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Transfer RNA Biogenesis - Shigella flexneri 8401 (serotype 5b)
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AEukaryotic type
B 5'processing factors
C Ribonucrease P
B 3'processing and CCA adding factors
C 3'processing factors
D SFV_2339 elaC; conserved hypothetical protein K00784 rnz; ribonuclease Z [EC:3.1.26.11]
C CCA adding factors
D SFV_3096 cca; tRNA nucleotidyl transferase K00974 cca; tRNA nucleotidyltransferase (CCA-adding enzyme) [EC:2.7.7.72 3.1.3.- 3.1.4.-]
B tRNA spricing factors
C tRNA splicing endonuclease complex
C tRNA splicing ligase complex
D SFV_3428 rtcB; conserved hypothetical protein K14415 RTCB; tRNA-splicing ligase RtcB (3'-phosphate/5'-hydroxy nucleic acid ligase) [EC:6.5.1.8]
C Other tRNA splicing factors
B tRNA transport factors
C tRNA export factors
C tRNA import factors
B Aminoacyl-tRNA synthetases (AARSs)
C Multi-aminoacyl-tRNA synthetase complex (MSC)
D SFV_2455 gltX; glutamate tRNA synthetase, catalytic subunit K01885 EARS; glutamyl-tRNA synthetase [EC:6.1.1.17]
D SFV_0178 proS; proline tRNA synthetase K01881 PARS; prolyl-tRNA synthetase [EC:6.1.1.15]
D SFV_0020 ileS; isoleucine tRNA synthetase K01870 IARS; isoleucyl-tRNA synthetase [EC:6.1.1.5]
D SFV_0684 leuS; leucine tRNA synthetase K01869 LARS; leucyl-tRNA synthetase [EC:6.1.1.4]
D SFV_2170 metG; methionine tRNA synthetase K01874 MARS; methionyl-tRNA synthetase [EC:6.1.1.10]
D SFV_0651 glnS; glutamine tRNA synthetase K01886 QARS; glutaminyl-tRNA synthetase [EC:6.1.1.18]
D SFV_1914 argS; arginine tRNA synthetase K01887 RARS; arginyl-tRNA synthetase [EC:6.1.1.19]
D SFV_2938 lysS; lysine tRNA synthetase K04567 KARS; lysyl-tRNA synthetase, class II [EC:6.1.1.6]
D SFV_1868 aspS; aspartate tRNA synthetase K01876 DARS2; aspartyl-tRNA synthetase [EC:6.1.1.12]
C Other AARSs
D SFV_2808 alaS; alanyl-tRNA synthetase K01872 AARS; alanyl-tRNA synthetase [EC:6.1.1.7]
D SFV_0932 asnS; asparagine tRNA synthetase K01893 NARS; asparaginyl-tRNA synthetase [EC:6.1.1.22]
D SFV_1504 thrS; threonine tRNA synthetase K01868 TARS; threonyl-tRNA synthetase [EC:6.1.1.3]
D SFV_0884 serS; serine tRNA synthetase K01875 SARS; seryl-tRNA synthetase [EC:6.1.1.11]
D SFV_0484 cysS; cysteine tRNA synthetase K01883 CARS; cysteinyl-tRNA synthetase [EC:6.1.1.16]
D SFV_4235 valS; valine tRNA synthetase K01873 VARS; valyl-tRNA synthetase [EC:6.1.1.9]
D SFV_2561 hisS; histidine tRNA synthetase K01892 HARS; histidyl-tRNA synthetase [EC:6.1.1.21]
D SFV_1509 pheS; phenylalanine tRNA synthetase, alpha-subunit K01889 FARSA; phenylalanyl-tRNA synthetase alpha chain [EC:6.1.1.20]
D SFV_1510 pheT; phenylalanine tRNA synthetase, beta-subunit K01890 FARSB; phenylalanyl-tRNA synthetase beta chain [EC:6.1.1.20]
D SFV_1654 tyrS; tyrosine tRNA synthetase K01866 YARS; tyrosyl-tRNA synthetase [EC:6.1.1.1]
D SFV_3389 trpS; tryptophan tRNA synthetase K01867 WARS; tryptophanyl-tRNA synthetase [EC:6.1.1.2]
C Trans-editing factors
D SFV_3612 yihZ; conserved hypothetical protein K07560 dtd; D-aminoacyl-tRNA deacylase [EC:3.1.1.96]
C AARS associated factors
D SFV_1123 ycfF; conserved hypothetical protein K02503 HINT1_2; histidine triad (HIT) family protein [EC:3.9.1.-]
B tRNA modification factors
C Deaminases
C Dihydorouridine synthases
C Methylthiotransferase
C Methyltransferases
D SFV_3018 yggH; conserved hypothetical protein K03439 trmB; tRNA (guanine-N7-)-methyltransferase [EC:2.1.1.33]
D SFV_0179 yaeB; conserved hypothetical protein K22900 TRMO; tRNA (adenine37-N6)-methyltransferase [EC:2.1.1.-]
C Psudouridine synthases
D SFV_2387 truA; pseudouridylate synthase I K06173 truA; tRNA pseudouridine38-40 synthase [EC:5.4.99.12]
D SFV_3196 truB; tRNA pseudouridine 5S synthase K03177 truB; tRNA pseudouridine55 synthase [EC:5.4.99.25]
D SFV_2753 ygbO; putative hydrogenase subunit K06176 truD; tRNA pseudouridine13 synthase [EC:5.4.99.27]
C Thiolation factors
D SFV_2578 yfhO; putative aminotransferase K04487 iscS; cysteine desulfurase [EC:2.8.1.7]
C KEOPS/EKC complex
C Elongator complex
C Elongator related proteins
C Other tRNA modification factors
D SFV_3303 yrdC; conserved hypothetical protein K07566 tsaC; L-threonylcarbamoyladenylate synthase [EC:2.7.7.87]
D SFV_4329 miaA; delta(2)-isopentenylpyrophosphate tRNA-adenosine transferase K00791 miaA; tRNA dimethylallyltransferase [EC:2.5.1.75]
D SFV_3806 thdF; GTP-binding protein in thiophene and furan oxidation K03650 mnmE; tRNA modification GTPase [EC:3.6.-.-]
D SFV_3767 gidA; glucose-inhibited division K03495 gidA; tRNA uridine 5-carboxymethylaminomethyl modification enzyme
D SFV_1453 selD; selenophosphate synthase K01008 selD; selenide, water dikinase [EC:2.7.9.3]
B tRNA degradation factors
C TRAMP complex
C Rapid tRNA decay (RTD) pathway factors
D SFV_4273 cysQ; CysQ protein K01082 cysQ; 3'(2'), 5'-bisphosphate nucleotidase [EC:3.1.3.7]
C Other tRNA degradation factors
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AProkaryotic type
B 5'processing factors
C Ribonucrease P
D SFV_3808 rnpA; ribonuclease P K03536 rnpA; ribonuclease P protein component [EC:3.1.26.5]
B 3'processing and CCA adding factors
C 3'processing factors
D SFV_2339 elaC; conserved hypothetical protein K00784 rnz; ribonuclease Z [EC:3.1.26.11]
D SFV_1672 rnt; RNase T K03683 rnt; ribonuclease T [EC:3.1.13.-]
D SFV_3887 rph; RNase PH K00989 rph; ribonuclease PH [EC:2.7.7.56]
D SFV_0564 rna; RNase I K01169 rna; ribonuclease I (enterobacter ribonuclease) [EC:4.6.1.21]
D SFV_1300 rnb; RNase II, mRNA degradation K01147 rnb; exoribonuclease II [EC:3.1.13.1]
D SFV_1425 rnd; RNase D, processes tRNA precursor K03684 rnd; ribonuclease D [EC:3.1.13.5]
C CCA adding factors
D SFV_3096 cca; tRNA nucleotidyl transferase K00974 cca; tRNA nucleotidyltransferase (CCA-adding enzyme) [EC:2.7.7.72 3.1.3.- 3.1.4.-]
B tRNA spricing factors
C tRNA splicing endonucleases
C tRNA splicing ligases
D SFV_3428 rtcB; conserved hypothetical protein K14415 RTCB; tRNA-splicing ligase RtcB (3'-phosphate/5'-hydroxy nucleic acid ligase) [EC:6.5.1.8]
C Other tRNA splicing factors
D SFV_0133 yadP; conserved hypothetical protein K01975 thpR; RNA 2',3'-cyclic 3'-phosphodiesterase [EC:3.1.4.58]
D SFV_4195 yjiI; conserved hypothetical protein K07559 kptA; putative RNA 2'-phosphotransferase [EC:2.7.1.-]
B tRNA transport factors
C tRNA export factors
D SFV_4425 yjjK; putative ATP-binding component of a transport system K06020 ettA; energy-dependent translational throttle protein EttA
B Aminoacyl-tRNA synthetases (AARSs)
C Multi-aminoacyl-tRNA synthetase complex (MSC)
D SFV_0684 leuS; leucine tRNA synthetase K01869 LARS; leucyl-tRNA synthetase [EC:6.1.1.4]
D SFV_0178 proS; proline tRNA synthetase K01881 PARS; prolyl-tRNA synthetase [EC:6.1.1.15]
C Other AARSs
D SFV_1654 tyrS; tyrosine tRNA synthetase K01866 YARS; tyrosyl-tRNA synthetase [EC:6.1.1.1]
D SFV_3389 trpS; tryptophan tRNA synthetase K01867 WARS; tryptophanyl-tRNA synthetase [EC:6.1.1.2]
D SFV_1504 thrS; threonine tRNA synthetase K01868 TARS; threonyl-tRNA synthetase [EC:6.1.1.3]
D SFV_0020 ileS; isoleucine tRNA synthetase K01870 IARS; isoleucyl-tRNA synthetase [EC:6.1.1.5]
D SFV_2938 lysS; lysine tRNA synthetase K04567 KARS; lysyl-tRNA synthetase, class II [EC:6.1.1.6]
D SFV_2808 alaS; alanyl-tRNA synthetase K01872 AARS; alanyl-tRNA synthetase [EC:6.1.1.7]
D SFV_4235 valS; valine tRNA synthetase K01873 VARS; valyl-tRNA synthetase [EC:6.1.1.9]
D SFV_2170 metG; methionine tRNA synthetase K01874 MARS; methionyl-tRNA synthetase [EC:6.1.1.10]
D SFV_0884 serS; serine tRNA synthetase K01875 SARS; seryl-tRNA synthetase [EC:6.1.1.11]
D SFV_1868 aspS; aspartate tRNA synthetase K01876 DARS2; aspartyl-tRNA synthetase [EC:6.1.1.12]
D SFV_3981 glyQ; glycine tRNA synthetase, alpha subunit K01878 glyQ; glycyl-tRNA synthetase alpha chain [EC:6.1.1.14]
D SFV_3982 glyS; glycine tRNA synthetase, beta subunit K01879 glyS; glycyl-tRNA synthetase beta chain [EC:6.1.1.14]
D SFV_0484 cysS; cysteine tRNA synthetase K01883 CARS; cysteinyl-tRNA synthetase [EC:6.1.1.16]
D SFV_2455 gltX; glutamate tRNA synthetase, catalytic subunit K01885 EARS; glutamyl-tRNA synthetase [EC:6.1.1.17]
D SFV_0651 glnS; glutamine tRNA synthetase K01886 QARS; glutaminyl-tRNA synthetase [EC:6.1.1.18]
D SFV_1914 argS; arginine tRNA synthetase K01887 RARS; arginyl-tRNA synthetase [EC:6.1.1.19]
D SFV_1509 pheS; phenylalanine tRNA synthetase, alpha-subunit K01889 FARSA; phenylalanyl-tRNA synthetase alpha chain [EC:6.1.1.20]
D SFV_1510 pheT; phenylalanine tRNA synthetase, beta-subunit K01890 FARSB; phenylalanyl-tRNA synthetase beta chain [EC:6.1.1.20]
D SFV_2561 hisS; histidine tRNA synthetase K01892 HARS; histidyl-tRNA synthetase [EC:6.1.1.21]
D SFV_0932 asnS; asparagine tRNA synthetase K01893 NARS; asparaginyl-tRNA synthetase [EC:6.1.1.22]
D SFV_0129 yadB; putative tRNA synthetase K01894 gluQ; glutamyl-Q tRNA(Asp) synthetase [EC:6.1.1.-]
C Trans-editing factors
D SFV_3612 yihZ; conserved hypothetical protein K07560 dtd; D-aminoacyl-tRNA deacylase [EC:3.1.1.96]
D SFV_0454 ybaK; conserved hypothetical protein K03976 ybaK; Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase [EC:3.1.1.-]
B tRNA modification factors
C Deaminases
D SFV_2607 yfhC; putative deaminase K11991 tadA; tRNA(adenine34) deaminase [EC:3.5.4.33]
C Dihydorouridine synthases
D SFV_4164 yjbN; conserved hypothetical protein K05539 dusA; tRNA-dihydrouridine synthase A [EC:1.-.-.-]
D SFV_3285 yhdG; putative dehydrogenase K05540 dusB; tRNA-dihydrouridine synthase B [EC:1.-.-.-]
D SFV_2215 yohI; putative regulator protein K05541 dusC; tRNA-dihydrouridine synthase C [EC:1.-.-.-]
C Methylthiotransferases
D SFV_0666 yleA; conserved hypothetical protein K06168 miaB; tRNA-2-methylthio-N6-dimethylallyladenosine synthase [EC:2.8.4.3]
C Methyltransferases
D SFV_1906 yecO; conserved hypothetical protein K15256 cmoA; tRNA (cmo5U34)-methyltransferase [EC:2.1.1.-]
D SFV_1907 yecP; putative enzyme K15257 cmoB; tRNA (mo5U34)-methyltransferase [EC:2.1.1.-]
D SFV_0922 smtA; S-adenosylmethionine-dependentmethyltransferase K06219 smtA; tRNA 5-carboxymethoxyuridine methyltransferase [EC:2.1.1.-]
D SFV_4436 lasT; conserved hypothetical protein K02533 lasT; tRNA/rRNA methyltransferase [EC:2.1.1.-]
D SFV_4038 trmA; tRNA (uracil-5-)-methyltransferase K00557 trmA; tRNA (uracil-5-)-methyltransferase [EC:2.1.1.35]
D SFV_3018 yggH; conserved hypothetical protein K03439 trmB; tRNA (guanine-N7-)-methyltransferase [EC:2.1.1.33]
D SFV_2863 trmD; tRNA methyltransferase K00554 trmD; tRNA (guanine37-N1)-methyltransferase [EC:2.1.1.228]
D SFV_3806 thdF; GTP-binding protein in thiophene and furan oxidation K03650 mnmE; tRNA modification GTPase [EC:3.6.-.-]
D SFV_2644 yfiF; conserved hypothetical protein K03214 yfiF; RNA methyltransferase, TrmH family [EC:2.1.1.-]
D SFV_3878 spoU; putative RNA methylase K00556 trmH; tRNA (guanosine-2'-O-)-methyltransferase [EC:2.1.1.34]
D SFV_2580 putative ATP synthase beta subunit K15396 trmJ; tRNA (cytidine32/uridine32-2'-O)-methyltransferase [EC:2.1.1.200]
D SFV_3925 yibK; conserved hypothetical protein K03216 trmL; tRNA (cytidine/uridine-2'-O-)-methyltransferase [EC:2.1.1.207]
D SFV_0179 yaeB; conserved hypothetical protein K22900 TRMO; tRNA (adenine37-N6)-methyltransferase [EC:2.1.1.-]
D SFV_2638 yfiC; putative enzyme K15460 yfiC; tRNA1Val (adenine37-N6)-methyltransferase [EC:2.1.1.223]
C Psudouridine synthases
D SFV_2387 truA; pseudouridylate synthase I K06173 truA; tRNA pseudouridine38-40 synthase [EC:5.4.99.12]
D SFV_3196 truB; tRNA pseudouridine 5S synthase K03177 truB; tRNA pseudouridine55 synthase [EC:5.4.99.25]
D SFV_2666 yqcB; conserved hypothetical protein K06175 truC; tRNA pseudouridine65 synthase [EC:5.4.99.26]
D SFV_2753 ygbO; putative hydrogenase subunit K06176 truD; tRNA pseudouridine13 synthase [EC:5.4.99.27]
D SFV_0050 yabO; conserved hypothetical protein K06177 rluA; tRNA pseudouridine32 synthase / 23S rRNA pseudouridine746 synthase [EC:5.4.99.28 5.4.99.29]
C Thiolation factors
D SFV_1168 ycfB; conserved hypothetical protein K00566 mnmA; tRNA-uridine 2-sulfurtransferase [EC:2.8.1.13]
D SFV_1814 ydaO; conserved hypothetical protein K14058 ttcA; tRNA 2-thiocytidine biosynthesis protein TtcA
D SFV_3473 yhhP; conserved hypothetical protein K04085 tusA; tRNA 2-thiouridine synthesizing protein A [EC:2.8.1.-]
D SFV_3348 yheL; conserved hypothetical protein K07237 tusB; tRNA 2-thiouridine synthesizing protein B
D SFV_3349 yheM; conserved hypothetical protein K07236 tusC; tRNA 2-thiouridine synthesizing protein C
D SFV_3350 yheN; conserved hypothetical protein K07235 tusD; tRNA 2-thiouridine synthesizing protein D [EC:2.8.1.-]
D SFV_0978 yccK; putative sulfite reductase K11179 tusE; tRNA 2-thiouridine synthesizing protein E [EC:2.8.1.-]
D SFV_2576 yfhF; putative regulator K13628 iscA; iron-sulfur cluster assembly protein
D SFV_2578 yfhO; putative aminotransferase K04487 iscS; cysteine desulfurase [EC:2.8.1.7]
D SFV_2946 ygfZ; conserved hypothetical protein K06980 ygfZ; tRNA-modifying protein YgfZ
C KEOPS/EKC complex
C Other tRNA modification factors
D SFV_3767 gidA; glucose-inhibited division K03495 gidA; tRNA uridine 5-carboxymethylaminomethyl modification enzyme
D SFV_4329 miaA; delta(2)-isopentenylpyrophosphate tRNA-adenosine transferase K00791 miaA; tRNA dimethylallyltransferase [EC:2.5.1.75]
D SFV_2393 putative peptidase K15461 mnmC; tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein [EC:2.1.1.61 1.5.-.-]
D SFV_0370 queA; probably S-adenosylmethionine:tRNA ribosyltransferase-isomerase K07568 queA; S-adenosylmethionine:tRNA ribosyltransferase-isomerase [EC:2.4.99.17]
D SFV_0418 ybaX; conserved hypothetical protein K06920 queC; 7-cyano-7-deazaguanine synthase [EC:6.3.4.20]
D SFV_2740 ygcM; putative 6-pyruvoyl tetrahydrobiopterin synthase K01737 queD; 6-pyruvoyltetrahydropterin/6-carboxytetrahydropterin synthase [EC:4.2.3.12 4.1.2.50]
D SFV_2678 ygcF; conserved hypothetical protein K10026 queE; 7-carboxy-7-deazaguanine synthase [EC:4.3.99.3]
D SFV_2663 yqcD; conserved hypothetical protein K06879 queF; 7-cyano-7-deazaguanine reductase [EC:1.7.1.13]
D SFV_4325 yjeS; conserved hypothetical protein K18979 queG; epoxyqueuosine reductase [EC:1.17.99.6]
D SFV_0736 conserved hypothetical protein K09765 queH; epoxyqueuosine reductase [EC:1.17.99.6]
D SFV_1453 selD; selenophosphate synthase K01008 selD; selenide, water dikinase [EC:2.7.9.3]
D SFV_0470 ybbB; putative capsule anchoring protein K06917 selU; tRNA 2-selenouridine synthase [EC:2.9.1.3]
D SFV_0371 tgt; tRNA-guanine transglycosylase K00773 tgt; queuine tRNA-ribosyltransferase [EC:2.4.2.29]
D SFV_0388 yajK; putative oxidoreductase K03151 thiI; tRNA uracil 4-sulfurtransferase [EC:2.8.1.4]
D SFV_2519 ypfI; conserved hypothetical protein K06957 tmcA; tRNA(Met) cytidine acetyltransferase [EC:2.3.1.193]
D SFV_1422 yeaZ; conserved hypothetical protein K14742 tsaB; tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
D SFV_3303 yrdC; conserved hypothetical protein K07566 tsaC; L-threonylcarbamoyladenylate synthase [EC:2.7.7.87]
D SFV_3104 ygjD; putative O-sialoglycoprotein endopeptidase K25706 tsaD; tRNA N6-adenosine threonylcarbamoyltransferase [EC:2.3.1.234]
D SFV_4326 yjeE; conserved hypothetical protein K06925 tsaE; tRNA threonylcarbamoyladenosine biosynthesis protein TsaE
D SFV_2891 ygdL; putative enzyme K22132 tcdA; tRNA threonylcarbamoyladenosine dehydratase
B tRNA degradation factors
C SFV_4337 vacB; putative enzyme K12573 rnr; ribonuclease R [EC:3.1.13.1]
C SFV_3194 pnp; Polyribonucleotide nucleotidyltransferase K00962 pnp; polyribonucleotide nucleotidyltransferase [EC:2.7.7.8]
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#[ BRITE | KEGG2 | KEGG ]
#Last updated: February 29, 2024