-- dump date 20120504_160526 -- class Genbank::misc_feature -- table misc_feature_note -- id note 1105112000001 Kinase/pyrophosphorylase; Region: Kinase-PPPase; cl00780 1105112000002 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 1105112000003 catalytic residues [active] 1105112000004 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 1105112000005 ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export. Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and...; Region: ABC_KpsT_Wzt; cd03220 1105112000006 Walker A/P-loop; other site 1105112000007 ATP binding site [chemical binding]; other site 1105112000008 Q-loop/lid; other site 1105112000009 ABC transporter signature motif; other site 1105112000010 Walker B; other site 1105112000011 D-loop; other site 1105112000012 H-loop/switch region; other site 1105112000013 ABC-2 type transporter; Region: ABC2_membrane; cl11417 1105112000014 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 1105112000015 FAD/NAD binding domain (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)-dihydroorotate...; Region: DHOD_e_trans_like; cd06192 1105112000016 FAD binding pocket [chemical binding]; other site 1105112000017 FAD binding motif [chemical binding]; other site 1105112000018 phosphate binding motif [ion binding]; other site 1105112000019 beta-alpha-beta structure motif; other site 1105112000020 NAD binding pocket [chemical binding]; other site 1105112000021 Iron coordination center [ion binding]; other site 1105112000022 PemK-like protein; Region: PemK; cl00995 1105112000023 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 1105112000024 potential frameshift: common BLAST hit: gi|67458519|ref|YP_246143.1| tellurite resistance protein-like protein 1105112000025 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 1105112000026 membrane protein insertase; Provisional; Region: PRK01318 1105112000027 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 1105112000028 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1105112000029 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 1105112000030 Uncharacterized conserved protein [Function unknown]; Region: COG1565 1105112000031 Putative S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_28; pfam02636 1105112000032 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112000033 Protein of unknown function (DUF1311); Region: DUF1311; cl01530 1105112000034 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 1105112000035 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 1105112000036 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 1105112000037 cofactor binding site; other site 1105112000038 FtsH Extracellular; Region: FtsH_ext; pfam06480 1105112000039 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 1105112000040 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 1105112000041 Walker A motif; other site 1105112000042 ATP binding site [chemical binding]; other site 1105112000043 Walker B motif; other site 1105112000044 arginine finger; other site 1105112000045 Peptidase family M41; Region: Peptidase_M41; pfam01434 1105112000046 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 1105112000047 Ligand Binding Site [chemical binding]; other site 1105112000048 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112000049 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 1105112000050 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 1105112000051 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 1105112000052 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 1105112000053 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 1105112000054 potential frameshift: common BLAST hit: gi|157827734|ref|YP_001496798.1| response regulator 1105112000055 Helix-turn-helix domains; Region: HTH; cl00088 1105112000056 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 1105112000057 Fatty acid desaturase; Region: FA_desaturase; pfam00487 1105112000058 Di-iron ligands [ion binding]; other site 1105112000059 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 1105112000060 UGMP family protein; Validated; Region: PRK09604 1105112000061 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 1105112000062 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 1105112000063 Clp amino terminal domain; Region: Clp_N; pfam02861 1105112000064 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 1105112000065 Walker A motif; other site 1105112000066 ATP binding site [chemical binding]; other site 1105112000067 Walker B motif; other site 1105112000068 arginine finger; other site 1105112000069 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 1105112000070 Walker A motif; other site 1105112000071 ATP binding site [chemical binding]; other site 1105112000072 Walker B motif; other site 1105112000073 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 1105112000074 potential frameshift: common BLAST hit: gi|67458545|ref|YP_246169.1| acetoacetyl-CoA reductase 1105112000075 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 1105112000076 Protein of unknown function (DUF2748); Region: DUF2748; pfam10871 1105112000077 potential frameshift: common BLAST hit: gi|341583274|ref|YP_004763765.1| cell surface antigen-like protein Sca10 1105112000078 potential frameshift: common BLAST hit: gi|229586241|ref|YP_002844742.1| Putative dihydrouridine synthase Dus 1105112000079 potential frameshift: common BLAST hit: gi|165932567|ref|YP_001649356.1| tRNA-dihydrouridine synthase 1105112000080 potential frameshift: common BLAST hit: gi|238650328|ref|YP_002916180.1| nifR3-like protein 1105112000081 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 1105112000082 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 1105112000083 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 1105112000084 intersubunit interface [polypeptide binding]; other site 1105112000085 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 1105112000086 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 1105112000087 active site 1105112000088 NTP binding site [chemical binding]; other site 1105112000089 metal binding triad [ion binding]; metal-binding site 1105112000090 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 1105112000091 potential frameshift: common BLAST hit: gi|341583241|ref|YP_004763732.1| ComEC/Rec2-like protein 1105112000092 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 1105112000093 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1105112000094 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 1105112000095 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 1105112000096 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1105112000097 ATP synthase subunit C; Region: ATP-synt_C; cl00466 1105112000098 ATP synthase A chain; Region: ATP-synt_A; cl00413 1105112000099 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; cl09754 1105112000100 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 1105112000101 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 1105112000102 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 1105112000103 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 1105112000104 S-adenosylmethionine binding site [chemical binding]; other site 1105112000105 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 1105112000106 recombination protein F; Reviewed; Region: recF; PRK00064 1105112000107 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105112000108 Walker A/P-loop; other site 1105112000109 ATP binding site [chemical binding]; other site 1105112000110 Q-loop/lid; other site 1105112000111 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105112000112 ABC transporter signature motif; other site 1105112000113 Walker B; other site 1105112000114 D-loop; other site 1105112000115 H-loop/switch region; other site 1105112000116 potential frameshift: common BLAST hit: gi|341583262|ref|YP_004763753.1| folate synthesis bifunctional protein 1105112000117 potential frameshift: common BLAST hit: gi|67458431|ref|YP_246055.1| folate synthesis bifunctional protein 1105112000118 potential frameshift: common BLAST hit: gi|67458431|ref|YP_246055.1| folate synthesis bifunctional protein 1105112000119 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 1105112000120 active site 1105112000121 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 1105112000122 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 1105112000123 Cu(I) binding site [ion binding]; other site 1105112000124 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 1105112000125 Colicin V production protein; Region: Colicin_V; cl00567 1105112000126 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 1105112000127 potential frameshift: common BLAST hit: gi|67458439|ref|YP_246063.1| cell surface antigen-like protein Sca10 1105112000128 potential frameshift: common BLAST hit: gi|341583274|ref|YP_004763765.1| cell surface antigen-like protein Sca10 1105112000129 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 1105112000130 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105112000131 Walker A/P-loop; other site 1105112000132 ATP binding site [chemical binding]; other site 1105112000133 Q-loop/lid; other site 1105112000134 ABC transporter signature motif; other site 1105112000135 Walker B; other site 1105112000136 D-loop; other site 1105112000137 H-loop/switch region; other site 1105112000138 Permease; Region: Permease; cl00510 1105112000139 alanine racemase; Reviewed; Region: alr; PRK00053 1105112000140 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 1105112000141 active site 1105112000142 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1105112000143 dimer interface [polypeptide binding]; other site 1105112000144 substrate binding site [chemical binding]; other site 1105112000145 catalytic residues [active] 1105112000146 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 1105112000147 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1105112000148 active site 1105112000149 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112000150 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; cl01074 1105112000151 VacJ like lipoprotein; Region: VacJ; cl01073 1105112000152 Tetratricopeptide repeat; Region: TPR_16; pfam13432 1105112000153 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 1105112000154 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 1105112000155 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 1105112000156 aspartate aminotransferase; Provisional; Region: PRK05764 1105112000157 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 1105112000158 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105112000159 homodimer interface [polypeptide binding]; other site 1105112000160 catalytic residue [active] 1105112000161 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 1105112000162 putative acyl-acceptor binding pocket; other site 1105112000163 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 1105112000164 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112000165 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 1105112000166 elongation factor Ts; Provisional; Region: tsf; PRK09377 1105112000167 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 1105112000168 Elongation factor TS; Region: EF_TS; pfam00889 1105112000169 Elongation factor TS; Region: EF_TS; pfam00889 1105112000170 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 1105112000171 rRNA interaction site [nucleotide binding]; other site 1105112000172 S8 interaction site; other site 1105112000173 putative laminin-1 binding site; other site 1105112000174 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 1105112000175 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1105112000176 active site 1105112000177 HIGH motif; other site 1105112000178 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1105112000179 KMSKS motif; other site 1105112000180 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1105112000181 tRNA binding surface [nucleotide binding]; other site 1105112000182 anticodon binding site; other site 1105112000183 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 1105112000184 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 1105112000185 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105112000186 putative substrate translocation pore; other site 1105112000187 EamA-like transporter family; Region: EamA; cl01037 1105112000188 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 1105112000189 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 1105112000190 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 1105112000191 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 1105112000192 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 1105112000193 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 1105112000194 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 1105112000195 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105112000196 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 1105112000197 active site 1105112000198 phosphorylation site [posttranslational modification] 1105112000199 intermolecular recognition site; other site 1105112000200 dimerization interface [polypeptide binding]; other site 1105112000201 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 1105112000202 DNA binding site [nucleotide binding] 1105112000203 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cd00557 1105112000204 SecA binding site; other site 1105112000205 Preprotein binding site; other site 1105112000206 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1105112000207 trimer interface [polypeptide binding]; other site 1105112000208 active site 1105112000209 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 1105112000210 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 1105112000211 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 1105112000212 CAP-like domain; other site 1105112000213 active site 1105112000214 primary dimer interface [polypeptide binding]; other site 1105112000215 Sporulation related domain; Region: SPOR; cl10051 1105112000216 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 1105112000217 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 1105112000218 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 1105112000219 active site 1105112000220 HIGH motif; other site 1105112000221 KMSK motif region; other site 1105112000222 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1105112000223 tRNA binding surface [nucleotide binding]; other site 1105112000224 anticodon binding site; other site 1105112000225 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 1105112000226 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 1105112000227 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 1105112000228 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 1105112000229 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 1105112000230 NeuB family; Region: NeuB; cl00496 1105112000231 Protein of unknown function (DUF2672); Region: DUF2672; pfam10878 1105112000232 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 1105112000233 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 1105112000234 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 1105112000235 ABC transporter; Region: ABC_tran_2; pfam12848 1105112000236 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 1105112000237 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 1105112000238 ParB-like nuclease domain; Region: ParBc; cl02129 1105112000239 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 1105112000240 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 1105112000241 P-loop; other site 1105112000242 Magnesium ion binding site [ion binding]; other site 1105112000243 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 1105112000244 Magnesium ion binding site [ion binding]; other site 1105112000245 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 1105112000246 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 1105112000247 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105112000248 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 1105112000249 Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside...; Region: NDPk_I; cd04413 1105112000250 active site 1105112000251 multimer interface [polypeptide binding]; other site 1105112000252 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 1105112000253 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 1105112000254 putative substrate translocation pore; other site 1105112000255 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105112000256 ATP/ADP translocase [Energy production and conversion]; Region: COG3202; cl03940 1105112000257 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 1105112000258 active site 1105112000259 catalytic residues [active] 1105112000260 metal binding site [ion binding]; metal-binding site 1105112000261 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 1105112000262 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 1105112000263 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 1105112000264 active site 1105112000265 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 1105112000266 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 1105112000267 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 1105112000268 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 1105112000269 trimer interface [polypeptide binding]; other site 1105112000270 active site 1105112000271 UDP-GlcNAc binding site [chemical binding]; other site 1105112000272 lipid binding site [chemical binding]; lipid-binding site 1105112000273 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 1105112000274 active site 1105112000275 potential frameshift: common BLAST hit: gi|67458401|ref|YP_246025.1| alpha-beta hydrolase family esterase 1105112000276 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 1105112000277 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 1105112000278 Predicted GTPase [General function prediction only]; Region: COG0218 1105112000279 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 1105112000280 G1 box; other site 1105112000281 GTP/Mg2+ binding site [chemical binding]; other site 1105112000282 Switch I region; other site 1105112000283 G2 box; other site 1105112000284 G3 box; other site 1105112000285 Switch II region; other site 1105112000286 G4 box; other site 1105112000287 G5 box; other site 1105112000288 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 1105112000289 nucleotide binding site [chemical binding]; other site 1105112000290 substrate binding site [chemical binding]; other site 1105112000291 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 1105112000292 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 1105112000293 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1105112000294 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105112000295 Walker A/P-loop; other site 1105112000296 ATP binding site [chemical binding]; other site 1105112000297 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 1105112000298 MAEBL; Provisional; Region: PTZ00121 1105112000299 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 1105112000300 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 1105112000301 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 1105112000302 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 1105112000303 aspartyl-tRNA synthetase; Provisional; Region: PTZ00401 1105112000304 potential frameshift: common BLAST hit: gi|67458488|ref|YP_246112.1| phosphate acetyltransferase 1105112000305 potential frameshift: common BLAST hit: gi|157825283|ref|YP_001493003.1| phosphate acetyltransferase 1105112000306 potential frameshift: common BLAST hit: gi|67458489|ref|YP_246113.1| acetate kinase 1105112000307 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 1105112000308 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 1105112000309 Uncharacterized protein conserved in bacteria (DUF2312); Region: DUF2312; cl11480 1105112000310 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 1105112000311 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 1105112000312 Protein export membrane protein; Region: SecD_SecF; cl14618 1105112000313 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 1105112000314 SLBB domain; Region: SLBB; pfam10531 1105112000315 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 1105112000316 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 1105112000317 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 1105112000318 Catalytic site [active] 1105112000319 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 1105112000320 ribonuclease III; Reviewed; Region: rnc; PRK00102 1105112000321 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 1105112000322 dimerization interface [polypeptide binding]; other site 1105112000323 active site 1105112000324 metal binding site [ion binding]; metal-binding site 1105112000325 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 1105112000326 dsRNA binding site [nucleotide binding]; other site 1105112000327 GTPase Era; Provisional; Region: era; PRK15494 1105112000328 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112000329 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 1105112000330 G1 box; other site 1105112000331 GTP/Mg2+ binding site [chemical binding]; other site 1105112000332 Switch I region; other site 1105112000333 G2 box; other site 1105112000334 Switch II region; other site 1105112000335 G3 box; other site 1105112000336 G4 box; other site 1105112000337 G5 box; other site 1105112000338 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 1105112000339 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 1105112000340 active site 1105112000341 putative DNA-binding cleft [nucleotide binding]; other site 1105112000342 dimer interface [polypeptide binding]; other site 1105112000343 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 1105112000344 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 1105112000345 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 1105112000346 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 1105112000347 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 1105112000348 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 1105112000349 Walker A motif; other site 1105112000350 Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflK; cd03404 1105112000351 HflK protein; Region: hflK; TIGR01933 1105112000352 FtsH protease regulator HflC; Provisional; Region: PRK11029 1105112000353 Band_7_HflC: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfC (High frequency of lysogenization C). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflC; cd03405 1105112000354 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 1105112000355 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 1105112000356 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 1105112000357 protein binding site [polypeptide binding]; other site 1105112000358 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 1105112000359 protein binding site [polypeptide binding]; other site 1105112000360 hypothetical protein; Validated; Region: PRK01415 1105112000361 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 1105112000362 active site residue [active] 1105112000363 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the...; Region: SQR_TypeC_SdhC; cd03499 1105112000364 Iron-sulfur protein interface; other site 1105112000365 proximal quinone binding site [chemical binding]; other site 1105112000366 SdhD (CybS) interface [polypeptide binding]; other site 1105112000367 proximal heme binding site [chemical binding]; other site 1105112000368 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory...; Region: SQR_TypeC_SdhD_like; cd03495 1105112000369 putative SdhC subunit interface [polypeptide binding]; other site 1105112000370 putative proximal heme binding site [chemical binding]; other site 1105112000371 putative Iron-sulfur protein interface [polypeptide binding]; other site 1105112000372 putative proximal quinone binding site; other site 1105112000373 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 1105112000374 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105112000375 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 1105112000376 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1105112000377 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 1105112000378 dimer interface [polypeptide binding]; other site 1105112000379 conserved gate region; other site 1105112000380 putative PBP binding loops; other site 1105112000381 ABC-ATPase subunit interface; other site 1105112000382 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 1105112000383 S17 interaction site [polypeptide binding]; other site 1105112000384 S8 interaction site; other site 1105112000385 16S rRNA interaction site [nucleotide binding]; other site 1105112000386 streptomycin interaction site [chemical binding]; other site 1105112000387 23S rRNA interaction site [nucleotide binding]; other site 1105112000388 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 1105112000389 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 1105112000390 elongation factor G; Reviewed; Region: PRK00007 1105112000391 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 1105112000392 G1 box; other site 1105112000393 putative GEF interaction site [polypeptide binding]; other site 1105112000394 GTP/Mg2+ binding site [chemical binding]; other site 1105112000395 Switch I region; other site 1105112000396 G2 box; other site 1105112000397 G3 box; other site 1105112000398 Switch II region; other site 1105112000399 G4 box; other site 1105112000400 G5 box; other site 1105112000401 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 1105112000402 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 1105112000403 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 1105112000404 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 1105112000405 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 1105112000406 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 1105112000407 putative homodimer interface [polypeptide binding]; other site 1105112000408 KOW motif; Region: KOW; cl00354 1105112000409 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 1105112000410 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 1105112000411 23S rRNA interface [nucleotide binding]; other site 1105112000412 putative thiostrepton binding site; other site 1105112000413 L7/L12 interface [polypeptide binding]; other site 1105112000414 L25 interface [polypeptide binding]; other site 1105112000415 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 1105112000416 mRNA/rRNA interface [nucleotide binding]; other site 1105112000417 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 1105112000418 23S rRNA interface [nucleotide binding]; other site 1105112000419 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 1105112000420 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 1105112000421 core dimer interface [polypeptide binding]; other site 1105112000422 peripheral dimer interface [polypeptide binding]; other site 1105112000423 L10 interface [polypeptide binding]; other site 1105112000424 L11 interface [polypeptide binding]; other site 1105112000425 putative EF-Tu interaction site [polypeptide binding]; other site 1105112000426 putative EF-G interaction site [polypeptide binding]; other site 1105112000427 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 1105112000428 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 1105112000429 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 1105112000430 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 1105112000431 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 1105112000432 RPB10 interaction site [polypeptide binding]; other site 1105112000433 RPB11 interaction site [polypeptide binding]; other site 1105112000434 RPB3 interaction site [polypeptide binding]; other site 1105112000435 RPB12 interaction site [polypeptide binding]; other site 1105112000436 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 1105112000437 RPB3 interaction site [polypeptide binding]; other site 1105112000438 RPB1 interaction site [polypeptide binding]; other site 1105112000439 RPB11 interaction site [polypeptide binding]; other site 1105112000440 RPB10 interaction site [polypeptide binding]; other site 1105112000441 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 1105112000442 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 1105112000443 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 1105112000444 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 1105112000445 DNA-directed RNA polymerase subunit beta'; Provisional; Region: rpoC2; PRK02597 1105112000446 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 1105112000447 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 1105112000448 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 1105112000449 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 1105112000450 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 1105112000451 DNA binding site [nucleotide binding] 1105112000452 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 1105112000453 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112000454 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 1105112000455 multifunctional aminopeptidase A; Provisional; Region: PRK00913 1105112000456 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 1105112000457 interface (dimer of trimers) [polypeptide binding]; other site 1105112000458 Substrate-binding/catalytic site; other site 1105112000459 Zn-binding sites [ion binding]; other site 1105112000460 ATPase MipZ; Region: MipZ; pfam09140 1105112000461 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 1105112000462 P-loop; other site 1105112000463 Magnesium ion binding site [ion binding]; other site 1105112000464 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 1105112000465 Magnesium ion binding site [ion binding]; other site 1105112000466 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 1105112000467 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 1105112000468 dimer interface [polypeptide binding]; other site 1105112000469 anticodon binding site; other site 1105112000470 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 1105112000471 homodimer interface [polypeptide binding]; other site 1105112000472 motif 1; other site 1105112000473 active site 1105112000474 motif 2; other site 1105112000475 GAD domain; Region: GAD; pfam02938 1105112000476 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 1105112000477 active site 1105112000478 motif 3; other site 1105112000479 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 1105112000480 dihydrodipicolinate reductase; Provisional; Region: PRK00048 1105112000481 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105112000482 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 1105112000483 Flavin Reductases; Region: FlaRed; cl00801 1105112000484 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1105112000485 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 1105112000486 substrate binding pocket [chemical binding]; other site 1105112000487 membrane-bound complex binding site; other site 1105112000488 hinge residues; other site 1105112000489 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 1105112000490 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 1105112000491 GatB domain; Region: GatB_Yqey; cl11497 1105112000492 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 1105112000493 Amidase; Region: Amidase; cl11426 1105112000494 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 1105112000495 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain superfamily; Region: NTP-PPase; cl16941 1105112000496 ribosome recycling factor; Reviewed; Region: frr; PRK00083 1105112000497 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 1105112000498 hinge region; other site 1105112000499 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 1105112000500 putative nucleotide binding site [chemical binding]; other site 1105112000501 uridine monophosphate binding site [chemical binding]; other site 1105112000502 homohexameric interface [polypeptide binding]; other site 1105112000503 Na+/H+ ion antiporter subunit; Region: MNHE; cl00807 1105112000504 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1105112000505 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 1105112000506 putative substrate translocation pore; other site 1105112000507 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 1105112000508 Protein of unknown function (DUF2674); Region: DUF2674; pfam10879 1105112000509 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 1105112000510 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 1105112000511 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 1105112000512 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 1105112000513 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 1105112000514 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 1105112000515 Surface antigen; Region: Bac_surface_Ag; cl03097 1105112000516 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 1105112000517 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 1105112000518 active site 1105112000519 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 1105112000520 protein binding site [polypeptide binding]; other site 1105112000521 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 1105112000522 putative substrate binding region [chemical binding]; other site 1105112000523 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 1105112000524 putative RNA binding site [nucleotide binding]; other site 1105112000525 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 1105112000526 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 1105112000527 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 1105112000528 putative coenzyme Q binding site [chemical binding]; other site 1105112000529 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112000530 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 1105112000531 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 1105112000532 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385; cl00611 1105112000533 RNA methyltransferase; Region: Methyltrans_RNA; pfam04452 1105112000534 Domain of unknown function (DUF378); Region: DUF378; cl00943 1105112000535 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105112000536 Protein export membrane protein; Region: SecD_SecF; cl14618 1105112000537 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 1105112000538 IHF dimer interface [polypeptide binding]; other site 1105112000539 IHF - DNA interface [nucleotide binding]; other site 1105112000540 DNA polymerase III subunit delta'; Validated; Region: PRK06581 1105112000541 signal recognition particle protein; Provisional; Region: PRK10867 1105112000542 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 1105112000543 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 1105112000544 P loop; other site 1105112000545 GTP binding site [chemical binding]; other site 1105112000546 Signal peptide binding domain; Region: SRP_SPB; pfam02978 1105112000547 potential frameshift: common BLAST hit: gi|51473374|ref|YP_067131.1| post-proline cleaving enzyme 1105112000548 potential frameshift: common BLAST hit: gi|15604049|ref|NP_220564.1| peptidase 1105112000549 potential frameshift: common BLAST hit: gi|67459496|ref|YP_247120.1| prolyl endopeptidase 1105112000550 coproporphyrinogen III oxidase; Provisional; Region: PRK06582 1105112000551 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 1105112000552 FeS/SAM binding site; other site 1105112000553 HemN C-terminal domain; Region: HemN_C; pfam06969 1105112000554 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; cl02529 1105112000555 potential frameshift: common BLAST hit: gi|157826898|ref|YP_001495962.1| cephalosporin hydroxylase 1105112000556 potential frameshift: common BLAST hit: gi|157826898|ref|YP_001495962.1| cephalosporin hydroxylase 1105112000557 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1105112000558 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 1105112000559 CutA1 divalent ion tolerance protein; Region: CutA1; cl00584 1105112000560 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 1105112000561 active site 1105112000562 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 1105112000563 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 1105112000564 E3 interaction surface; other site 1105112000565 lipoyl attachment site [posttranslational modification]; other site 1105112000566 e3 binding domain; Region: E3_binding; pfam02817 1105112000567 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 1105112000568 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 1105112000569 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 1105112000570 TPP-binding site [chemical binding]; other site 1105112000571 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 1105112000572 potential frameshift: common BLAST hit: gi|350273234|ref|YP_004884547.1| thermostable carboxypeptidase 1105112000573 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 1105112000574 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 1105112000575 Walker A/P-loop; other site 1105112000576 ATP binding site [chemical binding]; other site 1105112000577 Q-loop/lid; other site 1105112000578 Allexivirus 40kDa protein; Region: Allexi_40kDa; pfam05549 1105112000579 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 1105112000580 ABC transporter signature motif; other site 1105112000581 Walker B; other site 1105112000582 D-loop; other site 1105112000583 H-loop/switch region; other site 1105112000584 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 1105112000585 Tetratricopeptide repeat; Region: TPR_6; pfam13174 1105112000586 ChaB; Region: ChaB; cl01887 1105112000587 chaperone protein DnaJ; Provisional; Region: PRK14300 1105112000588 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 1105112000589 HSP70 interaction site [polypeptide binding]; other site 1105112000590 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 1105112000591 substrate binding site [polypeptide binding]; other site 1105112000592 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 1105112000593 Zn binding sites [ion binding]; other site 1105112000594 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 1105112000595 dimer interface [polypeptide binding]; other site 1105112000596 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 1105112000597 FGGY family of carbohydrate kinases; Region: FGGY; cl08364 1105112000598 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 1105112000599 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 1105112000600 Lipopolysaccharide-assembly; Region: LptE; cl01125 1105112000601 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 1105112000602 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 1105112000603 diiron binding motif [ion binding]; other site 1105112000604 Cytochrome c oxidase subunit III. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_III; cd01665 1105112000605 Subunit III/VIIa interface [polypeptide binding]; other site 1105112000606 Phospholipid binding site [chemical binding]; other site 1105112000607 Subunit I/III interface [polypeptide binding]; other site 1105112000608 Subunit III/VIb interface [polypeptide binding]; other site 1105112000609 Subunit III/VIa interface; other site 1105112000610 Subunit III/Vb interface [polypeptide binding]; other site 1105112000611 TrbC/VIRB2 family; Region: TrbC; cl01583 1105112000612 zinc-ribbon domain; Region: zinc_ribbon_5; cl11777 1105112000613 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 1105112000614 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA; Region: LbH_THP_succinylT; cd03350 1105112000615 trimer interface [polypeptide binding]; other site 1105112000616 active site 1105112000617 substrate binding site [chemical binding]; other site 1105112000618 CoA binding site [chemical binding]; other site 1105112000619 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 1105112000620 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 1105112000621 Ligand Binding Site [chemical binding]; other site 1105112000622 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 1105112000623 NMT1-like family; Region: NMT1_2; cl15260 1105112000624 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 1105112000625 catalytic loop [active] 1105112000626 iron binding site [ion binding]; other site 1105112000627 chaperone protein HscA; Provisional; Region: hscA; PRK01433 1105112000628 co-chaperone HscB; Provisional; Region: hscB; PRK01356 1105112000629 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 1105112000630 HSP70 interaction site [polypeptide binding]; other site 1105112000631 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 1105112000632 RNA/DNA hybrid binding site [nucleotide binding]; other site 1105112000633 active site 1105112000634 excinuclease ABC subunit B; Provisional; Region: PRK05298 1105112000635 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 1105112000636 ATP binding site [chemical binding]; other site 1105112000637 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 1105112000638 nucleotide binding region [chemical binding]; other site 1105112000639 ATP-binding site [chemical binding]; other site 1105112000640 Ultra-violet resistance protein B; Region: UvrB; pfam12344 1105112000641 UvrB/uvrC motif; Region: UVR; pfam02151 1105112000642 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 1105112000643 GSH binding site [chemical binding]; other site 1105112000644 catalytic residues [active] 1105112000645 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 1105112000646 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 1105112000647 ATM1 is an ABC transporter that is expressed in the mitochondria. Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to...; Region: ABCC_ATM1_transporter; cd03253 1105112000648 Walker A/P-loop; other site 1105112000649 ATP binding site [chemical binding]; other site 1105112000650 Q-loop/lid; other site 1105112000651 ABC transporter signature motif; other site 1105112000652 Walker B; other site 1105112000653 D-loop; other site 1105112000654 H-loop/switch region; other site 1105112000655 DNA gyrase subunit A; Validated; Region: PRK05560 1105112000656 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 1105112000657 CAP-like domain; other site 1105112000658 active site 1105112000659 primary dimer interface [polypeptide binding]; other site 1105112000660 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105112000661 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105112000662 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105112000663 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105112000664 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105112000665 Iron-sulphur cluster assembly; Region: Fe-S_assembly; cl01123 1105112000666 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 1105112000667 active site 1105112000668 catalytic residues [active] 1105112000669 metal binding site [ion binding]; metal-binding site 1105112000670 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 1105112000671 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 1105112000672 putative active site [active] 1105112000673 substrate binding site [chemical binding]; other site 1105112000674 putative cosubstrate binding site; other site 1105112000675 catalytic site [active] 1105112000676 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 1105112000677 substrate binding site [chemical binding]; other site 1105112000678 potential frameshift: common BLAST hit: gi|157826977|ref|YP_001496041.1| capsular polysaccharide biosynthesis protein 1105112000679 Predicted ATPase [General function prediction only]; Region: COG1485 1105112000680 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 1105112000681 Walker A motif; other site 1105112000682 ATP binding site [chemical binding]; other site 1105112000683 Walker B motif; other site 1105112000684 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 1105112000685 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 1105112000686 potential frameshift: common BLAST hit: gi|350273268|ref|YP_004884581.1| ankyrin 1105112000687 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1105112000688 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 1105112000689 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105112000690 Walker A/P-loop; other site 1105112000691 ATP binding site [chemical binding]; other site 1105112000692 Q-loop/lid; other site 1105112000693 ABC transporter signature motif; other site 1105112000694 Walker B; other site 1105112000695 D-loop; other site 1105112000696 H-loop/switch region; other site 1105112000697 Protein of unknown function (DUF2671); Region: DUF2671; pfam10877 1105112000698 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 1105112000699 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 1105112000700 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 1105112000701 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 1105112000702 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 1105112000703 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 1105112000704 putative metal binding site; other site 1105112000705 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1105112000706 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1105112000707 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1105112000708 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 1105112000709 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 1105112000710 ATP binding site [chemical binding]; other site 1105112000711 active site 1105112000712 substrate binding site [chemical binding]; other site 1105112000713 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 1105112000714 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 1105112000715 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 1105112000716 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 1105112000717 active site 1105112000718 dimer interface [polypeptide binding]; other site 1105112000719 motif 1; other site 1105112000720 motif 2; other site 1105112000721 motif 3; other site 1105112000722 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 1105112000723 anticodon binding site; other site 1105112000724 DDE superfamily endonuclease; Region: DDE_4; cl15789 1105112000725 DDE superfamily endonuclease; Region: DDE_4; cl15789 1105112000726 BolA-like protein; Region: BolA; cl00386 1105112000727 Oligomerisation domain; Region: Oligomerisation; cl00519 1105112000728 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 1105112000729 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 1105112000730 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105112000731 Bacterial SH3 domain; Region: SH3_3; cl02551 1105112000732 Bacterial SH3 domain; Region: SH3_3; cl02551 1105112000733 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112000734 potential frameshift: common BLAST hit: gi|67459672|ref|YP_247296.1| nucleotidyltransferase/HEPN domain-containing protein 1105112000735 potential frameshift: common BLAST hit: gi|91204878|ref|YP_537233.1| nucleotidyltransferase 1105112000736 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 1105112000737 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1105112000738 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 1105112000739 FeS/SAM binding site; other site 1105112000740 TRAM domain; Region: TRAM; cl01282 1105112000741 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 1105112000742 Transglycosylase; Region: Transgly; cl07896 1105112000743 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 1105112000744 potential frameshift: common BLAST hit: gi|67459667|ref|YP_247291.1| Beta-lactamase class D 1105112000745 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 1105112000746 dinuclear metal binding motif [ion binding]; other site 1105112000747 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 1105112000748 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105112000749 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105112000750 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1105112000751 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 1105112000752 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 1105112000753 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 1105112000754 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 1105112000755 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 1105112000756 beta subunit interaction interface [polypeptide binding]; other site 1105112000757 Walker A motif; other site 1105112000758 ATP binding site [chemical binding]; other site 1105112000759 Walker B motif; other site 1105112000760 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1105112000761 ATP synthase; Region: ATP-synt; cl00365 1105112000762 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 1105112000763 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 1105112000764 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 1105112000765 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 1105112000766 alpha subunit interaction interface [polypeptide binding]; other site 1105112000767 Walker A motif; other site 1105112000768 ATP binding site [chemical binding]; other site 1105112000769 Walker B motif; other site 1105112000770 inhibitor binding site; inhibition site 1105112000771 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1105112000772 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK01474 1105112000773 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 1105112000774 aconitate hydratase; Validated; Region: PRK09277 1105112000775 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 1105112000776 substrate binding site [chemical binding]; other site 1105112000777 ligand binding site [chemical binding]; other site 1105112000778 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 1105112000779 substrate binding site [chemical binding]; other site 1105112000780 Predicted membrane protein [Function unknown]; Region: COG3671 1105112000781 NADH dehydrogenase subunit G; Validated; Region: PRK09130 1105112000782 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 1105112000783 catalytic loop [active] 1105112000784 iron binding site [ion binding]; other site 1105112000785 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 1105112000786 MopB_Res_Cmplx1_Nad11: The second domain of the Nad11/75-kDa subunit of the NADH-quinone oxidoreductase/respiratory complex I/NADH dehydrogenase-1(NDH-1) of eukaryotes and the Nqo3/G subunit of alphaproteobacteria NDH-1. The NADH-quinone oxidoreductase...; Region: MopB_Res-Cmplx1_Nad11; cd02773 1105112000787 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 1105112000788 NADH dehydrogenase; Region: NADHdh; cl00469 1105112000789 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 1105112000790 4Fe-4S binding domain; Region: Fer4; cl02805 1105112000791 4Fe-4S binding domain; Region: Fer4; cl02805 1105112000792 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13541 1105112000793 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105112000794 Walker A/P-loop; other site 1105112000795 ATP binding site [chemical binding]; other site 1105112000796 Q-loop/lid; other site 1105112000797 ABC transporter signature motif; other site 1105112000798 Walker B; other site 1105112000799 D-loop; other site 1105112000800 H-loop/switch region; other site 1105112000801 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 1105112000802 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 1105112000803 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 1105112000804 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 1105112000805 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 1105112000806 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 1105112000807 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 1105112000808 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 1105112000809 Predicted transcriptional regulator [Transcription]; Region: COG2944 1105112000810 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 1105112000811 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 1105112000812 S-adenosylmethionine binding site [chemical binding]; other site 1105112000813 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 1105112000814 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 1105112000815 Integral membrane protein TerC family; Region: TerC; cl10468 1105112000816 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 1105112000817 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1105112000818 seryl-tRNA synthetase; Provisional; Region: PRK05431 1105112000819 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 1105112000820 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 1105112000821 dimer interface [polypeptide binding]; other site 1105112000822 active site 1105112000823 motif 1; other site 1105112000824 motif 2; other site 1105112000825 motif 3; other site 1105112000826 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 1105112000827 AmpG-like permease; Region: 2A0125; TIGR00901 1105112000828 muropeptide transporter; Validated; Region: ampG; PRK11010 1105112000829 Protein of unknown function; Region: DUF3971; pfam13116 1105112000830 AsmA-like C-terminal region; Region: AsmA_2; cl15864 1105112000831 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 1105112000832 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 1105112000833 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105112000834 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 1105112000835 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 1105112000836 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 1105112000837 generic binding surface I; other site 1105112000838 generic binding surface II; other site 1105112000839 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 1105112000840 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 1105112000841 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 1105112000842 DNA polymerase I; Provisional; Region: PRK05755 1105112000843 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 1105112000844 active site 1105112000845 metal binding site 1 [ion binding]; metal-binding site 1105112000846 putative 5' ssDNA interaction site; other site 1105112000847 metal binding site 3; metal-binding site 1105112000848 metal binding site 2 [ion binding]; metal-binding site 1105112000849 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 1105112000850 putative DNA binding site [nucleotide binding]; other site 1105112000851 putative metal binding site [ion binding]; other site 1105112000852 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 1105112000853 active site 1105112000854 substrate binding site [chemical binding]; other site 1105112000855 catalytic site [active] 1105112000856 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 1105112000857 active site 1105112000858 DNA binding site [nucleotide binding] 1105112000859 catalytic site [active] 1105112000860 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 1105112000861 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 1105112000862 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 1105112000863 P loop; other site 1105112000864 GTP binding site [chemical binding]; other site 1105112000865 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 1105112000866 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 1105112000867 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 1105112000868 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 1105112000869 dimer interface [polypeptide binding]; other site 1105112000870 active site 1105112000871 CoA binding pocket [chemical binding]; other site 1105112000872 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1105112000873 ligand binding site [chemical binding]; other site 1105112000874 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1105112000875 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 1105112000876 rod shape-determining protein MreB; Provisional; Region: PRK13927 1105112000877 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 1105112000878 ATP binding site [chemical binding]; other site 1105112000879 profilin binding site; other site 1105112000880 rod shape-determining protein MreC; Provisional; Region: PRK13922 1105112000881 rod shape-determining protein MreC; Region: MreC; pfam04085 1105112000882 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 1105112000883 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112000884 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 1105112000885 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 1105112000886 catalytic site [active] 1105112000887 G-X2-G-X-G-K; other site 1105112000888 potential frameshift: common BLAST hit: gi|238650596|ref|YP_002916448.1| ATPase 1105112000889 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1105112000890 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 1105112000891 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 1105112000892 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 1105112000893 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 1105112000894 dimer interface [polypeptide binding]; other site 1105112000895 active site 1105112000896 Phosphopantetheine attachment site; Region: PP-binding; cl09936 1105112000897 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 1105112000898 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 1105112000899 NAD(P) binding site [chemical binding]; other site 1105112000900 homotetramer interface [polypeptide binding]; other site 1105112000901 homodimer interface [polypeptide binding]; other site 1105112000902 active site 1105112000903 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 1105112000904 protein RecA; Region: tigrfam_recA; TIGR02012 1105112000905 hexamer interface [polypeptide binding]; other site 1105112000906 Walker A motif; other site 1105112000907 ATP binding site [chemical binding]; other site 1105112000908 Walker B motif; other site 1105112000909 potential frameshift: common BLAST hit: gi|341584339|ref|YP_004764830.1| putative multidrug resistance protein 1105112000910 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1105112000911 methyl viologen resistance protein SmvA; Provisional; Region: PRK14995 1105112000912 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 1105112000913 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 1105112000914 trmE is a tRNA modification GTPase; Region: trmE; cd04164 1105112000915 G1 box; other site 1105112000916 GTP/Mg2+ binding site [chemical binding]; other site 1105112000917 Switch I region; other site 1105112000918 G2 box; other site 1105112000919 Switch II region; other site 1105112000920 G3 box; other site 1105112000921 G4 box; other site 1105112000922 G5 box; other site 1105112000923 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 1105112000924 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]; Region: COG2902 1105112000925 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105112000926 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 1105112000927 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 1105112000928 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112000929 Cell division protein ZapA; Region: ZapA; cl01146 1105112000930 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 1105112000931 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105112000932 putative substrate translocation pore; other site 1105112000933 Peptidase M55, D-aminopeptidase dipeptide-binding protein family; Region: DAP_dppA; cl01007 1105112000934 aspartate kinase; Reviewed; Region: PRK06635 1105112000935 AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive...; Region: AAK_AKii-LysC-BS; cd04261 1105112000936 putative nucleotide binding site [chemical binding]; other site 1105112000937 putative catalytic residues [active] 1105112000938 putative Mg ion binding site [ion binding]; other site 1105112000939 putative aspartate binding site [chemical binding]; other site 1105112000940 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AKii-LysC-BS-like_2; cd04936 1105112000941 putative allosteric regulatory residue; other site 1105112000942 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 1105112000943 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 1105112000944 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 1105112000945 tetramer interfaces [polypeptide binding]; other site 1105112000946 binuclear metal-binding site [ion binding]; other site 1105112000947 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 1105112000948 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 1105112000949 putative ligand binding site [chemical binding]; other site 1105112000950 Predicted methyltransferases [General function prediction only]; Region: COG0313 1105112000951 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 1105112000952 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105112000953 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 1105112000954 Entericidin EcnA/B family; Region: Entericidin; cl02322 1105112000955 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 1105112000956 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1105112000957 minor groove reading motif; other site 1105112000958 helix-hairpin-helix signature motif; other site 1105112000959 substrate binding pocket [chemical binding]; other site 1105112000960 active site 1105112000961 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 1105112000962 Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain...; Region: GRX_PICOT_like; cd03028 1105112000963 putative GSH binding site [chemical binding]; other site 1105112000964 catalytic residues [active] 1105112000965 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 1105112000966 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 1105112000967 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 1105112000968 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 1105112000969 dimer interface [polypeptide binding]; other site 1105112000970 active site 1105112000971 glycine-pyridoxal phosphate binding site [chemical binding]; other site 1105112000972 folate binding site [chemical binding]; other site 1105112000973 lipoyl synthase; Provisional; Region: PRK05481 1105112000974 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 1105112000975 FeS/SAM binding site; other site 1105112000976 PemK-like protein; Region: PemK; cl00995 1105112000977 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 1105112000978 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 1105112000979 Transporter associated domain; Region: CorC_HlyC; cl08393 1105112000980 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity. They also contain a...; Region: Nudix_Hydrolase_1; cd03674 1105112000981 nudix motif; other site 1105112000982 ATP/ADP translocase [Energy production and conversion]; Region: COG3202; cl03940 1105112000983 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105112000984 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 1105112000985 potential frameshift: common BLAST hit: gi|350273857|ref|YP_004885170.1| acetyl-CoA acetyltransferase 1105112000986 potential frameshift: common BLAST hit: gi|350273857|ref|YP_004885170.1| acetyl-CoA acetyltransferase 1105112000987 potential frameshift: common BLAST hit: gi|350273857|ref|YP_004885170.1| acetyl-CoA acetyltransferase 1105112000988 potential frameshift: common BLAST hit: gi|341584292|ref|YP_004764783.1| superfamily I DNA/RNA helicase 1105112000989 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105112000990 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105112000991 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105112000992 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105112000993 Acyl transferase domain; Region: Acyl_transf_1; cl08282 1105112000994 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 1105112000995 double-strand break repair helicase AddA, alphaproteobacterial type; Region: addA_alphas; TIGR02784 1105112000996 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105112000997 Family description; Region: UvrD_C_2; cl15862 1105112000998 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cd06662 1105112000999 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 1105112001000 DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; Region: DNA_pol_III_epsilon_Ecoli_like; cd06131 1105112001001 active site 1105112001002 catalytic site [active] 1105112001003 substrate binding site [chemical binding]; other site 1105112001004 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 1105112001005 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 1105112001006 CoA-binding site [chemical binding]; other site 1105112001007 ATP-binding [chemical binding]; other site 1105112001008 Protein of unknown function (DUF1009); Region: DUF1009; cl09182 1105112001009 Stringent starvation protein B; Region: SspB; cl01120 1105112001010 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 1105112001011 RNA/DNA hybrid binding site [nucleotide binding]; other site 1105112001012 active site 1105112001013 NADH ubiquinone oxidoreductase subunit NDUFA12; Region: NDUFA12; cl01534 1105112001014 mce related protein; Region: MCE; pfam02470 1105112001015 potential frameshift: common BLAST hit: gi|67458578|ref|YP_246202.1| proline/betaine transporter 1105112001016 potential frameshift: common BLAST hit: gi|67458578|ref|YP_246202.1| proline/betaine transporter 1105112001017 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 1105112001018 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105112001019 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 1105112001020 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 1105112001021 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 1105112001022 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 1105112001023 NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction...; Region: LIGANc; cd00114 1105112001024 nucleotide binding pocket [chemical binding]; other site 1105112001025 K-X-D-G motif; other site 1105112001026 catalytic site [active] 1105112001027 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 1105112001028 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 1105112001029 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 1105112001030 Dimer interface [polypeptide binding]; other site 1105112001031 BRCT sequence motif; other site 1105112001032 potential frameshift: common BLAST hit: gi|238650377|ref|YP_002916229.1| protein involved in external DNA uptake 1105112001033 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105112001034 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 1105112001035 tetraacyldisaccharide 4'-kinase; Region: lpxK; TIGR00682 1105112001036 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 1105112001037 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 1105112001038 putative acyl-acceptor binding pocket; other site 1105112001039 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 1105112001040 catalytic triad [active] 1105112001041 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 1105112001042 IHF - DNA interface [nucleotide binding]; other site 1105112001043 IHF dimer interface [polypeptide binding]; other site 1105112001044 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 1105112001045 DNA binding residues [nucleotide binding] 1105112001046 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 1105112001047 potential frameshift: common BLAST hit: gi|157964855|ref|YP_001499679.1| guanosine polyphosphate pyrophosphohydrolase/synthetase 1105112001048 potential frameshift: common BLAST hit: gi|157964854|ref|YP_001499678.1| outer membrane protein OmpB 1105112001049 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 1105112001050 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 1105112001051 Domain of unknown function DUF21; Region: DUF21; pfam01595 1105112001052 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 1105112001053 Transporter associated domain; Region: CorC_HlyC; cl08393 1105112001054 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1105112001055 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 1105112001056 Walker A/P-loop; other site 1105112001057 ATP binding site [chemical binding]; other site 1105112001058 Q-loop/lid; other site 1105112001059 ABC transporter signature motif; other site 1105112001060 Walker B; other site 1105112001061 D-loop; other site 1105112001062 H-loop/switch region; other site 1105112001063 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 1105112001064 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1105112001065 FtsX-like permease family; Region: FtsX; cl15850 1105112001066 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 1105112001067 putative substrate translocation pore; other site 1105112001068 Protein of unknown function (DUF2673); Region: DUF2673; pfam10880 1105112001069 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 1105112001070 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 1105112001071 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105112001072 Walker A/P-loop; other site 1105112001073 ATP binding site [chemical binding]; other site 1105112001074 Q-loop/lid; other site 1105112001075 ABC transporter signature motif; other site 1105112001076 Walker B; other site 1105112001077 D-loop; other site 1105112001078 H-loop/switch region; other site 1105112001079 Uncharacterized protein family (UPF0150); Region: UPF0150; cl00691 1105112001080 HicB family; Region: HicB; pfam05534 1105112001081 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 1105112001082 Ligand Binding Site [chemical binding]; other site 1105112001083 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 1105112001084 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 1105112001085 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 1105112001086 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 1105112001087 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 1105112001088 Walker A motif; other site 1105112001089 ATP binding site [chemical binding]; other site 1105112001090 Walker B motif; other site 1105112001091 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 1105112001092 Predicted integral membrane protein (DUF2269); Region: DUF2269; cl02335 1105112001093 potential frameshift: common BLAST hit: gi|157826924|ref|YP_001495988.1| glycosyltransferase 1105112001094 RmuC family; Region: RmuC; pfam02646 1105112001095 potential frameshift: common BLAST hit: gi|67458618|ref|YP_246242.1| ATPase 1105112001096 potential frameshift: common BLAST hit: gi|67458618|ref|YP_246242.1| ATPase 1105112001097 LicD family; Region: LicD; cl01378 1105112001098 LicD family; Region: LicD; cl01378 1105112001099 valyl-tRNA synthetase; Reviewed; Region: valS; PRK13208 1105112001100 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105112001101 active site 1105112001102 HIGH motif; other site 1105112001103 nucleotide binding site [chemical binding]; other site 1105112001104 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1105112001105 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105112001106 active site 1105112001107 KMSKS motif; other site 1105112001108 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 1105112001109 tRNA binding surface [nucleotide binding]; other site 1105112001110 anticodon binding site; other site 1105112001111 potential frameshift: common BLAST hit: gi|350273815|ref|YP_004885128.1| transposase 1105112001112 UbiA prenyltransferase family; Region: UbiA; cl00337 1105112001113 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105112001114 thymidylate kinase; Validated; Region: tmk; PRK00698 1105112001115 Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step...; Region: TMPK; cd01672 1105112001116 TMP-binding site; other site 1105112001117 ATP-binding site [chemical binding]; other site 1105112001118 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 1105112001119 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 1105112001120 HIGH motif; other site 1105112001121 active site 1105112001122 KMSKS motif; other site 1105112001123 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 1105112001124 tRNA binding surface [nucleotide binding]; other site 1105112001125 anticodon binding site; other site 1105112001126 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 1105112001127 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 1105112001128 active site 1105112001129 potential frameshift: common BLAST hit: gi|157964831|ref|YP_001499655.1| Poly-beta-hydroxyalkanoate depolymerase 1105112001130 potential frameshift: common BLAST hit: gi|157964831|ref|YP_001499655.1| Poly-beta-hydroxyalkanoate depolymerase 1105112001131 potential frameshift: common BLAST hit: gi|67458633|ref|YP_246257.1| mannose-1-phosphate guanylyltransferase 1105112001132 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112001133 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105112001134 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 1105112001135 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 1105112001136 DNA binding site [nucleotide binding] 1105112001137 catalytic residue [active] 1105112001138 H2TH interface [polypeptide binding]; other site 1105112001139 putative catalytic residues [active] 1105112001140 turnover-facilitating residue; other site 1105112001141 intercalation triad [nucleotide binding]; other site 1105112001142 8OG recognition residue [nucleotide binding]; other site 1105112001143 putative reading head residues; other site 1105112001144 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 1105112001145 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 1105112001146 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 1105112001147 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 1105112001148 S-adenosylmethionine binding site [chemical binding]; other site 1105112001149 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 1105112001150 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 1105112001151 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs); Region: APH_ChoK_like; cd05120 1105112001152 active site 1105112001153 ATP binding site [chemical binding]; other site 1105112001154 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 1105112001155 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 1105112001156 GTP-binding protein Der; Reviewed; Region: PRK00093 1105112001157 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 1105112001158 G1 box; other site 1105112001159 GTP/Mg2+ binding site [chemical binding]; other site 1105112001160 Switch I region; other site 1105112001161 G2 box; other site 1105112001162 Switch II region; other site 1105112001163 G3 box; other site 1105112001164 G4 box; other site 1105112001165 G5 box; other site 1105112001166 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 1105112001167 G1 box; other site 1105112001168 GTP/Mg2+ binding site [chemical binding]; other site 1105112001169 Switch I region; other site 1105112001170 G2 box; other site 1105112001171 G3 box; other site 1105112001172 Switch II region; other site 1105112001173 G4 box; other site 1105112001174 G5 box; other site 1105112001175 PQ loop repeat; Region: PQ-loop; cl12056 1105112001176 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 1105112001177 putative catalytic site [active] 1105112001178 putative phosphate binding site [ion binding]; other site 1105112001179 active site 1105112001180 metal binding site A [ion binding]; metal-binding site 1105112001181 DNA binding site [nucleotide binding] 1105112001182 putative AP binding site [nucleotide binding]; other site 1105112001183 putative metal binding site B [ion binding]; other site 1105112001184 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 1105112001185 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 1105112001186 generic binding surface II; other site 1105112001187 generic binding surface I; other site 1105112001188 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 1105112001189 Organic solvent tolerance protein; Region: OstA_C; pfam04453 1105112001190 SurA N-terminal domain; Region: SurA_N_3; cl07813 1105112001191 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 1105112001192 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 1105112001193 S-adenosylmethionine binding site [chemical binding]; other site 1105112001194 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein; Region: CSP_CDS; cd04458 1105112001195 DNA-binding site [nucleotide binding]; DNA binding site 1105112001196 RNA-binding motif; other site 1105112001197 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 1105112001198 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 1105112001199 ATP binding site [chemical binding]; other site 1105112001200 Mg++ binding site [ion binding]; other site 1105112001201 motif III; other site 1105112001202 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 1105112001203 nucleotide binding region [chemical binding]; other site 1105112001204 ATP-binding site [chemical binding]; other site 1105112001205 muropeptide transporter; Validated; Region: ampG; PRK11010 1105112001206 AmpG-like permease; Region: 2A0125; TIGR00901 1105112001207 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; cl07364 1105112001208 NifU-like domain; Region: NifU; cl00484 1105112001209 Protease Inhibitor Ecotin; homodimeric protease inhibitor; Region: Ecotin; cl00178 1105112001210 primary substrate binding site; other site 1105112001211 inhibition loop; other site 1105112001212 cell division protein FtsZ; Validated; Region: PRK09330 1105112001213 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 1105112001214 nucleotide binding site [chemical binding]; other site 1105112001215 SulA interaction site; other site 1105112001216 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 1105112001217 putative active site [active] 1105112001218 homotetrameric interface [polypeptide binding]; other site 1105112001219 metal binding site [ion binding]; metal-binding site 1105112001220 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 1105112001221 fumarate hydratase; Reviewed; Region: fumC; PRK00485 1105112001222 Class II fumarases; Region: Fumarase_classII; cd01362 1105112001223 active site 1105112001224 tetramer interface [polypeptide binding]; other site 1105112001225 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 1105112001226 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 1105112001227 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 1105112001228 elongation factor Tu; Reviewed; Region: PRK00049 1105112001229 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 1105112001230 G1 box; other site 1105112001231 GEF interaction site [polypeptide binding]; other site 1105112001232 GTP/Mg2+ binding site [chemical binding]; other site 1105112001233 Switch I region; other site 1105112001234 G2 box; other site 1105112001235 G3 box; other site 1105112001236 Switch II region; other site 1105112001237 G4 box; other site 1105112001238 G5 box; other site 1105112001239 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 1105112001240 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 1105112001241 Antibiotic Binding Site [chemical binding]; other site 1105112001242 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 1105112001243 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 1105112001244 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 1105112001245 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 1105112001246 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 1105112001247 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 1105112001248 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 1105112001249 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 1105112001250 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 1105112001251 putative translocon binding site; other site 1105112001252 protein-rRNA interface [nucleotide binding]; other site 1105112001253 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 1105112001254 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 1105112001255 G-X-X-G motif; other site 1105112001256 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 1105112001257 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 1105112001258 23S rRNA interface [nucleotide binding]; other site 1105112001259 5S rRNA interface [nucleotide binding]; other site 1105112001260 putative antibiotic binding site [chemical binding]; other site 1105112001261 L25 interface [polypeptide binding]; other site 1105112001262 L27 interface [polypeptide binding]; other site 1105112001263 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; cl09943 1105112001264 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 1105112001265 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 1105112001266 KOW motif; Region: KOW; cl00354 1105112001267 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 1105112001268 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 1105112001269 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 1105112001270 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 1105112001271 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 1105112001272 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 1105112001273 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 1105112001274 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1105112001275 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1105112001276 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 1105112001277 5S rRNA interface [nucleotide binding]; other site 1105112001278 23S rRNA interface [nucleotide binding]; other site 1105112001279 L5 interface [polypeptide binding]; other site 1105112001280 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 1105112001281 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 1105112001282 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 1105112001283 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 1105112001284 23S rRNA binding site [nucleotide binding]; other site 1105112001285 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 1105112001286 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 1105112001287 SecY translocase; Region: SecY; pfam00344 1105112001288 adenylate kinase; Reviewed; Region: adk; PRK00279 1105112001289 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 1105112001290 AMP-binding site [chemical binding]; other site 1105112001291 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 1105112001292 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 1105112001293 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 1105112001294 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 1105112001295 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 1105112001296 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 1105112001297 alphaNTD - beta interaction site [polypeptide binding]; other site 1105112001298 alphaNTD homodimer interface [polypeptide binding]; other site 1105112001299 alphaNTD - beta' interaction site [polypeptide binding]; other site 1105112001300 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 1105112001301 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 1105112001302 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 1105112001303 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105112001304 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105112001305 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105112001306 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 1105112001307 Domain of unknown function DUF20; Region: UPF0118; pfam01594 1105112001308 Clusterin-associated protein-1; Region: Cluap1; pfam10234 1105112001309 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 1105112001310 dimer interface [polypeptide binding]; other site 1105112001311 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 1105112001312 Ribonuclease PH; Region: RNase_PH_bact; cd11362 1105112001313 hexamer interface [polypeptide binding]; other site 1105112001314 active site 1105112001315 potential frameshift: common BLAST hit: gi|67458799|ref|YP_246423.1| glycosyltransferase 1105112001316 potential frameshift: common BLAST hit: gi|67458799|ref|YP_246423.1| glycosyltransferase 1105112001317 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 1105112001318 oligomerisation interface [polypeptide binding]; other site 1105112001319 mobile loop; other site 1105112001320 roof hairpin; other site 1105112001321 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 1105112001322 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 1105112001323 ring oligomerisation interface [polypeptide binding]; other site 1105112001324 ATP/Mg binding site [chemical binding]; other site 1105112001325 stacking interactions; other site 1105112001326 hinge regions; other site 1105112001327 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 1105112001328 synthetase active site [active] 1105112001329 NTP binding site [chemical binding]; other site 1105112001330 metal binding site [ion binding]; metal-binding site 1105112001331 potential frameshift: common BLAST hit: gi|157964772|ref|YP_001499596.1| guanosine polyphosphate pyrophosphohydrolase/synthetase 1105112001332 potential frameshift: common BLAST hit: gi|157828820|ref|YP_001495062.1| chaperonin GroEL 1105112001333 Invasion associated locus B (IalB) protein; Region: IalB; cl02207 1105112001334 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 1105112001335 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105112001336 HIGH motif; other site 1105112001337 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105112001338 active site 1105112001339 KMSKS motif; other site 1105112001340 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112001341 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 1105112001342 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112001343 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 1105112001344 S-adenosylmethionine binding site [chemical binding]; other site 1105112001345 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; cl00462 1105112001346 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 1105112001347 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 1105112001348 putative substrate translocation pore; other site 1105112001349 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1105112001350 putative acyl-acceptor binding pocket; other site 1105112001351 AMP-binding enzyme; Region: AMP-binding; cl15778 1105112001352 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 1105112001353 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 1105112001354 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 1105112001355 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 1105112001356 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1105112001357 ATP-grasp domain; Region: ATP-grasp_4; cl03087 1105112001358 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 1105112001359 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 1105112001360 carboxyltransferase (CT) interaction site; other site 1105112001361 biotinylation site [posttranslational modification]; other site 1105112001362 TPR repeat; Region: TPR_11; pfam13414 1105112001363 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 1105112001364 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1105112001365 HIGH motif; other site 1105112001366 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1105112001367 active site 1105112001368 KMSKS motif; other site 1105112001369 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 1105112001370 tRNA binding surface [nucleotide binding]; other site 1105112001371 anticodon binding site; other site 1105112001372 Uncharacterized conserved protein [Function unknown]; Region: COG5590 1105112001373 Helix-turn-helix domains; Region: HTH; cl00088 1105112001374 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 1105112001375 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 1105112001376 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1105112001377 dimerization interface [polypeptide binding]; other site 1105112001378 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 1105112001379 dimer interface [polypeptide binding]; other site 1105112001380 phosphorylation site [posttranslational modification] 1105112001381 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 1105112001382 ATP binding site [chemical binding]; other site 1105112001383 Mg2+ binding site [ion binding]; other site 1105112001384 G-X-G motif; other site 1105112001385 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 1105112001386 potential frameshift: common BLAST hit: gi|15892870|ref|NP_360584.1| aminoglycoside 3-N-acetyltransferase 1105112001387 DDE superfamily endonuclease; Region: DDE_4; cl15789 1105112001388 DDE superfamily endonuclease; Region: DDE_4; cl15789 1105112001389 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 1105112001390 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 1105112001391 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105112001392 Ribonuclease P; Region: Ribonuclease_P; cl00457 1105112001393 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 1105112001394 ribosomal protein L20; Region: rpl20; CHL00068 1105112001395 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 1105112001396 23S rRNA binding site [nucleotide binding]; other site 1105112001397 L21 binding site [polypeptide binding]; other site 1105112001398 L13 binding site [polypeptide binding]; other site 1105112001399 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 1105112001400 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 1105112001401 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 1105112001402 FeS/SAM binding site; other site 1105112001403 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 1105112001404 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 1105112001405 5S rRNA interface [nucleotide binding]; other site 1105112001406 CTC domain interface [polypeptide binding]; other site 1105112001407 L16 interface [polypeptide binding]; other site 1105112001408 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 1105112001409 putative active site [active] 1105112001410 catalytic residue [active] 1105112001411 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 1105112001412 GTP-binding protein YchF; Reviewed; Region: PRK09601 1105112001413 YchF GTPase; Region: YchF; cd01900 1105112001414 G1 box; other site 1105112001415 GTP/Mg2+ binding site [chemical binding]; other site 1105112001416 Switch I region; other site 1105112001417 G2 box; other site 1105112001418 Switch II region; other site 1105112001419 G3 box; other site 1105112001420 G4 box; other site 1105112001421 G5 box; other site 1105112001422 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 1105112001423 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 1105112001424 metal binding triad [ion binding]; metal-binding site 1105112001425 HEPN domain; Region: HEPN; cl00824 1105112001426 potential frameshift: common BLAST hit: gi|350273736|ref|YP_004885049.1| bicyclomycin resistance protein 1105112001427 potential frameshift: common BLAST hit: gi|350273736|ref|YP_004885049.1| bicyclomycin resistance protein 1105112001428 Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17; Region: Pat17_PNPLA8_PNPLA9_like; cd07199 1105112001429 active site 1105112001430 nucleophile elbow; other site 1105112001431 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 1105112001432 DnaA N-terminal domain; Region: DnaA_N; pfam11638 1105112001433 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 1105112001434 Walker A motif; other site 1105112001435 ATP binding site [chemical binding]; other site 1105112001436 Walker B motif; other site 1105112001437 arginine finger; other site 1105112001438 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 1105112001439 DnaA box-binding interface [nucleotide binding]; other site 1105112001440 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins; Region: RHOD_1; cd01522 1105112001441 active site residue [active] 1105112001442 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 1105112001443 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 1105112001444 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 1105112001445 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 1105112001446 ATP binding site [chemical binding]; other site 1105112001447 putative Mg++ binding site [ion binding]; other site 1105112001448 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 1105112001449 nucleotide binding region [chemical binding]; other site 1105112001450 ATP-binding site [chemical binding]; other site 1105112001451 TRCF domain; Region: TRCF; cl04088 1105112001452 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 1105112001453 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105112001454 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105112001455 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105112001456 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105112001457 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 1105112001458 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105112001459 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105112001460 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 1105112001461 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 1105112001462 Mg++ binding site [ion binding]; other site 1105112001463 putative catalytic motif [active] 1105112001464 putative substrate binding site [chemical binding]; other site 1105112001465 V-type ATP synthase subunit I; Validated; Region: PRK05771 1105112001466 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 1105112001467 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 1105112001468 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 1105112001469 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 1105112001470 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 1105112001471 ssDNA binding site; other site 1105112001472 generic binding surface II; other site 1105112001473 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 1105112001474 ATP binding site [chemical binding]; other site 1105112001475 putative Mg++ binding site [ion binding]; other site 1105112001476 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 1105112001477 nucleotide binding region [chemical binding]; other site 1105112001478 ATP-binding site [chemical binding]; other site 1105112001479 TraX protein; Region: TraX; cl05434 1105112001480 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112001481 MviN-like protein; Region: MVIN; pfam03023 1105112001482 Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers; Region: pyrophosphatase; cd00412 1105112001483 dimer interface [polypeptide binding]; other site 1105112001484 substrate binding site [chemical binding]; other site 1105112001485 metal binding sites [ion binding]; metal-binding site 1105112001486 CcmE; Region: CcmE; cl00994 1105112001487 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 1105112001488 Cu(I) binding site [ion binding]; other site 1105112001489 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 1105112001490 Protein export membrane protein; Region: SecD_SecF; cl14618 1105112001491 Preprotein translocase subunit; Region: YajC; cl00806 1105112001492 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105112001493 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15783 1105112001494 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 1105112001495 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 1105112001496 MgtE intracellular N domain; Region: MgtE_N; cl15244 1105112001497 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 1105112001498 Divalent cation transporter; Region: MgtE; cl00786 1105112001499 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 1105112001500 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 1105112001501 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 1105112001502 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 1105112001503 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 1105112001504 ATP binding site [chemical binding]; other site 1105112001505 Mg2+ binding site [ion binding]; other site 1105112001506 G-X-G motif; other site 1105112001507 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 1105112001508 anchoring element; other site 1105112001509 dimer interface [polypeptide binding]; other site 1105112001510 ATP binding site [chemical binding]; other site 1105112001511 TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the...; Region: TOPRIM_TopoIIA_GyrB; cd03366 1105112001512 active site 1105112001513 putative metal-binding site [ion binding]; other site 1105112001514 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1105112001515 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 1105112001516 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 1105112001517 hinge; other site 1105112001518 active site 1105112001519 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 1105112001520 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 1105112001521 peptidylprolyl isomerase; Reviewed; Region: prsA; PRK03002 1105112001522 PPIC-type PPIASE domain; Region: Rotamase; cl08278 1105112001523 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 1105112001524 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105112001525 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 1105112001526 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 1105112001527 nucleotide binding region [chemical binding]; other site 1105112001528 ATP-binding site [chemical binding]; other site 1105112001529 SEC-C motif; Region: SEC-C; pfam02810 1105112001530 potential frameshift: common BLAST hit: gi|67459332|ref|YP_246956.1| nucleotidyltransferase/HEPN domain-containing protein 1105112001531 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; cl02529 1105112001532 potential frameshift: common BLAST hit: gi|91205221|ref|YP_537576.1| Type I restriction-modification system, M subunit 1105112001533 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 1105112001534 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 1105112001535 DNA binding site [nucleotide binding] 1105112001536 active site 1105112001537 A new structural DNA glycosylase; Region: AlkD_like; cd06561 1105112001538 active site 1105112001539 Protein of unknown function (DUF461); Region: DUF461; cl01071 1105112001540 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 1105112001541 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 1105112001542 GIY-YIG motif/motif A; other site 1105112001543 active site 1105112001544 catalytic site [active] 1105112001545 putative DNA binding site [nucleotide binding]; other site 1105112001546 metal binding site [ion binding]; metal-binding site 1105112001547 UvrB/uvrC motif; Region: UVR; pfam02151 1105112001548 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 1105112001549 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 1105112001550 Na binding site [ion binding]; other site 1105112001551 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 1105112001552 MraZ protein; Region: MraZ; pfam02381 1105112001553 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 1105112001554 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 1105112001555 S-adenosylmethionine binding site [chemical binding]; other site 1105112001556 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 1105112001557 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 1105112001558 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1105112001559 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 1105112001560 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 1105112001561 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1105112001562 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 1105112001563 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 1105112001564 secreted effector protein PipB2; Provisional; Region: PRK15196 1105112001565 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105112001566 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1105112001567 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 1105112001568 active site 1105112001569 phosphorylation site [posttranslational modification] 1105112001570 intermolecular recognition site; other site 1105112001571 dimerization interface [polypeptide binding]; other site 1105112001572 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 1105112001573 Walker A motif; other site 1105112001574 ATP binding site [chemical binding]; other site 1105112001575 Walker B motif; other site 1105112001576 arginine finger; other site 1105112001577 Helix-turn-helix domains; Region: HTH; cl00088 1105112001578 Multiple resistance and pH regulation protein F (MrpF / PhaF); Region: MrpF_PhaF; cl09154 1105112001579 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112001580 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK06617 1105112001581 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105112001582 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105112001583 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105112001584 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105112001585 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105112001586 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 1105112001587 Alpha-2-macroglobulin family N-terminal region; Region: A2M_N_2; pfam07703 1105112001588 Alpha-2-macroglobulin family; Region: A2M; pfam00207 1105112001589 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 1105112001590 surface patch; other site 1105112001591 thioester region; other site 1105112001592 specificity defining residues; other site 1105112001593 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 1105112001594 Protein of unknown function (DUF3680); Region: DUF3680; cl02189 1105112001595 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 1105112001596 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 1105112001597 active site 1105112001598 HIGH motif; other site 1105112001599 dimer interface [polypeptide binding]; other site 1105112001600 KMSKS motif; other site 1105112001601 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 1105112001602 RNA binding surface [nucleotide binding]; other site 1105112001603 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 1105112001604 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 1105112001605 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 1105112001606 Helix-turn-helix domains; Region: HTH; cl00088 1105112001607 Rrf2 family protein; Region: rrf2_super; TIGR00738 1105112001608 ribosome maturation protein RimP; Reviewed; Region: PRK00092 1105112001609 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 1105112001610 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 1105112001611 Sm1 motif; other site 1105112001612 D1 - D2 interaction site; other site 1105112001613 D3 - B interaction site; other site 1105112001614 Hfq - Hfq interaction site; other site 1105112001615 RNA binding pocket [nucleotide binding]; other site 1105112001616 Sm2 motif; other site 1105112001617 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 1105112001618 NusA N-terminal domain; Region: NusA_N; pfam08529 1105112001619 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 1105112001620 RNA binding site [nucleotide binding]; other site 1105112001621 homodimer interface [polypeptide binding]; other site 1105112001622 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 1105112001623 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 1105112001624 G-X-X-G motif; other site 1105112001625 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 1105112001626 translation initiation factor IF-2; Validated; Region: infB; PRK05306 1105112001627 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 1105112001628 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 1105112001629 G1 box; other site 1105112001630 putative GEF interaction site [polypeptide binding]; other site 1105112001631 GTP/Mg2+ binding site [chemical binding]; other site 1105112001632 Switch I region; other site 1105112001633 G2 box; other site 1105112001634 G3 box; other site 1105112001635 Switch II region; other site 1105112001636 G4 box; other site 1105112001637 G5 box; other site 1105112001638 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 1105112001639 Translation-initiation factor 2; Region: IF-2; pfam11987 1105112001640 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 1105112001641 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 1105112001642 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 1105112001643 Recombination protein O N terminal; Region: RecO_N; cl15812 1105112001644 Recombination protein O C terminal; Region: RecO_C; pfam02565 1105112001645 DNA repair protein RadA; Provisional; Region: PRK11823 1105112001646 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 1105112001647 Walker A motif/ATP binding site; other site 1105112001648 ATP binding site [chemical binding]; other site 1105112001649 Walker B motif; other site 1105112001650 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 1105112001651 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 1105112001652 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105112001653 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105112001654 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 1105112001655 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105112001656 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 1105112001657 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 1105112001658 RNA binding surface [nucleotide binding]; other site 1105112001659 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 1105112001660 active site 1105112001661 potential frameshift: common BLAST hit: gi|67459254|ref|YP_246878.1| to amino acid permeases 1105112001662 replicative DNA helicase; Provisional; Region: PRK09165 1105112001663 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 1105112001664 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 1105112001665 Walker A motif; other site 1105112001666 ATP binding site [chemical binding]; other site 1105112001667 Walker B motif; other site 1105112001668 DNA binding loops [nucleotide binding] 1105112001669 polyprenyl P-hydroxybenzoate and phenylacrylic acid decarboxylases; Region: ubiX_pad; TIGR00421 1105112001670 Flavoprotein; Region: Flavoprotein; cl08021 1105112001671 primosome assembly protein PriA; Validated; Region: PRK05580 1105112001672 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 1105112001673 ATP binding site [chemical binding]; other site 1105112001674 putative Mg++ binding site [ion binding]; other site 1105112001675 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105112001676 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS_aspartate_rich; cd04823 1105112001677 dimer interface [polypeptide binding]; other site 1105112001678 allosteric magnesium binding site [ion binding]; other site 1105112001679 active site 1105112001680 aspartate-rich active site metal binding site; other site 1105112001681 Schiff base residues; other site 1105112001682 NADH dehydrogenase subunit 2; Provisional; Region: ND2; MTH00196 1105112001683 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 1105112001684 potential frameshift: common BLAST hit: gi|67458839|ref|YP_246463.1| NACHT domain-containing protein 1105112001685 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 1105112001686 Predicted transcriptional regulator [Transcription]; Region: COG1959 1105112001687 Helix-turn-helix domains; Region: HTH; cl00088 1105112001688 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 1105112001689 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 1105112001690 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1105112001691 catalytic residue [active] 1105112001692 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 1105112001693 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 1105112001694 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1105112001695 catalytic residue [active] 1105112001696 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 1105112001697 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 1105112001698 trimerization site [polypeptide binding]; other site 1105112001699 active site 1105112001700 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 1105112001701 arginine:agmatin antiporter; Provisional; Region: PRK10644 1105112001702 Spore germination protein; Region: Spore_permease; cl15802 1105112001703 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 1105112001704 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 1105112001705 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112001706 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 1105112001707 active site 1105112001708 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 1105112001709 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 1105112001710 substrate binding pocket [chemical binding]; other site 1105112001711 chain length determination region; other site 1105112001712 substrate-Mg2+ binding site; other site 1105112001713 catalytic residues [active] 1105112001714 aspartate-rich region 1; other site 1105112001715 active site lid residues [active] 1105112001716 aspartate-rich region 2; other site 1105112001717 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105112001718 ATP/ADP translocase [Energy production and conversion]; Region: COG3202; cl03940 1105112001719 potential frameshift: common BLAST hit: gi|67459228|ref|YP_246852.1| lipopolysaccharide 1,2-glucosyltransferase RfaJ 1105112001720 muropeptide transporter; Validated; Region: ampG; PRK11010 1105112001721 AmpG-like permease; Region: 2A0125; TIGR00901 1105112001722 muropeptide transporter; Validated; Region: ampG; PRK11010 1105112001723 LysE type translocator; Region: LysE; cl00565 1105112001724 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 1105112001725 active site 1105112001726 Uroporphyrinogen-III synthase HemD; Region: HEM4; pfam02602 1105112001727 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 1105112001728 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemY; COG3071 1105112001729 HemY protein N-terminus; Region: HemY_N; pfam07219 1105112001730 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 1105112001731 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 1105112001732 RelB antitoxin; Region: RelB; cl01171 1105112001733 Protein required for attachment to host cells; Region: Host_attach; cl02398 1105112001734 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1105112001735 putative acyl-acceptor binding pocket; other site 1105112001736 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 1105112001737 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 1105112001738 active site 1105112001739 HIGH motif; other site 1105112001740 dimer interface [polypeptide binding]; other site 1105112001741 KMSKS motif; other site 1105112001742 Protein of unknown function (DUF497); Region: DUF497; cl01108 1105112001743 potential frameshift: common BLAST hit: gi|91205198|ref|YP_537553.1| ATPase AAA 1105112001744 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 1105112001745 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cd00494 1105112001746 domain interfaces; other site 1105112001747 active site 1105112001748 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 1105112001749 dimer interface [polypeptide binding]; other site 1105112001750 catalytic triad [active] 1105112001751 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 1105112001752 ATP binding site [chemical binding]; other site 1105112001753 G-X-G motif; other site 1105112001754 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 1105112001755 dimer interface [polypeptide binding]; other site 1105112001756 phosphorylation site [posttranslational modification] 1105112001757 potential frameshift: common BLAST hit: gi|15604329|ref|NP_220845.1| alkaline phosphatase synthesis sensor protein PhoR 1105112001758 potential frameshift: common BLAST hit: gi|157964645|ref|YP_001499469.1| ankyrin repeat-containing protein 1105112001759 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 1105112001760 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 1105112001761 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 1105112001762 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 1105112001763 Uncharacterized ACR, YagE family COG1723; Region: DUF155; cl00751 1105112001764 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 1105112001765 catalytic site [active] 1105112001766 putative active site [active] 1105112001767 putative substrate binding site [chemical binding]; other site 1105112001768 HRDC domain; Region: HRDC; cl02578 1105112001769 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 1105112001770 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 1105112001771 glycerol-3-phosphate dehydrogenase, anaerobic, B subunit; Region: glycerol3P_GlpB; TIGR03378 1105112001772 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105112001773 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1105112001774 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 1105112001775 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 1105112001776 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 1105112001777 Protein of unknown function (DUF2532); Region: DUF2532; pfam10811 1105112001778 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1105112001779 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 1105112001780 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1105112001781 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 1105112001782 Transcriptional regulator; Region: Transcrip_reg; cl00361 1105112001783 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 1105112001784 Substrate binding site; other site 1105112001785 Mg++ binding site; other site 1105112001786 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 1105112001787 putative CoA binding site [chemical binding]; other site 1105112001788 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 1105112001789 putative CoA binding site [chemical binding]; other site 1105112001790 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 1105112001791 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 1105112001792 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105112001793 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105112001794 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1105112001795 Coenzyme A binding pocket [chemical binding]; other site 1105112001796 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 1105112001797 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 1105112001798 Isopentenyl-diphosphate:dimethylallyl diphosphate isomerase type 2 (IDI-2) FMN-binding domain. Two types of IDIs have been characterized at present. The long known IDI-1 is only dependent on divalent metals for activity, whereas IDI-2 requires a metal; Region: IDI-2_FMN; cd02811 1105112001799 homotetramer interface [polypeptide binding]; other site 1105112001800 FMN binding site [chemical binding]; other site 1105112001801 homodimer contacts [polypeptide binding]; other site 1105112001802 putative active site [active] 1105112001803 putative substrate binding site [chemical binding]; other site 1105112001804 Acetyltransferase (GNAT) domain; Region: Acetyltransf_8; pfam13523 1105112001805 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 1105112001806 Clp protease; Region: CLP_protease; pfam00574 1105112001807 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 1105112001808 oligomer interface [polypeptide binding]; other site 1105112001809 active site residues [active] 1105112001810 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 1105112001811 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 1105112001812 RNA binding site [nucleotide binding]; other site 1105112001813 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 1105112001814 RNA binding site [nucleotide binding]; other site 1105112001815 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec3; cd05688 1105112001816 RNA binding site [nucleotide binding]; other site 1105112001817 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 1105112001818 RNA binding site [nucleotide binding]; other site 1105112001819 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 1105112001820 RNA binding site [nucleotide binding]; other site 1105112001821 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 1105112001822 RNA binding site [nucleotide binding]; other site 1105112001823 cytidylate kinase; Provisional; Region: cmk; PRK00023 1105112001824 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 1105112001825 CMP-binding site; other site 1105112001826 The sites determining sugar specificity; other site 1105112001827 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 1105112001828 sequence-specific DNA binding site [nucleotide binding]; other site 1105112001829 salt bridge; other site 1105112001830 Protein of unknown function (DUF328); Region: DUF328; cl01143 1105112001831 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 1105112001832 IHF - DNA interface [nucleotide binding]; other site 1105112001833 IHF dimer interface [polypeptide binding]; other site 1105112001834 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1105112001835 tandem repeat interface [polypeptide binding]; other site 1105112001836 oligomer interface [polypeptide binding]; other site 1105112001837 active site residues [active] 1105112001838 transcription termination factor Rho; Provisional; Region: rho; PRK09376 1105112001839 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 1105112001840 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 1105112001841 RNA binding site [nucleotide binding]; other site 1105112001842 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 1105112001843 multimer interface [polypeptide binding]; other site 1105112001844 Walker A motif; other site 1105112001845 ATP binding site [chemical binding]; other site 1105112001846 Walker B motif; other site 1105112001847 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1, 4-benzoquinol methylase [Coenzyme metabolism]; Region: UbiG; COG2227 1105112001848 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 1105112001849 S-adenosylmethionine binding site [chemical binding]; other site 1105112001850 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 1105112001851 DHH family; Region: DHH; pfam01368 1105112001852 DHHA1 domain; Region: DHHA1; pfam02272 1105112001853 peptide chain release factor 1; Validated; Region: prfA; PRK00591 1105112001854 RF-1 domain; Region: RF-1; cl02875 1105112001855 RF-1 domain; Region: RF-1; cl02875 1105112001856 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 1105112001857 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 1105112001858 E3 interaction surface; other site 1105112001859 lipoyl attachment site [posttranslational modification]; other site 1105112001860 e3 binding domain; Region: E3_binding; pfam02817 1105112001861 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 1105112001862 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 1105112001863 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 1105112001864 Predicted membrane protein (DUF2335); Region: DUF2335; cl02210 1105112001865 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 1105112001866 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl08495 1105112001867 potential frameshift: common BLAST hit: gi|67459142|ref|YP_246766.1| HK97 family phage prohead protease/phage major capsid protein 1105112001868 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 1105112001869 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 1105112001870 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 1105112001871 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 1105112001872 ExoU and VipD-like proteins; homologus to patatin, cPLA2, and iPLA2; Region: Pat_ExoU_VipD_like; cd07207 1105112001873 active site 1105112001874 nucleophile elbow; other site 1105112001875 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 1105112001876 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 1105112001877 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 1105112001878 folylpolyglutamate synthase/dihydrofolate synthase; Region: folC; TIGR01499 1105112001879 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; cl01942 1105112001880 Uncharacterized conserved protein [Function unknown]; Region: COG4285 1105112001881 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP); Region: GATase1_ScBLP_like; cd03144 1105112001882 conserved cys residue [active] 1105112001883 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 1105112001884 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 1105112001885 GSH binding site (G-site) [chemical binding]; other site 1105112001886 C-terminal domain interface [polypeptide binding]; other site 1105112001887 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 1105112001888 N-terminal domain interface [polypeptide binding]; other site 1105112001889 dimer interface [polypeptide binding]; other site 1105112001890 substrate binding pocket (H-site) [chemical binding]; other site 1105112001891 pyruvate phosphate dikinase; Provisional; Region: PRK09279 1105112001892 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 1105112001893 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 1105112001894 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 1105112001895 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 1105112001896 intersubunit interface [polypeptide binding]; other site 1105112001897 active site 1105112001898 Zn2+ binding site [ion binding]; other site 1105112001899 potential frameshift: common BLAST hit: gi|67459124|ref|YP_246748.1| toxin of toxin-antitoxin system 1105112001900 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 1105112001901 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112001902 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 1105112001903 active site 1105112001904 catalytic residues [active] 1105112001905 metal binding site [ion binding]; metal-binding site 1105112001906 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 1105112001907 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 1105112001908 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1105112001909 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 1105112001910 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 1105112001911 non-specific DNA binding site [nucleotide binding]; other site 1105112001912 salt bridge; other site 1105112001913 sequence-specific DNA binding site [nucleotide binding]; other site 1105112001914 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 1105112001915 ATP/ADP translocase [Energy production and conversion]; Region: COG3202; cl03940 1105112001916 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105112001917 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK14846 1105112001918 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 1105112001919 RNA binding site [nucleotide binding]; other site 1105112001920 active site 1105112001921 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112001922 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 1105112001923 16S/18S rRNA binding site [nucleotide binding]; other site 1105112001924 S13e-L30e interaction site [polypeptide binding]; other site 1105112001925 25S rRNA binding site [nucleotide binding]; other site 1105112001926 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 1105112001927 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 1105112001928 RNase E interface [polypeptide binding]; other site 1105112001929 trimer interface [polypeptide binding]; other site 1105112001930 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 1105112001931 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 1105112001932 RNase E interface [polypeptide binding]; other site 1105112001933 trimer interface [polypeptide binding]; other site 1105112001934 active site 1105112001935 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 1105112001936 putative nucleic acid binding region [nucleotide binding]; other site 1105112001937 G-X-X-G motif; other site 1105112001938 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 1105112001939 RNA binding site [nucleotide binding]; other site 1105112001940 domain interface; other site 1105112001941 KpsF/GutQ family protein; Region: kpsF; TIGR00393 1105112001942 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 1105112001943 putative active site [active] 1105112001944 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 1105112001945 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 1105112001946 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112001947 OstA-like protein; Region: OstA; cl00844 1105112001948 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 1105112001949 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 1105112001950 Walker A/P-loop; other site 1105112001951 ATP binding site [chemical binding]; other site 1105112001952 Q-loop/lid; other site 1105112001953 ABC transporter signature motif; other site 1105112001954 Walker B; other site 1105112001955 D-loop; other site 1105112001956 H-loop/switch region; other site 1105112001957 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 1105112001958 The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a...; Region: PMM_PGM; cd03089 1105112001959 active site 1105112001960 substrate binding site [chemical binding]; other site 1105112001961 metal binding site [ion binding]; metal-binding site 1105112001962 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105112001963 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 1105112001964 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 1105112001965 dimer interface [polypeptide binding]; other site 1105112001966 diiron center [ion binding]; other site 1105112001967 putative radical transfer pathway; other site 1105112001968 tyrosyl radical; other site 1105112001969 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 1105112001970 Class I ribonucleotide reductase; Region: RNR_I; cd01679 1105112001971 active site 1105112001972 dimer interface [polypeptide binding]; other site 1105112001973 catalytic residues [active] 1105112001974 effector binding site; other site 1105112001975 R2 peptide binding site; other site 1105112001976 DDE superfamily endonuclease; Region: DDE_4; cl15789 1105112001977 DDE superfamily endonuclease; Region: DDE_4; cl15789 1105112001978 Chitin binding domain; Region: Chitin_bind_3; cl03871 1105112001979 Spore Coat Protein U domain; Region: SCPU; cl02253 1105112001980 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 1105112001981 potential frameshift: common BLAST hit: gi|157827080|ref|YP_001496144.1| P pilus assembly, fimbrial usher protein 1105112001982 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 1105112001983 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 1105112001984 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 1105112001985 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105112001986 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105112001987 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14171 1105112001988 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 1105112001989 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 1105112001990 homodimer interface [polypeptide binding]; other site 1105112001991 NADP binding site [chemical binding]; other site 1105112001992 substrate binding site [chemical binding]; other site 1105112001993 potential frameshift: common BLAST hit: gi|229586740|ref|YP_002845241.1| Carbonic anhydrases/acetyltransferase, isoleucine patch superfamily 1105112001994 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 1105112001995 30S subunit binding site; other site 1105112001996 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 1105112001997 Found in ATP-dependent protease La (LON); Region: LON; smart00464 1105112001998 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 1105112001999 Walker A motif; other site 1105112002000 ATP binding site [chemical binding]; other site 1105112002001 Walker B motif; other site 1105112002002 arginine finger; other site 1105112002003 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 1105112002004 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 1105112002005 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 1105112002006 tetramer interface [polypeptide binding]; other site 1105112002007 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105112002008 catalytic residue [active] 1105112002009 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 1105112002010 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105112002011 Family description; Region: UvrD_C_2; cl15862 1105112002012 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 1105112002013 active site 1105112002014 potential frameshift: common BLAST hit: gi|165933216|ref|YP_001650005.1| succinate-semialdehyde dehydrogenase (NADP+) 1105112002015 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 1105112002016 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105112002017 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1105112002018 Membrane transport protein; Region: Mem_trans; cl09117 1105112002019 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 1105112002020 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105112002021 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 1105112002022 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 1105112002023 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 1105112002024 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 1105112002025 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 1105112002026 recombination protein RecR; Reviewed; Region: recR; PRK00076 1105112002027 RecR protein; Region: RecR; pfam02132 1105112002028 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 1105112002029 putative active site [active] 1105112002030 putative metal-binding site [ion binding]; other site 1105112002031 tetramer interface [polypeptide binding]; other site 1105112002032 RDD family; Region: RDD; cl00746 1105112002033 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 1105112002034 Ribosome-binding factor A; Region: RBFA; cl00542 1105112002035 Tim44-like domain; Region: Tim44; cl09208 1105112002036 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 1105112002037 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 1105112002038 substrate binding pocket [chemical binding]; other site 1105112002039 catalytic triad [active] 1105112002040 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 1105112002041 potential frameshift: common BLAST hit: gi|229586712|ref|YP_002845213.1| Putative nucleic-acid-binding protein, containing PIN domain 1105112002042 potential frameshift: common BLAST hit: gi|229586712|ref|YP_002845213.1| Putative nucleic-acid-binding protein, containing PIN domain 1105112002043 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 1105112002044 ATP-grasp domain; Region: ATP-grasp_4; cl03087 1105112002045 CoA-ligase; Region: Ligase_CoA; cl02894 1105112002046 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 1105112002047 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105112002048 CoA-ligase; Region: Ligase_CoA; cl02894 1105112002049 DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC...; Region: DsbA_Com1_like; cd03023 1105112002050 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 1105112002051 catalytic residues [active] 1105112002052 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 1105112002053 SmpB-tmRNA interface; other site 1105112002054 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 1105112002055 dihydrodipicolinate synthase; Region: dapA; TIGR00674 1105112002056 dimer interface [polypeptide binding]; other site 1105112002057 active site 1105112002058 catalytic residue [active] 1105112002059 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 1105112002060 homodimer interface [polypeptide binding]; other site 1105112002061 substrate-cofactor binding pocket; other site 1105112002062 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105112002063 catalytic residue [active] 1105112002064 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105112002065 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 1105112002066 active site 1105112002067 phosphorylation site [posttranslational modification] 1105112002068 intermolecular recognition site; other site 1105112002069 dimerization interface [polypeptide binding]; other site 1105112002070 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 1105112002071 DNA binding site [nucleotide binding] 1105112002072 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105112002073 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 1105112002074 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 1105112002075 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 1105112002076 ATP binding site [chemical binding]; other site 1105112002077 Mg2+ binding site [ion binding]; other site 1105112002078 G-X-G motif; other site 1105112002079 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cl00230 1105112002080 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 1105112002081 catalytic residue [active] 1105112002082 putative FPP diphosphate binding site; other site 1105112002083 putative FPP binding hydrophobic cleft; other site 1105112002084 dimer interface [polypeptide binding]; other site 1105112002085 putative IPP diphosphate binding site; other site 1105112002086 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 1105112002087 Septum formation initiator; Region: DivIC; cl11433 1105112002088 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 1105112002089 catalytic site [active] 1105112002090 putative active site [active] 1105112002091 putative substrate binding site [chemical binding]; other site 1105112002092 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 1105112002093 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 1105112002094 HIGH motif; other site 1105112002095 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1105112002096 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105112002097 active site 1105112002098 KMSKS motif; other site 1105112002099 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 1105112002100 tRNA binding surface [nucleotide binding]; other site 1105112002101 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 1105112002102 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 1105112002103 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 1105112002104 DNA polymerase III subunit beta; Validated; Region: PRK05643 1105112002105 putative DNA binding surface [nucleotide binding]; other site 1105112002106 dimer interface [polypeptide binding]; other site 1105112002107 beta-clamp/clamp loader binding surface; other site 1105112002108 beta-clamp/translesion DNA polymerase binding surface; other site 1105112002109 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 1105112002110 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 1105112002111 putative tRNA-binding site [nucleotide binding]; other site 1105112002112 B3/4 domain; Region: B3_4; cl11458 1105112002113 tRNA synthetase B5 domain; Region: B5; cl08394 1105112002114 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 1105112002115 dimer interface [polypeptide binding]; other site 1105112002116 motif 1; other site 1105112002117 motif 3; other site 1105112002118 motif 2; other site 1105112002119 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 1105112002120 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 1105112002121 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 1105112002122 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 1105112002123 dimer interface [polypeptide binding]; other site 1105112002124 motif 1; other site 1105112002125 active site 1105112002126 motif 2; other site 1105112002127 motif 3; other site 1105112002128 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 1105112002129 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1105112002130 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 1105112002131 FeS/SAM binding site; other site 1105112002132 diaminopimelate epimerase; Region: DapF; TIGR00652 1105112002133 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1105112002134 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1105112002135 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105112002136 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105112002137 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 1105112002138 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1105112002139 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 1105112002140 DDE superfamily endonuclease; Region: DDE_4; cl15789 1105112002141 DDE superfamily endonuclease; Region: DDE_4; cl15789 1105112002142 potential frameshift: common BLAST hit: gi|157827177|ref|YP_001496241.1| RND family efflux transporter 1105112002143 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 1105112002144 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 1105112002145 active site 1105112002146 homodimer interface [polypeptide binding]; other site 1105112002147 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 1105112002148 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01368 1105112002149 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105112002150 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105112002151 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105112002152 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 1105112002153 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 1105112002154 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 1105112002155 putative peptidase; Provisional; Region: PRK11649 1105112002156 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105112002157 active site 1105112002158 HIGH motif; other site 1105112002159 nucleotide binding site [chemical binding]; other site 1105112002160 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112002161 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 1105112002162 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 1105112002163 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 1105112002164 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 1105112002165 CoA binding site [chemical binding]; other site 1105112002166 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 1105112002167 Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_I; cd01663 1105112002168 Subunit I/III interface [polypeptide binding]; other site 1105112002169 D-pathway; other site 1105112002170 Subunit I/VIIc interface [polypeptide binding]; other site 1105112002171 Subunit I/IV interface [polypeptide binding]; other site 1105112002172 Subunit I/II interface [polypeptide binding]; other site 1105112002173 Low-spin heme (heme a) binding site [chemical binding]; other site 1105112002174 Subunit I/VIIa interface [polypeptide binding]; other site 1105112002175 Subunit I/VIa interface [polypeptide binding]; other site 1105112002176 Dimer interface; other site 1105112002177 Putative water exit pathway; other site 1105112002178 Binuclear center (heme a3/CuB) [ion binding]; other site 1105112002179 K-pathway; other site 1105112002180 Subunit I/Vb interface [polypeptide binding]; other site 1105112002181 Putative proton exit pathway; other site 1105112002182 Subunit I/VIb interface; other site 1105112002183 Subunit I/VIc interface [polypeptide binding]; other site 1105112002184 Electron transfer pathway; other site 1105112002185 Subunit I/VIIIb interface [polypeptide binding]; other site 1105112002186 Subunit I/VIIb interface [polypeptide binding]; other site 1105112002187 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 1105112002188 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 1105112002189 catalytic triad [active] 1105112002190 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 1105112002191 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 1105112002192 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 1105112002193 dimer interface [polypeptide binding]; other site 1105112002194 catalytic triad [active] 1105112002195 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 1105112002196 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1105112002197 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 1105112002198 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1105112002199 catalytic residue [active] 1105112002200 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1105112002201 trimer interface [polypeptide binding]; other site 1105112002202 active site 1105112002203 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1105112002204 tandem repeat interface [polypeptide binding]; other site 1105112002205 oligomer interface [polypeptide binding]; other site 1105112002206 active site residues [active] 1105112002207 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 1105112002208 catalytic residues [active] 1105112002209 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 1105112002210 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 1105112002211 active site 1105112002212 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 1105112002213 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 1105112002214 Iron permease FTR1 family; Region: FTR1; cl00475 1105112002215 Intracellular septation protein A; Region: IspA; cl01098 1105112002216 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 1105112002217 BON domain; Region: BON; cl02771 1105112002218 BON domain; Region: BON; cl02771 1105112002219 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112002220 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105112002221 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 1105112002222 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 1105112002223 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 1105112002224 muropeptide transporter; Validated; Region: ampG; PRK11010 1105112002225 muropeptide transporter; Reviewed; Region: ampG; PRK11902 1105112002226 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1105112002227 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 1105112002228 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 1105112002229 Walker A/P-loop; other site 1105112002230 ATP binding site [chemical binding]; other site 1105112002231 Q-loop/lid; other site 1105112002232 ABC transporter signature motif; other site 1105112002233 Walker B; other site 1105112002234 D-loop; other site 1105112002235 H-loop/switch region; other site 1105112002236 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 1105112002237 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 1105112002238 Walker A motif; other site 1105112002239 ATP binding site [chemical binding]; other site 1105112002240 Walker B motif; other site 1105112002241 arginine finger; other site 1105112002242 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 1105112002243 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 1105112002244 RuvA N terminal domain; Region: RuvA_N; pfam01330 1105112002245 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 1105112002246 Fic family protein [Function unknown]; Region: COG3177 1105112002247 Fic/DOC family; Region: Fic; cl00960 1105112002248 prolyl-tRNA synthetase; Provisional; Region: PRK12325 1105112002249 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_prok; cd00779 1105112002250 dimer interface [polypeptide binding]; other site 1105112002251 motif 1; other site 1105112002252 active site 1105112002253 motif 2; other site 1105112002254 motif 3; other site 1105112002255 ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding; Region: ProRS_anticodon_short; cd00861 1105112002256 anticodon binding site; other site 1105112002257 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 1105112002258 GTP cyclohydrolase I; Provisional; Region: PLN03044 1105112002259 active site 1105112002260 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_19; cd04678 1105112002261 nudix motif; other site 1105112002262 Protein of unknown function (DUF3680); Region: DUF3680; cl02189 1105112002263 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 1105112002264 Ligand binding site; other site 1105112002265 oligomer interface; other site 1105112002266 CTP synthetase; Validated; Region: pyrG; PRK05380 1105112002267 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 1105112002268 Catalytic site [active] 1105112002269 active site 1105112002270 UTP binding site [chemical binding]; other site 1105112002271 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 1105112002272 active site 1105112002273 putative oxyanion hole; other site 1105112002274 catalytic triad [active] 1105112002275 ATP/ADP translocase [Energy production and conversion]; Region: COG3202; cl03940 1105112002276 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105112002277 malate dehydrogenase; Reviewed; Region: PRK06223 1105112002278 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 1105112002279 NAD(P) binding site [chemical binding]; other site 1105112002280 dimer interface [polypeptide binding]; other site 1105112002281 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1105112002282 substrate binding site [chemical binding]; other site 1105112002283 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105112002284 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 1105112002285 PIN domain of ribonucleases (toxins), VapC, FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs; Region: PIN_VapC-like; cd09861 1105112002286 putative active site [active] 1105112002287 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 1105112002288 Malic enzyme, N-terminal domain; Region: malic; pfam00390 1105112002289 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 1105112002290 putative NAD(P) binding site [chemical binding]; other site 1105112002291 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 1105112002292 Membrane transport protein; Region: Mem_trans; cl09117 1105112002293 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 1105112002294 catalytic core domain of class I lysyl tRNA synthetase; Region: LysRS_core_class_I; cd00674 1105112002295 active site 1105112002296 HIGH motif; other site 1105112002297 KMSKS motif; other site 1105112002298 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 1105112002299 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 1105112002300 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 1105112002301 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 1105112002302 potential frameshift: common BLAST hit: gi|15892423|ref|NP_360137.1| ABC transporter ATP-binding protein 1105112002303 potential frameshift: common BLAST hit: gi|229586633|ref|YP_002845134.1| ABC transporter substrate-binding protein 1105112002304 potential frameshift: common BLAST hit: gi|165933077|ref|YP_001649866.1| ABC transporter substrate-binding protein 1105112002305 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1105112002306 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 1105112002307 amidase catalytic site [active] 1105112002308 Zn binding residues [ion binding]; other site 1105112002309 substrate binding site [chemical binding]; other site 1105112002310 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 1105112002311 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 1105112002312 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 1105112002313 putative active site [active] 1105112002314 catalytic triad [active] 1105112002315 putative dimer interface [polypeptide binding]; other site 1105112002316 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 1105112002317 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 1105112002318 NAD binding site [chemical binding]; other site 1105112002319 homotetramer interface [polypeptide binding]; other site 1105112002320 homodimer interface [polypeptide binding]; other site 1105112002321 substrate binding site [chemical binding]; other site 1105112002322 active site 1105112002323 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 1105112002324 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 1105112002325 active site 1105112002326 DNA binding site [nucleotide binding] 1105112002327 Int/Topo IB signature motif; other site 1105112002328 potential frameshift: common BLAST hit: gi|67458962|ref|YP_246586.1| phage protein 1105112002329 Uncharacterized protein conserved in bacteria (DUF2155); Region: DUF2155; cl01970 1105112002330 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 1105112002331 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 1105112002332 NADH dehydrogenase subunit B; Provisional; Region: PRK14816 1105112002333 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl15792 1105112002334 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 1105112002335 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl16917 1105112002336 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 1105112002337 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; pfam00346 1105112002338 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 1105112002339 catalytic site [active] 1105112002340 metal binding site [ion binding]; metal-binding site 1105112002341 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 1105112002342 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 1105112002343 putative dimer interface [polypeptide binding]; other site 1105112002344 [2Fe-2S] cluster binding site [ion binding]; other site 1105112002345 Haemolytic domain; Region: Haemolytic; cl00506 1105112002346 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 1105112002347 active site 1105112002348 DNA binding site [nucleotide binding] 1105112002349 Protein of unknown function (DUF3680); Region: DUF3680; cl02189 1105112002350 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 1105112002351 AsmA-like C-terminal region; Region: AsmA_2; cl15864 1105112002352 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 1105112002353 RimM N-terminal domain; Region: RimM; pfam01782 1105112002354 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce...; Region: PRCH; cl09959 1105112002355 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 1105112002356 AsmA-like C-terminal region; Region: AsmA_2; cl15864 1105112002357 Domain of unknown function (DUF4385); Region: DUF4385; pfam14328 1105112002358 spore photoproduct lyase; Region: photo_TT_lyase; cl15393 1105112002359 UbiA prenyltransferase family; Region: UbiA; cl00337 1105112002360 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 1105112002361 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 1105112002362 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 1105112002363 RNA binding surface [nucleotide binding]; other site 1105112002364 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1105112002365 This family is most closely related to the GT1 family of glycosyltransferases. WavL in Vibrio cholerae has been shown to be involved in the biosynthesis of the lipopolysaccharide core; Region: GT1_WavL_like; cd03819 1105112002366 putative ADP-binding pocket [chemical binding]; other site 1105112002367 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1105112002368 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 1105112002369 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 1105112002370 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 1105112002371 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 1105112002372 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 1105112002373 active site 1105112002374 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 1105112002375 active site 1105112002376 potential frameshift: common BLAST hit: gi|238651057|ref|YP_002916914.1| methyltransferase 1105112002377 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 1105112002378 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 1105112002379 active site 1105112002380 homodimer interface [polypeptide binding]; other site 1105112002381 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 1105112002382 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 1105112002383 NAD(P) binding site [chemical binding]; other site 1105112002384 homodimer interface [polypeptide binding]; other site 1105112002385 substrate binding site [chemical binding]; other site 1105112002386 active site 1105112002387 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 1105112002388 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 1105112002389 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 1105112002390 NADP binding site [chemical binding]; other site 1105112002391 active site 1105112002392 putative substrate binding site [chemical binding]; other site 1105112002393 potential frameshift: common BLAST hit: gi|157964412|ref|YP_001499236.1| plasmid maintenance system antidote protein 1105112002394 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 1105112002395 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 1105112002396 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 1105112002397 Sulfatase; Region: Sulfatase; cl10460 1105112002398 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1105112002399 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 1105112002400 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1105112002401 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 1105112002402 dimer interface [polypeptide binding]; other site 1105112002403 decamer (pentamer of dimers) interface [polypeptide binding]; other site 1105112002404 catalytic triad [active] 1105112002405 peroxidatic and resolving cysteines [active] 1105112002406 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 1105112002407 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 1105112002408 DNA topoisomerase I; Validated; Region: PRK06599 1105112002409 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 1105112002410 active site 1105112002411 interdomain interaction site; other site 1105112002412 putative metal-binding site [ion binding]; other site 1105112002413 nucleotide binding site [chemical binding]; other site 1105112002414 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 1105112002415 domain I; other site 1105112002416 DNA binding groove [nucleotide binding] 1105112002417 phosphate binding site [ion binding]; other site 1105112002418 domain II; other site 1105112002419 domain III; other site 1105112002420 nucleotide binding site [chemical binding]; other site 1105112002421 catalytic site [active] 1105112002422 domain IV; other site 1105112002423 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1105112002424 Uncharacterized C-terminal domain of topoisomerase IA [General function prediction only]; Region: COG1754 1105112002425 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 1105112002426 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105112002427 HIGH motif; other site 1105112002428 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105112002429 active site 1105112002430 KMSKS motif; other site 1105112002431 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 1105112002432 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 1105112002433 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 1105112002434 Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in...; Region: Frataxin; cd00503 1105112002435 putative iron binding site [ion binding]; other site 1105112002436 YceG-like family; Region: YceG; pfam02618 1105112002437 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 1105112002438 dimerization interface [polypeptide binding]; other site 1105112002439 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 1105112002440 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 1105112002441 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105112002442 potential frameshift: common BLAST hit: gi|67458910|ref|YP_246534.1| Mg chelatase-like protein 1105112002443 potential frameshift: common BLAST hit: gi|67458910|ref|YP_246534.1| Mg chelatase-like protein 1105112002444 potential frameshift: common BLAST hit: gi|157827341|ref|YP_001496405.1| Mg chelatase-like protein 1105112002445 potential frameshift: common BLAST hit: gi|91205630|ref|YP_537985.1| Mg chelatase-like protein 1105112002446 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 1105112002447 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 1105112002448 Walker A motif; other site 1105112002449 ATP binding site [chemical binding]; other site 1105112002450 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105112002451 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 1105112002452 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 1105112002453 active site 1105112002454 HslU subunit interaction site [polypeptide binding]; other site 1105112002455 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105112002456 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 1105112002457 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 1105112002458 nucleotide binding site/active site [active] 1105112002459 HIT family signature motif; other site 1105112002460 catalytic residue [active] 1105112002461 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 1105112002462 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105112002463 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 1105112002464 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 1105112002465 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 1105112002466 This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain. They export...; Region: ABCC_Protease_Secretion; cd03246 1105112002467 Walker A/P-loop; other site 1105112002468 ATP binding site [chemical binding]; other site 1105112002469 Q-loop/lid; other site 1105112002470 ABC transporter signature motif; other site 1105112002471 Walker B; other site 1105112002472 D-loop; other site 1105112002473 H-loop/switch region; other site 1105112002474 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 1105112002475 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 1105112002476 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 1105112002477 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 1105112002478 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105112002479 putative substrate translocation pore; other site 1105112002480 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 1105112002481 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 1105112002482 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 1105112002483 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105112002484 Walker A/P-loop; other site 1105112002485 ATP binding site [chemical binding]; other site 1105112002486 Q-loop/lid; other site 1105112002487 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 1105112002488 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 1105112002489 dimer interface [polypeptide binding]; other site 1105112002490 motif 1; other site 1105112002491 active site 1105112002492 motif 2; other site 1105112002493 motif 3; other site 1105112002494 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 1105112002495 anticodon binding site; other site 1105112002496 amino acid transporter; Region: 2A0306; TIGR00909 1105112002497 Spore germination protein; Region: Spore_permease; cl15802 1105112002498 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 1105112002499 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 1105112002500 Ligand Binding Site [chemical binding]; other site 1105112002501 Cytochrome c oxidase assembly protein CtaG/Cox11; Region: CtaG_Cox11; cl01240 1105112002502 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 1105112002503 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1105112002504 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1105112002505 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 1105112002506 translocation protein TolB; Provisional; Region: tolB; PRK05137 1105112002507 TolB amino-terminal domain; Region: TolB_N; cl00639 1105112002508 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105112002509 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105112002510 Thymidylate synthase complementing protein; Region: Thy1; cl03630 1105112002511 potential frameshift: common BLAST hit: gi|229586557|ref|YP_002845058.1| Putative metal-dependent hydrolase 1105112002512 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105112002513 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 1105112002514 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 1105112002515 MutS domain I; Region: MutS_I; pfam01624 1105112002516 MutS domain II; Region: MutS_II; pfam05188 1105112002517 MutS family domain IV; Region: MutS_IV; pfam05190 1105112002518 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 1105112002519 Walker A/P-loop; other site 1105112002520 ATP binding site [chemical binding]; other site 1105112002521 Q-loop/lid; other site 1105112002522 ABC transporter signature motif; other site 1105112002523 Walker B; other site 1105112002524 D-loop; other site 1105112002525 H-loop/switch region; other site 1105112002526 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in cysteine...; Region: CysQ; cd01638 1105112002527 active site 1105112002528 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 1105112002529 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 1105112002530 Phage-related protein [Function unknown]; Region: COG4695; cl01923 1105112002531 bifunctional glutathionylspermidine amidase/glutathionylspermidine synthetase; Provisional; Region: PRK10507 1105112002532 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 1105112002533 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 1105112002534 type IV secretion system component VirD4; Provisional; Region: PRK13897 1105112002535 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer...; Region: TraG_VirD4; cd01126 1105112002536 Walker A motif; other site 1105112002537 ATP binding site [chemical binding]; other site 1105112002538 Walker B motif; other site 1105112002539 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 1105112002540 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 1105112002541 Walker A motif; other site 1105112002542 hexamer interface [polypeptide binding]; other site 1105112002543 ATP binding site [chemical binding]; other site 1105112002544 Walker B motif; other site 1105112002545 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 1105112002546 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 1105112002547 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 1105112002548 VirB8 protein; Region: VirB8; cl01500 1105112002549 Protein of unknown function (DUF2706); Region: DUF2706; pfam10913 1105112002550 VirB8 protein; Region: VirB8; cl01500 1105112002551 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 1105112002552 VirB7 interaction site; other site 1105112002553 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 1105112002554 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06591 1105112002555 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 1105112002556 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06589 1105112002557 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 1105112002558 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 1105112002559 oligomeric interface; other site 1105112002560 putative active site [active] 1105112002561 homodimer interface [polypeptide binding]; other site 1105112002562 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06588 1105112002563 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 1105112002564 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 1105112002565 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105112002566 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 1105112002567 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 1105112002568 potential frameshift: common BLAST hit: gi|67458844|ref|YP_246468.1| MFS type sugar transporter 1105112002569 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105112002570 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 1105112002571 HEAT repeats; Region: HEAT_2; pfam13646 1105112002572 potential frameshift: common BLAST hit: gi|67459245|ref|YP_246869.1| NTPase 1105112002573 potential frameshift: common BLAST hit: gi|15892293|ref|NP_360007.1| ATP-dependent protease subunit C (ClpC) 1105112002574 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 1105112002575 hydrophobic ligand binding site; other site 1105112002576 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 1105112002577 bifunctional preprotein translocase subunit SecD/SecF; Reviewed; Region: PRK13024 1105112002578 potential frameshift: common BLAST hit: gi|165933830|ref|YP_001650619.1| outer membrane protein A 1105112002579 potential frameshift: common BLAST hit: gi|341584421|ref|YP_004764912.1| 190-kDa cell surface antigen 1105112002580 Phage capsid family; Region: Phage_capsid; pfam05065 1105112002581 GTP-binding protein LepA; Provisional; Region: PRK05433 1105112002582 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 1105112002583 G1 box; other site 1105112002584 putative GEF interaction site [polypeptide binding]; other site 1105112002585 GTP/Mg2+ binding site [chemical binding]; other site 1105112002586 Switch I region; other site 1105112002587 G2 box; other site 1105112002588 G3 box; other site 1105112002589 Switch II region; other site 1105112002590 G4 box; other site 1105112002591 G5 box; other site 1105112002592 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 1105112002593 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 1105112002594 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 1105112002595 RF-1 domain; Region: RF-1; cl02875 1105112002596 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 1105112002597 RF-1 domain; Region: RF-1; cl02875 1105112002598 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105112002599 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 1105112002600 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 1105112002601 putative dimer interface [polypeptide binding]; other site 1105112002602 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 1105112002603 Cytochrome c; Region: Cytochrom_C; cl11414 1105112002604 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 1105112002605 catalytic site [active] 1105112002606 metal binding site [ion binding]; metal-binding site 1105112002607 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cd00284 1105112002608 Qi binding site; other site 1105112002609 cytochrome b; Provisional; Region: CYTB; MTH00191 1105112002610 intrachain domain interface; other site 1105112002611 interchain domain interface [polypeptide binding]; other site 1105112002612 heme bH binding site [chemical binding]; other site 1105112002613 heme bL binding site [chemical binding]; other site 1105112002614 Qo binding site; other site 1105112002615 Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: cytochrome_b_C; cd00290 1105112002616 interchain domain interface [polypeptide binding]; other site 1105112002617 intrachain domain interface; other site 1105112002618 Qi binding site; other site 1105112002619 Qo binding site; other site 1105112002620 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 1105112002621 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 1105112002622 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including...; Region: Rieske_cytochrome_bc1; cd03470 1105112002623 [2Fe-2S] cluster binding site [ion binding]; other site 1105112002624 Protein of unknown function (DUF2670); Region: DUF2670; pfam10875 1105112002625 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12507 1105112002626 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 1105112002627 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 1105112002628 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; cl00583 1105112002629 isocitrate dehydrogenase; Validated; Region: PRK09222 1105112002630 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 1105112002631 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: HlpA; COG2825 1105112002632 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 1105112002633 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 1105112002634 G1 box; other site 1105112002635 putative GEF interaction site [polypeptide binding]; other site 1105112002636 GTP/Mg2+ binding site [chemical binding]; other site 1105112002637 Switch I region; other site 1105112002638 G2 box; other site 1105112002639 G3 box; other site 1105112002640 Switch II region; other site 1105112002641 G4 box; other site 1105112002642 G5 box; other site 1105112002643 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 1105112002644 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 1105112002645 pyruvate dehydrogenase subunit beta; Validated; Region: PRK09212 1105112002646 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 1105112002647 alpha subunit interface [polypeptide binding]; other site 1105112002648 TPP binding site [chemical binding]; other site 1105112002649 heterodimer interface [polypeptide binding]; other site 1105112002650 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1105112002651 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 1105112002652 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 1105112002653 tetramer interface [polypeptide binding]; other site 1105112002654 TPP-binding site [chemical binding]; other site 1105112002655 heterodimer interface [polypeptide binding]; other site 1105112002656 phosphorylation loop region [posttranslational modification] 1105112002657 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 1105112002658 putative catalytic site [active] 1105112002659 putative phosphate binding site [ion binding]; other site 1105112002660 active site 1105112002661 metal binding site A [ion binding]; metal-binding site 1105112002662 DNA binding site [nucleotide binding] 1105112002663 putative AP binding site [nucleotide binding]; other site 1105112002664 putative metal binding site B [ion binding]; other site 1105112002665 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 1105112002666 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 1105112002667 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1105112002668 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 1105112002669 RNA binding surface [nucleotide binding]; other site 1105112002670 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1105112002671 active site 1105112002672 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 1105112002673 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 1105112002674 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 1105112002675 RNA binding site [nucleotide binding]; other site 1105112002676 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 1105112002677 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 1105112002678 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 1105112002679 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 1105112002680 Cytochrome c; Region: Cytochrom_C; cl11414 1105112002681 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 1105112002682 cell division protein FtsA; Region: ftsA; TIGR01174 1105112002683 Cell division protein FtsA; Region: FtsA; cl11496 1105112002684 Cell division protein FtsA; Region: FtsA; cl11496 1105112002685 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 1105112002686 Cell division protein FtsQ; Region: FtsQ; pfam03799 1105112002687 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 1105112002688 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 1105112002689 ATP-grasp domain; Region: ATP-grasp_4; cl03087 1105112002690 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 1105112002691 FAD binding domain; Region: FAD_binding_4; pfam01565 1105112002692 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 1105112002693 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 1105112002694 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105112002695 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105112002696 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105112002697 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1105112002698 BolA-like protein; Region: BolA; cl00386 1105112002699 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105112002700 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105112002701 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 1105112002702 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 1105112002703 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 1105112002704 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 1105112002705 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 1105112002706 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 1105112002707 Domain of unknown function (DUF2610); Region: DUF2610; pfam11020 1105112002708 Inositol-monophosphatase-like domains. This family of phosphatases is dependent on bivalent metal ions such as Mg++, and many members are inhibited by Li+ (which is thought to displace a bivalent ion in the active site). Substrates include fructose-1; Region: IMPase_like; cd01637 1105112002709 active site 1105112002710 elongation factor P; Validated; Region: PRK00529 1105112002711 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 1105112002712 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 1105112002713 RNA binding site [nucleotide binding]; other site 1105112002714 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 1105112002715 RNA binding site [nucleotide binding]; other site 1105112002716 response regulator PleD; Reviewed; Region: pleD; PRK09581 1105112002717 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 1105112002718 active site 1105112002719 phosphorylation site [posttranslational modification] 1105112002720 intermolecular recognition site; other site 1105112002721 dimerization interface [polypeptide binding]; other site 1105112002722 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 1105112002723 active site 1105112002724 phosphorylation site [posttranslational modification] 1105112002725 intermolecular recognition site; other site 1105112002726 dimerization interface [polypeptide binding]; other site 1105112002727 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1105112002728 metal binding site [ion binding]; metal-binding site 1105112002729 active site 1105112002730 I-site; other site 1105112002731 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 1105112002732 putative active site [active] 1105112002733 Ap4A binding site [chemical binding]; other site 1105112002734 nudix motif; other site 1105112002735 putative metal binding site [ion binding]; other site 1105112002736 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_a; cd00913 1105112002737 aromatic arch; other site 1105112002738 DCoH dimer interaction site [polypeptide binding]; other site 1105112002739 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 1105112002740 DCoH tetramer interaction site [polypeptide binding]; other site 1105112002741 substrate binding site [chemical binding]; other site 1105112002742 D-alanyl-D-alanine carboxypeptidase; Region: VanY; cl00813 1105112002743 D-alanyl-D-alanine carboxypeptidase; Region: VanY; cl00813 1105112002744 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 1105112002745 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 1105112002746 23S rRNA interface [nucleotide binding]; other site 1105112002747 L3 interface [polypeptide binding]; other site 1105112002748 FOG: WD40-like repeat [Function unknown]; Region: COG1520 1105112002749 Beta-barrel assembly machinery (Bam) complex component B and related proteins; Region: BamB_YfgL; cd10276 1105112002750 Trp docking motif [polypeptide binding]; other site 1105112002751 Protein of unknown function (DUF2659); Region: DUF2659; pfam10858 1105112002752 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 1105112002753 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 1105112002754 dimer interface [polypeptide binding]; other site 1105112002755 phosphorylation site [posttranslational modification] 1105112002756 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 1105112002757 ATP binding site [chemical binding]; other site 1105112002758 Mg2+ binding site [ion binding]; other site 1105112002759 G-X-G motif; other site 1105112002760 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 1105112002761 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 1105112002762 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 1105112002763 protein binding site [polypeptide binding]; other site 1105112002764 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 1105112002765 Catalytic dyad [active] 1105112002766 DNA topoisomerase IV, B subunit, proteobacterial; Region: parE_Gneg; TIGR01055 1105112002767 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 1105112002768 ATP binding site [chemical binding]; other site 1105112002769 Mg2+ binding site [ion binding]; other site 1105112002770 G-X-G motif; other site 1105112002771 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 1105112002772 anchoring element; other site 1105112002773 dimer interface [polypeptide binding]; other site 1105112002774 ATP binding site [chemical binding]; other site 1105112002775 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 1105112002776 active site 1105112002777 metal binding site [ion binding]; metal-binding site 1105112002778 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1105112002779 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 1105112002780 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 1105112002781 Protein of unknown function (DUF2497); Region: DUF2497; cl11534 1105112002782 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1105112002783 Protein of unknown function (DUF2660); Region: DUF2660; pfam10859 1105112002784 potential frameshift: common BLAST hit: gi|67459373|ref|YP_246997.1| multidrug ABC transporter ATPase and permease 1105112002785 DDE superfamily endonuclease; Region: DDE_4; cl15789 1105112002786 DDE superfamily endonuclease; Region: DDE_4; cl15789 1105112002787 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105112002788 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105112002789 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105112002790 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 1105112002791 rRNA binding site [nucleotide binding]; other site 1105112002792 predicted 30S ribosome binding site; other site 1105112002793 Maf-like protein; Region: Maf; pfam02545 1105112002794 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 1105112002795 active site 1105112002796 dimer interface [polypeptide binding]; other site 1105112002797 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 1105112002798 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 1105112002799 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 1105112002800 active site 1105112002801 DNA binding site [nucleotide binding] 1105112002802 Int/Topo IB signature motif; other site 1105112002803 potential frameshift: common BLAST hit: gi|67459688|ref|YP_247312.1| phasin family protein 1105112002804 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 1105112002805 PLD-like domain; Region: PLDc_2; pfam13091 1105112002806 putative active site [active] 1105112002807 catalytic site [active] 1105112002808 potential frameshift: common BLAST hit: gi|67459690|ref|YP_247314.1| Poly(3-hydroxyalkanoate) synthetase 1105112002809 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 1105112002810 periplasmic folding chaperone; Provisional; Region: PRK10788 1105112002811 PPIC-type PPIASE domain; Region: Rotamase; cl08278 1105112002812 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 1105112002813 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 1105112002814 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105112002815 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; cl02529 1105112002816 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 1105112002817 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105112002818 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 1105112002819 potential frameshift: common BLAST hit: gi|229587187|ref|YP_002845688.1| Putative acyltransferase 1105112002820 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 1105112002821 active site 1105112002822 DNA repair proteins [DNA replication, recombination, and repair]; Region: RadC; COG2003 1105112002823 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 1105112002824 MPN+ (JAMM) motif; other site 1105112002825 Zinc-binding site [ion binding]; other site 1105112002826 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 1105112002827 The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine precursor; Region: GT_WbpL_WbcO_like; cd06854 1105112002828 Mg++ binding site [ion binding]; other site 1105112002829 putative catalytic motif [active] 1105112002830 putative substrate binding site [chemical binding]; other site 1105112002831 Protein of unknown function (DUF721); Region: DUF721; cl02324 1105112002832 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 1105112002833 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 1105112002834 Ferredoxin [Energy production and conversion]; Region: COG1146 1105112002835 4Fe-4S binding domain; Region: Fer4; cl02805 1105112002836 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 1105112002837 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 1105112002838 nucleoside/Zn binding site; other site 1105112002839 dimer interface [polypeptide binding]; other site 1105112002840 catalytic motif [active] 1105112002841 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 1105112002842 Cation efflux family; Region: Cation_efflux; cl00316 1105112002843 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 1105112002844 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 1105112002845 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 1105112002846 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of...; Region: ABC_Metallic_Cations; cd03235 1105112002847 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 1105112002848 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 1105112002849 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 1105112002850 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 1105112002851 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 1105112002852 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 1105112002853 dimer interface [polypeptide binding]; other site 1105112002854 ssDNA binding site [nucleotide binding]; other site 1105112002855 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1105112002856 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 1105112002857 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 1105112002858 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 1105112002859 heat shock protein 90; Provisional; Region: PRK05218 1105112002860 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 1105112002861 ATP binding site [chemical binding]; other site 1105112002862 Mg2+ binding site [ion binding]; other site 1105112002863 G-X-G motif; other site 1105112002864 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 1105112002865 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 1105112002866 substrate-cofactor binding pocket; other site 1105112002867 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105112002868 catalytic residue [active] 1105112002869 falcipain-2; Provisional; Region: PTZ00021 1105112002870 trigger factor; Provisional; Region: tig; PRK01490 1105112002871 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 1105112002872 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 1105112002873 GTPase CgtA; Reviewed; Region: obgE; PRK12299 1105112002874 GTP1/OBG; Region: GTP1_OBG; pfam01018 1105112002875 Obg GTPase; Region: Obg; cd01898 1105112002876 G1 box; other site 1105112002877 GTP/Mg2+ binding site [chemical binding]; other site 1105112002878 Switch I region; other site 1105112002879 G2 box; other site 1105112002880 G3 box; other site 1105112002881 Switch II region; other site 1105112002882 G4 box; other site 1105112002883 G5 box; other site 1105112002884 Escherichia coli (Ec) citrate synthase (CS) GltA_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS...; Region: EcCS_like; cd06114 1105112002885 dimer interface [polypeptide binding]; other site 1105112002886 Citrate synthase; Region: Citrate_synt; pfam00285 1105112002887 active site 1105112002888 citrylCoA binding site [chemical binding]; other site 1105112002889 NADH binding [chemical binding]; other site 1105112002890 cationic pore residues; other site 1105112002891 oxalacetate/citrate binding site [chemical binding]; other site 1105112002892 coenzyme A binding site [chemical binding]; other site 1105112002893 catalytic triad [active] 1105112002894 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 1105112002895 ATP10 protein; Region: ATP-synt_10; pfam05176 1105112002896 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 1105112002897 Fe-S cluster binding site [ion binding]; other site 1105112002898 active site 1105112002899 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1105112002900 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 1105112002901 RNA binding surface [nucleotide binding]; other site 1105112002902 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1105112002903 active site 1105112002904 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed; Region: PRK01544 1105112002905 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 1105112002906 S-adenosylmethionine binding site [chemical binding]; other site 1105112002907 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 1105112002908 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 1105112002909 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 1105112002910 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 1105112002911 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1105112002912 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 1105112002913 motif 1; other site 1105112002914 dimer interface [polypeptide binding]; other site 1105112002915 active site 1105112002916 motif 2; other site 1105112002917 motif 3; other site 1105112002918 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 1105112002919 oligomeric interface; other site 1105112002920 putative active site [active] 1105112002921 homodimer interface [polypeptide binding]; other site 1105112002922 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 1105112002923 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 1105112002924 potential frameshift: common BLAST hit: gi|67459741|ref|YP_247365.1| proline/betaine transporter 1105112002925 potential frameshift: common BLAST hit: gi|67459741|ref|YP_247365.1| proline/betaine transporter 1105112002926 potential frameshift: common BLAST hit: gi|157827810|ref|YP_001496874.1| oxidoreductase 1105112002927 Zinc-finger domain; Region: zf-CHCC; cl01821 1105112002928 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 1105112002929 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 1105112002930 ATP binding site [chemical binding]; other site 1105112002931 Mg2+ binding site [ion binding]; other site 1105112002932 G-X-G motif; other site 1105112002933 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 1105112002934 ATP binding site [chemical binding]; other site 1105112002935 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 1105112002936 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 1105112002937 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 1105112002938 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1105112002939 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 1105112002940 amidase catalytic site [active] 1105112002941 Zn binding residues [ion binding]; other site 1105112002942 substrate binding site [chemical binding]; other site 1105112002943 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 1105112002944 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 1105112002945 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; cl00630 1105112002946 putative active site [active] 1105112002947 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 1105112002948 potential frameshift: common BLAST hit: gi|157827849|ref|YP_001496913.1| Type I restriction-modification system methyltransferase subunit 1105112002949 potential frameshift: common BLAST hit: gi|157827849|ref|YP_001496913.1| Type I restriction-modification system methyltransferase subunit 1105112002950 potential frameshift: common BLAST hit: gi|157827849|ref|YP_001496913.1| Type I restriction-modification system methyltransferase subunit 1105112002951 potential frameshift: common BLAST hit: gi|238651120|ref|YP_002916978.1| putative type I restriction enzyme S subunit 1105112002952 potential frameshift: common BLAST hit: gi|15893271|ref|NP_360985.1| type I restriction enzyme S subunit 1105112002953 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 1105112002954 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 1105112002955 metal binding site [ion binding]; metal-binding site 1105112002956 dimer interface [polypeptide binding]; other site 1105112002957 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 1105112002958 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 1105112002959 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1105112002960 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 1105112002961 RelB antitoxin; Region: RelB; cl01171 1105112002962 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cd01610 1105112002963 active site 1105112002964 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 1105112002965 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 1105112002966 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105112002967 Walker A/P-loop; other site 1105112002968 ATP binding site [chemical binding]; other site 1105112002969 Q-loop/lid; other site 1105112002970 ABC transporter signature motif; other site 1105112002971 Walker B; other site 1105112002972 D-loop; other site 1105112002973 H-loop/switch region; other site 1105112002974 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 1105112002975 Predicted aspartyl protease [General function prediction only]; Region: COG3577 1105112002976 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 1105112002977 catalytic motif [active] 1105112002978 Catalytic residue [active] 1105112002979 YbaB/EbfC DNA-binding family; Region: YbaB_DNA_bd; cl00494 1105112002980 potential frameshift: common BLAST hit: gi|157965023|ref|YP_001499847.1| DNA polymerase III subunits gamma and tau 1105112002981 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 1105112002982 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 1105112002983 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 1105112002984 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 1105112002985 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 1105112002986 NAD(P) binding site [chemical binding]; other site 1105112002987 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 1105112002988 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 1105112002989 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 1105112002990 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1105112002991 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 1105112002992 DNA primase, catalytic core; Region: dnaG; TIGR01391 1105112002993 CHC2 zinc finger; Region: zf-CHC2; cl15369 1105112002994 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 1105112002995 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 1105112002996 active site 1105112002997 metal binding site [ion binding]; metal-binding site 1105112002998 interdomain interaction site; other site 1105112002999 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 1105112003000 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 1105112003001 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1105112003002 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1105112003003 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1105112003004 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 1105112003005 DNA binding residues [nucleotide binding] 1105112003006 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 1105112003007 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 1105112003008 dimerization interface 3.5A [polypeptide binding]; other site 1105112003009 active site 1105112003010 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 1105112003011 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 1105112003012 motif 1; other site 1105112003013 active site 1105112003014 motif 2; other site 1105112003015 motif 3; other site 1105112003016 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 1105112003017 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105112003018 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 1105112003019 TPR motif; other site 1105112003020 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 1105112003021 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105112003022 putative substrate translocation pore; other site 1105112003023 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 1105112003024 potential frameshift: common BLAST hit: gi|67459789|ref|YP_247413.1| prophage antirepressor 1105112003025 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 1105112003026 ferrochelatase; Reviewed; Region: hemH; PRK00035 1105112003027 Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_N; cd03411 1105112003028 C-terminal domain interface [polypeptide binding]; other site 1105112003029 active site 1105112003030 Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_C; cd00419 1105112003031 active site 1105112003032 N-terminal domain interface [polypeptide binding]; other site 1105112003033 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction...; Region: URO-D; cd00717 1105112003034 substrate binding site [chemical binding]; other site 1105112003035 active site 1105112003036 ParA-like protein; Provisional; Region: PHA02518 1105112003037 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 1105112003038 P-loop; other site 1105112003039 Magnesium ion binding site [ion binding]; other site 1105112003040 HicB family; Region: HicB; pfam05534 1105112003041 putative transposase; Provisional; Region: PRK09857 1105112003042 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 1105112003043 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 1105112003044 catalytic residues [active] 1105112003045 catalytic nucleophile [active] 1105112003046 Presynaptic Site I dimer interface [polypeptide binding]; other site 1105112003047 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 1105112003048 Synaptic Flat tetramer interface [polypeptide binding]; other site 1105112003049 Synaptic Site I dimer interface [polypeptide binding]; other site 1105112003050 DNA binding site [nucleotide binding] 1105112003051 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 1105112003052 DNA-binding interface [nucleotide binding]; DNA binding site 1105112003053 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 1105112003054 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 1105112003055 synthetase active site [active] 1105112003056 NTP binding site [chemical binding]; other site 1105112003057 metal binding site [ion binding]; metal-binding site 1105112003058 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 1105112003059 Leucine-rich repeats; other site 1105112003060 Substrate binding site [chemical binding]; other site 1105112003061 DnaA N-terminal domain; Region: DnaA_N; pfam11638