GapMind for catabolism of small carbon sources

 

L-leucine catabolism

Analysis of pathway leucine in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 natA, natB, natC*, natD, natE, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Acidithiobacillus ferrooxidans ATCC 23270 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Acidovorax sp. GW101-3H11 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Algiphilus aromaticivorans DG1253 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Alicycliphilus denitrificans K601 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Alkalihalobacterium alkalinitrilicum DSM 22532 brnQ, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Allochromatium vinosum DSM 180 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Ammonifex degensii KC4 livF, livG, livJ, livH, livM, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Anaerobutyricum hallii DSM 3353 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Aquimarina longa SW024 brnQ, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Archaeoglobus veneficus SNP6 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Arcobacter nitrofigilis DSM 7299 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Azoarcus olearius BH72 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Azohydromonas australica DSM 1124 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Azorhizobium caulinodans ORS 571 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Azospirillum brasilense Sp245 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Azospirillum sp. B510 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Bacteroides thetaiotaomicron VPI-5482 leuT, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Beijerinckia indica ATCC 9039 aapJ, aapQ, aapM, aapP, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Beijerinckia mobilis UQM 1969 aapJ, aapQ, aapM, aapP, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Billgrantia desiderata SP1 aapJ, aapQ, aapM, aapP, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA*, atoD, atoB
Bradyrhizobium sp. BTAi1 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Brevundimonas sp. GW460-12-10-14-LB2 leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Burkholderia phytofirmans PsJN livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Burkholderia vietnamiensis G4 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Calditerrivibrio nitroreducens DSM 19672 livF, livG, livJ, livH, livM, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Caminibacter mediatlanticus TB-2 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Carboxydothermus pertinax Ug1 livF, livG, livJ, livH, livM, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Caulobacter crescentus NA1000 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Cereibacter sphaeroides ATCC 17029 aapJ, aapQ, aapM, aapP, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Chlorobaculum parvum NCIB 8327 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Chlorobaculum tepidum TLS leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Chlorobium limicola DSM 245 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Chlorobium phaeobacteroides BS1 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Clostridium acetobutylicum ATCC 824 leuT, ilvE, ofoA, ofoB, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Clostridium kluyveri DSM 555 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Clostridium tyrobutyricum FAM22553 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Crocosphaera subtropica ATCC 51142 natA, natB, natC, natD, natE, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Cupriavidus basilensis FW507-4G11 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Dechloromonas agitata is5 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Dechlorosoma suillum PS livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Dehalococcoides mccartyi 195 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Denitrovibrio acetiphilus DSM 12809 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Derxia gummosa DSM 723 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Desulfacinum hydrothermale DSM 13146 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Desulfacinum infernum DSM 9756 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Desulfarculus baarsii DSM 2075 livF, livG, livJ, livH, livM, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Desulfatibacillum aliphaticivorans DSM 15576 livF, livG, livJ, livH, livM, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Desulfatiglans anilini DSM 4660 livF, livG, livJ, livH, livM, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Desulfitobacterium hafniense DCB-2 brnQ, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Desulfobacca acetoxidans DSM 11109 livF, livG, livJ, livH, livM, ilvE, ofoA, ofoB, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Desulfobacter vibrioformis DSM 8776 livF, livG, livJ, livH, livM, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Desulfogranum mediterraneum DSM 13871 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Desulforamulus ruminis DSM 2154 livF, livG, livJ, livH, livM, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Desulfoscipio geothermicus DSM 3669 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Desulfotalea psychrophila LSv54 aapJ, aapQ, aapM, aapP, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Desulfovibrio oxyclinae DSM 11498 livF, livG, livJ, livH, livM, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Desulfovibrio vulgaris Hildenborough JW710 livF, livG, livJ, livH, livM, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Desulfovibrio vulgaris Miyazaki F livF, livG, livJ, livH, livM, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Desulfurobacterium atlanticum DSM 15668 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Desulfuromonas acetexigens leuT, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Desulfuromusa kysingii DSM 7343 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Dinoroseobacter shibae DFL-12 aapJ, aapQ, aapM, aapP, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Dyella japonica UNC79MFTsu3.2 leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Echinicola vietnamensis KMM 6221, DSM 17526 leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Escherichia coli BW25113 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Ferroglobus placidus DSM 10642 livF, livG, livJ, livH, livM, ilvE, ofoA, ofoB, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Frankia alni ACN14a livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Geobacter metallireducens GS-15 leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Geotalea uraniireducens Rf4 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Halococcus hamelinensis 100A6 bcaP, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Haloechinothrix alba DSM 45207 natA, natB, natC, natD, natE, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Haloferax volcanii DS2 leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Haloglycomyces albus DSM 45210 leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Halorhodospira halophila SL1 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Heliomicrobium modesticaldum Ice1; ATCC 51547 livF, livG, livJ, livH, livM, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Herbaspirillum autotrophicum IAM 14942 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Herbaspirillum seropedicae SmR1 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Hippea alviniae EP5-r livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Hydrogenophaga taeniospiralis NBRC 102512 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Hydrogenovibrio halophilus DSM 15072 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Hydrogenovibrio kuenenii DSM 12350 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Hydrogenovibrio marinus DSM 11271 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Hyphomicrobium sulfonivorans WDL6 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Klebsiella michiganensis M5al livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Klebsiella variicola At-22 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Kyrpidia tusciae DSM 2912 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Leptospirillum ferrooxidans C2-3 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Magnetospirillum magneticum AMB-1 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Malonomonas rubra DSM 5091 livF, livG, livJ, livH, livM, ilvE, vorA, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Maridesulfovibrio bastinii DSM 16055 livF, livG, livJ, livH, livM, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Maridesulfovibrio zosterae DSM 11974 livF, livG, livJ, livH, livM, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Marinobacter adhaerens HP15 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Mesorhizobium ciceri WSM1271 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Methanobacterium lacus AL-21 leuT, ilvE, vorA, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Methanococcus aeolicus Nankai-3 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Methanococcus maripaludis C5 leuT, ilvE, vorA, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Methanosarcina acetivorans C2A leuT, ilvE, vorA, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Methanosarcina mazei Go1 leuT, ilvE, vorA, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Methanospirillum lacunae Ki8-1 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Methanothermobacter thermautotrophicus Delta H leuT, ilvE, vorA, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Methylobacterium nodulans ORS 2060 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Methylobacterium sp. 4-46 Apr-46 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Methylocapsa acidiphila B2 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Methylocapsa aurea KYG livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Methylocella silvestris BL2 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Methylococcus capsulatus Bath leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Methylocystis bryophila S285 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Methyloferula stellata AR4T livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Methylohalobius crimeensis 10Ki leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Methylomonas methanica MC09 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Methylosarcina fibrata AML-C10 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Methylotuvimicrobium alcaliphilum 20Z leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Methylovulum miyakonense HT12 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Mycolicibacterium vanbaalenii PYR-1 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Nitratifractor salsuginis DSM 16511 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Nitratiruptor tergarcus DSM 16512 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Nitriliruptor alkaliphilus DSM 45188 natA, natB, natC, natD, natE, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Nocardioides dokdonensis FR1436 natA, natB, natC, natD, natE, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Nocardiopsis lucentensis DSM 44048 natA, natB, natC, natD, natE, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Nostoc punctiforme ATCC 29133; PCC 73102 natA, natB, natC, natD, natE, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Novosphingobium aromaticivorans DSM 12444 leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Oleispira antarctica leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Paraburkholderia atlantica CCGE1002 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Paraburkholderia bryophila 376MFSha3.1 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Paraburkholderia phymatum STM815 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Paucidesulfovibrio gracilis DSM 16080 livF, livG, livJ, livH, livM, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Pedobacter sp. GW460-11-11-14-LB5 leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Pelobacter propionicus DSM 2379 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Persephonella marina EX-H1 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Phaeacidiphilus oryzae TH49 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Phaeobacter inhibens BS107 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Polaromonas naphthalenivorans CJ2 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Prosthecochloris aestuarii DSM 271 leuT, ilvE, ofoA, ofoB, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Pseudarthrobacter sulfonivorans Ar51 natA, natB, natC, natD, natE, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Pseudomonas benzenivorans DSM 8628 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Pseudomonas fluorescens FW300-N1B4 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Pseudomonas fluorescens FW300-N2C3 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Pseudomonas fluorescens FW300-N2E2 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Pseudomonas fluorescens FW300-N2E3 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Pseudomonas fluorescens GW456-L13 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Pseudomonas putida KT2440 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Pseudomonas simiae WCS417 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Pseudomonas stutzeri RCH2 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Pyrolobus fumarii 1A leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Rhizobium etli CFN 42 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Rhizobium johnstonii 3841 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Rhizobium leguminosarum WSM1325 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Rhizorhabdus wittichii RW1 leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Rhodanobacter denitrificans FW104-10B01 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Rhodomicrobium vannielii ATCC 17100 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Rhodopseudomonas palustris CGA009 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Rhodospirillum centenum SW; ATCC 51521 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Rhodospirillum rubrum ATCC 11170 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Roseburia faecis M72 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Saccharomonospora cyanea NA-134 leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Sedimenticola selenatireducens DSM 17993 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Shewanella amazonensis SB2B brnQ, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Shewanella loihica PV-4 brnQ, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Shewanella oneidensis MR-1 brnQ, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Shewanella sp. ANA-3 brnQ, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Sinorhizobium fredii NGR234 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Sinorhizobium medicae WSM419 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Sinorhizobium meliloti 1021 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Sphingomonas koreensis DSMZ 15582 leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Stenotrophomonas chelatiphaga DSM 21508 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Steroidobacter denitrificans DSM 18526 leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Stutzerimonas stutzeri A1501 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Sulfuricurvum kujiense DSM 16994 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Sulfurihydrogenibium azorense Az-Fu1 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Sulfurihydrogenibium subterraneum DSM 15120 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Sulfurimonas denitrificans DSM 1251 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Sulfuritalea hydrogenivorans DSM 22779 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Sulfurivirga caldicuralii DSM 17737 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Synechococcus elongatus PCC 7942 natA, natB, natC, natD, natE, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Teredinibacter turnerae T7901 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Thauera aminoaromatica S2 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Thermithiobacillus tepidarius DSM 3134 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Thermocrinis albus DSM 14484 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Thermodesulforhabdus norvegica DSM 9990 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Thermomonospora curvata DSM 43183 livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Thermovibrio ammonificans HB-1 leuT, ilvE, ofoA, ofoB, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Thermus aquaticus YT-1 livF, livG, livJ, livH, livM, ilvE, ofoA, ofoB, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Thioalkalivibrio denitrificans ALJD leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Thioalkalivibrio halophilus HL17 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Thioalkalivibrio paradoxus ARh 1 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Thioalkalivibrio thiocyanodenitrificans ARhD 1 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Thiohalomonas denitrificans HLD2 leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Thiohalospira halophila HL 3 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Thiomicrorhabdus arctica DSM 13458 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Thiomicrorhabdus chilensis DSM 12352 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Thiomicrospira cyclica ALM1 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Thiomicrospira microaerophila ASL8-2 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Thiomicrospira pelophila DSM 1534 leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Thiothrix lacustris DSM 21227 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Tistlia consotensis USBA 355 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Trichlorobacter lovleyi SZ leuT, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Trichormus variabilis ATCC 29413 natA, natB, natC, natD, natE, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
Xanthobacter autotrophicus Py2 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
Xenophilus azovorans DSM 13620 livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory