaction site [chemical binding]; other site 553174005757 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 553174005758 Peptidase M15; Region: Peptidase_M15_3; cl01194 553174005759 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cl00257 553174005760 IHF dimer interface [polypeptide binding]; other site 553174005761 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 553174005762 Acyltransferase family; Region: Acyl_transf_3; pfam01757 553174005763 Bacterial membrane protein YfhO; Region: YfhO; pfam09586 553174005764 S-Ribosylhomocysteinase (LuxS); Region: LuxS; cl00802 553174005765 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174005766 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 553174005767 Protein of unknown function (Porph_ging); Region: Porph_ging; cl09903 553174005768 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 553174005769 ligand binding site [chemical binding]; other site 553174005770 prolyl-tRNA synthetase; Provisional; Region: PRK08661 553174005771 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of...; Region: ProRS_core_arch_euk; cd00778 553174005772 dimer interface [polypeptide binding]; other site 553174005773 motif 1; other site 553174005774 active site 553174005775 motif 2; other site 553174005776 motif 3; other site 553174005777 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 553174005778 anticodon binding site; other site 553174005779 zinc-binding site [ion binding]; other site 553174005780 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 553174005781 RNA polymerase sigma factor, cyanobacterial RpoD-like family; Region: Sig70-cyanoRpoD; TIGR02997 553174005782 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 553174005783 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 553174005784 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 553174005785 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174005786 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 553174005787 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; cl01155 553174005788 Domain of unknown function (DUF4249); Region: DUF4249; pfam14054 553174005789 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174005790 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; cl01155 553174005791 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 553174005792 active site 553174005793 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; cl01155 553174005794 KWG Leptospira; Region: KWG; pfam07656 553174005795 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 553174005796 MatE; Region: MatE; cl10513 553174005797 MatE; Region: MatE; cl10513 553174005798 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 553174005799 Membrane transport protein; Region: Mem_trans; cl09117 553174005800 Low molecular weight phosphatase family; Region: LMWPc; cd00115 553174005801 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 553174005802 active site 553174005803 Anion-transporting ATPase; Region: ArsA_ATPase; pfam02374 553174005804 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 553174005805 P loop; other site 553174005806 Nucleotide binding site [chemical binding]; other site 553174005807 DTAP/Switch II; other site 553174005808 Switch I; other site 553174005809 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 553174005810 P loop; other site 553174005811 Nucleotide binding site [chemical binding]; other site 553174005812 DTAP/Switch II; other site 553174005813 Switch I; other site 553174005814 Arsenical resistance operon trans-acting repressor ArsD; Region: ArsD; pfam06953 553174005815 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 553174005816 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 553174005817 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 553174005818 dimerization interface [polypeptide binding]; other site 553174005819 putative DNA binding site [nucleotide binding]; other site 553174005820 putative Zn2+ binding site [ion binding]; other site 553174005821 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 553174005822 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 553174005823 ankyrin-like protein; Provisional; Region: PHA03095 553174005824 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 553174005825 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174005826 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174005827 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 553174005828 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; cl01155 553174005829 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174005830 Domain of unknown function (DUF4302); Region: DUF4302; pfam14135 553174005831 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 553174005832 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 553174005833 Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and...; Region: rubredoxin_SM; cd00729 553174005834 iron binding site [ion binding]; other site 553174005835 Rubrerythrin [Energy production and conversion]; Region: COG1592 553174005836 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 553174005837 binuclear metal center [ion binding]; other site 553174005838 Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and...; Region: rubredoxin_SM; cd00729 553174005839 iron binding site [ion binding]; other site 553174005840 Galactose mutarotase-like; Region: Gal_mutarotas_2; pfam13802 553174005841 CPE1046 is an uncharacterized Clostridium perfringens protein with a glycosyl hydrolase family 31 (GH31) domain. The domain architecture of CPE1046 and its orthologs includes a C-terminal fibronectin type 3 (FN3) domain and a coagulation factor 5/8 type...; Region: GH31_CPE1046; cd06596 553174005842 putative active site [active] 553174005843 putative catalytic site [active] 553174005844 putative alpha-glucosidase; Provisional; Region: PRK10658 553174005845 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 553174005846 Interdomain contacts; other site 553174005847 Cytokine receptor motif; other site 553174005848 Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes; Region: FA58C; cl12042 553174005849 Domains similar to the eukaryotic reeler domain and bacterial cohesins; Region: Reeler_cohesin_like; cl14606 553174005850 Peptidase M60-like family; Region: M60-like; pfam13402 553174005851 LabA_like proteins; Region: LabA_like; cd06167 553174005852 putative metal binding site [ion binding]; other site 553174005853 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 553174005854 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 553174005855 Walker A/P-loop; other site 553174005856 ATP binding site [chemical binding]; other site 553174005857 Q-loop/lid; other site 553174005858 ABC transporter signature motif; other site 553174005859 Walker B; other site 553174005860 D-loop; other site 553174005861 H-loop/switch region; other site 553174005862 ABC transporter; Region: ABC_tran_2; pfam12848 553174005863 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 553174005864 KilA-N domain; Region: KilA-N; pfam04383 553174005865 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 553174005866 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 553174005867 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; cl01155 553174005868 Protein of unknown function (DUF3308); Region: DUF3308; cl14675 553174005869 starch binding outer membrane protein SusD; Region: SusD; cd08977 553174005870 starch binding outer membrane protein SusD; Region: SusD; cl15876 553174005871 Immune inhibitor A peptidase M6; Region: Peptidase_M6; cl11525 553174005872 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 553174005873 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 553174005874 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 553174005875 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 553174005876 Probable Catalytic site; other site 553174005877 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 553174005878 recombination protein RecR; Reviewed; Region: recR; PRK00076 553174005879 RecR protein; Region: RecR; pfam02132 553174005880 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 553174005881 putative active site [active] 553174005882 putative metal-binding site [ion binding]; other site 553174005883 tetramer interface [polypeptide binding]; other site 553174005884 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 553174005885 Inorganic pyrophosphatase [Energy production and conversion]; Region: OVP1; cl11452 553174005886 Inorganic H+ pyrophosphatase; Region: H_PPase; pfam03030 553174005887 This family contains NADPH-dependent flavin reductase and oxygen-insensitive nitroreductase. These enzymes are homodimeric flavoproteins that contain one FMN per monomer as a cofactor. Flavin reductase catalyzes the reduction of flavin by using NADPH as...; Region: NfsA_FRP; cd02146 553174005888 dimer interface [polypeptide binding]; other site 553174005889 FMN binding site [chemical binding]; other site 553174005890 NADPH bind site [chemical binding]; other site 553174005891 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 553174005892 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 553174005893 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 553174005894 active site 553174005895 dimer interface [polypeptide binding]; other site 553174005896 effector binding site; other site 553174005897 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 553174005898 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK08665 553174005899 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 553174005900 homooctamer interface [polypeptide binding]; other site 553174005901 active site 553174005902 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 553174005903 active site 553174005904 metal binding site [ion binding]; metal-binding site 553174005905 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 553174005906 mce related protein; Region: MCE; pfam02470