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Transfer RNA Biogenesis - Shewanella benthica
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AEukaryotic type
B 5'processing factors
C Ribonucrease P
B 3'processing and CCA adding factors
C 3'processing factors
C CCA adding factors
D SHEWBE_1578 cca; fused tRNA nucleotidyl transferase; 2'3'-cyclic phosphodiesterase and 2'nucleotidase and phosphatase 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
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 SHEWBE_3451 gltX; glutamyl-tRNA synthetase K01885 EARS; glutamyl-tRNA synthetase [EC:6.1.1.17]
D SHEWBE_1955 proS; prolyl-tRNA synthetase K01881 PARS; prolyl-tRNA synthetase [EC:6.1.1.15]
D SHEWBE_1696 ileS; isoleucyl-tRNA synthetase K01870 IARS; isoleucyl-tRNA synthetase [EC:6.1.1.5]
D SHEWBE_4029 leuS; leucyl-tRNA synthetase K01869 LARS; leucyl-tRNA synthetase [EC:6.1.1.4]
D SHEWBE_3050 metG; methionyl-tRNA synthetase K01874 MARS; methionyl-tRNA synthetase [EC:6.1.1.10]
D SHEWBE_2105 glnS; glutamyl-tRNA synthetase K01886 QARS; glutaminyl-tRNA synthetase [EC:6.1.1.18]
D SHEWBE_0925 argS; arginyl-tRNA synthetase K01887 RARS; arginyl-tRNA synthetase [EC:6.1.1.19]
D SHEWBE_1311 lysS; lysine tRNA synthetase, constitutive K04567 KARS; lysyl-tRNA synthetase, class II [EC:6.1.1.6]
D SHEWBE_2583 aspS; aspartyl-tRNA synthetase K01876 DARS2; aspartyl-tRNA synthetase [EC:6.1.1.12]
C Other AARSs
D SHEWBE_3825 alaS; alanyl-tRNA synthetase K01872 AARS; alanyl-tRNA synthetase [EC:6.1.1.7]
D SHEWBE_2844 asnS; asparaginyl tRNA synthetase K01893 NARS; asparaginyl-tRNA synthetase [EC:6.1.1.22]
D SHEWBE_2629 thrS; threonyl-tRNA synthetase K01868 TARS; threonyl-tRNA synthetase [EC:6.1.1.3]
D SHEWBE_2641 serS; seryl-tRNA synthetase; also charges selenocystein tRNA with serine K01875 SARS; seryl-tRNA synthetase [EC:6.1.1.11]
D SHEWBE_2110 cysS; cysteinyl-tRNA synthetase K01883 CARS; cysteinyl-tRNA synthetase [EC:6.1.1.16]
D SHEWBE_4179 valS; valyl-tRNA synthetase K01873 VARS; valyl-tRNA synthetase [EC:6.1.1.9]
D SHEWBE_3653 hisS; histidyl tRNA synthetase K01892 HARS; histidyl-tRNA synthetase [EC:6.1.1.21]
D SHEWBE_2442 pheS; phenylalanyl-tRNA synthetase, alpha-subunit K01889 FARSA; phenylalanyl-tRNA synthetase alpha chain [EC:6.1.1.20]
D SHEWBE_2443 pheT; phenylalanine tRNA synthetase, beta subunit K01890 FARSB; phenylalanyl-tRNA synthetase beta chain [EC:6.1.1.20]
D SHEWBE_1599 tyrS; Tyrosine--tRNA ligase K01866 YARS; tyrosyl-tRNA synthetase [EC:6.1.1.1]
D SHEWBE_0886 trpS; Tryptophan--tRNA ligase K01867 WARS; tryptophanyl-tRNA synthetase [EC:6.1.1.2]
C Trans-editing factors
D SHEWBE_0250 dtd; D-tyr-tRNA(Tyr) deacylase K07560 dtd; D-aminoacyl-tRNA deacylase [EC:3.1.1.96]
C AARS associated factors
D SHEWBE_3129 hinT; purine nucleoside phosphoramidase 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 SHEWBE_1760 yggH; tRNA (m7G46) methyltransferase, SAM-dependent K03439 trmB; tRNA (guanine-N7-)-methyltransferase [EC:2.1.1.33]
D SHEWBE_1962 yaeB; conserved hypothetical protein K22900 TRMO; tRNA (adenine37-N6)-methyltransferase [EC:2.1.1.-]
C Psudouridine synthases
D SHEWBE_2238 truA; pseudouridylate synthase I K06173 truA; tRNA pseudouridine38-40 synthase [EC:5.4.99.12]
D SHEWBE_3929 truB; tRNA pseudouridine synthase K03177 truB; tRNA pseudouridine55 synthase [EC:5.4.99.25]
D SHEWBE_3835 truD; pseudoruidine synthase K06176 truD; tRNA pseudouridine13 synthase [EC:5.4.99.27]
C Thiolation factors
D SHEWBE_3405 iscS; cysteine desulfurase used in synthesis of Fe-S cluster (tRNA 4-thiouridine sulfurtransferase) K04487 iscS; cysteine desulfurase [EC:2.8.1.7]
D SHEWBE_4452 Aminotransferase, class V 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 SHEWBE_0630 tsaC; Threonylcarbamoyl-AMP synthase K07566 tsaC; L-threonylcarbamoyladenylate synthase [EC:2.7.7.87]
D SHEWBE_1151 miaA; delta(2)-isopentenylpyrophosphate tRNA-adenosine transferase K00791 miaA; tRNA dimethylallyltransferase [EC:2.5.1.75]
D SHEWBE_0571 trmE; GTPase K03650 mnmE; tRNA modification GTPase [EC:3.6.-.-]
D SHEWBE_0539 gidA; glucose-inhibited cell-division protein K03495 gidA; tRNA uridine 5-carboxymethylaminomethyl modification enzyme
D SHEWBE_0359 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 SHEWBE_0362 cysQ; 3'(2'),5'-bisphosphate nucleotidase CysQ K01082 cysQ; 3'(2'), 5'-bisphosphate nucleotidase [EC:3.1.3.7]
C Other tRNA degradation factors
#
AProkaryotic type
B 5'processing factors
C Ribonucrease P
D SHEWBE_0574 rnpA; protein C5 component of RNase P K03536 rnpA; ribonuclease P protein component [EC:3.1.26.5]
D SHEWBE_MISCRNA7 RNaseP_bact_a K01978 rnpB; RNase P catalytic RNA component
B 3'processing and CCA adding factors
C 3'processing factors
D SHEWBE_2328 rnt; ribonuclease T (RNase T) K03683 rnt; ribonuclease T [EC:3.1.13.-]
D SHEWBE_0205 rph; ribonuclease PH (RNase PH), tRNA nucleotidyltransferase K00989 rph; ribonuclease PH [EC:2.7.7.56]
D SHEWBE_2464 rnd; ribonuclease D K03684 rnd; ribonuclease D [EC:3.1.13.5]
C CCA adding factors
D SHEWBE_1578 cca; fused tRNA nucleotidyl transferase; 2'3'-cyclic phosphodiesterase and 2'nucleotidase and phosphatase 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
C Other tRNA splicing factors
D SHEWBE_1258 RNA 2',3'-cyclic phosphodiesterase K01975 thpR; RNA 2',3'-cyclic 3'-phosphodiesterase [EC:3.1.4.58]
B tRNA transport factors
C tRNA export factors
D SHEWBE_3860 yjjK; fused putative transporter subunits of ABC superfamily: ATP-binding components K06020 ettA; energy-dependent translational throttle protein EttA
B Aminoacyl-tRNA synthetases (AARSs)
C Multi-aminoacyl-tRNA synthetase complex (MSC)
D SHEWBE_4029 leuS; leucyl-tRNA synthetase K01869 LARS; leucyl-tRNA synthetase [EC:6.1.1.4]
D SHEWBE_1955 proS; prolyl-tRNA synthetase K01881 PARS; prolyl-tRNA synthetase [EC:6.1.1.15]
C Other AARSs
D SHEWBE_1599 tyrS; Tyrosine--tRNA ligase K01866 YARS; tyrosyl-tRNA synthetase [EC:6.1.1.1]
D SHEWBE_0886 trpS; Tryptophan--tRNA ligase K01867 WARS; tryptophanyl-tRNA synthetase [EC:6.1.1.2]
D SHEWBE_2629 thrS; threonyl-tRNA synthetase K01868 TARS; threonyl-tRNA synthetase [EC:6.1.1.3]
D SHEWBE_1696 ileS; isoleucyl-tRNA synthetase K01870 IARS; isoleucyl-tRNA synthetase [EC:6.1.1.5]
D SHEWBE_1311 lysS; lysine tRNA synthetase, constitutive K04567 KARS; lysyl-tRNA synthetase, class II [EC:6.1.1.6]
D SHEWBE_3825 alaS; alanyl-tRNA synthetase K01872 AARS; alanyl-tRNA synthetase [EC:6.1.1.7]
D SHEWBE_4179 valS; valyl-tRNA synthetase K01873 VARS; valyl-tRNA synthetase [EC:6.1.1.9]
D SHEWBE_3050 metG; methionyl-tRNA synthetase K01874 MARS; methionyl-tRNA synthetase [EC:6.1.1.10]
D SHEWBE_2641 serS; seryl-tRNA synthetase; also charges selenocystein tRNA with serine K01875 SARS; seryl-tRNA synthetase [EC:6.1.1.11]
D SHEWBE_2583 aspS; aspartyl-tRNA synthetase K01876 DARS2; aspartyl-tRNA synthetase [EC:6.1.1.12]
D SHEWBE_0584 glyQ; glycyl-tRNA synthetase, alpha chain K01878 glyQ; glycyl-tRNA synthetase alpha chain [EC:6.1.1.14]
D SHEWBE_0583 glyS; glycine tRNA synthetase, beta subunit K01879 glyS; glycyl-tRNA synthetase beta chain [EC:6.1.1.14]
D SHEWBE_2110 cysS; cysteinyl-tRNA synthetase K01883 CARS; cysteinyl-tRNA synthetase [EC:6.1.1.16]
D SHEWBE_3451 gltX; glutamyl-tRNA synthetase K01885 EARS; glutamyl-tRNA synthetase [EC:6.1.1.17]
D SHEWBE_2105 glnS; glutamyl-tRNA synthetase K01886 QARS; glutaminyl-tRNA synthetase [EC:6.1.1.18]
D SHEWBE_0925 argS; arginyl-tRNA synthetase K01887 RARS; arginyl-tRNA synthetase [EC:6.1.1.19]
D SHEWBE_2442 pheS; phenylalanyl-tRNA synthetase, alpha-subunit K01889 FARSA; phenylalanyl-tRNA synthetase alpha chain [EC:6.1.1.20]
D SHEWBE_2443 pheT; phenylalanine tRNA synthetase, beta subunit K01890 FARSB; phenylalanyl-tRNA synthetase beta chain [EC:6.1.1.20]
D SHEWBE_3653 hisS; histidyl tRNA synthetase K01892 HARS; histidyl-tRNA synthetase [EC:6.1.1.21]
D SHEWBE_2844 asnS; asparaginyl tRNA synthetase K01893 NARS; asparaginyl-tRNA synthetase [EC:6.1.1.22]
D SHEWBE_1251 yadB; glutamyl-Q tRNA(Asp) synthetase K01894 gluQ; glutamyl-Q tRNA(Asp) synthetase [EC:6.1.1.-]
C Trans-editing factors
D SHEWBE_0250 dtd; D-tyr-tRNA(Tyr) deacylase K07560 dtd; D-aminoacyl-tRNA deacylase [EC:3.1.1.96]
D SHEWBE_0588 ybaK; Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK K03976 ybaK; Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase [EC:3.1.1.-]
D SHEWBE_1475 conserved protein of unknown function, low identity with Prolyl-tRNA synthetase K19055 prdX; Ala-tRNA(Pro) deacylase [EC:3.1.1.-]
D SHEWBE_1806 conserved protein of unknown function K19055 prdX; Ala-tRNA(Pro) deacylase [EC:3.1.1.-]
D SHEWBE_3054 conserved protein of unknown function,might belong to YbaK/prolyl-tRNA synthetase associated region K19055 prdX; Ala-tRNA(Pro) deacylase [EC:3.1.1.-]
B tRNA modification factors
C Deaminases
D SHEWBE_3639 tadA; tRNA-specific adenosine deaminase K11991 tadA; tRNA(adenine34) deaminase [EC:3.5.4.33]
C Dihydorouridine synthases
D SHEWBE_1120 yjbN; tRNA-dihydrouridine synthase A K05539 dusA; tRNA-dihydrouridine synthase A [EC:1.-.-.-]
D SHEWBE_4508 dusB; tRNA-dihydrouridine synthase B K05540 dusB; tRNA-dihydrouridine synthase B [EC:1.-.-.-]
D SHEWBE_3238 dusC; tRNA-dihydrouridine synthase C K05541 dusC; tRNA-dihydrouridine synthase C [EC:1.-.-.-]
C Methylthiotransferases
D SHEWBE_4019 putative tRNA-i(6)A37 modification enzyme (MiaB) K06168 miaB; tRNA-2-methylthio-N6-dimethylallyladenosine synthase [EC:2.8.4.3]
C Methyltransferases
D SHEWBE_2581 yecO; AdoMet-dependent methyltransferase K15256 cmoA; tRNA (cmo5U34)-methyltransferase [EC:2.1.1.-]
D SHEWBE_2580 yecP; conserved hypothetical protein K15257 cmoB; tRNA (mo5U34)-methyltransferase [EC:2.1.1.-]
D SHEWBE_2701 lasT; Uncharacterized tRNA/rRNA methyltransferase LasT K02533 lasT; tRNA/rRNA methyltransferase [EC:2.1.1.-]
D SHEWBE_0356 trmA; tRNA (uracil-5-)-methyltransferase K00557 trmA; tRNA (uracil-5-)-methyltransferase [EC:2.1.1.35]
D SHEWBE_1760 yggH; tRNA (m7G46) methyltransferase, SAM-dependent K03439 trmB; tRNA (guanine-N7-)-methyltransferase [EC:2.1.1.33]
D SHEWBE_1650 trmD; tRNA (guanine-1-)-methyltransferase K00554 trmD; tRNA (guanine37-N1)-methyltransferase [EC:2.1.1.228]
D SHEWBE_0571 trmE; GTPase K03650 mnmE; tRNA modification GTPase [EC:3.6.-.-]
D SHEWBE_0221 trmH; tRNA (Guanosine-2'-O-)-methyltransferase K00556 trmH; tRNA (guanosine-2'-O-)-methyltransferase [EC:2.1.1.34]
D SHEWBE_3408 yfhQ; putative methyltransferase K15396 trmJ; tRNA (cytidine32/uridine32-2'-O)-methyltransferase [EC:2.1.1.200]
D SHEWBE_0819 yibK; tRNA (cytidine(34)-2'-O)-methyltransferase K03216 trmL; tRNA (cytidine/uridine-2'-O-)-methyltransferase [EC:2.1.1.207]
D SHEWBE_1962 yaeB; conserved hypothetical protein K22900 TRMO; tRNA (adenine37-N6)-methyltransferase [EC:2.1.1.-]
D SHEWBE_1468 tRNA1(Val) (adenine(37)-N6)-methyltransferase K15460 yfiC; tRNA1Val (adenine37-N6)-methyltransferase [EC:2.1.1.223]
C Psudouridine synthases
D SHEWBE_2238 truA; pseudouridylate synthase I K06173 truA; tRNA pseudouridine38-40 synthase [EC:5.4.99.12]
D SHEWBE_3929 truB; tRNA pseudouridine synthase K03177 truB; tRNA pseudouridine55 synthase [EC:5.4.99.25]
D SHEWBE_1920 truC; tRNA pseudouridine synthase K06175 truC; tRNA pseudouridine65 synthase [EC:5.4.99.26]
D SHEWBE_3835 truD; pseudoruidine synthase K06176 truD; tRNA pseudouridine13 synthase [EC:5.4.99.27]
D SHEWBE_0409 Uncharacterized RNA pseudouridine synthase HI_0042 K06177 rluA; tRNA pseudouridine32 synthase / 23S rRNA pseudouridine746 synthase [EC:5.4.99.28 5.4.99.29]
D SHEWBE_1292 rluA; pseudouridine synthase for 23S rRNA (position 746) and tRNAphe(position 32) K06177 rluA; tRNA pseudouridine32 synthase / 23S rRNA pseudouridine746 synthase [EC:5.4.99.28 5.4.99.29]
D SHEWBE_1986 Ribosomal large subunit pseudouridine synthase A K06177 rluA; tRNA pseudouridine32 synthase / 23S rRNA pseudouridine746 synthase [EC:5.4.99.28 5.4.99.29]
D SHEWBE_2720 rluA; Ribosomal large subunit pseudouridine synthase A K06177 rluA; tRNA pseudouridine32 synthase / 23S rRNA pseudouridine746 synthase [EC:5.4.99.28 5.4.99.29]
D SHEWBE_3426 rluA; Ribosomal large subunit pseudouridine synthase A K06177 rluA; tRNA pseudouridine32 synthase / 23S rRNA pseudouridine746 synthase [EC:5.4.99.28 5.4.99.29]
D SHEWBE_4448 YabO/YceC/SfhB family protein K06177 rluA; tRNA pseudouridine32 synthase / 23S rRNA pseudouridine746 synthase [EC:5.4.99.28 5.4.99.29]
C Thiolation factors
D SHEWBE_2368 trmU; tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase K00566 mnmA; tRNA-uridine 2-sulfurtransferase [EC:2.8.1.13]
D SHEWBE_2692 ydaO; putative C32 tRNA thiolase K14058 ttcA; tRNA 2-thiocytidine biosynthesis protein TtcA
D SHEWBE_0587 tusA; sulfurtransferase K04085 tusA; tRNA 2-thiouridine synthesizing protein A [EC:2.8.1.-]
D SHEWBE_2934 conserved protein of unknown function K04085 tusA; tRNA 2-thiouridine synthesizing protein A [EC:2.8.1.-]
D SHEWBE_2644 dsrH; Sulfurtransferase complex subunit TusB K07237 tusB; tRNA 2-thiouridine synthesizing protein B
D SHEWBE_2645 conserved protein of unknown function K07236 tusC; tRNA 2-thiouridine synthesizing protein C
D SHEWBE_2646 tusD; methylsulfur transfer protein K07235 tusD; tRNA 2-thiouridine synthesizing protein D [EC:2.8.1.-]
D SHEWBE_2643 tusE; subunit of enzyme for 2-thio modification of mnm5s2U of tRNA anticodon U K11179 tusE; tRNA 2-thiouridine synthesizing protein E [EC:2.8.1.-]
D SHEWBE_3403 iscA; iron-binding protein, believed to be involved in Fe-S protein formation or repair K13628 iscA; iron-sulfur cluster assembly protein
D SHEWBE_3405 iscS; cysteine desulfurase used in synthesis of Fe-S cluster (tRNA 4-thiouridine sulfurtransferase) K04487 iscS; cysteine desulfurase [EC:2.8.1.7]
D SHEWBE_4452 Aminotransferase, class V K04487 iscS; cysteine desulfurase [EC:2.8.1.7]
D SHEWBE_4340 tRNA-modifying protein YgfZ K06980 ygfZ; tRNA-modifying protein YgfZ
C KEOPS/EKC complex
C Other tRNA modification factors
D SHEWBE_0539 gidA; glucose-inhibited cell-division protein K03495 gidA; tRNA uridine 5-carboxymethylaminomethyl modification enzyme
D SHEWBE_1151 miaA; delta(2)-isopentenylpyrophosphate tRNA-adenosine transferase K00791 miaA; tRNA dimethylallyltransferase [EC:2.5.1.75]
D SHEWBE_2107 miaE; tRNA-(ms[2]io[6]A)-hydroxylase K06169 miaE; tRNA 2-(methylsulfanyl)-N6-isopentenyladenosine37 hydroxylase [EC:1.14.99.69]
D SHEWBE_2224 mnmC; tRNA (mnm(5)s(2)U34)-methyltransferase / FAD-dependent cmnm(5)s(2)U34 oxidoreductase K15461 mnmC; tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein [EC:2.1.1.61 1.5.-.-]
D SHEWBE_3423 queA; S-adenosylmethionine:tRNA ribosyltransferase-isomerase K07568 queA; S-adenosylmethionine:tRNA ribosyltransferase-isomerase [EC:2.4.99.17]
D SHEWBE_2603 queC; queuosine biosynthesis protein K06920 queC; 7-cyano-7-deazaguanine synthase [EC:6.3.4.20]
D SHEWBE_2605 ygcF; conserved hypothetical protein K10026 queE; 7-carboxy-7-deazaguanine synthase [EC:4.3.99.3]
D SHEWBE_1909 queF; NADPH-dependent 7-cyano-7-deazaguanine reductase K06879 queF; 7-cyano-7-deazaguanine reductase [EC:1.7.1.13]
D SHEWBE_4090 yjeS; putative Fe-S electron transport protein K18979 queG; epoxyqueuosine reductase [EC:1.17.99.6]
D SHEWBE_0359 selD; selenophosphate synthase K01008 selD; selenide, water dikinase [EC:2.7.9.3]
D SHEWBE_0360 selU; tRNA 2-selenouridine synthase K06917 selU; tRNA 2-selenouridine synthase [EC:2.9.1.3]
D SHEWBE_3422 tgt; queuine tRNA-ribosyltransferase (tRNA-guanine transglycosylase) (Guanine insertion enzyme) K00773 tgt; queuine tRNA-ribosyltransferase [EC:2.4.2.29]
D SHEWBE_1836 thiI; sulfurtransferase required for thiamine and 4-thiouridine biosynthesis K03151 thiI; tRNA uracil 4-sulfurtransferase [EC:2.8.1.4]
D SHEWBE_1945 tilS; tRNA(Ile)-lysidine synthase K04075 tilS; tRNA(Ile)-lysidine synthase [EC:6.3.4.19]
D SHEWBE_2458 yeaZ; putative peptidase K14742 tsaB; tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
D SHEWBE_0630 tsaC; Threonylcarbamoyl-AMP synthase K07566 tsaC; L-threonylcarbamoyladenylate synthase [EC:2.7.7.87]
D SHEWBE_1569 putative O-sialoglycoprotein endopeptidase gcp K25706 tsaD; tRNA N6-adenosine threonylcarbamoyltransferase [EC:2.3.1.234]
D SHEWBE_1148 yjeE; ATPase with strong ADP affinity K06925 tsaE; tRNA threonylcarbamoyladenosine biosynthesis protein TsaE
D SHEWBE_4385 ygdL; conserved hypothetical protein K22132 tcdA; tRNA threonylcarbamoyladenosine dehydratase
B tRNA degradation factors
C SHEWBE_1099 rnr; exoribonuclease R, RNase R K12573 rnr; ribonuclease R [EC:3.1.13.1]
C SHEWBE_3926 pnp; polyribonucleotide nucleotidyltransferase (Polynucleotide phosphorylase) (PNPase) K00962 pnp; polyribonucleotide nucleotidyltransferase [EC:2.7.7.8]
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#[ BRITE | KEGG2 | KEGG ]
#Last updated: June 17, 2025