-- dump date 20111121_011036 -- class Genbank::misc_feature -- table misc_feature_note -- id note 387662000001 Predicted GTPase [General function prediction only]; Region: ThdF; COG0486 387662000002 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 387662000003 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 387662000004 G1 box; other site 387662000005 GTP/Mg2+ binding site [chemical binding]; other site 387662000006 G2 box; other site 387662000007 Switch I region; other site 387662000008 G3 box; other site 387662000009 Switch II region; other site 387662000010 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; cl11520 387662000011 Glucose inhibited division protein A; Region: GIDA; pfam01134 387662000012 ATP synthase A chain; Region: ATP-synt_A; cl00413 387662000013 ATP synthase subunit C; Region: ATP-synt_C; cl00466 387662000014 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 387662000015 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 387662000016 beta subunit interaction interface [polypeptide binding]; other site 387662000017 Walker A motif; other site 387662000018 ATP binding site [chemical binding]; other site 387662000019 Walker B motif; other site 387662000020 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 387662000021 ATP synthase; Region: ATP-synt; cl00365 387662000022 ATP synthase; Region: ATP-synt; cl00365 387662000023 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 387662000024 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 387662000025 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 387662000026 alpha subunit interaction interface [polypeptide binding]; other site 387662000027 Walker A motif; other site 387662000028 ATP binding site [chemical binding]; other site 387662000029 Walker B motif; other site 387662000030 inhibitor binding site; inhibition site 387662000031 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 387662000032 Ornithine carbamoyltransferase [Amino acid transport and metabolism]; Region: ArgF; COG0078 387662000033 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 387662000034 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 387662000035 Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway...; Region: DHQase_II; cd00466 387662000036 trimer interface [polypeptide binding]; other site 387662000037 active site 387662000038 dimer interface [polypeptide binding]; other site 387662000039 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 387662000040 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin...; Region: TPP_enzymes; cl01629 387662000041 TPP-binding site [chemical binding]; other site 387662000042 Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins; Region: TPP_PYR_DXS_TK_like; cd07033 387662000043 PYR/PP interface [polypeptide binding]; other site 387662000044 dimer interface [polypeptide binding]; other site 387662000045 TPP binding site [chemical binding]; other site 387662000046 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09209 387662000047 Methylenetetrahydrofolate reductase; Region: MTHFR; pfam02219 387662000048 Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine...; Region: MTHFR; cl00246 387662000049 FAD binding site [chemical binding]; other site 387662000050 M28, and M42; Region: Zinc_peptidase_like; cl14876 387662000051 metal binding site [ion binding]; metal-binding site 387662000052 Putative 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (THP succinyltransferase), C-terminal left-handed parallel alpha-helix (LbH) domain: This group is composed of mostly uncharacterized proteins containing an N-terminal...; Region: LbH_THP_succinylT_putative; cd04649 387662000053 putative trimer interface [polypeptide binding]; other site 387662000054 putative CoA binding site [chemical binding]; other site 387662000055 A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate...; Region: APP_MetAP; cl00279 387662000056 active site 387662000057 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; cl00315 387662000058 rRNA interaction site [nucleotide binding]; other site 387662000059 S8 interaction site; other site 387662000060 DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]; Region: DnaE; COG0587 387662000061 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 387662000062 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 387662000063 The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases, as well as cobalamine (B12) independent methionine...; Region: URO-D_CIMS_like; cl00464 387662000064 The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases, as well as cobalamine (B12) independent methionine...; Region: URO-D_CIMS_like; cl00464 387662000065 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 387662000066 active site 387662000067 NAD binding site [chemical binding]; other site 387662000068 metal binding site [ion binding]; metal-binding site 387662000069 Dehydratase family; Region: ILVD_EDD; cl00340 387662000070 dihydroxy-acid dehydratase; Region: ilvD; TIGR00110 387662000071 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 387662000072 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 387662000073 catalytic residue [active] 387662000074 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 387662000075 FeS assembly protein SufB; Region: sufB; TIGR01980 387662000076 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 387662000077 Walker A/P-loop; other site 387662000078 ATP binding site [chemical binding]; other site 387662000079 Q-loop/lid; other site 387662000080 ABC transporter signature motif; other site 387662000081 Walker B; other site 387662000082 D-loop; other site 387662000083 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 387662000084 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 387662000085 catalytic residue [active] 387662000086 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 387662000087 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 387662000088 rRNA binding site [nucleotide binding]; other site 387662000089 predicted 30S ribosome binding site; other site 387662000090 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 387662000091 catalytic residues [active] 387662000092 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 387662000093 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 387662000094 peptide chain release factor 1; Validated; Region: prfA; PRK00591 387662000095 RF-1 domain; Region: RF-1; cl02875 387662000096 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 387662000097 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 387662000098 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 387662000099 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 387662000100 This domain family includes the Enolpyruvate transferase (EPT) family and the RNA 3' phosphate cyclase family (RTPC). These 2 families differ in that EPT is formed by 3 repeats of an alpha-beta structural domain while RTPC has 3 similar repeats with a...; Region: EPT_RTPC-like; cl00288 387662000101 putative active site [active] 387662000102 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 387662000103 RNA binding site [nucleotide binding]; other site 387662000104 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 387662000105 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 387662000106 ring oligomerisation interface [polypeptide binding]; other site 387662000107 ATP/Mg binding site [chemical binding]; other site 387662000108 stacking interactions; other site 387662000109 hinge regions; other site 387662000110 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 387662000111 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 387662000112 Walker A motif; other site 387662000113 ATP binding site [chemical binding]; other site 387662000114 Walker B motif; other site 387662000115 CHC2 zinc finger; Region: zf-CHC2; cl02597 387662000116 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 387662000117 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication...; Region: TOPRIM_primases; cd01029 387662000118 active site 387662000119 metal binding site [ion binding]; metal-binding site 387662000120 interdomain interaction site; other site 387662000121 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...; Region: Sigma70_r4; cl01055 387662000122 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 387662000123 dimer interface [polypeptide binding]; other site 387662000124 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 387662000125 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 387662000126 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 387662000127 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 387662000128 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; pfam00988 387662000129 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 387662000130 conserved cys residue [active] 387662000131 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 387662000132 Carbamoylphosphate synthase large subunit (split gene in MJ) [Amino acid transport and metabolism / Nucleotide transport and metabolism]; Region: CarB; COG0458 387662000133 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 387662000134 carbamoyl-phosphate synthase, large subunit; Region: CPSaseII_lrg; TIGR01369 387662000135 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 387662000136 translation initiation factor 2; Provisional; Region: infB; CHL00189 387662000137 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 387662000138 G1 box; other site 387662000139 GTP/Mg2+ binding site [chemical binding]; other site 387662000140 G2 box; other site 387662000141 Switch I region; other site 387662000142 G3 box; other site 387662000143 Switch II region; other site 387662000144 G4 box; other site 387662000145 G5 box; other site 387662000146 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding...; Region: Translation_Factor_II_like; cl02787 387662000147 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 387662000148 active site 387662000149 HIGH motif; other site 387662000150 nucleotide binding site [chemical binding]; other site 387662000151 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 387662000152 active site 387662000153 HIGH motif; other site 387662000154 nucleotide binding site [chemical binding]; other site 387662000155 glutaminyl-tRNA synthetase/YqeY domain fusion protein; Provisional; Region: PRK14703 387662000156 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 387662000157 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 387662000158 oligomer interface [polypeptide binding]; other site 387662000159 active site residues [active] 387662000160 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 387662000161 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...; Region: AAA; cd00009 387662000162 Walker A motif; other site 387662000163 ATP binding site [chemical binding]; other site 387662000164 Walker B motif; other site 387662000165 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 387662000166 putative active site [active] 387662000167 catalytic site [active] 387662000168 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 387662000169 motif 1; other site 387662000170 dimer interface [polypeptide binding]; other site 387662000171 active site 387662000172 motif 2; other site 387662000173 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 387662000174 active site 387662000175 motif 3; other site 387662000176 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 387662000177 phosphate binding site [ion binding]; other site 387662000178 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 387662000179 Proline dehydrogenase; Region: Pro_dh; cl03282 387662000180 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 387662000181 Glutamate binding site [chemical binding]; other site 387662000182 NAD binding site [chemical binding]; other site 387662000183 catalytic residues [active] 387662000184 DRE-TIM metallolyase superfamily; Region: DRE_TIM_metallolyase; cl07974 387662000185 active site 387662000186 catalytic residues [active] 387662000187 metal binding site [ion binding]; metal-binding site 387662000188 (R)-citramalate synthase; Provisional; Region: PRK09389 387662000189 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 387662000190 Tetramer interface [polypeptide binding]; other site 387662000191 Active site [active] 387662000192 FMN-binding site [chemical binding]; other site 387662000193 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 387662000194 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 387662000195 substrate binding site [chemical binding]; other site 387662000196 ligand binding site [chemical binding]; other site 387662000197 Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate 3-...; Region: IPMI_Swivel; cd01577 387662000198 substrate binding site [chemical binding]; other site 387662000199 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 387662000200 isocitrate dehydrogenase; Validated; Region: PRK06451 387662000201 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 387662000202 Semialdehyde dehydrogenase, dimerisation domain; Region: Semialdhyde_dhC; pfam02774 387662000203 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 387662000204 motif 1; other site 387662000205 dimer interface [polypeptide binding]; other site 387662000206 active site 387662000207 motif 2; other site 387662000208 motif 3; other site 387662000209 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 387662000210 active site 387662000211 substrate binding site [chemical binding]; other site 387662000212 catalytic site [active] 387662000213 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 387662000214 23S rRNA binding site [nucleotide binding]; other site 387662000215 L13 binding site [polypeptide binding]; other site 387662000216 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 387662000217 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 387662000218 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 387662000219 NeuB family; Region: NeuB; cl00496 387662000220 Radical SAM; Region: Elp3; smart00729 387662000221 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; cl14056 387662000222 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 387662000223 active site 387662000224 HIGH motif; other site 387662000225 nucleotide binding site [chemical binding]; other site 387662000226 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 387662000227 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 387662000228 succinyl-CoA synthetase, alpha subunit; Region: sucCoAalpha; TIGR01019 387662000229 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 387662000230 succinyl-CoA synthetase, beta subunit; Region: sucCoAbeta; TIGR01016 387662000231 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 387662000232 CoA-ligase; Region: Ligase_CoA; pfam00549 387662000233 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 387662000234 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 387662000235 active site 387662000236 KMSKS motif; other site 387662000237 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 387662000238 active site 387662000239 HIGH motif; other site 387662000240 nucleotide binding site [chemical binding]; other site 387662000241 argininosuccinate synthase; Provisional; Region: PLN00200 387662000242 Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In...; Region: Argininosuccinate_Synthase; cd01999 387662000243 ANP binding site [chemical binding]; other site 387662000244 Substrate Binding Site II [chemical binding]; other site 387662000245 Substrate Binding Site I [chemical binding]; other site 387662000246 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 387662000247 Predicted dehydrogenase [General function prediction only]; Region: COG0579 387662000248 aspartate kinase; Reviewed; Region: PRK06635 387662000249 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 387662000250 nucleotide binding site [chemical binding]; other site 387662000251 substrate binding site [chemical binding]; other site 387662000252 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins; Region: ACT_AKii-LysC-BS-like_1; cd04913 387662000253 putative allosteric regulatory site; other site 387662000254 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AK-LysC-DapG-like_2; cd04923 387662000255 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 387662000256 dimer interface [polypeptide binding]; other site 387662000257 motif 2; other site 387662000258 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 387662000259 Walker A motif; other site 387662000260 ATP binding site [chemical binding]; other site 387662000261 Walker B motif; other site 387662000262 Valyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ValS; COG0525 387662000263 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 387662000264 active site 387662000265 HIGH motif; other site 387662000266 nucleotide binding site [chemical binding]; other site 387662000267 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 387662000268 peroxiredoxin; Region: AhpC; TIGR03137 387662000269 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...; Region: PRX_Typ2cys; cd03015 387662000270 dimer interface [polypeptide binding]; other site 387662000271 decamer (pentamer of dimers) interface [polypeptide binding]; other site 387662000272 catalytic triad [active] 387662000273 peroxidatic and resolving cysteines [active] 387662000274 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 387662000275 active site 387662000276 catalytic residue [active] 387662000277 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 387662000278 active site 387662000279 HIGH motif; other site 387662000280 nucleotide binding site [chemical binding]; other site 387662000281 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 387662000282 active site 387662000283 dimer interface [polypeptide binding]; other site 387662000284 motif 2; other site 387662000285 motif 3; other site 387662000286 peptide chain release factor 2; Validated; Region: prfB; PRK00578 387662000287 RF-1 domain; Region: RF-1; cl02875 387662000288 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD)...; Region: Trp-synth-beta_II; cl00342 387662000289 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 387662000290 catalytic residue [active] 387662000291 Homoserine dehydrogenase [Amino acid transport and metabolism]; Region: ThrA; COG0460 387662000292 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 387662000293 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 387662000294 ketol-acid reductoisomerase; Provisional; Region: PRK05479 387662000295 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 387662000296 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 387662000297 acetolactate synthase catalytic subunit; Reviewed; Region: PRK07282 387662000298 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 387662000299 PYR/PP interface [polypeptide binding]; other site 387662000300 dimer interface [polypeptide binding]; other site 387662000301 TPP binding site [chemical binding]; other site 387662000302 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 387662000303 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin...; Region: TPP_enzymes; cl01629 387662000304 TPP-binding site [chemical binding]; other site 387662000305 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 387662000306 active site 387662000307 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 387662000308 Isoleucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: IleS; COG0060 387662000309 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 387662000310 active site 387662000311 HIGH motif; other site 387662000312 nucleotide binding site [chemical binding]; other site 387662000313 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 387662000314 active site 387662000315 KMSKS motif; other site 387662000316 GTP1/OBG; Region: GTP1_OBG; pfam01018 387662000317 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 387662000318 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 387662000319 dimer interface [polypeptide binding]; other site 387662000320 DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type; Region: rpoA; TIGR02027 387662000321 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 387662000322 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 387662000323 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 387662000324 RNA binding surface [nucleotide binding]; other site 387662000325 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 387662000326 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 387662000327 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 387662000328 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 387662000329 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 387662000330 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 387662000331 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 387662000332 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 387662000333 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 387662000334 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 387662000335 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 387662000336 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 387662000337 23S rRNA interface [nucleotide binding]; other site 387662000338 5S rRNA interface [nucleotide binding]; other site 387662000339 putative antibiotic binding site [chemical binding]; other site 387662000340 L25 interface [polypeptide binding]; other site 387662000341 L27 interface [polypeptide binding]; other site 387662000342 ribosomal protein S3, bacterial type; Region: rpsC_bact; TIGR01009 387662000343 Ribosomal protein S3, N-terminal domain; Region: Ribosomal_S3_N; pfam00417 387662000344 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 387662000345 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 387662000346 protein-rRNA interface [nucleotide binding]; other site 387662000347 putative translocon binding site; other site 387662000348 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 387662000349 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 387662000350 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 387662000351 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 387662000352 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 387662000353 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 387662000354 elongation factor Tu; Reviewed; Region: PRK00049 387662000355 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 387662000356 G1 box; other site 387662000357 GEF interaction site [polypeptide binding]; other site 387662000358 GTP/Mg2+ binding site [chemical binding]; other site 387662000359 Switch I region; other site 387662000360 G2 box; other site 387662000361 G3 box; other site 387662000362 Switch II region; other site 387662000363 G4 box; other site 387662000364 G5 box; other site 387662000365 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 387662000366 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 387662000367 Antibiotic Binding Site [chemical binding]; other site 387662000368 elongation factor G; Reviewed; Region: PRK00007 387662000369 Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved...; Region: EF-G; cd01886 387662000370 G1 box; other site 387662000371 putative GEF interaction site [polypeptide binding]; other site 387662000372 GTP/Mg2+ binding site [chemical binding]; other site 387662000373 Switch I region; other site 387662000374 G2 box; other site 387662000375 G3 box; other site 387662000376 Switch II region; other site 387662000377 G4 box; other site 387662000378 G5 box; other site 387662000379 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...; Region: EFG_mtEFG_II; cd04088 387662000380 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...; Region: EFG_mtEFG1_IV; cd01434 387662000381 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...; Region: EFG_mtEFG_C; cd03713 387662000382 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 387662000383 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 387662000384 S17 interaction site [polypeptide binding]; other site 387662000385 S8 interaction site; other site 387662000386 16S rRNA interaction site [nucleotide binding]; other site 387662000387 streptomycin interaction site [chemical binding]; other site 387662000388 23S rRNA interaction site [nucleotide binding]; other site 387662000389 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 387662000390 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 387662000391 DNA-directed RNA polymerase, beta' subunit, predominant form; Region: rpoC_TIGR; TIGR02386 387662000392 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 387662000393 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 387662000394 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 387662000395 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 387662000396 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 387662000397 DNA binding site [nucleotide binding] 387662000398 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 387662000399 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 387662000400 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 387662000401 RPB11 interaction site [polypeptide binding]; other site 387662000402 RPB12 interaction site [polypeptide binding]; other site 387662000403 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 387662000404 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 387662000405 RPB1 interaction site [polypeptide binding]; other site 387662000406 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 387662000407 peripheral dimer interface [polypeptide binding]; other site 387662000408 core dimer interface [polypeptide binding]; other site 387662000409 L10 interface [polypeptide binding]; other site 387662000410 L11 interface [polypeptide binding]; other site 387662000411 putative EF-Tu interaction site [polypeptide binding]; other site 387662000412 putative EF-G interaction site [polypeptide binding]; other site 387662000413 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...; Region: Ribosomal_L1; cl00322 387662000414 Ribosomal protein L11/L12; Region: RL11; smart00649 387662000415 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 387662000416 putative thiostrepton binding site; other site 387662000417 23S rRNA interface [nucleotide binding]; other site 387662000418 L7/L12 interface [polypeptide binding]; other site 387662000419 L25 interface [polypeptide binding]; other site 387662000420 Heme-copper oxidase subunit III. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The...; Region: Heme_Cu_Oxidase_III_like; cl00211 387662000421 Subunit I/III interface [polypeptide binding]; other site 387662000422 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily...; Region: Heme_Cu_Oxidase_I; cl00275 387662000423 D-pathway; other site 387662000424 Low-spin heme binding site [chemical binding]; other site 387662000425 Putative water exit pathway; other site 387662000426 Binuclear center (active site) [active] 387662000427 K-pathway; other site 387662000428 Putative proton exit pathway; other site 387662000429 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 387662000430 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 387662000431 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and 4-amino-4-deoxychorismate...; Region: PLPDE_IV; cl00224 387662000432 homodimer interface [polypeptide binding]; other site 387662000433 substrate-cofactor binding pocket; other site 387662000434 pyridoxal 5'-phosphate binding site [chemical binding]; other site 387662000435 catalytic residue [active] 387662000436 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 387662000437 dimer interface [polypeptide binding]; other site 387662000438 motif 1; other site 387662000439 active site 387662000440 motif 2; other site 387662000441 motif 3; other site 387662000442 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(...; Region: Pep_deformylase; cl00234 387662000443 active site 387662000444 catalytic residues [active] 387662000445 metal binding site [ion binding]; metal-binding site 387662000446 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 387662000447 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 387662000448 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 387662000449 catalytic residue [active] 387662000450 Diaminopimelate epimerase [Amino acid transport and metabolism]; Region: DapF; COG0253 387662000451 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 387662000452 motif 1; other site 387662000453 dimer interface [polypeptide binding]; other site 387662000454 active site 387662000455 motif 2; other site 387662000456 motif 3; other site 387662000457 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 387662000458 DNA-binding site [nucleotide binding]; DNA binding site 387662000459 RNA-binding motif; other site