GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism

Analysis of pathway isoleucine in 150 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 natA, natB, natC*, natD, natE, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Acidithiobacillus ferrooxidans ATCC 23270 Bap2, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
Alicycliphilus denitrificans K601 livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
Allochromatium vinosum DSM 180 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
Ammonifex degensii KC4 livF, livG, livJ, livH, livM, vorA*, vorB, vorC, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
Archaeoglobus veneficus SNP6 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
Arcobacter nitrofigilis DSM 7299 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
Azoarcus sp. BH72 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Azohydromonas australica DSM 1124 livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Azorhizobium caulinodans ORS 571 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Azospirillum lipoferum B510 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
Bacillus alkalinitrilicus DSM 22532 brnQ, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Beijerinckia indica ATCC 9039 Bap2, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Beijerinckia mobilis UQM 1969 Bap2, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Bradyrhizobium sp. BTAi1 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
Burkholderia vietnamiensis G4 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
Calditerrivibrio nitroreducens DSM 19672 livF, livG, livJ, livH, livM, vorA*, vorB, vorC, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Caminibacter mediatlanticus TB-2 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Chlorobaculum parvum NCIB 8327 Bap2, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Chlorobaculum tepidum TLS Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Chlorobium limicola DSM 245 Bap2, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Chlorobium phaeobacteroides BS1 Bap2, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Clostridium acetobutylicum ATCC 824 Bap2, ofoA, ofoB, acdH, ech, ivdG, fadA, pco, hpcD, dddA, iolA
Clostridium kluyveri DSM 555 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pco, hpcD, dddA, iolA
Crocosphaera subtropica ATCC 51142 natA, natB, natC, natD, natE, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Dechloromonas agitata is5 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Dehalococcoides mccartyi 195 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
Denitrovibrio acetiphilus DSM 12809 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Derxia gummosa DSM 723 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
Desulfacinum hydrothermale DSM 13146 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Desulfacinum infernum DSM 9756 livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Desulfallas geothermicus DSM 3669 Bap2, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Desulfarculus baarsii DSM 2075 livF, livG, livJ, livH, livM, vorA*, vorB, vorC, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Desulfatibacillum aliphaticivorans DSM 15576 livF, livG, livJ, livH, livM, vorA*, vorB, vorC, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Desulfatiglans anilini DSM 4660 livF, livG, livJ, livH, livM, vorA*, vorB, vorC, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Desulfitobacterium hafniense DCB-2 brnQ, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Desulfobacca acetoxidans DSM 11109 livF, livG, livJ, livH, livM, ofoA, ofoB, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Desulfobacter vibrioformis DSM 8776 livF, livG, livJ, livH, livM, vorA*, vorB, vorC, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
Desulfobulbus mediterraneus DSM 13871 livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Desulfotalea psychrophila LSv54 brnQ, ofo, acdH, ech, ivdG, fadA, pco, hpcD, dddA, iolA
Desulfotomaculum ruminis DSM 2154 livF, livG, livJ, livH, livM, vorA*, vorB, vorC, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
Desulfovibrio bastinii DSM 16055 livF, livG, livJ, livH, livM, vorA*, vorB, vorC, acdH, ech, ivdG, fadA, pco, hpcD, dddA, iolA
Desulfovibrio gracilis DSM 16080 livF, livG, livJ, livH, livM, vorA*, vorB, vorC, acdH, ech, ivdG, fadA, pco, hpcD, dddA, iolA
Desulfovibrio oxyclinae DSM 11498 livF, livG, livJ, livH, livM, vorA*, vorB, vorC, acdH, ech, ivdG, fadA, pco, hpcD, dddA, iolA
Desulfovibrio zosterae DSM 11974 livF, livG, livJ, livH, livM, vorA*, vorB, vorC, acdH, ech, ivdG, fadA, pco, hpcD, dddA, iolA
Desulfurobacterium atlanticum DSM 15668 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
Desulfuromonas acetexigens Bap2, vorA*, vorB, vorC, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Desulfuromusa kysingii DSM 7343 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Ferroglobus placidus DSM 10642 livF, livG, livJ, livH, livM, ofoA, ofoB, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Frankia alni ACN14A livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Geobacter lovleyi SZ Bap2, vorA*, vorB, vorC, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Geobacter metallireducens GS-15 Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Geobacter uraniireducens Rf4 livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Haloechinothrix alba DSM 45207 natA, natB, natC, natD, natE, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
Haloglycomyces albus DSM 45210 Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Halomonas desiderata SP1 natA, natB, natC, natD, natE, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
Halorhodospira halophila SL1 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Heliobacterium modesticaldum Ice1; ATCC 51547 livF, livG, livJ, livH, livM, vorA*, vorB, vorC, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Herbaspirillum autotrophicum IAM 14942 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
Hydrogenophaga taeniospiralis NBRC 102512 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Hydrogenovibrio halophilus DSM 15072 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Hydrogenovibrio kuenenii DSM 12350 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Hydrogenovibrio marinus DSM 11271 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Hyphomicrobium sulfonivorans WDL6 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Klebsiella variicola At-22 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
Kyrpidia tusciae DSM 2912 livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Leptospirillum ferrooxidans C2-3 Bap2, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
Malonomonas rubra DSM 5091 livF, livG, livJ, livH, livM, vorA, vorB, vorC, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Mesorhizobium ciceri WSM1271 livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Methanobacterium lacus AL-21 Bap2, vorA, vorB, vorC, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
Methanococcus aeolicus Nankai-3 Bap2, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
Methanococcus maripaludis C5 Bap2, vorA, vorB, vorC, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
Methanosarcina acetivorans C2A Bap2, vorA, vorB, vorC, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Methanosarcina barkeri Fusaro Bap2, vorA, vorB, vorC, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Methanosarcina mazei Go1 Bap2, vorA, vorB, vorC, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Methanothermobacter thermautotrophicus Delta H Bap2, vorA, vorB, vorC, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
Methylobacterium nodulans ORS 2060 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
Methylobacterium sp. 4-46 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
Methylocapsa acidiphila B2 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Methylocapsa aurea KYG T livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Methylocella silvestris BL2 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Methylococcus capsulatus Bath Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Methylocystis bryophila S285 Bap2, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Methyloferula stellata AR4T livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Methylohalobius crimeensis 10Ki Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Methylomicrobium alcaliphilum 20Z Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Methylomonas methanica MC09 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Methylosarcina fibrata AML-C10 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Methylovulum miyakonense HT12 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Mycolicibacterium vanbaalenii PYR-1 livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Nitratifractor salsuginis DSM 16511 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Nitratiruptor tergarcus DSM 16512 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Nitriliruptor alkaliphilus DSM 45188 natA, natB, natC, natD, natE, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Nocardiopsis lucentensis DSM 44048 Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Nostoc punctiforme ATCC 29133; PCC 73102 natA, natB, natC, natD, natE, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Novosphingobium aromaticivorans DSM 12444 Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Oleispira antarctica Bap2, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Paraburkholderia phymatum STM815 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
Paraburkholderia sp. CCGE1002 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
Pelobacter propionicus DSM 2379 Bap2, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Persephonella marina EX-H1 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Polaromonas naphthalenivorans CJ2 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Prosthecochloris aestuarii DSM 271 Bap2, ofoA, ofoB, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Pseudarthrobacter sulfonivorans Ar51 natA, natB, natC, natD, natE, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Pseudomonas benzenivorans DSM 8628 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
Pseudomonas stutzeri A1501 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
Pyrolobus fumarii 1A Bap2, ofo, acdH, ech, ivdG, fadA, pco, hpcD, dddA, iolA
Rhizobium etli CFN 42 livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Rhizobium leguminosarum 3841 livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Rhizobium leguminosarum WSM1325 livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Rhodobacter sphaeroides ATCC 17029 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Rhodomicrobium vannielii ATCC 17100 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Rhodopseudomonas palustris CGA009 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
Rhodospirillum centenum SW; ATCC 51521 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Rhodospirillum rubrum ATCC 11170 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Saccharomonospora cyanea NA-134 Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Sedimenticola selenatireducens DSM 17993 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Sinorhizobium fredii NGR234 livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Sinorhizobium medicae WSM419 livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Sphingomonas wittichii RW1 Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
Stenotrophomonas chelatiphaga DSM 21508 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
Steroidobacter denitrificans DSM 18526 Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Sulfuricurvum kujiense DSM 16994 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Sulfurihydrogenibium azorense Az-Fu1 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Sulfurihydrogenibium subterraneum DSM 15120 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Sulfurimonas denitrificans DSM 1251 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Sulfuritalea hydrogenivorans DSM 22779 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Sulfurivirga caldicuralii DSM 17737 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Teredinibacter turnerae T7901 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Thauera aminoaromatica S2 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Thermithiobacillus tepidarius DSM 3134 Bap2, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
Thermocrinis albus DSM 14484 Bap2, ofo, acdH, ech, ivdG, fadA, pco, hpcD, dddA, iolA
Thermodesulforhabdus norvegica DSM 9990 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Thermomonospora curvata DSM 43183 livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Thermovibrio ammonificans HB-1 Bap2, ofoA, ofoB, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
Thioalkalivibrio denitrificans ALJD Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Thioalkalivibrio halophilus HL17 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Thioalkalivibrio paradoxus ARh 1 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Thioalkalivibrio thiocyanodenitrificans ARhD 1 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Thiohalomonas denitrificans HLD2 Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Thiomicrorhabdus arctica DSM 13458 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Thiomicrorhabdus chilensis DSM 12352 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Thiomicrospira cyclica ALM1 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Thiomicrospira microaerophila ASL8-2 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Thiomicrospira pelophila DSM 1534 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Thiothrix lacustris DSM 21227 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
Trichodesmium erythraeum IMS101 Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Trichormus variabilis ATCC 29413 natA, natB, natC, natD, natE, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
Xanthobacter autotrophicus Py2 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
Xenophilus azovorans DSM 13620 livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small

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 Sep 24 2021. 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