-- dump date 20120504_160706 -- class Genbank::misc_feature -- table misc_feature_note -- id note 1105101000001 Kinase/pyrophosphorylase; Region: Kinase-PPPase; cl00780 1105101000002 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 1105101000003 catalytic residues [active] 1105101000004 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 1105101000005 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 1105101000006 Walker A/P-loop; other site 1105101000007 ATP binding site [chemical binding]; other site 1105101000008 Q-loop/lid; other site 1105101000009 ABC transporter signature motif; other site 1105101000010 Walker B; other site 1105101000011 D-loop; other site 1105101000012 H-loop/switch region; other site 1105101000013 ABC-2 type transporter; Region: ABC2_membrane; cl11417 1105101000014 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 1105101000015 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 1105101000016 FAD binding pocket [chemical binding]; other site 1105101000017 FAD binding motif [chemical binding]; other site 1105101000018 phosphate binding motif [ion binding]; other site 1105101000019 beta-alpha-beta structure motif; other site 1105101000020 NAD binding pocket [chemical binding]; other site 1105101000021 Iron coordination center [ion binding]; other site 1105101000022 PemK-like protein; Region: PemK; cl00995 1105101000023 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 1105101000024 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 1105101000025 active site 1105101000026 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 1105101000027 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 1105101000028 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 1105101000029 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 1105101000030 trimer interface [polypeptide binding]; other site 1105101000031 active site 1105101000032 UDP-GlcNAc binding site [chemical binding]; other site 1105101000033 lipid binding site [chemical binding]; lipid-binding site 1105101000034 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 1105101000035 active site 1105101000036 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 1105101000037 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105101000038 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 1105101000039 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 1105101000040 FMN binding site [chemical binding]; other site 1105101000041 active site 1105101000042 catalytic residues [active] 1105101000043 substrate binding site [chemical binding]; other site 1105101000044 Putative catalytic NodB homology domain of uncharacterized protein RC0012 from Rickettsia conorii and its bacterial homologs; Region: CE4_RC0012_like; cd10963 1105101000045 NodB motif; other site 1105101000046 putative active site [active] 1105101000047 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 1105101000048 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 1105101000049 intersubunit interface [polypeptide binding]; other site 1105101000050 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 1105101000051 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 1105101000052 active site 1105101000053 NTP binding site [chemical binding]; other site 1105101000054 metal binding triad [ion binding]; metal-binding site 1105101000055 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 1105101000056 Competence protein; Region: Competence; cl00471 1105101000057 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 1105101000058 AAA domain; Region: AAA_22; pfam13401 1105101000059 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 1105101000060 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 1105101000061 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1105101000062 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 1105101000063 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1105101000064 ATP synthase subunit C; Region: ATP-synt_C; cl00466 1105101000065 ATP synthase A chain; Region: ATP-synt_A; cl00413 1105101000066 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; cl09754 1105101000067 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 1105101000068 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 1105101000069 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 1105101000070 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 1105101000071 S-adenosylmethionine binding site [chemical binding]; other site 1105101000072 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 1105101000073 recombination protein F; Reviewed; Region: recF; PRK00064 1105101000074 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101000075 Walker A/P-loop; other site 1105101000076 ATP binding site [chemical binding]; other site 1105101000077 Q-loop/lid; other site 1105101000078 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101000079 ABC transporter signature motif; other site 1105101000080 Walker B; other site 1105101000081 D-loop; other site 1105101000082 H-loop/switch region; other site 1105101000083 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cl15243 1105101000084 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cd00209 1105101000085 folate binding site [chemical binding]; other site 1105101000086 NADP+ binding site [chemical binding]; other site 1105101000087 potential frameshift: common BLAST hit: gi|157827907|ref|YP_001494149.1| folate synthesis bifunctional protein 1105101000088 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 1105101000089 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 1105101000090 Cu(I) binding site [ion binding]; other site 1105101000091 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 1105101000092 Colicin V production protein; Region: Colicin_V; cl00567 1105101000093 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 1105101000094 Protein of unknown function (DUF2748); Region: DUF2748; pfam10871 1105101000095 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105101000096 active site 1105101000097 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105101000098 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 1105101000099 Clp amino terminal domain; Region: Clp_N; pfam02861 1105101000100 Pal1 cell morphology protein; Region: Pal1; pfam08316 1105101000101 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 1105101000102 Walker A motif; other site 1105101000103 ATP binding site [chemical binding]; other site 1105101000104 Walker B motif; other site 1105101000105 arginine finger; other site 1105101000106 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 1105101000107 Walker A motif; other site 1105101000108 ATP binding site [chemical binding]; other site 1105101000109 Walker B motif; other site 1105101000110 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 1105101000111 UGMP family protein; Validated; Region: PRK09604 1105101000112 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 1105101000113 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 1105101000114 Fatty acid desaturase; Region: FA_desaturase; pfam00487 1105101000115 Di-iron ligands [ion binding]; other site 1105101000116 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 1105101000117 Helix-turn-helix domains; Region: HTH; cl00088 1105101000118 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 1105101000119 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 1105101000120 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 1105101000121 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 1105101000122 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 1105101000123 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 1105101000124 Ligand Binding Site [chemical binding]; other site 1105101000125 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101000126 FtsH Extracellular; Region: FtsH_ext; pfam06480 1105101000127 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 1105101000128 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 1105101000129 Walker A motif; other site 1105101000130 ATP binding site [chemical binding]; other site 1105101000131 Walker B motif; other site 1105101000132 arginine finger; other site 1105101000133 Peptidase family M41; Region: Peptidase_M41; pfam01434 1105101000134 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 1105101000135 cofactor binding site; other site 1105101000136 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 1105101000137 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 1105101000138 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 1105101000139 Uncharacterized conserved protein [Function unknown]; Region: COG1565 1105101000140 Putative S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_28; pfam02636 1105101000141 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101000142 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 1105101000143 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 1105101000144 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1105101000145 membrane protein insertase; Provisional; Region: PRK01318 1105101000146 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 1105101000147 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 1105101000148 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 1105101000149 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 1105101000150 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 1105101000151 active site 1105101000152 catalytic residues [active] 1105101000153 metal binding site [ion binding]; metal-binding site 1105101000154 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105101000155 ATP/ADP translocase [Energy production and conversion]; Region: COG3202; cl03940 1105101000156 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 1105101000157 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 1105101000158 putative substrate translocation pore; other site 1105101000159 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 1105101000160 active site 1105101000161 multimer interface [polypeptide binding]; other site 1105101000162 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 1105101000163 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105101000164 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 1105101000165 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 1105101000166 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 1105101000167 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 1105101000168 P-loop; other site 1105101000169 Magnesium ion binding site [ion binding]; other site 1105101000170 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 1105101000171 Magnesium ion binding site [ion binding]; other site 1105101000172 ParB-like nuclease domain; Region: ParBc; cl02129 1105101000173 KorB domain; Region: KorB; pfam08535 1105101000174 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 1105101000175 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 1105101000176 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 1105101000177 ABC transporter; Region: ABC_tran_2; pfam12848 1105101000178 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 1105101000179 Protein of unknown function (DUF2672); Region: DUF2672; pfam10878 1105101000180 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 1105101000181 NeuB family; Region: NeuB; cl00496 1105101000182 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 1105101000183 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 1105101000184 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 1105101000185 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 1105101000186 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 1105101000187 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 1105101000188 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 1105101000189 active site 1105101000190 HIGH motif; other site 1105101000191 KMSK motif region; other site 1105101000192 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1105101000193 tRNA binding surface [nucleotide binding]; other site 1105101000194 anticodon binding site; other site 1105101000195 Sporulation related domain; Region: SPOR; cl10051 1105101000196 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 1105101000197 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 1105101000198 CAP-like domain; other site 1105101000199 active site 1105101000200 primary dimer interface [polypeptide binding]; other site 1105101000201 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 1105101000202 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1105101000203 trimer interface [polypeptide binding]; other site 1105101000204 active site 1105101000205 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 1105101000206 SecA binding site; other site 1105101000207 Preprotein binding site; other site 1105101000208 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105101000209 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 1105101000210 active site 1105101000211 phosphorylation site [posttranslational modification] 1105101000212 intermolecular recognition site; other site 1105101000213 dimerization interface [polypeptide binding]; other site 1105101000214 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 1105101000215 DNA binding site [nucleotide binding] 1105101000216 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 1105101000217 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 1105101000218 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 1105101000219 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 1105101000220 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 1105101000221 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 1105101000222 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 1105101000223 EamA-like transporter family; Region: EamA; cl01037 1105101000224 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 1105101000225 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 1105101000226 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105101000227 putative substrate translocation pore; other site 1105101000228 Preprotein translocase SecG subunit; Region: SecG; cl09123 1105101000229 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 1105101000230 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 1105101000231 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1105101000232 active site 1105101000233 HIGH motif; other site 1105101000234 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1105101000235 KMSKS motif; other site 1105101000236 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1105101000237 tRNA binding surface [nucleotide binding]; other site 1105101000238 anticodon binding site; other site 1105101000239 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 1105101000240 rRNA interaction site [nucleotide binding]; other site 1105101000241 S8 interaction site; other site 1105101000242 putative laminin-1 binding site; other site 1105101000243 elongation factor Ts; Provisional; Region: tsf; PRK09377 1105101000244 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 1105101000245 Elongation factor TS; Region: EF_TS; pfam00889 1105101000246 Elongation factor TS; Region: EF_TS; pfam00889 1105101000247 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 1105101000248 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101000249 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 1105101000250 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 1105101000251 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 1105101000252 putative acyl-acceptor binding pocket; other site 1105101000253 aspartate aminotransferase; Provisional; Region: PRK05764 1105101000254 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 1105101000255 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105101000256 homodimer interface [polypeptide binding]; other site 1105101000257 catalytic residue [active] 1105101000258 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 1105101000259 Tetratricopeptide repeat; Region: TPR_16; pfam13432 1105101000260 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 1105101000261 VacJ like lipoprotein; Region: VacJ; cl01073 1105101000262 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; cl01074 1105101000263 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 1105101000264 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 1105101000265 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1105101000266 active site 1105101000267 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101000268 alanine racemase; Reviewed; Region: alr; PRK00053 1105101000269 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 1105101000270 active site 1105101000271 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1105101000272 dimer interface [polypeptide binding]; other site 1105101000273 substrate binding site [chemical binding]; other site 1105101000274 catalytic residues [active] 1105101000275 Permease; Region: Permease; cl00510 1105101000276 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 1105101000277 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101000278 Walker A/P-loop; other site 1105101000279 ATP binding site [chemical binding]; other site 1105101000280 Q-loop/lid; other site 1105101000281 ABC transporter signature motif; other site 1105101000282 Walker B; other site 1105101000283 D-loop; other site 1105101000284 H-loop/switch region; other site 1105101000285 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 1105101000286 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 1105101000287 Predicted GTPase [General function prediction only]; Region: COG0218 1105101000288 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 1105101000289 G1 box; other site 1105101000290 GTP/Mg2+ binding site [chemical binding]; other site 1105101000291 Switch I region; other site 1105101000292 G2 box; other site 1105101000293 G3 box; other site 1105101000294 Switch II region; other site 1105101000295 G4 box; other site 1105101000296 G5 box; other site 1105101000297 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 1105101000298 nucleotide binding site [chemical binding]; other site 1105101000299 substrate binding site [chemical binding]; other site 1105101000300 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 1105101000301 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 1105101000302 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1105101000303 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101000304 Walker A motif; other site 1105101000305 ATP binding site [chemical binding]; other site 1105101000306 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 1105101000307 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 1105101000308 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 1105101000309 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 1105101000310 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 1105101000311 aspartyl-tRNA synthetase; Provisional; Region: PTZ00401 1105101000312 potential frameshift: common BLAST hit: gi|67458488|ref|YP_246112.1| phosphate acetyltransferase 1105101000313 potential frameshift: common BLAST hit: gi|67458489|ref|YP_246113.1| acetate kinase 1105101000314 potential frameshift: common BLAST hit: gi|67458489|ref|YP_246113.1| acetate kinase 1105101000315 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 1105101000316 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 1105101000317 Uncharacterized protein conserved in bacteria (DUF2312); Region: DUF2312; cl11480 1105101000318 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 1105101000319 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 1105101000320 Protein export membrane protein; Region: SecD_SecF; cl14618 1105101000321 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 1105101000322 SLBB domain; Region: SLBB; pfam10531 1105101000323 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 1105101000324 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 1105101000325 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 1105101000326 Catalytic site [active] 1105101000327 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 1105101000328 ribonuclease III; Reviewed; Region: rnc; PRK00102 1105101000329 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 1105101000330 dimerization interface [polypeptide binding]; other site 1105101000331 active site 1105101000332 metal binding site [ion binding]; metal-binding site 1105101000333 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 1105101000334 dsRNA binding site [nucleotide binding]; other site 1105101000335 GTPase Era; Provisional; Region: era; PRK15494 1105101000336 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101000337 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 1105101000338 G1 box; other site 1105101000339 GTP/Mg2+ binding site [chemical binding]; other site 1105101000340 Switch I region; other site 1105101000341 G2 box; other site 1105101000342 Switch II region; other site 1105101000343 G3 box; other site 1105101000344 G4 box; other site 1105101000345 G5 box; other site 1105101000346 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 1105101000347 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 1105101000348 active site 1105101000349 putative DNA-binding cleft [nucleotide binding]; other site 1105101000350 dimer interface [polypeptide binding]; other site 1105101000351 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 1105101000352 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 1105101000353 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl08495 1105101000354 potential frameshift: common BLAST hit: gi|165932732|ref|YP_001649521.1| nucleotidyltransferase 1105101000355 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 1105101000356 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 1105101000357 AAA domain; Region: AAA_31; pfam13614 1105101000358 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 1105101000359 Walker A motif; other site 1105101000360 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 1105101000361 HflK protein; Region: hflK; TIGR01933 1105101000362 FtsH protease regulator HflC; Provisional; Region: PRK11029 1105101000363 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 1105101000364 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 1105101000365 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 1105101000366 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 1105101000367 protein binding site [polypeptide binding]; other site 1105101000368 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 1105101000369 protein binding site [polypeptide binding]; other site 1105101000370 hypothetical protein; Validated; Region: PRK01415 1105101000371 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 1105101000372 active site residue [active] 1105101000373 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 1105101000374 Iron-sulfur protein interface; other site 1105101000375 proximal quinone binding site [chemical binding]; other site 1105101000376 SdhD (CybS) interface [polypeptide binding]; other site 1105101000377 proximal heme binding site [chemical binding]; other site 1105101000378 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 1105101000379 putative SdhC subunit interface [polypeptide binding]; other site 1105101000380 putative proximal heme binding site [chemical binding]; other site 1105101000381 putative Iron-sulfur protein interface [polypeptide binding]; other site 1105101000382 putative proximal quinone binding site; other site 1105101000383 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 1105101000384 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105101000385 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 1105101000386 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1105101000387 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 1105101000388 dimer interface [polypeptide binding]; other site 1105101000389 conserved gate region; other site 1105101000390 putative PBP binding loops; other site 1105101000391 ABC-ATPase subunit interface; other site 1105101000392 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 1105101000393 S17 interaction site [polypeptide binding]; other site 1105101000394 S8 interaction site; other site 1105101000395 16S rRNA interaction site [nucleotide binding]; other site 1105101000396 streptomycin interaction site [chemical binding]; other site 1105101000397 23S rRNA interaction site [nucleotide binding]; other site 1105101000398 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 1105101000399 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 1105101000400 elongation factor G; Reviewed; Region: PRK00007 1105101000401 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 1105101000402 G1 box; other site 1105101000403 putative GEF interaction site [polypeptide binding]; other site 1105101000404 GTP/Mg2+ binding site [chemical binding]; other site 1105101000405 Switch I region; other site 1105101000406 G2 box; other site 1105101000407 G3 box; other site 1105101000408 Switch II region; other site 1105101000409 G4 box; other site 1105101000410 G5 box; other site 1105101000411 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 1105101000412 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 1105101000413 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 1105101000414 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 1105101000415 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 1105101000416 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 1105101000417 putative homodimer interface [polypeptide binding]; other site 1105101000418 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 1105101000419 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 1105101000420 23S rRNA interface [nucleotide binding]; other site 1105101000421 putative thiostrepton binding site; other site 1105101000422 L7/L12 interface [polypeptide binding]; other site 1105101000423 L25 interface [polypeptide binding]; other site 1105101000424 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 1105101000425 mRNA/rRNA interface [nucleotide binding]; other site 1105101000426 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 1105101000427 23S rRNA interface [nucleotide binding]; other site 1105101000428 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 1105101000429 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 1105101000430 core dimer interface [polypeptide binding]; other site 1105101000431 peripheral dimer interface [polypeptide binding]; other site 1105101000432 L10 interface [polypeptide binding]; other site 1105101000433 L11 interface [polypeptide binding]; other site 1105101000434 putative EF-Tu interaction site [polypeptide binding]; other site 1105101000435 putative EF-G interaction site [polypeptide binding]; other site 1105101000436 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 1105101000437 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 1105101000438 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 1105101000439 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 1105101000440 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 1105101000441 RPB10 interaction site [polypeptide binding]; other site 1105101000442 RPB11 interaction site [polypeptide binding]; other site 1105101000443 RPB3 interaction site [polypeptide binding]; other site 1105101000444 RPB12 interaction site [polypeptide binding]; other site 1105101000445 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 1105101000446 RPB3 interaction site [polypeptide binding]; other site 1105101000447 RPB1 interaction site [polypeptide binding]; other site 1105101000448 RPB11 interaction site [polypeptide binding]; other site 1105101000449 RPB10 interaction site [polypeptide binding]; other site 1105101000450 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 1105101000451 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 1105101000452 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 1105101000453 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 1105101000454 DNA-directed RNA polymerase subunit beta'; Provisional; Region: rpoC2; PRK02597 1105101000455 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 1105101000456 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 1105101000457 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 1105101000458 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 1105101000459 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 1105101000460 DNA binding site [nucleotide binding] 1105101000461 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 1105101000462 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 1105101000463 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101000464 multifunctional aminopeptidase A; Provisional; Region: PRK00913 1105101000465 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 1105101000466 interface (dimer of trimers) [polypeptide binding]; other site 1105101000467 Substrate-binding/catalytic site; other site 1105101000468 Zn-binding sites [ion binding]; other site 1105101000469 ATPase MipZ; Region: MipZ; pfam09140 1105101000470 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 1105101000471 P-loop; other site 1105101000472 Magnesium ion binding site [ion binding]; other site 1105101000473 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 1105101000474 Magnesium ion binding site [ion binding]; other site 1105101000475 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 1105101000476 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 1105101000477 dimer interface [polypeptide binding]; other site 1105101000478 anticodon binding site; other site 1105101000479 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 1105101000480 homodimer interface [polypeptide binding]; other site 1105101000481 motif 1; other site 1105101000482 active site 1105101000483 motif 2; other site 1105101000484 GAD domain; Region: GAD; pfam02938 1105101000485 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 1105101000486 active site 1105101000487 motif 3; other site 1105101000488 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 1105101000489 dihydrodipicolinate reductase; Provisional; Region: PRK00048 1105101000490 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105101000491 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 1105101000492 Flavin Reductases; Region: FlaRed; cl00801 1105101000493 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1105101000494 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 1105101000495 substrate binding pocket [chemical binding]; other site 1105101000496 membrane-bound complex binding site; other site 1105101000497 hinge residues; other site 1105101000498 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 1105101000499 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 1105101000500 GatB domain; Region: GatB_Yqey; cl11497 1105101000501 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 1105101000502 Amidase; Region: Amidase; cl11426 1105101000503 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 1105101000504 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain superfamily; Region: NTP-PPase; cl16941 1105101000505 ribosome recycling factor; Reviewed; Region: frr; PRK00083 1105101000506 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 1105101000507 hinge region; other site 1105101000508 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 1105101000509 putative nucleotide binding site [chemical binding]; other site 1105101000510 uridine monophosphate binding site [chemical binding]; other site 1105101000511 homohexameric interface [polypeptide binding]; other site 1105101000512 Na+/H+ ion antiporter subunit; Region: MNHE; cl00807 1105101000513 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1105101000514 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 1105101000515 putative substrate translocation pore; other site 1105101000516 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 1105101000517 Protein of unknown function (DUF2674); Region: DUF2674; pfam10879 1105101000518 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 1105101000519 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 1105101000520 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 1105101000521 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 1105101000522 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 1105101000523 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 1105101000524 Surface antigen; Region: Bac_surface_Ag; cl03097 1105101000525 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 1105101000526 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 1105101000527 active site 1105101000528 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 1105101000529 protein binding site [polypeptide binding]; other site 1105101000530 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 1105101000531 putative substrate binding region [chemical binding]; other site 1105101000532 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 1105101000533 putative RNA binding site [nucleotide binding]; other site 1105101000534 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 1105101000535 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 1105101000536 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 1105101000537 putative coenzyme Q binding site [chemical binding]; other site 1105101000538 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101000539 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 1105101000540 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 1105101000541 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385; cl00611 1105101000542 RNA methyltransferase; Region: Methyltrans_RNA; pfam04452 1105101000543 Domain of unknown function (DUF378); Region: DUF378; cl00943 1105101000544 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105101000545 Protein export membrane protein; Region: SecD_SecF; cl14618 1105101000546 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 1105101000547 IHF dimer interface [polypeptide binding]; other site 1105101000548 IHF - DNA interface [nucleotide binding]; other site 1105101000549 DNA polymerase III subunit delta'; Validated; Region: PRK06581 1105101000550 signal recognition particle protein; Provisional; Region: PRK10867 1105101000551 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 1105101000552 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 1105101000553 P loop; other site 1105101000554 GTP binding site [chemical binding]; other site 1105101000555 Signal peptide binding domain; Region: SRP_SPB; pfam02978 1105101000556 potential frameshift: common BLAST hit: gi|51473374|ref|YP_067131.1| post-proline cleaving enzyme 1105101000557 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105101000558 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105101000559 potential frameshift: common BLAST hit: gi|67459496|ref|YP_247120.1| prolyl endopeptidase 1105101000560 coproporphyrinogen III oxidase; Provisional; Region: PRK06582 1105101000561 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 1105101000562 FeS/SAM binding site; other site 1105101000563 HemN C-terminal domain; Region: HemN_C; pfam06969 1105101000564 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 1105101000565 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105101000566 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 1105101000567 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1105101000568 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 1105101000569 CutA1 divalent ion tolerance protein; Region: CutA1; cl00584 1105101000570 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 1105101000571 active site 1105101000572 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 1105101000573 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 1105101000574 E3 interaction surface; other site 1105101000575 lipoyl attachment site [posttranslational modification]; other site 1105101000576 e3 binding domain; Region: E3_binding; pfam02817 1105101000577 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 1105101000578 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 1105101000579 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 1105101000580 TPP-binding site [chemical binding]; other site 1105101000581 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 1105101000582 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 1105101000583 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 1105101000584 active site 1105101000585 Zn binding site [ion binding]; other site 1105101000586 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 1105101000587 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 1105101000588 Walker A/P-loop; other site 1105101000589 ATP binding site [chemical binding]; other site 1105101000590 Q-loop/lid; other site 1105101000591 Allexivirus 40kDa protein; Region: Allexi_40kDa; pfam05549 1105101000592 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 1105101000593 ABC transporter signature motif; other site 1105101000594 Walker B; other site 1105101000595 D-loop; other site 1105101000596 H-loop/switch region; other site 1105101000597 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 1105101000598 Tetratricopeptide repeat; Region: TPR_6; pfam13174 1105101000599 ChaB; Region: ChaB; cl01887 1105101000600 ChaB; Region: ChaB; cl01887 1105101000601 chaperone protein DnaJ; Provisional; Region: PRK14300 1105101000602 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 1105101000603 HSP70 interaction site [polypeptide binding]; other site 1105101000604 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 1105101000605 substrate binding site [polypeptide binding]; other site 1105101000606 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 1105101000607 Zn binding sites [ion binding]; other site 1105101000608 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 1105101000609 dimer interface [polypeptide binding]; other site 1105101000610 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 1105101000611 FGGY family of carbohydrate kinases; Region: FGGY; cl08364 1105101000612 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 1105101000613 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 1105101000614 Lipopolysaccharide-assembly; Region: LptE; cl01125 1105101000615 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 1105101000616 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 1105101000617 diiron binding motif [ion binding]; other site 1105101000618 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 1105101000619 Subunit III/VIIa interface [polypeptide binding]; other site 1105101000620 Phospholipid binding site [chemical binding]; other site 1105101000621 Subunit I/III interface [polypeptide binding]; other site 1105101000622 Subunit III/VIb interface [polypeptide binding]; other site 1105101000623 Subunit III/VIa interface; other site 1105101000624 Subunit III/Vb interface [polypeptide binding]; other site 1105101000625 TrbC/VIRB2 family; Region: TrbC; cl01583 1105101000626 zinc-ribbon domain; Region: zinc_ribbon_5; cl11777 1105101000627 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 1105101000628 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 1105101000629 trimer interface [polypeptide binding]; other site 1105101000630 active site 1105101000631 substrate binding site [chemical binding]; other site 1105101000632 CoA binding site [chemical binding]; other site 1105101000633 potential frameshift: common BLAST hit: gi|15892172|ref|NP_359886.1| bifunctional penicillin-binding protein 1C 1105101000634 potential frameshift: common BLAST hit: gi|229586439|ref|YP_002844940.1| Bifunctional penicillin-binding protein 1C 1105101000635 potential frameshift: common BLAST hit: gi|15892172|ref|NP_359886.1| bifunctional penicillin-binding protein 1C 1105101000636 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 1105101000637 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 1105101000638 Ligand Binding Site [chemical binding]; other site 1105101000639 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 1105101000640 NMT1-like family; Region: NMT1_2; cl15260 1105101000641 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 1105101000642 catalytic loop [active] 1105101000643 iron binding site [ion binding]; other site 1105101000644 chaperone protein HscA; Provisional; Region: hscA; PRK01433 1105101000645 co-chaperone HscB; Provisional; Region: hscB; PRK01356 1105101000646 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 1105101000647 HSP70 interaction site [polypeptide binding]; other site 1105101000648 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 1105101000649 RNA/DNA hybrid binding site [nucleotide binding]; other site 1105101000650 active site 1105101000651 excinuclease ABC subunit B; Provisional; Region: PRK05298 1105101000652 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 1105101000653 ATP binding site [chemical binding]; other site 1105101000654 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 1105101000655 nucleotide binding region [chemical binding]; other site 1105101000656 ATP-binding site [chemical binding]; other site 1105101000657 Ultra-violet resistance protein B; Region: UvrB; pfam12344 1105101000658 UvrB/uvrC motif; Region: UVR; pfam02151 1105101000659 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 1105101000660 GSH binding site [chemical binding]; other site 1105101000661 catalytic residues [active] 1105101000662 potential frameshift: common BLAST hit: gi|157964270|ref|YP_001499094.1| multidrug resistance protein Atm1 1105101000663 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 1105101000664 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101000665 Walker A/P-loop; other site 1105101000666 ATP binding site [chemical binding]; other site 1105101000667 Q-loop/lid; other site 1105101000668 DNA gyrase subunit A; Validated; Region: PRK05560 1105101000669 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 1105101000670 CAP-like domain; other site 1105101000671 active site 1105101000672 primary dimer interface [polypeptide binding]; other site 1105101000673 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105101000674 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105101000675 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105101000676 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105101000677 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105101000678 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 1105101000679 Iron-sulphur cluster assembly; Region: Fe-S_assembly; cl01123 1105101000680 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 1105101000681 active site 1105101000682 catalytic residues [active] 1105101000683 metal binding site [ion binding]; metal-binding site 1105101000684 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 1105101000685 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 1105101000686 putative active site [active] 1105101000687 substrate binding site [chemical binding]; other site 1105101000688 putative cosubstrate binding site; other site 1105101000689 catalytic site [active] 1105101000690 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 1105101000691 substrate binding site [chemical binding]; other site 1105101000692 potential RNA of insufficient length (23S ribosomal RNA) 1105101000693 potential frameshift: common BLAST hit: gi|157826977|ref|YP_001496041.1| capsular polysaccharide biosynthesis protein 1105101000694 Predicted ATPase [General function prediction only]; Region: COG1485 1105101000695 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 1105101000696 Walker A motif; other site 1105101000697 ATP binding site [chemical binding]; other site 1105101000698 Walker B motif; other site 1105101000699 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 1105101000700 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 1105101000701 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 1105101000702 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 1105101000703 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1105101000704 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 1105101000705 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101000706 Walker A/P-loop; other site 1105101000707 ATP binding site [chemical binding]; other site 1105101000708 Q-loop/lid; other site 1105101000709 ABC transporter signature motif; other site 1105101000710 Walker B; other site 1105101000711 D-loop; other site 1105101000712 H-loop/switch region; other site 1105101000713 Protein of unknown function (DUF2671); Region: DUF2671; pfam10877 1105101000714 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 1105101000715 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 1105101000716 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 1105101000717 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 1105101000718 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 1105101000719 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 1105101000720 putative metal binding site; other site 1105101000721 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1105101000722 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1105101000723 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1105101000724 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 1105101000725 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 1105101000726 ATP binding site [chemical binding]; other site 1105101000727 active site 1105101000728 substrate binding site [chemical binding]; other site 1105101000729 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 1105101000730 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 1105101000731 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 1105101000732 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 1105101000733 active site 1105101000734 dimer interface [polypeptide binding]; other site 1105101000735 motif 1; other site 1105101000736 motif 2; other site 1105101000737 motif 3; other site 1105101000738 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 1105101000739 anticodon binding site; other site 1105101000740 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101000741 Walker A/P-loop; other site 1105101000742 ATP binding site [chemical binding]; other site 1105101000743 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101000744 ABC transporter signature motif; other site 1105101000745 Walker B; other site 1105101000746 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101000747 H-loop/switch region; other site 1105101000748 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); Region: DUF2310; cl02380 1105101000749 Protein of unknown function (DUF2660); Region: DUF2660; pfam10859 1105101000750 glutamyl-tRNA(Gln) amidotransferase subunit E; Validated; Region: PRK04028 1105101000751 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1105101000752 Protein of unknown function (DUF2497); Region: DUF2497; cl11534 1105101000753 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 1105101000754 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 1105101000755 DNA topoisomerase IV, B subunit, proteobacterial; Region: parE_Gneg; TIGR01055 1105101000756 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 1105101000757 ATP binding site [chemical binding]; other site 1105101000758 Mg2+ binding site [ion binding]; other site 1105101000759 G-X-G motif; other site 1105101000760 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 1105101000761 anchoring element; other site 1105101000762 dimer interface [polypeptide binding]; other site 1105101000763 ATP binding site [chemical binding]; other site 1105101000764 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 1105101000765 active site 1105101000766 metal binding site [ion binding]; metal-binding site 1105101000767 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1105101000768 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 1105101000769 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 1105101000770 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 1105101000771 protein binding site [polypeptide binding]; other site 1105101000772 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 1105101000773 Catalytic dyad [active] 1105101000774 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 1105101000775 dimer interface [polypeptide binding]; other site 1105101000776 phosphorylation site [posttranslational modification] 1105101000777 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 1105101000778 ATP binding site [chemical binding]; other site 1105101000779 Mg2+ binding site [ion binding]; other site 1105101000780 G-X-G motif; other site 1105101000781 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 1105101000782 Protein of unknown function (DUF2659); Region: DUF2659; pfam10858 1105101000783 FOG: WD40-like repeat [Function unknown]; Region: COG1520 1105101000784 Beta-barrel assembly machinery (Bam) complex component B and related proteins; Region: BamB_YfgL; cd10276 1105101000785 Trp docking motif [polypeptide binding]; other site 1105101000786 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 1105101000787 23S rRNA interface [nucleotide binding]; other site 1105101000788 L3 interface [polypeptide binding]; other site 1105101000789 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 1105101000790 potential protein location (hypothetical protein RPK_01760 [Rickettsia rickettsii str. Hlp#2]) that overlaps RNA (tRNA-M) 1105101000791 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; cl00942 1105101000792 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 1105101000793 DCoH tetramer interaction site [polypeptide binding]; other site 1105101000794 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 1105101000795 putative active site [active] 1105101000796 Ap4A binding site [chemical binding]; other site 1105101000797 nudix motif; other site 1105101000798 putative metal binding site [ion binding]; other site 1105101000799 response regulator PleD; Reviewed; Region: pleD; PRK09581 1105101000800 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 1105101000801 active site 1105101000802 phosphorylation site [posttranslational modification] 1105101000803 intermolecular recognition site; other site 1105101000804 dimerization interface [polypeptide binding]; other site 1105101000805 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 1105101000806 active site 1105101000807 phosphorylation site [posttranslational modification] 1105101000808 intermolecular recognition site; other site 1105101000809 dimerization interface [polypeptide binding]; other site 1105101000810 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1105101000811 metal binding site [ion binding]; metal-binding site 1105101000812 active site 1105101000813 I-site; other site 1105101000814 elongation factor P; Validated; Region: PRK00529 1105101000815 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 1105101000816 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 1105101000817 RNA binding site [nucleotide binding]; other site 1105101000818 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 1105101000819 RNA binding site [nucleotide binding]; other site 1105101000820 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 1105101000821 active site 1105101000822 Domain of unknown function (DUF2610); Region: DUF2610; pfam11020 1105101000823 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 1105101000824 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 1105101000825 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 1105101000826 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 1105101000827 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 1105101000828 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 1105101000829 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105101000830 BolA-like protein; Region: BolA; cl00386 1105101000831 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 1105101000832 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 1105101000833 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105101000834 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105101000835 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105101000836 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 1105101000837 FAD binding domain; Region: FAD_binding_4; pfam01565 1105101000838 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 1105101000839 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 1105101000840 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 1105101000841 ATP-grasp domain; Region: ATP-grasp_4; cl03087 1105101000842 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 1105101000843 Cell division protein FtsQ; Region: FtsQ; pfam03799 1105101000844 cell division protein FtsA; Region: ftsA; TIGR01174 1105101000845 Cell division protein FtsA; Region: FtsA; cl11496 1105101000846 Cell division protein FtsA; Region: FtsA; cl11496 1105101000847 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 1105101000848 Cytochrome c; Region: Cytochrom_C; cl11414 1105101000849 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 1105101000850 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 1105101000851 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 1105101000852 RNA binding site [nucleotide binding]; other site 1105101000853 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 1105101000854 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 1105101000855 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 1105101000856 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 1105101000857 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1105101000858 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 1105101000859 RNA binding surface [nucleotide binding]; other site 1105101000860 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1105101000861 active site 1105101000862 potential frameshift: common BLAST hit: gi|15892268|ref|NP_359982.1| penicillin-binding protein 4* 1105101000863 potential frameshift: common BLAST hit: gi|341583576|ref|YP_004764067.1| penicillin-binding protein 4* 1105101000864 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 1105101000865 putative catalytic site [active] 1105101000866 putative phosphate binding site [ion binding]; other site 1105101000867 active site 1105101000868 metal binding site A [ion binding]; metal-binding site 1105101000869 DNA binding site [nucleotide binding] 1105101000870 putative AP binding site [nucleotide binding]; other site 1105101000871 putative metal binding site B [ion binding]; other site 1105101000872 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 1105101000873 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 1105101000874 tetramer interface [polypeptide binding]; other site 1105101000875 TPP-binding site [chemical binding]; other site 1105101000876 heterodimer interface [polypeptide binding]; other site 1105101000877 phosphorylation loop region [posttranslational modification] 1105101000878 pyruvate dehydrogenase subunit beta; Validated; Region: PRK09212 1105101000879 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 1105101000880 alpha subunit interface [polypeptide binding]; other site 1105101000881 TPP binding site [chemical binding]; other site 1105101000882 heterodimer interface [polypeptide binding]; other site 1105101000883 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1105101000884 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 1105101000885 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 1105101000886 G1 box; other site 1105101000887 putative GEF interaction site [polypeptide binding]; other site 1105101000888 GTP/Mg2+ binding site [chemical binding]; other site 1105101000889 Switch I region; other site 1105101000890 G2 box; other site 1105101000891 G3 box; other site 1105101000892 Switch II region; other site 1105101000893 G4 box; other site 1105101000894 G5 box; other site 1105101000895 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 1105101000896 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 1105101000897 haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; Region: HAD-SF-IA-v3; TIGR01509 1105101000898 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: HlpA; COG2825 1105101000899 isocitrate dehydrogenase; Validated; Region: PRK09222 1105101000900 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 1105101000901 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; cl00583 1105101000902 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12507 1105101000903 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 1105101000904 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 1105101000905 Protein of unknown function (DUF2670); Region: DUF2670; pfam10875 1105101000906 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 1105101000907 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 1105101000908 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 1105101000909 [2Fe-2S] cluster binding site [ion binding]; other site 1105101000910 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 1105101000911 Qi binding site; other site 1105101000912 cytochrome b; Provisional; Region: CYTB; MTH00191 1105101000913 intrachain domain interface; other site 1105101000914 interchain domain interface [polypeptide binding]; other site 1105101000915 heme bH binding site [chemical binding]; other site 1105101000916 heme bL binding site [chemical binding]; other site 1105101000917 Qo binding site; other site 1105101000918 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 1105101000919 interchain domain interface [polypeptide binding]; other site 1105101000920 intrachain domain interface; other site 1105101000921 Qi binding site; other site 1105101000922 Qo binding site; other site 1105101000923 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 1105101000924 catalytic site [active] 1105101000925 metal binding site [ion binding]; metal-binding site 1105101000926 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 1105101000927 Cytochrome c; Region: Cytochrom_C; cl11414 1105101000928 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 1105101000929 putative dimer interface [polypeptide binding]; other site 1105101000930 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 1105101000931 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105101000932 RF-1 domain; Region: RF-1; cl02875 1105101000933 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 1105101000934 RF-1 domain; Region: RF-1; cl02875 1105101000935 GTP-binding protein LepA; Provisional; Region: PRK05433 1105101000936 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 1105101000937 G1 box; other site 1105101000938 putative GEF interaction site [polypeptide binding]; other site 1105101000939 GTP/Mg2+ binding site [chemical binding]; other site 1105101000940 Switch I region; other site 1105101000941 G2 box; other site 1105101000942 G3 box; other site 1105101000943 Switch II region; other site 1105101000944 G4 box; other site 1105101000945 G5 box; other site 1105101000946 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 1105101000947 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 1105101000948 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 1105101000949 potential frameshift: common BLAST hit: gi|15892293|ref|NP_360007.1| ATP-dependent protease subunit C (ClpC) 1105101000950 potential frameshift: common BLAST hit: gi|67458839|ref|YP_246463.1| NACHT domain-containing protein 1105101000951 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101000952 AAA domain; Region: AAA_18; pfam13238 1105101000953 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 1105101000954 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs'; Region: NTP-PPase_MazG_Cterm; cd11529 1105101000955 active site 1105101000956 homodimer interface [polypeptide binding]; other site 1105101000957 putative chemical substrate binding site [chemical binding]; other site 1105101000958 metal binding site [ion binding]; metal-binding site 1105101000959 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 1105101000960 Substrate binding site; other site 1105101000961 Mg++ binding site; other site 1105101000962 Transcriptional regulator; Region: Transcrip_reg; cl00361 1105101000963 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 1105101000964 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1105101000965 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 1105101000966 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1105101000967 Protein of unknown function (DUF2532); Region: DUF2532; pfam10811 1105101000968 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 1105101000969 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 1105101000970 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 1105101000971 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 1105101000972 glycerol-3-phosphate dehydrogenase, anaerobic, B subunit; Region: glycerol3P_GlpB; TIGR03378 1105101000973 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105101000974 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1105101000975 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 1105101000976 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 1105101000977 catalytic site [active] 1105101000978 putative active site [active] 1105101000979 putative substrate binding site [chemical binding]; other site 1105101000980 HRDC domain; Region: HRDC; cl02578 1105101000981 Uncharacterized ACR, YagE family COG1723; Region: DUF155; cl00751 1105101000982 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 1105101000983 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 1105101000984 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 1105101000985 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 1105101000986 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 1105101000987 potential frameshift: common BLAST hit: gi|15892625|ref|NP_360339.1| sodium/pantothenate symporter 1105101000988 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 1105101000989 dimer interface [polypeptide binding]; other site 1105101000990 phosphorylation site [posttranslational modification] 1105101000991 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 1105101000992 G-X-G motif; other site 1105101000993 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 1105101000994 dimer interface [polypeptide binding]; other site 1105101000995 catalytic triad [active] 1105101000996 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 1105101000997 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 1105101000998 domain interfaces; other site 1105101000999 active site 1105101001000 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101001001 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 1105101001002 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 1105101001003 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 1105101001004 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 1105101001005 active site 1105101001006 HIGH motif; other site 1105101001007 dimer interface [polypeptide binding]; other site 1105101001008 KMSKS motif; other site 1105101001009 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1105101001010 putative acyl-acceptor binding pocket; other site 1105101001011 Protein required for attachment to host cells; Region: Host_attach; cl02398 1105101001012 RelB antitoxin; Region: RelB; cl01171 1105101001013 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 1105101001014 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 1105101001015 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemY; COG3071 1105101001016 HemY protein N-terminus; Region: HemY_N; pfam07219 1105101001017 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 1105101001018 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 1105101001019 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 1105101001020 active site 1105101001021 LysE type translocator; Region: LysE; cl00565 1105101001022 muropeptide transporter; Validated; Region: ampG; PRK11010 1105101001023 AmpG-like permease; Region: 2A0125; TIGR00901 1105101001024 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 1105101001025 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 1105101001026 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105101001027 ATP/ADP translocase [Energy production and conversion]; Region: COG3202; cl03940 1105101001028 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 1105101001029 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 1105101001030 substrate binding pocket [chemical binding]; other site 1105101001031 chain length determination region; other site 1105101001032 substrate-Mg2+ binding site; other site 1105101001033 catalytic residues [active] 1105101001034 aspartate-rich region 1; other site 1105101001035 active site lid residues [active] 1105101001036 aspartate-rich region 2; other site 1105101001037 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 1105101001038 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 1105101001039 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 1105101001040 active site 1105101001041 Spore germination protein; Region: Spore_permease; cl15802 1105101001042 arginine:agmatin antiporter; Provisional; Region: PRK10644 1105101001043 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 1105101001044 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 1105101001045 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 1105101001046 trimerization site [polypeptide binding]; other site 1105101001047 active site 1105101001048 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 1105101001049 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 1105101001050 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1105101001051 catalytic residue [active] 1105101001052 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 1105101001053 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 1105101001054 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1105101001055 Predicted transcriptional regulator [Transcription]; Region: COG1959 1105101001056 Helix-turn-helix domains; Region: HTH; cl00088 1105101001057 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 1105101001058 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105101001059 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1105101001060 Coenzyme A binding pocket [chemical binding]; other site 1105101001061 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 1105101001062 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 1105101001063 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 1105101001064 homotetramer interface [polypeptide binding]; other site 1105101001065 FMN binding site [chemical binding]; other site 1105101001066 homodimer contacts [polypeptide binding]; other site 1105101001067 putative active site [active] 1105101001068 putative substrate binding site [chemical binding]; other site 1105101001069 Clp protease; Region: CLP_protease; pfam00574 1105101001070 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 1105101001071 oligomer interface [polypeptide binding]; other site 1105101001072 active site residues [active] 1105101001073 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 1105101001074 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 1105101001075 RNA binding site [nucleotide binding]; other site 1105101001076 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 1105101001077 RNA binding site [nucleotide binding]; other site 1105101001078 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 1105101001079 RNA binding site [nucleotide binding]; other site 1105101001080 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 1105101001081 RNA binding site [nucleotide binding]; other site 1105101001082 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 1105101001083 RNA binding site [nucleotide binding]; other site 1105101001084 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 1105101001085 RNA binding site [nucleotide binding]; other site 1105101001086 cytidylate kinase; Provisional; Region: cmk; PRK00023 1105101001087 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 1105101001088 CMP-binding site; other site 1105101001089 The sites determining sugar specificity; other site 1105101001090 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 1105101001091 non-specific DNA binding site [nucleotide binding]; other site 1105101001092 salt bridge; other site 1105101001093 sequence-specific DNA binding site [nucleotide binding]; other site 1105101001094 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 1105101001095 Bacteriophage head to tail connecting protein; Region: Head-tail_con; cl10251 1105101001096 Bacteriophage head to tail connecting protein; Region: Head-tail_con; cl10251 1105101001097 Protein of unknown function (DUF328); Region: DUF328; cl01143 1105101001098 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 1105101001099 IHF - DNA interface [nucleotide binding]; other site 1105101001100 IHF dimer interface [polypeptide binding]; other site 1105101001101 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1105101001102 tandem repeat interface [polypeptide binding]; other site 1105101001103 oligomer interface [polypeptide binding]; other site 1105101001104 active site residues [active] 1105101001105 transcription termination factor Rho; Provisional; Region: rho; PRK09376 1105101001106 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 1105101001107 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 1105101001108 RNA binding site [nucleotide binding]; other site 1105101001109 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 1105101001110 multimer interface [polypeptide binding]; other site 1105101001111 Walker A motif; other site 1105101001112 ATP binding site [chemical binding]; other site 1105101001113 Walker B motif; other site 1105101001114 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1, 4-benzoquinol methylase [Coenzyme metabolism]; Region: UbiG; COG2227 1105101001115 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 1105101001116 S-adenosylmethionine binding site [chemical binding]; other site 1105101001117 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 1105101001118 DHH family; Region: DHH; pfam01368 1105101001119 DHHA1 domain; Region: DHHA1; pfam02272 1105101001120 peptide chain release factor 1; Validated; Region: prfA; PRK00591 1105101001121 RF-1 domain; Region: RF-1; cl02875 1105101001122 RF-1 domain; Region: RF-1; cl02875 1105101001123 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 1105101001124 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 1105101001125 E3 interaction surface; other site 1105101001126 lipoyl attachment site [posttranslational modification]; other site 1105101001127 e3 binding domain; Region: E3_binding; pfam02817 1105101001128 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 1105101001129 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 1105101001130 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 1105101001131 Predicted membrane protein (DUF2335); Region: DUF2335; cl02210 1105101001132 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 1105101001133 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 1105101001134 Conserved hypothetical protein 2217 (DUF2460); Region: DUF2460; cl02268 1105101001135 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 1105101001136 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 1105101001137 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 1105101001138 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105101001139 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105101001140 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105101001141 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 1105101001142 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 1105101001143 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 1105101001144 folylpolyglutamate synthase/dihydrofolate synthase; Region: folC; TIGR01499 1105101001145 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; cl01942 1105101001146 Uncharacterized conserved protein [Function unknown]; Region: COG4285 1105101001147 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP); Region: GATase1_ScBLP_like; cd03144 1105101001148 conserved cys residue [active] 1105101001149 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 1105101001150 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 1105101001151 GSH binding site (G-site) [chemical binding]; other site 1105101001152 C-terminal domain interface [polypeptide binding]; other site 1105101001153 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 1105101001154 N-terminal domain interface [polypeptide binding]; other site 1105101001155 dimer interface [polypeptide binding]; other site 1105101001156 substrate binding pocket (H-site) [chemical binding]; other site 1105101001157 pyruvate phosphate dikinase; Provisional; Region: PRK09279 1105101001158 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 1105101001159 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 1105101001160 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 1105101001161 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 1105101001162 intersubunit interface [polypeptide binding]; other site 1105101001163 active site 1105101001164 Zn2+ binding site [ion binding]; other site 1105101001165 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 1105101001166 putative active site [active] 1105101001167 homotetrameric interface [polypeptide binding]; other site 1105101001168 metal binding site [ion binding]; metal-binding site 1105101001169 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101001170 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; cl00234 1105101001171 catalytic residues [active] 1105101001172 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 1105101001173 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 1105101001174 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1105101001175 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 1105101001176 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 1105101001177 non-specific DNA binding site [nucleotide binding]; other site 1105101001178 salt bridge; other site 1105101001179 sequence-specific DNA binding site [nucleotide binding]; other site 1105101001180 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 1105101001181 ATP/ADP translocase [Energy production and conversion]; Region: COG3202; cl03940 1105101001182 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105101001183 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK14846 1105101001184 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 1105101001185 RNA binding site [nucleotide binding]; other site 1105101001186 active site 1105101001187 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101001188 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 1105101001189 16S/18S rRNA binding site [nucleotide binding]; other site 1105101001190 S13e-L30e interaction site [polypeptide binding]; other site 1105101001191 25S rRNA binding site [nucleotide binding]; other site 1105101001192 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 1105101001193 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 1105101001194 RNase E interface [polypeptide binding]; other site 1105101001195 trimer interface [polypeptide binding]; other site 1105101001196 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 1105101001197 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 1105101001198 RNase E interface [polypeptide binding]; other site 1105101001199 trimer interface [polypeptide binding]; other site 1105101001200 active site 1105101001201 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 1105101001202 putative nucleic acid binding region [nucleotide binding]; other site 1105101001203 G-X-X-G motif; other site 1105101001204 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 1105101001205 RNA binding site [nucleotide binding]; other site 1105101001206 domain interface; other site 1105101001207 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 1105101001208 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 1105101001209 putative active site [active] 1105101001210 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 1105101001211 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 1105101001212 OstA-like protein; Region: OstA; cl00844 1105101001213 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 1105101001214 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 1105101001215 Walker A/P-loop; other site 1105101001216 ATP binding site [chemical binding]; other site 1105101001217 Q-loop/lid; other site 1105101001218 ABC transporter signature motif; other site 1105101001219 Walker B; other site 1105101001220 D-loop; other site 1105101001221 H-loop/switch region; other site 1105101001222 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 1105101001223 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 1105101001224 active site 1105101001225 substrate binding site [chemical binding]; other site 1105101001226 metal binding site [ion binding]; metal-binding site 1105101001227 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101001228 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 1105101001229 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 1105101001230 dimer interface [polypeptide binding]; other site 1105101001231 putative radical transfer pathway; other site 1105101001232 diiron center [ion binding]; other site 1105101001233 tyrosyl radical; other site 1105101001234 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 1105101001235 Class I ribonucleotide reductase; Region: RNR_I; cd01679 1105101001236 active site 1105101001237 dimer interface [polypeptide binding]; other site 1105101001238 catalytic residues [active] 1105101001239 effector binding site; other site 1105101001240 R2 peptide binding site; other site 1105101001241 Spore Coat Protein U domain; Region: SCPU; cl02253 1105101001242 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 1105101001243 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 1105101001244 potential frameshift: common BLAST hit: gi|91205792|ref|YP_538147.1| P pilus assembly, fimbrial usher protein 1105101001245 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 1105101001246 Spore Coat Protein U domain; Region: SCPU; cl02253 1105101001247 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 1105101001248 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105101001249 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105101001250 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14171 1105101001251 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 1105101001252 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 1105101001253 homodimer interface [polypeptide binding]; other site 1105101001254 NADP binding site [chemical binding]; other site 1105101001255 substrate binding site [chemical binding]; other site 1105101001256 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 1105101001257 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 1105101001258 30S subunit binding site; other site 1105101001259 potential frameshift: common BLAST hit: gi|67459085|ref|YP_246709.1| cell surface antigen Sca3 1105101001260 potential frameshift: common BLAST hit: gi|67459085|ref|YP_246709.1| cell surface antigen Sca3 1105101001261 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 1105101001262 Found in ATP-dependent protease La (LON); Region: LON; smart00464 1105101001263 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 1105101001264 Walker A motif; other site 1105101001265 ATP binding site [chemical binding]; other site 1105101001266 Walker B motif; other site 1105101001267 arginine finger; other site 1105101001268 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 1105101001269 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 1105101001270 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 1105101001271 tetramer interface [polypeptide binding]; other site 1105101001272 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105101001273 catalytic residue [active] 1105101001274 Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: AlaS; COG0013 1105101001275 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 1105101001276 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101001277 Family description; Region: UvrD_C_2; cl15862 1105101001278 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 1105101001279 active site 1105101001280 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 1105101001281 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 1105101001282 tetramerization interface [polypeptide binding]; other site 1105101001283 NAD(P) binding site [chemical binding]; other site 1105101001284 catalytic residues [active] 1105101001285 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 1105101001286 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105101001287 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1105101001288 Membrane transport protein; Region: Mem_trans; cl09117 1105101001289 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 1105101001290 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105101001291 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 1105101001292 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 1105101001293 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 1105101001294 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 1105101001295 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 1105101001296 recombination protein RecR; Reviewed; Region: recR; PRK00076 1105101001297 RecR protein; Region: RecR; pfam02132 1105101001298 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 1105101001299 putative active site [active] 1105101001300 putative metal-binding site [ion binding]; other site 1105101001301 tetramer interface [polypeptide binding]; other site 1105101001302 RDD family; Region: RDD; cl00746 1105101001303 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 1105101001304 Ribosome-binding factor A; Region: RBFA; cl00542 1105101001305 OpgC protein; Region: OpgC_C; cl00792 1105101001306 Tim44-like domain; Region: Tim44; cl09208 1105101001307 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 1105101001308 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 1105101001309 substrate binding pocket [chemical binding]; other site 1105101001310 catalytic triad [active] 1105101001311 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 1105101001312 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 1105101001313 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 1105101001314 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 1105101001315 ATP-grasp domain; Region: ATP-grasp_4; cl03087 1105101001316 CoA-ligase; Region: Ligase_CoA; cl02894 1105101001317 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 1105101001318 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105101001319 CoA-ligase; Region: Ligase_CoA; cl02894 1105101001320 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 1105101001321 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 1105101001322 catalytic residues [active] 1105101001323 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 1105101001324 SmpB-tmRNA interface; other site 1105101001325 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 1105101001326 dihydrodipicolinate synthase; Region: dapA; TIGR00674 1105101001327 dimer interface [polypeptide binding]; other site 1105101001328 active site 1105101001329 catalytic residue [active] 1105101001330 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and...; Region: BCAT_beta_family; cd01557 1105101001331 homodimer interface [polypeptide binding]; other site 1105101001332 substrate-cofactor binding pocket; other site 1105101001333 catalytic residue [active] 1105101001334 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105101001335 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 1105101001336 active site 1105101001337 phosphorylation site [posttranslational modification] 1105101001338 intermolecular recognition site; other site 1105101001339 dimerization interface [polypeptide binding]; other site 1105101001340 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 1105101001341 DNA binding site [nucleotide binding] 1105101001342 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105101001343 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 1105101001344 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 1105101001345 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 1105101001346 ATP binding site [chemical binding]; other site 1105101001347 Mg2+ binding site [ion binding]; other site 1105101001348 G-X-G motif; other site 1105101001349 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 1105101001350 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 1105101001351 catalytic residue [active] 1105101001352 putative FPP diphosphate binding site; other site 1105101001353 putative FPP binding hydrophobic cleft; other site 1105101001354 dimer interface [polypeptide binding]; other site 1105101001355 putative IPP diphosphate binding site; other site 1105101001356 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 1105101001357 Septum formation initiator; Region: DivIC; cl11433 1105101001358 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 1105101001359 catalytic site [active] 1105101001360 putative active site [active] 1105101001361 putative substrate binding site [chemical binding]; other site 1105101001362 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 1105101001363 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 1105101001364 HIGH motif; other site 1105101001365 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1105101001366 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105101001367 active site 1105101001368 KMSKS motif; other site 1105101001369 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 1105101001370 tRNA binding surface [nucleotide binding]; other site 1105101001371 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 1105101001372 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 1105101001373 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 1105101001374 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 1105101001375 DNA polymerase III subunit beta; Validated; Region: PRK05643 1105101001376 putative DNA binding surface [nucleotide binding]; other site 1105101001377 dimer interface [polypeptide binding]; other site 1105101001378 beta-clamp/clamp loader binding surface; other site 1105101001379 beta-clamp/translesion DNA polymerase binding surface; other site 1105101001380 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 1105101001381 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 1105101001382 putative tRNA-binding site [nucleotide binding]; other site 1105101001383 B3/4 domain; Region: B3_4; cl11458 1105101001384 tRNA synthetase B5 domain; Region: B5; cl08394 1105101001385 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 1105101001386 dimer interface [polypeptide binding]; other site 1105101001387 motif 1; other site 1105101001388 motif 3; other site 1105101001389 motif 2; other site 1105101001390 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 1105101001391 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 1105101001392 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 1105101001393 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 1105101001394 dimer interface [polypeptide binding]; other site 1105101001395 motif 1; other site 1105101001396 active site 1105101001397 motif 2; other site 1105101001398 motif 3; other site 1105101001399 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 1105101001400 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1105101001401 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 1105101001402 FeS/SAM binding site; other site 1105101001403 diaminopimelate epimerase; Region: DapF; TIGR00652 1105101001404 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1105101001405 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1105101001406 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105101001407 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105101001408 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 1105101001409 potential frameshift: common BLAST hit: gi|67459035|ref|YP_246659.1| RND efflux system, outer membrane protein 1105101001410 potential frameshift: common BLAST hit: gi|67459034|ref|YP_246658.1| RND family transporter membrane-fusion protein 1105101001411 potential frameshift: common BLAST hit: gi|67459034|ref|YP_246658.1| RND family transporter membrane-fusion protein 1105101001412 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 1105101001413 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 1105101001414 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 1105101001415 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 1105101001416 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 1105101001417 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 1105101001418 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 1105101001419 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 1105101001420 active site 1105101001421 homodimer interface [polypeptide binding]; other site 1105101001422 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 1105101001423 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01368 1105101001424 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105101001425 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105101001426 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105101001427 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 1105101001428 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 1105101001429 putative peptidase; Provisional; Region: PRK11649 1105101001430 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101001431 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 1105101001432 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 1105101001433 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 1105101001434 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 1105101001435 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 1105101001436 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 1105101001437 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 1105101001438 Subunit I/III interface [polypeptide binding]; other site 1105101001439 D-pathway; other site 1105101001440 Subunit I/VIIc interface [polypeptide binding]; other site 1105101001441 Subunit I/IV interface [polypeptide binding]; other site 1105101001442 Subunit I/II interface [polypeptide binding]; other site 1105101001443 Low-spin heme (heme a) binding site [chemical binding]; other site 1105101001444 Subunit I/VIIa interface [polypeptide binding]; other site 1105101001445 Subunit I/VIa interface [polypeptide binding]; other site 1105101001446 Dimer interface; other site 1105101001447 Putative water exit pathway; other site 1105101001448 Binuclear center (heme a3/CuB) [ion binding]; other site 1105101001449 K-pathway; other site 1105101001450 Subunit I/Vb interface [polypeptide binding]; other site 1105101001451 Putative proton exit pathway; other site 1105101001452 Subunit I/VIb interface; other site 1105101001453 Subunit I/VIc interface [polypeptide binding]; other site 1105101001454 Electron transfer pathway; other site 1105101001455 Subunit I/VIIIb interface [polypeptide binding]; other site 1105101001456 Subunit I/VIIb interface [polypeptide binding]; other site 1105101001457 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 1105101001458 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 1105101001459 catalytic triad [active] 1105101001460 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 1105101001461 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 1105101001462 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 1105101001463 dimer interface [polypeptide binding]; other site 1105101001464 catalytic triad [active] 1105101001465 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1105101001466 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 1105101001467 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1105101001468 catalytic residue [active] 1105101001469 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1105101001470 trimer interface [polypeptide binding]; other site 1105101001471 active site 1105101001472 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1105101001473 tandem repeat interface [polypeptide binding]; other site 1105101001474 oligomer interface [polypeptide binding]; other site 1105101001475 active site residues [active] 1105101001476 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 1105101001477 catalytic residues [active] 1105101001478 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 1105101001479 Protocatechuate 3,4-dioxygenase (3,4-PCD) catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis,cis-muconate. 3,4-PCDs are large aggregates of 12 protomers, each composed of an alpha- and beta-subunit and an Fe3+ ion...; Region: 3,4-PCD; cd03459 1105101001480 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 1105101001481 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 1105101001482 Iron permease FTR1 family; Region: FTR1; cl00475 1105101001483 Intracellular septation protein A; Region: IspA; cl01098 1105101001484 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 1105101001485 BON domain; Region: BON; cl02771 1105101001486 BON domain; Region: BON; cl02771 1105101001487 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101001488 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105101001489 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 1105101001490 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 1105101001491 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 1105101001492 muropeptide transporter; Validated; Region: ampG; PRK11010 1105101001493 muropeptide transporter; Reviewed; Region: ampG; PRK11902 1105101001494 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1105101001495 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 1105101001496 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 1105101001497 Walker A/P-loop; other site 1105101001498 ATP binding site [chemical binding]; other site 1105101001499 Q-loop/lid; other site 1105101001500 ABC transporter signature motif; other site 1105101001501 Walker B; other site 1105101001502 D-loop; other site 1105101001503 H-loop/switch region; other site 1105101001504 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 1105101001505 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 1105101001506 Walker A motif; other site 1105101001507 ATP binding site [chemical binding]; other site 1105101001508 Walker B motif; other site 1105101001509 arginine finger; other site 1105101001510 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 1105101001511 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 1105101001512 RuvA N terminal domain; Region: RuvA_N; pfam01330 1105101001513 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 1105101001514 Fic family protein [Function unknown]; Region: COG3177 1105101001515 Fic/DOC family; Region: Fic; cl00960 1105101001516 prolyl-tRNA synthetase; Provisional; Region: PRK12325 1105101001517 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 1105101001518 dimer interface [polypeptide binding]; other site 1105101001519 motif 1; other site 1105101001520 active site 1105101001521 motif 2; other site 1105101001522 motif 3; other site 1105101001523 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 1105101001524 anticodon binding site; other site 1105101001525 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 1105101001526 GTP cyclohydrolase I; Provisional; Region: PLN03044 1105101001527 active site 1105101001528 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 1105101001529 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 1105101001530 Ligand binding site; other site 1105101001531 oligomer interface; other site 1105101001532 CTP synthetase; Validated; Region: pyrG; PRK05380 1105101001533 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 1105101001534 Catalytic site [active] 1105101001535 active site 1105101001536 UTP binding site [chemical binding]; other site 1105101001537 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 1105101001538 active site 1105101001539 putative oxyanion hole; other site 1105101001540 catalytic triad [active] 1105101001541 ATP/ADP translocase [Energy production and conversion]; Region: COG3202; cl03940 1105101001542 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105101001543 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105101001544 malate dehydrogenase; Reviewed; Region: PRK06223 1105101001545 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 1105101001546 NAD(P) binding site [chemical binding]; other site 1105101001547 dimer interface [polypeptide binding]; other site 1105101001548 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1105101001549 substrate binding site [chemical binding]; other site 1105101001550 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105101001551 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 1105101001552 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 1105101001553 putative active site [active] 1105101001554 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 1105101001555 Malic enzyme, N-terminal domain; Region: malic; pfam00390 1105101001556 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 1105101001557 putative NAD(P) binding site [chemical binding]; other site 1105101001558 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 1105101001559 Membrane transport protein; Region: Mem_trans; cl09117 1105101001560 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 1105101001561 catalytic core domain of class I lysyl tRNA synthetase; Region: LysRS_core_class_I; cd00674 1105101001562 active site 1105101001563 HIGH motif; other site 1105101001564 KMSKS motif; other site 1105101001565 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 1105101001566 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 1105101001567 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 1105101001568 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC...; Region: ABC_cobalt_CbiO_domain1; cd03225 1105101001569 Walker A/P-loop; other site 1105101001570 ATP binding site [chemical binding]; other site 1105101001571 Q-loop/lid; other site 1105101001572 ABC transporter signature motif; other site 1105101001573 Walker B; other site 1105101001574 D-loop; other site 1105101001575 H-loop/switch region; other site 1105101001576 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cd06574 1105101001577 TM-ABC transporter signature motif; other site 1105101001578 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 1105101001579 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1105101001580 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 1105101001581 amidase catalytic site [active] 1105101001582 Zn binding residues [ion binding]; other site 1105101001583 substrate binding site [chemical binding]; other site 1105101001584 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 1105101001585 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 1105101001586 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 1105101001587 putative active site [active] 1105101001588 catalytic triad [active] 1105101001589 putative dimer interface [polypeptide binding]; other site 1105101001590 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 1105101001591 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 1105101001592 NAD binding site [chemical binding]; other site 1105101001593 homotetramer interface [polypeptide binding]; other site 1105101001594 homodimer interface [polypeptide binding]; other site 1105101001595 substrate binding site [chemical binding]; other site 1105101001596 active site 1105101001597 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 1105101001598 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 1105101001599 active site 1105101001600 DNA binding site [nucleotide binding] 1105101001601 Int/Topo IB signature motif; other site 1105101001602 potential frameshift: common BLAST hit: gi|67458962|ref|YP_246586.1| phage protein 1105101001603 Uncharacterized protein conserved in bacteria (DUF2155); Region: DUF2155; cl01970 1105101001604 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 1105101001605 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 1105101001606 NADH dehydrogenase subunit B; Provisional; Region: PRK14816 1105101001607 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl15792 1105101001608 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 1105101001609 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl16917 1105101001610 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 1105101001611 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; pfam00346 1105101001612 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 1105101001613 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 1105101001614 putative dimer interface [polypeptide binding]; other site 1105101001615 [2Fe-2S] cluster binding site [ion binding]; other site 1105101001616 Haemolytic domain; Region: Haemolytic; cl00506 1105101001617 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 1105101001618 active site 1105101001619 DNA binding site [nucleotide binding] 1105101001620 Protein of unknown function (DUF3680); Region: DUF3680; cl02189 1105101001621 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 1105101001622 AsmA-like C-terminal region; Region: AsmA_2; cl15864 1105101001623 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 1105101001624 RimM N-terminal domain; Region: RimM; pfam01782 1105101001625 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 1105101001626 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 1105101001627 AsmA-like C-terminal region; Region: AsmA_2; cl15864 1105101001628 TPR repeat; Region: TPR_11; pfam13414 1105101001629 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 1105101001630 TPR motif; other site 1105101001631 binding surface 1105101001632 Domain of unknown function (DUF4385); Region: DUF4385; pfam14328 1105101001633 spore photoproduct lyase; Region: photo_TT_lyase; cl15393 1105101001634 UbiA prenyltransferase family; Region: UbiA; cl00337 1105101001635 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 1105101001636 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 1105101001637 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 1105101001638 RNA binding surface [nucleotide binding]; other site 1105101001639 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1105101001640 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 1105101001641 putative ADP-binding pocket [chemical binding]; other site 1105101001642 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1105101001643 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 1105101001644 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 1105101001645 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 1105101001646 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 1105101001647 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 1105101001648 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 1105101001649 active site 1105101001650 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 1105101001651 active site 1105101001652 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 1105101001653 S-adenosylmethionine binding site [chemical binding]; other site 1105101001654 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 1105101001655 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 1105101001656 active site 1105101001657 homodimer interface [polypeptide binding]; other site 1105101001658 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 1105101001659 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 1105101001660 NAD(P) binding site [chemical binding]; other site 1105101001661 homodimer interface [polypeptide binding]; other site 1105101001662 substrate binding site [chemical binding]; other site 1105101001663 active site 1105101001664 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 1105101001665 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 1105101001666 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 1105101001667 NADP binding site [chemical binding]; other site 1105101001668 active site 1105101001669 putative substrate binding site [chemical binding]; other site 1105101001670 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 1105101001671 sequence-specific DNA binding site [nucleotide binding]; other site 1105101001672 salt bridge; other site 1105101001673 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 1105101001674 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 1105101001675 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 1105101001676 Sulfatase; Region: Sulfatase; cl10460 1105101001677 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1105101001678 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 1105101001679 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1105101001680 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 1105101001681 dimer interface [polypeptide binding]; other site 1105101001682 decamer (pentamer of dimers) interface [polypeptide binding]; other site 1105101001683 catalytic triad [active] 1105101001684 peroxidatic and resolving cysteines [active] 1105101001685 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 1105101001686 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 1105101001687 DNA topoisomerase I; Validated; Region: PRK06599 1105101001688 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 1105101001689 active site 1105101001690 interdomain interaction site; other site 1105101001691 putative metal-binding site [ion binding]; other site 1105101001692 nucleotide binding site [chemical binding]; other site 1105101001693 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 1105101001694 domain I; other site 1105101001695 DNA binding groove [nucleotide binding] 1105101001696 phosphate binding site [ion binding]; other site 1105101001697 domain II; other site 1105101001698 domain III; other site 1105101001699 nucleotide binding site [chemical binding]; other site 1105101001700 catalytic site [active] 1105101001701 domain IV; other site 1105101001702 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1105101001703 Uncharacterized C-terminal domain of topoisomerase IA [General function prediction only]; Region: COG1754 1105101001704 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 1105101001705 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 1105101001706 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105101001707 HIGH motif; other site 1105101001708 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105101001709 active site 1105101001710 KMSKS motif; other site 1105101001711 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 1105101001712 putative iron binding site [ion binding]; other site 1105101001713 YceG-like family; Region: YceG; pfam02618 1105101001714 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 1105101001715 dimerization interface [polypeptide binding]; other site 1105101001716 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 1105101001717 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 1105101001718 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105101001719 Uncharacterized conserved protein [Function unknown]; Region: COG5464 1105101001720 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105101001721 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105101001722 potential frameshift: common BLAST hit: gi|67458910|ref|YP_246534.1| Mg chelatase-like protein 1105101001723 potential frameshift: common BLAST hit: gi|157827341|ref|YP_001496405.1| Mg chelatase-like protein 1105101001724 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 1105101001725 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 1105101001726 Walker A motif; other site 1105101001727 ATP binding site [chemical binding]; other site 1105101001728 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101001729 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 1105101001730 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 1105101001731 active site 1105101001732 HslU subunit interaction site [polypeptide binding]; other site 1105101001733 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105101001734 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 1105101001735 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 1105101001736 nucleotide binding site/active site [active] 1105101001737 HIT family signature motif; other site 1105101001738 catalytic residue [active] 1105101001739 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 1105101001740 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105101001741 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 1105101001742 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 1105101001743 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 1105101001744 Walker A/P-loop; other site 1105101001745 ATP binding site [chemical binding]; other site 1105101001746 Q-loop/lid; other site 1105101001747 ABC transporter signature motif; other site 1105101001748 Walker B; other site 1105101001749 D-loop; other site 1105101001750 H-loop/switch region; other site 1105101001751 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 1105101001752 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 1105101001753 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 1105101001754 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 1105101001755 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105101001756 putative substrate translocation pore; other site 1105101001757 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 1105101001758 Gram-negative bacterial tonB protein; Region: TonB; cl10048 1105101001759 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 1105101001760 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 1105101001761 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 1105101001762 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 1105101001763 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 1105101001764 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 1105101001765 dimer interface [polypeptide binding]; other site 1105101001766 motif 1; other site 1105101001767 active site 1105101001768 motif 2; other site 1105101001769 motif 3; other site 1105101001770 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 1105101001771 anticodon binding site; other site 1105101001772 amino acid transporter; Region: 2A0306; TIGR00909 1105101001773 Spore germination protein; Region: Spore_permease; cl15802 1105101001774 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 1105101001775 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 1105101001776 Ligand Binding Site [chemical binding]; other site 1105101001777 Cytochrome c oxidase assembly protein CtaG/Cox11; Region: CtaG_Cox11; cl01240 1105101001778 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 1105101001779 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1105101001780 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1105101001781 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 1105101001782 translocation protein TolB; Provisional; Region: tolB; PRK05137 1105101001783 TolB amino-terminal domain; Region: TolB_N; cl00639 1105101001784 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105101001785 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105101001786 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105101001787 Thymidylate synthase complementing protein; Region: Thy1; cl03630 1105101001788 Protein of unknown function DUF45; Region: DUF45; cl00636 1105101001789 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105101001790 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 1105101001791 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 1105101001792 MutS domain I; Region: MutS_I; pfam01624 1105101001793 MutS domain II; Region: MutS_II; pfam05188 1105101001794 MutS family domain IV; Region: MutS_IV; pfam05190 1105101001795 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 1105101001796 Walker A/P-loop; other site 1105101001797 ATP binding site [chemical binding]; other site 1105101001798 Q-loop/lid; other site 1105101001799 ABC transporter signature motif; other site 1105101001800 Walker B; other site 1105101001801 D-loop; other site 1105101001802 H-loop/switch region; other site 1105101001803 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 1105101001804 active site 1105101001805 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 1105101001806 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 1105101001807 Phage portal protein; Region: Phage_portal; pfam04860 1105101001808 Phage portal protein; Region: Phage_portal; pfam04860 1105101001809 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 1105101001810 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 1105101001811 type IV secretion system component VirD4; Provisional; Region: PRK13897 1105101001812 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 1105101001813 Walker A motif; other site 1105101001814 ATP binding site [chemical binding]; other site 1105101001815 Walker B motif; other site 1105101001816 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 1105101001817 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 1105101001818 Walker A motif; other site 1105101001819 hexamer interface [polypeptide binding]; other site 1105101001820 ATP binding site [chemical binding]; other site 1105101001821 Walker B motif; other site 1105101001822 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 1105101001823 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 1105101001824 VirB8 protein; Region: VirB8; cl01500 1105101001825 Protein of unknown function (DUF2706); Region: DUF2706; pfam10913 1105101001826 VirB8 protein; Region: VirB8; cl01500 1105101001827 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 1105101001828 VirB7 interaction site; other site 1105101001829 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 1105101001830 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06591 1105101001831 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 1105101001832 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06589 1105101001833 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 1105101001834 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 1105101001835 oligomeric interface; other site 1105101001836 putative active site [active] 1105101001837 homodimer interface [polypeptide binding]; other site 1105101001838 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06588 1105101001839 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 1105101001840 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 1105101001841 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105101001842 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 1105101001843 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 1105101001844 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 1105101001845 NADH dehydrogenase subunit 2; Provisional; Region: ND2; MTH00196 1105101001846 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 1105101001847 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 1105101001848 dimer interface [polypeptide binding]; other site 1105101001849 allosteric magnesium binding site [ion binding]; other site 1105101001850 active site 1105101001851 aspartate-rich active site metal binding site; other site 1105101001852 Schiff base residues; other site 1105101001853 primosome assembly protein PriA; Validated; Region: PRK05580 1105101001854 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 1105101001855 ATP binding site [chemical binding]; other site 1105101001856 putative Mg++ binding site [ion binding]; other site 1105101001857 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101001858 aromatic acid decarboxylase; Validated; Region: PRK05920 1105101001859 Flavoprotein; Region: Flavoprotein; cl08021 1105101001860 SacI restriction endonuclease; Region: RE_SacI; pfam09566 1105101001861 replicative DNA helicase; Provisional; Region: PRK09165 1105101001862 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 1105101001863 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 1105101001864 Walker A motif; other site 1105101001865 ATP binding site [chemical binding]; other site 1105101001866 Walker B motif; other site 1105101001867 DNA binding loops [nucleotide binding] 1105101001868 potential frameshift: common BLAST hit: gi|67459254|ref|YP_246878.1| to amino acid permeases 1105101001869 Transmembrane amino acid transporter protein; Region: Aa_trans; cl15776 1105101001870 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 1105101001871 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 1105101001872 RNA binding surface [nucleotide binding]; other site 1105101001873 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 1105101001874 active site 1105101001875 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 1105101001876 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105101001877 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 1105101001878 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105101001879 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105101001880 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 1105101001881 DNA repair protein RadA; Provisional; Region: PRK11823 1105101001882 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 1105101001883 Walker A motif/ATP binding site; other site 1105101001884 ATP binding site [chemical binding]; other site 1105101001885 Walker B motif; other site 1105101001886 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 1105101001887 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 1105101001888 Recombination protein O N terminal; Region: RecO_N; cl15812 1105101001889 Recombination protein O C terminal; Region: RecO_C; pfam02565 1105101001890 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 1105101001891 translation initiation factor IF-2; Validated; Region: infB; PRK05306 1105101001892 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 1105101001893 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 1105101001894 G1 box; other site 1105101001895 putative GEF interaction site [polypeptide binding]; other site 1105101001896 GTP/Mg2+ binding site [chemical binding]; other site 1105101001897 Switch I region; other site 1105101001898 G2 box; other site 1105101001899 G3 box; other site 1105101001900 Switch II region; other site 1105101001901 G4 box; other site 1105101001902 G5 box; other site 1105101001903 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 1105101001904 Translation-initiation factor 2; Region: IF-2; pfam11987 1105101001905 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 1105101001906 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 1105101001907 NusA N-terminal domain; Region: NusA_N; pfam08529 1105101001908 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 1105101001909 RNA binding site [nucleotide binding]; other site 1105101001910 homodimer interface [polypeptide binding]; other site 1105101001911 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 1105101001912 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 1105101001913 G-X-X-G motif; other site 1105101001914 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 1105101001915 ribosome maturation protein RimP; Reviewed; Region: PRK00092 1105101001916 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 1105101001917 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 1105101001918 Sm1 motif; other site 1105101001919 D1 - D2 interaction site; other site 1105101001920 D3 - B interaction site; other site 1105101001921 Hfq - Hfq interaction site; other site 1105101001922 RNA binding pocket [nucleotide binding]; other site 1105101001923 Sm2 motif; other site 1105101001924 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cl06868 1105101001925 NAD binding pocket [chemical binding]; other site 1105101001926 Helix-turn-helix domains; Region: HTH; cl00088 1105101001927 Rrf2 family protein; Region: rrf2_super; TIGR00738 1105101001928 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 1105101001929 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 1105101001930 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 1105101001931 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 1105101001932 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 1105101001933 active site 1105101001934 HIGH motif; other site 1105101001935 dimer interface [polypeptide binding]; other site 1105101001936 KMSKS motif; other site 1105101001937 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 1105101001938 RNA binding surface [nucleotide binding]; other site 1105101001939 Protein of unknown function (DUF3680); Region: DUF3680; cl02189 1105101001940 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 1105101001941 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 1105101001942 Leucine-rich repeats; other site 1105101001943 Substrate binding site [chemical binding]; other site 1105101001944 proline/glycine betaine transporter; Provisional; Region: PRK10642 1105101001945 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 1105101001946 potential frameshift: common BLAST hit: gi|157964695|ref|YP_001499519.1| large extracellular alpha-helical protein 1105101001947 potential frameshift: common BLAST hit: gi|350273648|ref|YP_004884961.1| large extracellular alpha-helical protein 1105101001948 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 1105101001949 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 1105101001950 potential frameshift: common BLAST hit: gi|341584023|ref|YP_004764514.1| large extracellular alpha-helical protein 1105101001951 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105101001952 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105101001953 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105101001954 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105101001955 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 1105101001956 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101001957 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK06617 1105101001958 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105101001959 Multiple resistance and pH regulation protein F (MrpF / PhaF); Region: MrpF_PhaF; cl09154 1105101001960 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1105101001961 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 1105101001962 active site 1105101001963 phosphorylation site [posttranslational modification] 1105101001964 intermolecular recognition site; other site 1105101001965 dimerization interface [polypeptide binding]; other site 1105101001966 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 1105101001967 Walker A motif; other site 1105101001968 ATP binding site [chemical binding]; other site 1105101001969 Walker B motif; other site 1105101001970 arginine finger; other site 1105101001971 Helix-turn-helix domains; Region: HTH; cl00088 1105101001972 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105101001973 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105101001974 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105101001975 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105101001976 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105101001977 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105101001978 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 1105101001979 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 1105101001980 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1105101001981 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 1105101001982 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 1105101001983 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1105101001984 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 1105101001985 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 1105101001986 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 1105101001987 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 1105101001988 S-adenosylmethionine binding site [chemical binding]; other site 1105101001989 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 1105101001990 MraZ protein; Region: MraZ; pfam02381 1105101001991 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 1105101001992 Na binding site [ion binding]; other site 1105101001993 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 1105101001994 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 1105101001995 GIY-YIG motif/motif A; other site 1105101001996 active site 1105101001997 catalytic site [active] 1105101001998 putative DNA binding site [nucleotide binding]; other site 1105101001999 metal binding site [ion binding]; metal-binding site 1105101002000 UvrB/uvrC motif; Region: UVR; pfam02151 1105101002001 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 1105101002002 Protein of unknown function (DUF461); Region: DUF461; cl01071 1105101002003 A new structural DNA glycosylase; Region: AlkD_like; cd06561 1105101002004 active site 1105101002005 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 1105101002006 active site 1105101002007 DNA binding site [nucleotide binding] 1105101002008 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 1105101002009 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 1105101002010 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 1105101002011 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 1105101002012 DNA binding site [nucleotide binding] 1105101002013 active site 1105101002014 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 1105101002015 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 1105101002016 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101002017 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 1105101002018 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 1105101002019 nucleotide binding region [chemical binding]; other site 1105101002020 ATP-binding site [chemical binding]; other site 1105101002021 SEC-C motif; Region: SEC-C; pfam02810 1105101002022 peptidylprolyl isomerase; Reviewed; Region: prsA; PRK03002 1105101002023 PPIC-type PPIASE domain; Region: Rotamase; cl08278 1105101002024 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 1105101002025 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 1105101002026 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 1105101002027 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 1105101002028 hinge; other site 1105101002029 active site 1105101002030 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 1105101002031 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 1105101002032 ATP binding site [chemical binding]; other site 1105101002033 Mg2+ binding site [ion binding]; other site 1105101002034 G-X-G motif; other site 1105101002035 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 1105101002036 anchoring element; other site 1105101002037 dimer interface [polypeptide binding]; other site 1105101002038 ATP binding site [chemical binding]; other site 1105101002039 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 1105101002040 active site 1105101002041 putative metal-binding site [ion binding]; other site 1105101002042 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1105101002043 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 1105101002044 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 1105101002045 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 1105101002046 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 1105101002047 MgtE intracellular N domain; Region: MgtE_N; cl15244 1105101002048 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 1105101002049 Divalent cation transporter; Region: MgtE; cl00786 1105101002050 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 1105101002051 GMP synthetase; Region: PLN02347 1105101002052 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15783 1105101002053 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105101002054 Preprotein translocase subunit; Region: YajC; cl00806 1105101002055 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 1105101002056 Protein export membrane protein; Region: SecD_SecF; cl14618 1105101002057 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 1105101002058 Cu(I) binding site [ion binding]; other site 1105101002059 CcmE; Region: CcmE; cl00994 1105101002060 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 1105101002061 dimer interface [polypeptide binding]; other site 1105101002062 substrate binding site [chemical binding]; other site 1105101002063 metal binding sites [ion binding]; metal-binding site 1105101002064 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101002065 MviN-like protein; Region: MVIN; pfam03023 1105101002066 TraX protein; Region: TraX; cl05434 1105101002067 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 1105101002068 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 1105101002069 ssDNA binding site; other site 1105101002070 generic binding surface II; other site 1105101002071 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 1105101002072 ATP binding site [chemical binding]; other site 1105101002073 putative Mg++ binding site [ion binding]; other site 1105101002074 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 1105101002075 nucleotide binding region [chemical binding]; other site 1105101002076 ATP-binding site [chemical binding]; other site 1105101002077 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 1105101002078 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 1105101002079 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 1105101002080 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 1105101002081 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 1105101002082 Mg++ binding site [ion binding]; other site 1105101002083 putative catalytic motif [active] 1105101002084 putative substrate binding site [chemical binding]; other site 1105101002085 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105101002086 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 1105101002087 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105101002088 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105101002089 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 1105101002090 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105101002091 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105101002092 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105101002093 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 1105101002094 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 1105101002095 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 1105101002096 ATP binding site [chemical binding]; other site 1105101002097 putative Mg++ binding site [ion binding]; other site 1105101002098 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 1105101002099 nucleotide binding region [chemical binding]; other site 1105101002100 ATP-binding site [chemical binding]; other site 1105101002101 TRCF domain; Region: TRCF; cl04088 1105101002102 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 1105101002103 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 1105101002104 active site residue [active] 1105101002105 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 1105101002106 DnaA N-terminal domain; Region: DnaA_N; pfam11638 1105101002107 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 1105101002108 Walker A motif; other site 1105101002109 ATP binding site [chemical binding]; other site 1105101002110 Walker B motif; other site 1105101002111 arginine finger; other site 1105101002112 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 1105101002113 DnaA box-binding interface [nucleotide binding]; other site 1105101002114 Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17; Region: Pat17_PNPLA8_PNPLA9_like; cd07199 1105101002115 active site 1105101002116 nucleophile elbow; other site 1105101002117 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105101002118 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105101002119 HEPN domain; Region: HEPN; cl00824 1105101002120 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 1105101002121 active site 1105101002122 NTP binding site [chemical binding]; other site 1105101002123 metal binding triad [ion binding]; metal-binding site 1105101002124 GTP-binding protein YchF; Reviewed; Region: PRK09601 1105101002125 YchF GTPase; Region: YchF; cd01900 1105101002126 G1 box; other site 1105101002127 GTP/Mg2+ binding site [chemical binding]; other site 1105101002128 Switch I region; other site 1105101002129 G2 box; other site 1105101002130 Switch II region; other site 1105101002131 G3 box; other site 1105101002132 G4 box; other site 1105101002133 G5 box; other site 1105101002134 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 1105101002135 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 1105101002136 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 1105101002137 putative active site [active] 1105101002138 catalytic residue [active] 1105101002139 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 1105101002140 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 1105101002141 5S rRNA interface [nucleotide binding]; other site 1105101002142 CTC domain interface [polypeptide binding]; other site 1105101002143 L16 interface [polypeptide binding]; other site 1105101002144 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 1105101002145 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 1105101002146 FeS/SAM binding site; other site 1105101002147 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 1105101002148 ribosomal protein L20; Region: rpl20; CHL00068 1105101002149 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 1105101002150 23S rRNA binding site [nucleotide binding]; other site 1105101002151 L21 binding site [polypeptide binding]; other site 1105101002152 L13 binding site [polypeptide binding]; other site 1105101002153 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 1105101002154 Ribonuclease P; Region: Ribonuclease_P; cl00457 1105101002155 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105101002156 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 1105101002157 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 1105101002158 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 1105101002159 substrate binding site [chemical binding]; other site 1105101002160 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 1105101002161 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 1105101002162 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 1105101002163 dimerization interface [polypeptide binding]; other site 1105101002164 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 1105101002165 dimer interface [polypeptide binding]; other site 1105101002166 phosphorylation site [posttranslational modification] 1105101002167 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 1105101002168 ATP binding site [chemical binding]; other site 1105101002169 Mg2+ binding site [ion binding]; other site 1105101002170 G-X-G motif; other site 1105101002171 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 1105101002172 Uncharacterized conserved protein [Function unknown]; Region: COG5590 1105101002173 Helix-turn-helix domains; Region: HTH; cl00088 1105101002174 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 1105101002175 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1105101002176 HIGH motif; other site 1105101002177 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1105101002178 active site 1105101002179 KMSKS motif; other site 1105101002180 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 1105101002181 tRNA binding surface [nucleotide binding]; other site 1105101002182 anticodon binding site; other site 1105101002183 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 1105101002184 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 1105101002185 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1105101002186 ATP-grasp domain; Region: ATP-grasp_4; cl03087 1105101002187 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 1105101002188 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 1105101002189 carboxyltransferase (CT) interaction site; other site 1105101002190 biotinylation site [posttranslational modification]; other site 1105101002191 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 1105101002192 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 1105101002193 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 1105101002194 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 1105101002195 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 1105101002196 putative substrate translocation pore; other site 1105101002197 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1105101002198 putative acyl-acceptor binding pocket; other site 1105101002199 AMP-binding enzyme; Region: AMP-binding; cl15778 1105101002200 TfoX N-terminal domain; Region: TfoX_N; cl01167 1105101002201 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 1105101002202 ABC-ATPase subunit interface; other site 1105101002203 dimer interface [polypeptide binding]; other site 1105101002204 putative PBP binding regions; other site 1105101002205 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 1105101002206 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101002207 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 1105101002208 S-adenosylmethionine binding site [chemical binding]; other site 1105101002209 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 1105101002210 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105101002211 HIGH motif; other site 1105101002212 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105101002213 active site 1105101002214 KMSKS motif; other site 1105101002215 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101002216 Invasion associated locus B (IalB) protein; Region: IalB; cl02207 1105101002217 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 1105101002218 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 1105101002219 ring oligomerisation interface [polypeptide binding]; other site 1105101002220 ATP/Mg binding site [chemical binding]; other site 1105101002221 stacking interactions; other site 1105101002222 hinge regions; other site 1105101002223 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 1105101002224 oligomerisation interface [polypeptide binding]; other site 1105101002225 mobile loop; other site 1105101002226 roof hairpin; other site 1105101002227 potential frameshift: common BLAST hit: gi|67458799|ref|YP_246423.1| glycosyltransferase 1105101002228 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 1105101002229 potential frameshift: common BLAST hit: gi|67458799|ref|YP_246423.1| glycosyltransferase 1105101002230 ribonuclease PH; Reviewed; Region: rph; PRK00173 1105101002231 Ribonuclease PH; Region: RNase_PH_bact; cd11362 1105101002232 hexamer interface [polypeptide binding]; other site 1105101002233 active site 1105101002234 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 1105101002235 dimer interface [polypeptide binding]; other site 1105101002236 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 1105101002237 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 1105101002238 Domain of unknown function DUF20; Region: UPF0118; pfam01594 1105101002239 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101002240 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105101002241 potential frameshift: common BLAST hit: gi|67458789|ref|YP_246413.1| MFS type sugar transporter 1105101002242 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 1105101002243 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 1105101002244 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 1105101002245 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 1105101002246 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 1105101002247 alphaNTD - beta interaction site [polypeptide binding]; other site 1105101002248 alphaNTD homodimer interface [polypeptide binding]; other site 1105101002249 alphaNTD - beta' interaction site [polypeptide binding]; other site 1105101002250 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 1105101002251 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 1105101002252 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 1105101002253 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 1105101002254 adenylate kinase; Reviewed; Region: adk; PRK00279 1105101002255 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 1105101002256 AMP-binding site [chemical binding]; other site 1105101002257 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 1105101002258 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 1105101002259 SecY translocase; Region: SecY; pfam00344 1105101002260 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 1105101002261 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 1105101002262 23S rRNA binding site [nucleotide binding]; other site 1105101002263 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 1105101002264 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 1105101002265 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 1105101002266 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 1105101002267 5S rRNA interface [nucleotide binding]; other site 1105101002268 23S rRNA interface [nucleotide binding]; other site 1105101002269 L5 interface [polypeptide binding]; other site 1105101002270 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 1105101002271 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1105101002272 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1105101002273 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 1105101002274 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 1105101002275 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 1105101002276 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 1105101002277 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 1105101002278 KOW motif; Region: KOW; cl00354 1105101002279 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 1105101002280 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 1105101002281 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 1105101002282 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 1105101002283 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 1105101002284 23S rRNA interface [nucleotide binding]; other site 1105101002285 5S rRNA interface [nucleotide binding]; other site 1105101002286 putative antibiotic binding site [chemical binding]; other site 1105101002287 L25 interface [polypeptide binding]; other site 1105101002288 L27 interface [polypeptide binding]; other site 1105101002289 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 1105101002290 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 1105101002291 G-X-X-G motif; other site 1105101002292 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 1105101002293 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 1105101002294 putative translocon binding site; other site 1105101002295 protein-rRNA interface [nucleotide binding]; other site 1105101002296 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 1105101002297 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 1105101002298 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 1105101002299 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 1105101002300 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 1105101002301 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 1105101002302 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 1105101002303 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 1105101002304 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101002305 elongation factor Tu; Reviewed; Region: PRK00049 1105101002306 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 1105101002307 G1 box; other site 1105101002308 GEF interaction site [polypeptide binding]; other site 1105101002309 GTP/Mg2+ binding site [chemical binding]; other site 1105101002310 Switch I region; other site 1105101002311 G2 box; other site 1105101002312 G3 box; other site 1105101002313 Switch II region; other site 1105101002314 G4 box; other site 1105101002315 G5 box; other site 1105101002316 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 1105101002317 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 1105101002318 Antibiotic Binding Site [chemical binding]; other site 1105101002319 potential protein location (hypothetical protein RPK_05560 [Rickettsia rickettsii str. Hlp#2]) that overlaps RNA (tRNA-G) 1105101002320 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 1105101002321 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 1105101002322 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 1105101002323 fumarate hydratase; Reviewed; Region: fumC; PRK00485 1105101002324 Class II fumarases; Region: Fumarase_classII; cd01362 1105101002325 active site 1105101002326 tetramer interface [polypeptide binding]; other site 1105101002327 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 1105101002328 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 1105101002329 putative active site [active] 1105101002330 homotetrameric interface [polypeptide binding]; other site 1105101002331 cell division protein FtsZ; Validated; Region: PRK09330 1105101002332 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 1105101002333 nucleotide binding site [chemical binding]; other site 1105101002334 SulA interaction site; other site 1105101002335 Protease Inhibitor Ecotin; homodimeric protease inhibitor; Region: Ecotin; cl00178 1105101002336 secondary substrate binding site; other site 1105101002337 primary substrate binding site; other site 1105101002338 inhibition loop; other site 1105101002339 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; cl07364 1105101002340 NifU-like domain; Region: NifU; cl00484 1105101002341 muropeptide transporter; Validated; Region: ampG; PRK11010 1105101002342 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 1105101002343 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 1105101002344 ATP binding site [chemical binding]; other site 1105101002345 Mg++ binding site [ion binding]; other site 1105101002346 motif III; other site 1105101002347 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 1105101002348 nucleotide binding region [chemical binding]; other site 1105101002349 ATP-binding site [chemical binding]; other site 1105101002350 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 1105101002351 DNA-binding site [nucleotide binding]; DNA binding site 1105101002352 RNA-binding motif; other site 1105101002353 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 1105101002354 S-adenosylmethionine binding site [chemical binding]; other site 1105101002355 SurA N-terminal domain; Region: SurA_N_3; cl07813 1105101002356 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 1105101002357 Organic solvent tolerance protein; Region: OstA_C; pfam04453 1105101002358 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 1105101002359 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 1105101002360 generic binding surface II; other site 1105101002361 generic binding surface I; other site 1105101002362 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 1105101002363 putative catalytic site [active] 1105101002364 putative phosphate binding site [ion binding]; other site 1105101002365 active site 1105101002366 metal binding site A [ion binding]; metal-binding site 1105101002367 DNA binding site [nucleotide binding] 1105101002368 putative AP binding site [nucleotide binding]; other site 1105101002369 putative metal binding site B [ion binding]; other site 1105101002370 PQ loop repeat; Region: PQ-loop; cl12056 1105101002371 GTP-binding protein Der; Reviewed; Region: PRK00093 1105101002372 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 1105101002373 G1 box; other site 1105101002374 GTP/Mg2+ binding site [chemical binding]; other site 1105101002375 Switch I region; other site 1105101002376 G2 box; other site 1105101002377 Switch II region; other site 1105101002378 G3 box; other site 1105101002379 G4 box; other site 1105101002380 G5 box; other site 1105101002381 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 1105101002382 G1 box; other site 1105101002383 GTP/Mg2+ binding site [chemical binding]; other site 1105101002384 Switch I region; other site 1105101002385 G2 box; other site 1105101002386 G3 box; other site 1105101002387 Switch II region; other site 1105101002388 G4 box; other site 1105101002389 G5 box; other site 1105101002390 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101002391 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 1105101002392 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 1105101002393 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 1105101002394 active site 1105101002395 ATP binding site [chemical binding]; other site 1105101002396 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 1105101002397 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 1105101002398 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 1105101002399 S-adenosylmethionine binding site [chemical binding]; other site 1105101002400 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 1105101002401 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 1105101002402 DNA binding site [nucleotide binding] 1105101002403 catalytic residue [active] 1105101002404 H2TH interface [polypeptide binding]; other site 1105101002405 putative catalytic residues [active] 1105101002406 turnover-facilitating residue; other site 1105101002407 intercalation triad [nucleotide binding]; other site 1105101002408 8OG recognition residue [nucleotide binding]; other site 1105101002409 putative reading head residues; other site 1105101002410 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 1105101002411 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 1105101002412 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101002413 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105101002414 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 1105101002415 active site 1105101002416 potential frameshift: common BLAST hit: gi|15892963|ref|NP_360677.1| mannose-1-phosphate guanylyltransferase 1105101002417 potential frameshift: common BLAST hit: gi|157826925|ref|YP_001495989.1| Poly-beta-hydroxyalkanoate depolymerase 1105101002418 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105101002419 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105101002420 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105101002421 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 1105101002422 active site 1105101002423 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 1105101002424 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 1105101002425 HIGH motif; other site 1105101002426 active site 1105101002427 KMSKS motif; other site 1105101002428 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 1105101002429 tRNA binding surface [nucleotide binding]; other site 1105101002430 anticodon binding site; other site 1105101002431 thymidylate kinase; Validated; Region: tmk; PRK00698 1105101002432 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 1105101002433 TMP-binding site; other site 1105101002434 ATP-binding site [chemical binding]; other site 1105101002435 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105101002436 UbiA prenyltransferase family; Region: UbiA; cl00337 1105101002437 potential frameshift: common BLAST hit: gi|350273815|ref|YP_004885128.1| transposase 1105101002438 potential frameshift: common BLAST hit: gi|67458622|ref|YP_246246.1| transposase 1105101002439 valyl-tRNA synthetase; Reviewed; Region: valS; PRK13208 1105101002440 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105101002441 active site 1105101002442 HIGH motif; other site 1105101002443 nucleotide binding site [chemical binding]; other site 1105101002444 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1105101002445 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105101002446 active site 1105101002447 KMSKS motif; other site 1105101002448 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 1105101002449 tRNA binding surface [nucleotide binding]; other site 1105101002450 anticodon binding site; other site 1105101002451 LicD family; Region: LicD; cl01378 1105101002452 LicD family; Region: LicD; cl01378 1105101002453 potential frameshift: common BLAST hit: gi|157804076|ref|YP_001492625.1| ATPase 1105101002454 RmuC family; Region: RmuC; pfam02646 1105101002455 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 1105101002456 DoxX-like family; Region: DoxX_3; pfam13781 1105101002457 potential frameshift: common BLAST hit: gi|157826437|ref|YP_001495501.1| integral membrane protein 1105101002458 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 1105101002459 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 1105101002460 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 1105101002461 Walker A motif; other site 1105101002462 ATP binding site [chemical binding]; other site 1105101002463 Walker B motif; other site 1105101002464 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 1105101002465 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 1105101002466 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 1105101002467 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 1105101002468 Ligand Binding Site [chemical binding]; other site 1105101002469 Uncharacterized protein family (UPF0150); Region: UPF0150; cl00691 1105101002470 HicB family; Region: HicB; pfam05534 1105101002471 YcfA-like protein; Region: YcfA; cl00752 1105101002472 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 1105101002473 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 1105101002474 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101002475 Walker A/P-loop; other site 1105101002476 ATP binding site [chemical binding]; other site 1105101002477 Q-loop/lid; other site 1105101002478 ABC transporter signature motif; other site 1105101002479 Walker B; other site 1105101002480 D-loop; other site 1105101002481 H-loop/switch region; other site 1105101002482 Protein of unknown function (DUF2673); Region: DUF2673; pfam10880 1105101002483 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105101002484 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 1105101002485 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 1105101002486 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1105101002487 FtsX-like permease family; Region: FtsX; cl15850 1105101002488 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1105101002489 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 1105101002490 Walker A/P-loop; other site 1105101002491 ATP binding site [chemical binding]; other site 1105101002492 Q-loop/lid; other site 1105101002493 ABC transporter signature motif; other site 1105101002494 Walker B; other site 1105101002495 D-loop; other site 1105101002496 H-loop/switch region; other site 1105101002497 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 1105101002498 Domain of unknown function DUF21; Region: DUF21; pfam01595 1105101002499 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 1105101002500 Transporter associated domain; Region: CorC_HlyC; cl08393 1105101002501 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 1105101002502 Rickettsia outer membrane protein B; Region: rOmpB; pfam12334 1105101002503 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 1105101002504 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 1105101002505 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 1105101002506 synthetase active site [active] 1105101002507 NTP binding site [chemical binding]; other site 1105101002508 metal binding site [ion binding]; metal-binding site 1105101002509 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 1105101002510 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 1105101002511 DNA binding residues [nucleotide binding] 1105101002512 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 1105101002513 IHF dimer interface [polypeptide binding]; other site 1105101002514 IHF - DNA interface [nucleotide binding]; other site 1105101002515 valyl-tRNA synthetase-like protein; Provisional; Region: PTZ00419 1105101002516 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 1105101002517 catalytic triad [active] 1105101002518 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 1105101002519 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 1105101002520 putative acyl-acceptor binding pocket; other site 1105101002521 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 1105101002522 tetraacyldisaccharide 4'-kinase; Region: lpxK; TIGR00682 1105101002523 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105101002524 Protein of unknown function (DUF519); Region: DUF519; pfam04378 1105101002525 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 1105101002526 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 1105101002527 nucleotide binding pocket [chemical binding]; other site 1105101002528 K-X-D-G motif; other site 1105101002529 catalytic site [active] 1105101002530 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 1105101002531 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 1105101002532 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 1105101002533 Dimer interface [polypeptide binding]; other site 1105101002534 BRCT sequence motif; other site 1105101002535 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 1105101002536 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 1105101002537 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 1105101002538 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 1105101002539 mce related protein; Region: MCE; pfam02470 1105101002540 NADH ubiquinone oxidoreductase subunit NDUFA12; Region: NDUFA12; cl01534 1105101002541 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 1105101002542 RNA/DNA hybrid binding site [nucleotide binding]; other site 1105101002543 active site 1105101002544 Stringent starvation protein B; Region: SspB; cl01120 1105101002545 Protein of unknown function (DUF1009); Region: DUF1009; cl09182 1105101002546 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 1105101002547 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 1105101002548 CoA-binding site [chemical binding]; other site 1105101002549 ATP-binding [chemical binding]; other site 1105101002550 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 1105101002551 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 1105101002552 active site 1105101002553 catalytic site [active] 1105101002554 substrate binding site [chemical binding]; other site 1105101002555 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 1105101002556 double-strand break repair helicase AddA, alphaproteobacterial type; Region: addA_alphas; TIGR02784 1105101002557 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101002558 Family description; Region: UvrD_C_2; cl15862 1105101002559 Acyl transferase domain; Region: Acyl_transf_1; cl08282 1105101002560 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 1105101002561 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105101002562 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105101002563 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105101002564 potential frameshift: common BLAST hit: gi|341584292|ref|YP_004764783.1| superfamily I DNA/RNA helicase 1105101002565 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 1105101002566 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 1105101002567 ATP/ADP translocase [Energy production and conversion]; Region: COG3202; cl03940 1105101002568 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105101002569 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 1105101002570 nudix motif; other site 1105101002571 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 1105101002572 Transporter associated domain; Region: CorC_HlyC; cl08393 1105101002573 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 1105101002574 PemK-like protein; Region: PemK; cl00995 1105101002575 lipoyl synthase; Provisional; Region: PRK05481 1105101002576 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 1105101002577 FeS/SAM binding site; other site 1105101002578 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 1105101002579 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 1105101002580 dimer interface [polypeptide binding]; other site 1105101002581 active site 1105101002582 glycine-pyridoxal phosphate binding site [chemical binding]; other site 1105101002583 folate binding site [chemical binding]; other site 1105101002584 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 1105101002585 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 1105101002586 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 1105101002587 putative GSH binding site [chemical binding]; other site 1105101002588 catalytic residues [active] 1105101002589 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 1105101002590 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1105101002591 minor groove reading motif; other site 1105101002592 helix-hairpin-helix signature motif; other site 1105101002593 substrate binding pocket [chemical binding]; other site 1105101002594 active site 1105101002595 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 1105101002596 Entericidin EcnA/B family; Region: Entericidin; cl02322 1105101002597 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105101002598 Predicted methyltransferases [General function prediction only]; Region: COG0313 1105101002599 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 1105101002600 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 1105101002601 putative ligand binding site [chemical binding]; other site 1105101002602 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 1105101002603 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 1105101002604 tetramer interfaces [polypeptide binding]; other site 1105101002605 binuclear metal-binding site [ion binding]; other site 1105101002606 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 1105101002607 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 1105101002608 aspartate kinase; Reviewed; Region: PRK06635 1105101002609 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 1105101002610 putative nucleotide binding site [chemical binding]; other site 1105101002611 putative catalytic residues [active] 1105101002612 putative Mg ion binding site [ion binding]; other site 1105101002613 putative aspartate binding site [chemical binding]; other site 1105101002614 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 1105101002615 putative allosteric regulatory residue; other site 1105101002616 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 1105101002617 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 1105101002618 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 1105101002619 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 1105101002620 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105101002621 putative substrate translocation pore; other site 1105101002622 Cell division protein ZapA; Region: ZapA; cl01146 1105101002623 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 1105101002624 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101002625 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 1105101002626 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]; Region: COG2902 1105101002627 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105101002628 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 1105101002629 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 1105101002630 trmE is a tRNA modification GTPase; Region: trmE; cd04164 1105101002631 G1 box; other site 1105101002632 GTP/Mg2+ binding site [chemical binding]; other site 1105101002633 Switch I region; other site 1105101002634 G2 box; other site 1105101002635 Switch II region; other site 1105101002636 G3 box; other site 1105101002637 G4 box; other site 1105101002638 G5 box; other site 1105101002639 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 1105101002640 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1105101002641 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 1105101002642 protein RecA; Region: tigrfam_recA; TIGR02012 1105101002643 hexamer interface [polypeptide binding]; other site 1105101002644 Walker A motif; other site 1105101002645 ATP binding site [chemical binding]; other site 1105101002646 Walker B motif; other site 1105101002647 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 1105101002648 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105101002649 NAD(P) binding site [chemical binding]; other site 1105101002650 active site 1105101002651 Phosphopantetheine attachment site; Region: PP-binding; cl09936 1105101002652 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 1105101002653 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 1105101002654 dimer interface [polypeptide binding]; other site 1105101002655 active site 1105101002656 ABC transporter ATPase component; Reviewed; Region: PRK11147 1105101002657 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 1105101002658 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 1105101002659 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 1105101002660 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101002661 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 1105101002662 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101002663 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 1105101002664 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 1105101002665 catalytic site [active] 1105101002666 G-X2-G-X-G-K; other site 1105101002667 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 1105101002668 rod shape-determining protein MreC; Provisional; Region: PRK13922 1105101002669 rod shape-determining protein MreC; Region: MreC; pfam04085 1105101002670 rod shape-determining protein MreB; Provisional; Region: PRK13927 1105101002671 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 1105101002672 ATP binding site [chemical binding]; other site 1105101002673 profilin binding site; other site 1105101002674 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 1105101002675 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1105101002676 putative outer membrane lipoprotein; Provisional; Region: PRK09967 1105101002677 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1105101002678 ligand binding site [chemical binding]; other site 1105101002679 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101002680 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 1105101002681 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 1105101002682 dimer interface [polypeptide binding]; other site 1105101002683 active site 1105101002684 CoA binding pocket [chemical binding]; other site 1105101002685 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 1105101002686 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 1105101002687 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 1105101002688 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 1105101002689 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 1105101002690 P loop; other site 1105101002691 GTP binding site [chemical binding]; other site 1105101002692 DNA polymerase I; Provisional; Region: PRK05755 1105101002693 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 1105101002694 active site 1105101002695 metal binding site 1 [ion binding]; metal-binding site 1105101002696 putative 5' ssDNA interaction site; other site 1105101002697 metal binding site 3; metal-binding site 1105101002698 metal binding site 2 [ion binding]; metal-binding site 1105101002699 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 1105101002700 putative DNA binding site [nucleotide binding]; other site 1105101002701 putative metal binding site [ion binding]; other site 1105101002702 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 1105101002703 active site 1105101002704 substrate binding site [chemical binding]; other site 1105101002705 catalytic site [active] 1105101002706 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 1105101002707 active site 1105101002708 DNA binding site [nucleotide binding] 1105101002709 catalytic site [active] 1105101002710 potential frameshift: common BLAST hit: gi|157826229|ref|YP_001493949.1| S-adenosylmethionine synthetase 1105101002711 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 1105101002712 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 1105101002713 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 1105101002714 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 1105101002715 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 1105101002716 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 1105101002717 generic binding surface I; other site 1105101002718 generic binding surface II; other site 1105101002719 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 1105101002720 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 1105101002721 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105101002722 Protein of unknown function; Region: DUF3971; pfam13116 1105101002723 AsmA-like C-terminal region; Region: AsmA_2; cl15864 1105101002724 AmpG-like permease; Region: 2A0125; TIGR00901 1105101002725 muropeptide transporter; Validated; Region: ampG; PRK11010 1105101002726 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 1105101002727 seryl-tRNA synthetase; Provisional; Region: PRK05431 1105101002728 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 1105101002729 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 1105101002730 dimer interface [polypeptide binding]; other site 1105101002731 active site 1105101002732 motif 1; other site 1105101002733 motif 2; other site 1105101002734 motif 3; other site 1105101002735 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105101002736 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 1105101002737 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1105101002738 Integral membrane protein TerC family; Region: TerC; cl10468 1105101002739 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 1105101002740 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 1105101002741 S-adenosylmethionine binding site [chemical binding]; other site 1105101002742 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 1105101002743 Predicted transcriptional regulator [Transcription]; Region: COG2944 1105101002744 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 1105101002745 salt bridge; other site 1105101002746 non-specific DNA binding site [nucleotide binding]; other site 1105101002747 sequence-specific DNA binding site [nucleotide binding]; other site 1105101002748 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 1105101002749 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 1105101002750 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 1105101002751 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 1105101002752 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 1105101002753 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 1105101002754 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 1105101002755 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 1105101002756 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13541 1105101002757 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101002758 Walker A/P-loop; other site 1105101002759 ATP binding site [chemical binding]; other site 1105101002760 Q-loop/lid; other site 1105101002761 ABC transporter signature motif; other site 1105101002762 Walker B; other site 1105101002763 D-loop; other site 1105101002764 H-loop/switch region; other site 1105101002765 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 1105101002766 4Fe-4S binding domain; Region: Fer4; cl02805 1105101002767 4Fe-4S binding domain; Region: Fer4; cl02805 1105101002768 NADH dehydrogenase; Region: NADHdh; cl00469 1105101002769 NADH dehydrogenase subunit G; Validated; Region: PRK09130 1105101002770 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 1105101002771 catalytic loop [active] 1105101002772 iron binding site [ion binding]; other site 1105101002773 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 1105101002774 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 1105101002775 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 1105101002776 Predicted membrane protein [Function unknown]; Region: COG3671 1105101002777 aconitate hydratase; Validated; Region: PRK09277 1105101002778 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 1105101002779 substrate binding site [chemical binding]; other site 1105101002780 ligand binding site [chemical binding]; other site 1105101002781 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 1105101002782 substrate binding site [chemical binding]; other site 1105101002783 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK01474 1105101002784 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 1105101002785 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 1105101002786 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 1105101002787 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 1105101002788 alpha subunit interaction interface [polypeptide binding]; other site 1105101002789 Walker A motif; other site 1105101002790 ATP binding site [chemical binding]; other site 1105101002791 Walker B motif; other site 1105101002792 inhibitor binding site; inhibition site 1105101002793 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1105101002794 ATP synthase; Region: ATP-synt; cl00365 1105101002795 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 1105101002796 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 1105101002797 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 1105101002798 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 1105101002799 beta subunit interaction interface [polypeptide binding]; other site 1105101002800 Walker A motif; other site 1105101002801 ATP binding site [chemical binding]; other site 1105101002802 Walker B motif; other site 1105101002803 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1105101002804 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 1105101002805 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 1105101002806 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 1105101002807 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105101002808 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105101002809 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1105101002810 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 1105101002811 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 1105101002812 dimerization interface [polypeptide binding]; other site 1105101002813 DPS ferroxidase diiron center [ion binding]; other site 1105101002814 ion pore; other site 1105101002815 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 1105101002816 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 1105101002817 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 1105101002818 Transglycosylase; Region: Transgly; cl07896 1105101002819 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 1105101002820 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 1105101002821 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1105101002822 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; cl15377 1105101002823 TRAM domain; Region: TRAM; cl01282 1105101002824 potential frameshift: common BLAST hit: gi|67459332|ref|YP_246956.1| nucleotidyltransferase/HEPN domain-containing protein 1105101002825 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105101002826 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105101002827 Bacterial SH3 domain; Region: SH3_3; cl02551 1105101002828 Bacterial SH3 domain; Region: SH3_3; cl02551 1105101002829 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 1105101002830 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 1105101002831 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105101002832 Oligomerisation domain; Region: Oligomerisation; cl00519 1105101002833 BolA-like protein; Region: BolA; cl00386 1105101002834 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105101002835 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105101002836 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105101002837 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105101002838 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 1105101002839 rRNA binding site [nucleotide binding]; other site 1105101002840 predicted 30S ribosome binding site; other site 1105101002841 Maf-like protein; Region: Maf; pfam02545 1105101002842 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 1105101002843 active site 1105101002844 dimer interface [polypeptide binding]; other site 1105101002845 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 1105101002846 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 1105101002847 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 1105101002848 active site 1105101002849 DNA binding site [nucleotide binding] 1105101002850 Int/Topo IB signature motif; other site 1105101002851 Phasin protein; Region: Phasin_2; cl11491 1105101002852 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 1105101002853 PLD-like domain; Region: PLDc_2; pfam13091 1105101002854 putative active site [active] 1105101002855 catalytic site [active] 1105101002856 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 1105101002857 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 1105101002858 periplasmic folding chaperone; Provisional; Region: PRK10788 1105101002859 PPIC-type PPIASE domain; Region: Rotamase; cl08278 1105101002860 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 1105101002861 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 1105101002862 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 1105101002863 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101002864 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 1105101002865 OpgC protein; Region: OpgC_C; cl00792 1105101002866 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 1105101002867 active site 1105101002868 DNA repair proteins [DNA replication, recombination, and repair]; Region: RadC; COG2003 1105101002869 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 1105101002870 MPN+ (JAMM) motif; other site 1105101002871 Zinc-binding site [ion binding]; other site 1105101002872 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 1105101002873 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 1105101002874 Mg++ binding site [ion binding]; other site 1105101002875 putative catalytic motif [active] 1105101002876 putative substrate binding site [chemical binding]; other site 1105101002877 Protein of unknown function (DUF721); Region: DUF721; cl02324 1105101002878 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 1105101002879 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 1105101002880 Ferredoxin [Energy production and conversion]; Region: COG1146 1105101002881 4Fe-4S binding domain; Region: Fer4; cl02805 1105101002882 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 1105101002883 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 1105101002884 nucleoside/Zn binding site; other site 1105101002885 dimer interface [polypeptide binding]; other site 1105101002886 catalytic motif [active] 1105101002887 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 1105101002888 Cation efflux family; Region: Cation_efflux; cl00316 1105101002889 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 1105101002890 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 1105101002891 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 1105101002892 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 1105101002893 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 1105101002894 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 1105101002895 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 1105101002896 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 1105101002897 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 1105101002898 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 1105101002899 dimer interface [polypeptide binding]; other site 1105101002900 ssDNA binding site [nucleotide binding]; other site 1105101002901 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1105101002902 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 1105101002903 heat shock protein 90; Provisional; Region: PRK05218 1105101002904 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 1105101002905 ATP binding site [chemical binding]; other site 1105101002906 Mg2+ binding site [ion binding]; other site 1105101002907 G-X-G motif; other site 1105101002908 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 1105101002909 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 1105101002910 substrate-cofactor binding pocket; other site 1105101002911 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105101002912 catalytic residue [active] 1105101002913 trigger factor; Provisional; Region: tig; PRK01490 1105101002914 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 1105101002915 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 1105101002916 GTPase CgtA; Reviewed; Region: obgE; PRK12299 1105101002917 GTP1/OBG; Region: GTP1_OBG; pfam01018 1105101002918 Obg GTPase; Region: Obg; cd01898 1105101002919 G1 box; other site 1105101002920 GTP/Mg2+ binding site [chemical binding]; other site 1105101002921 Switch I region; other site 1105101002922 G2 box; other site 1105101002923 G3 box; other site 1105101002924 Switch II region; other site 1105101002925 G4 box; other site 1105101002926 G5 box; other site 1105101002927 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 1105101002928 dimer interface [polypeptide binding]; other site 1105101002929 Citrate synthase; Region: Citrate_synt; pfam00285 1105101002930 active site 1105101002931 citrylCoA binding site [chemical binding]; other site 1105101002932 NADH binding [chemical binding]; other site 1105101002933 cationic pore residues; other site 1105101002934 oxalacetate/citrate binding site [chemical binding]; other site 1105101002935 coenzyme A binding site [chemical binding]; other site 1105101002936 catalytic triad [active] 1105101002937 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 1105101002938 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 1105101002939 Fe-S cluster binding site [ion binding]; other site 1105101002940 active site 1105101002941 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1105101002942 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 1105101002943 RNA binding surface [nucleotide binding]; other site 1105101002944 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1105101002945 active site 1105101002946 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed; Region: PRK01544 1105101002947 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 1105101002948 S-adenosylmethionine binding site [chemical binding]; other site 1105101002949 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 1105101002950 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 1105101002951 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 1105101002952 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 1105101002953 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1105101002954 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 1105101002955 motif 1; other site 1105101002956 dimer interface [polypeptide binding]; other site 1105101002957 active site 1105101002958 motif 2; other site 1105101002959 motif 3; other site 1105101002960 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 1105101002961 oligomeric interface; other site 1105101002962 putative active site [active] 1105101002963 homodimer interface [polypeptide binding]; other site 1105101002964 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 1105101002965 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 1105101002966 potential frameshift: common BLAST hit: gi|350273988|ref|YP_004885301.1| proline/betaine transporter 1105101002967 ADP-specific Phosphofructokinase/Glucokinase conserved region; Region: ADP_PFK_GK; cl14060 1105101002968 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 1105101002969 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 1105101002970 motif 1; other site 1105101002971 active site 1105101002972 motif 2; other site 1105101002973 motif 3; other site 1105101002974 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 1105101002975 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 1105101002976 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 1105101002977 dimerization interface 3.5A [polypeptide binding]; other site 1105101002978 active site 1105101002979 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 1105101002980 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 1105101002981 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1105101002982 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1105101002983 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1105101002984 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 1105101002985 DNA binding residues [nucleotide binding] 1105101002986 DNA primase, catalytic core; Region: dnaG; TIGR01391 1105101002987 CHC2 zinc finger; Region: zf-CHC2; cl15369 1105101002988 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 1105101002989 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 1105101002990 active site 1105101002991 metal binding site [ion binding]; metal-binding site 1105101002992 interdomain interaction site; other site 1105101002993 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 1105101002994 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 1105101002995 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 1105101002996 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1105101002997 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 1105101002998 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 1105101002999 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 1105101003000 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 1105101003001 NAD(P) binding site [chemical binding]; other site 1105101003002 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 1105101003003 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 1105101003004 DNA polymerase III subunits gamma and tau; Validated; Region: PRK06645 1105101003005 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 1105101003006 Walker A motif; other site 1105101003007 ATP binding site [chemical binding]; other site 1105101003008 Walker B motif; other site 1105101003009 arginine finger; other site 1105101003010 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 1105101003011 YbaB/EbfC DNA-binding family; Region: YbaB_DNA_bd; cl00494 1105101003012 Predicted aspartyl protease [General function prediction only]; Region: COG3577 1105101003013 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 1105101003014 catalytic motif [active] 1105101003015 Catalytic residue [active] 1105101003016 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 1105101003017 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 1105101003018 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 1105101003019 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105101003020 Walker A/P-loop; other site 1105101003021 ATP binding site [chemical binding]; other site 1105101003022 Q-loop/lid; other site 1105101003023 ABC transporter signature motif; other site 1105101003024 Walker B; other site 1105101003025 D-loop; other site 1105101003026 H-loop/switch region; other site 1105101003027 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 1105101003028 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 1105101003029 active site 1105101003030 RelB antitoxin; Region: RelB; cl01171 1105101003031 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 1105101003032 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 1105101003033 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1105101003034 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 1105101003035 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 1105101003036 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 1105101003037 metal binding site [ion binding]; metal-binding site 1105101003038 dimer interface [polypeptide binding]; other site 1105101003039 potential frameshift: common BLAST hit: gi|341584500|ref|YP_004764991.1| putative type I restriction enzyme S subunit 1105101003040 potential frameshift: common BLAST hit: gi|157827849|ref|YP_001496913.1| Type I restriction-modification system methyltransferase subunit 1105101003041 potential frameshift: common BLAST hit: gi|157827849|ref|YP_001496913.1| Type I restriction-modification system methyltransferase subunit 1105101003042 potential frameshift: common BLAST hit: gi|157965011|ref|YP_001499835.1| Na+/H+ antiporter NhaA 1105101003043 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 1105101003044 putative active site [active] 1105101003045 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 1105101003046 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1105101003047 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 1105101003048 amidase catalytic site [active] 1105101003049 Zn binding residues [ion binding]; other site 1105101003050 substrate binding site [chemical binding]; other site 1105101003051 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 1105101003052 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 1105101003053 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 1105101003054 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 1105101003055 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 1105101003056 ATP binding site [chemical binding]; other site 1105101003057 Mg2+ binding site [ion binding]; other site 1105101003058 G-X-G motif; other site 1105101003059 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 1105101003060 ATP binding site [chemical binding]; other site 1105101003061 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 1105101003062 Zinc-finger domain; Region: zf-CHCC; cl01821 1105101003063 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105101003064 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1105101003065 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 1105101003066 TPR motif; other site 1105101003067 TPR repeat; Region: TPR_11; pfam13414 1105101003068 binding surface 1105101003069 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 1105101003070 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105101003071 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 1105101003072 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 1105101003073 potential frameshift: common BLAST hit: gi|67459789|ref|YP_247413.1| prophage antirepressor 1105101003074 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 1105101003075 ferrochelatase; Reviewed; Region: hemH; PRK00035 1105101003076 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 1105101003077 C-terminal domain interface [polypeptide binding]; other site 1105101003078 active site 1105101003079 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 1105101003080 active site 1105101003081 N-terminal domain interface [polypeptide binding]; other site 1105101003082 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 1105101003083 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 1105101003084 substrate binding site [chemical binding]; other site 1105101003085 active site