GapMind for catabolism of small carbon sources

 

myo-inositol catabolism

Analysis of pathway myoinositol in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Acidithiobacillus ferrooxidans ATCC 23270 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Acidovorax sp. GW101-3H11 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Algiphilus aromaticivorans DG1253 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Alicycliphilus denitrificans K601 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Alkalihalobacterium alkalinitrilicum DSM 22532 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Allochromatium vinosum DSM 180 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Ammonifex degensii KC4 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Anaerobutyricum hallii DSM 3353 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Aquimarina longa SW024 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Archaeoglobus veneficus SNP6 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Arcobacter nitrofigilis DSM 7299 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Azoarcus olearius BH72 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Azohydromonas australica DSM 1124 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Azorhizobium caulinodans ORS 571 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Azospirillum brasilense Sp245 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Azospirillum sp. B510 iatP, iatA, ibpA, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Bacteroides thetaiotaomicron VPI-5482 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Beijerinckia indica ATCC 9039 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Beijerinckia mobilis UQM 1969 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Billgrantia desiderata SP1 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Bradyrhizobium sp. BTAi1 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Brevundimonas sp. GW460-12-10-14-LB2 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Burkholderia phytofirmans PsJN PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Burkholderia vietnamiensis G4 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Calditerrivibrio nitroreducens DSM 19672 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Caminibacter mediatlanticus TB-2 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Carboxydothermus pertinax Ug1 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Caulobacter crescentus NA1000 iatP, iatA, ibpA, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Cereibacter sphaeroides ATCC 17029 iatP, iatA, ibpA, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Chlorobaculum parvum NCIB 8327 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Chlorobaculum tepidum TLS iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Chlorobium limicola DSM 245 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Chlorobium phaeobacteroides BS1 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Clostridium acetobutylicum ATCC 824 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Clostridium kluyveri DSM 555 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Clostridium tyrobutyricum FAM22553 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Crocosphaera subtropica ATCC 51142 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Cupriavidus basilensis FW507-4G11 PS417_11885, PS417_11890, PS417_11895, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Dechloromonas agitata is5 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Dechlorosoma suillum PS iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Dehalococcoides mccartyi 195 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Denitrovibrio acetiphilus DSM 12809 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Derxia gummosa DSM 723 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Desulfacinum hydrothermale DSM 13146 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Desulfacinum infernum DSM 9756 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Desulfarculus baarsii DSM 2075 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Desulfatibacillum aliphaticivorans DSM 15576 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Desulfatiglans anilini DSM 4660 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Desulfitobacterium hafniense DCB-2 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Desulfobacca acetoxidans DSM 11109 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Desulfobacter vibrioformis DSM 8776 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Desulfogranum mediterraneum DSM 13871 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Desulforamulus ruminis DSM 2154 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Desulfoscipio geothermicus DSM 3669 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Desulfotalea psychrophila LSv54 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Desulfovibrio oxyclinae DSM 11498 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Desulfovibrio vulgaris Hildenborough JW710 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Desulfovibrio vulgaris Miyazaki F iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Desulfurobacterium atlanticum DSM 15668 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Desulfuromonas acetexigens iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Desulfuromusa kysingii DSM 7343 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Dinoroseobacter shibae DFL-12 PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Dyella japonica UNC79MFTsu3.2 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Echinicola vietnamensis KMM 6221, DSM 17526 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Escherichia coli BW25113 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Ferroglobus placidus DSM 10642 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Frankia alni ACN14a iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Geobacter metallireducens GS-15 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Geotalea uraniireducens Rf4 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Halococcus hamelinensis 100A6 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Haloechinothrix alba DSM 45207 PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Haloferax volcanii DS2 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Haloglycomyces albus DSM 45210 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Halorhodospira halophila SL1 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Heliomicrobium modesticaldum Ice1; ATCC 51547 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Herbaspirillum autotrophicum IAM 14942 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Herbaspirillum seropedicae SmR1 PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Hippea alviniae EP5-r iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Hydrogenophaga taeniospiralis NBRC 102512 PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Hydrogenovibrio halophilus DSM 15072 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Hydrogenovibrio kuenenii DSM 12350 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Hydrogenovibrio marinus DSM 11271 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Hyphomicrobium sulfonivorans WDL6 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Klebsiella michiganensis M5al PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Klebsiella variicola At-22 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Kyrpidia tusciae DSM 2912 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Leptospirillum ferrooxidans C2-3 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Magnetospirillum magneticum AMB-1 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Malonomonas rubra DSM 5091 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Maridesulfovibrio bastinii DSM 16055 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Maridesulfovibrio zosterae DSM 11974 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Marinobacter adhaerens HP15 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Mesorhizobium ciceri WSM1271 iatP, iatA, ibpA, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Methanobacterium lacus AL-21 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Methanococcus aeolicus Nankai-3 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Methanococcus maripaludis C5 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Methanosarcina acetivorans C2A iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Methanosarcina mazei Go1 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Methanospirillum lacunae Ki8-1 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Methanothermobacter thermautotrophicus Delta H iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Methylobacterium nodulans ORS 2060 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Methylobacterium sp. 4-46 Apr-46 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Methylocapsa acidiphila B2 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Methylocapsa aurea KYG iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Methylocella silvestris BL2 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Methylococcus capsulatus Bath iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Methylocystis bryophila S285 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Methyloferula stellata AR4T iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Methylohalobius crimeensis 10Ki iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Methylomonas methanica MC09 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Methylosarcina fibrata AML-C10 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Methylotuvimicrobium alcaliphilum 20Z iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Methylovulum miyakonense HT12 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Mycolicibacterium vanbaalenii PYR-1 PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Nitratifractor salsuginis DSM 16511 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Nitratiruptor tergarcus DSM 16512 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Nitriliruptor alkaliphilus DSM 45188 PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Nocardioides dokdonensis FR1436 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Nocardiopsis lucentensis DSM 44048 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Nostoc punctiforme ATCC 29133; PCC 73102 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Novosphingobium aromaticivorans DSM 12444 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Oleispira antarctica iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Paraburkholderia atlantica CCGE1002 PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Paraburkholderia bryophila 376MFSha3.1 PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Paraburkholderia phymatum STM815 PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Paucidesulfovibrio gracilis DSM 16080 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Pedobacter sp. GW460-11-11-14-LB5 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Pelobacter propionicus DSM 2379 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Persephonella marina EX-H1 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Phaeacidiphilus oryzae TH49 PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Phaeobacter inhibens BS107 PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Polaromonas naphthalenivorans CJ2 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Prosthecochloris aestuarii DSM 271 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Pseudarthrobacter sulfonivorans Ar51 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Pseudomonas benzenivorans DSM 8628 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Pseudomonas fluorescens FW300-N1B4 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Pseudomonas fluorescens FW300-N2C3 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Pseudomonas fluorescens FW300-N2E2 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Pseudomonas fluorescens FW300-N2E3 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Pseudomonas fluorescens GW456-L13 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Pseudomonas putida KT2440 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Pseudomonas simiae WCS417 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Pseudomonas stutzeri RCH2 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Pyrolobus fumarii 1A iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Rhizobium etli CFN 42 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Rhizobium johnstonii 3841 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Rhizobium leguminosarum WSM1325 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Rhizorhabdus wittichii RW1 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Rhodanobacter denitrificans FW104-10B01 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Rhodomicrobium vannielii ATCC 17100 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Rhodopseudomonas palustris CGA009 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Rhodospirillum centenum SW; ATCC 51521 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Rhodospirillum rubrum ATCC 11170 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Roseburia faecis M72 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Saccharomonospora cyanea NA-134 PS417_11885, PS417_11890, PS417_11895, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Sedimenticola selenatireducens DSM 17993 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Shewanella amazonensis SB2B iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Shewanella loihica PV-4 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Shewanella oneidensis MR-1 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Shewanella sp. ANA-3 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Sinorhizobium fredii NGR234 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Sinorhizobium medicae WSM419 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Sinorhizobium meliloti 1021 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Sphingomonas koreensis DSMZ 15582 iolF, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Stenotrophomonas chelatiphaga DSM 21508 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Steroidobacter denitrificans DSM 18526 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Stutzerimonas stutzeri A1501 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Sulfuricurvum kujiense DSM 16994 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Sulfurihydrogenibium azorense Az-Fu1 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Sulfurihydrogenibium subterraneum DSM 15120 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Sulfurimonas denitrificans DSM 1251 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Sulfuritalea hydrogenivorans DSM 22779 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Sulfurivirga caldicuralii DSM 17737 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Synechococcus elongatus PCC 7942 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Teredinibacter turnerae T7901 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Thauera aminoaromatica S2 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Thermithiobacillus tepidarius DSM 3134 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Thermocrinis albus DSM 14484 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Thermodesulforhabdus norvegica DSM 9990 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Thermomonospora curvata DSM 43183 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Thermovibrio ammonificans HB-1 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Thermus aquaticus YT-1 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Thioalkalivibrio denitrificans ALJD iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Thioalkalivibrio halophilus HL17 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Thioalkalivibrio paradoxus ARh 1 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Thioalkalivibrio thiocyanodenitrificans ARhD 1 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Thiohalomonas denitrificans HLD2 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Thiohalospira halophila HL 3 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Thiomicrorhabdus arctica DSM 13458 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Thiomicrorhabdus chilensis DSM 12352 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Thiomicrospira cyclica ALM1 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Thiomicrospira microaerophila ASL8-2 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Thiomicrospira pelophila DSM 1534 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Thiothrix lacustris DSM 21227 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Tistlia consotensis USBA 355 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Trichlorobacter lovleyi SZ iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Trichormus variabilis ATCC 29413 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Xanthobacter autotrophicus Py2 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Xenophilus azovorans DSM 13620 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi

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.

Links

Downloads

Related tools

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