GapMind for catabolism of small carbon sources

 

L-threonine catabolism

Analysis of pathway threonine in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Acidithiobacillus ferrooxidans ATCC 23270 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Acidovorax sp. GW101-3H11 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Algiphilus aromaticivorans DG1253 tdcC, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Alicycliphilus denitrificans K601 sstT, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Alkalihalobacterium alkalinitrilicum DSM 22532 tdcC, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Allochromatium vinosum DSM 180 phtA, tdcB, tdcE, prpC, acnD, prpF, acn, prpB
Ammonifex degensii KC4 braC, braD*, braE, braF, braG, tdh, tynA, yvgN, aldA, L-LDH
Anaerobutyricum hallii DSM 3353 sstT, tdh, tynA, gloA, gloB, lctB, lctC, lctD
Aquimarina longa SW024 tdcC, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Archaeoglobus veneficus SNP6 snatA, tdcB, tdcE, pccA, pccB, epi, mcmA
Arcobacter nitrofigilis DSM 7299 snatA, tdcB, tdcE, prpC, acnD, prpF, acn, prpB
Azoarcus olearius BH72 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Azohydromonas australica DSM 1124 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Azorhizobium caulinodans ORS 571 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Azospirillum brasilense Sp245 braC, braD, braE, braF, braG, tdcB, tdcE, pccA, pccB, epi, mcm-large, mcm-small
Azospirillum sp. B510 braC, braD, braE, braF, braG, tdcB, tdcE, pccA, pccB, epi, mcmA
Bacteroides thetaiotaomicron VPI-5482 snatA, tdh, kbl, gcvP, gcvT, gcvH, lpd
Beijerinckia indica ATCC 9039 phtA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Beijerinckia mobilis UQM 1969 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Billgrantia desiderata SP1 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Bradyrhizobium sp. BTAi1 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Brevundimonas sp. GW460-12-10-14-LB2 tdcC, tdh, kbl, gcvP, gcvT, gcvH, lpd
Burkholderia phytofirmans PsJN snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Burkholderia vietnamiensis G4 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Calditerrivibrio nitroreducens DSM 19672 phtA, tdcB, tdcE, pccA, pccB, epi, mcm-large, mcm-small
Caminibacter mediatlanticus TB-2 snatA, tdh, tynA, yvgN, aldA, L-LDH
Carboxydothermus pertinax Ug1 RR42_RS28305, ltaE, ald-dh-CoA, grdA, grdE, grdB, grdD, grdC, ackA
Caulobacter crescentus NA1000 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Cereibacter sphaeroides ATCC 17029 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Chlorobaculum parvum NCIB 8327 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Chlorobaculum tepidum TLS snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Chlorobium limicola DSM 245 tdcC, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Chlorobium phaeobacteroides BS1 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Clostridium acetobutylicum ATCC 824 RR42_RS28305, tdh, tynA, gloA, gloB, lctB, lctC, lctD
Clostridium kluyveri DSM 555 serP1, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Clostridium tyrobutyricum FAM22553 RR42_RS28305, tdcB, tdcE, pco, hpcD, dddA, iolA
Crocosphaera subtropica ATCC 51142 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Cupriavidus basilensis FW507-4G11 RR42_RS28305, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Dechloromonas agitata is5 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Dechlorosoma suillum PS phtA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Dehalococcoides mccartyi 195 snatA, tdh, tynA, gloA, gloB, D-LDH
Denitrovibrio acetiphilus DSM 12809 braC, braD, braE, braF, braG, tdcB, tdcE, pccA, pccB, epi, mcm-large, mcm-small
Derxia gummosa DSM 723 braC, braD, braE, braF, braG, ltaE, ald-dh-CoA, gcvP, gcvT, gcvH, lpd
Desulfacinum hydrothermale DSM 13146 braC, braD, braE, braF, braG, ltaE, ald-dh-CoA, gcvP, gcvT, gcvH, lpd
Desulfacinum infernum DSM 9756 braC, braD, braE, braF, braG, ltaE, ald-dh-CoA, gcvP, gcvT, gcvH, lpd
Desulfarculus baarsii DSM 2075 snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Desulfatibacillum aliphaticivorans DSM 15576 braC, braD, braE, braF, braG, tdcB, tdcE, pccA, pccB, epi, mcm-large, mcm-small
Desulfatiglans anilini DSM 4660 braC, braD, braE, braF, braG, tdcB, tdcE, pccA, pccB, epi, mcm-large, mcm-small
Desulfitobacterium hafniense DCB-2 sstT, ltaE, ald-dh-CoA, gcvP, gcvT, gcvH, lpd
Desulfobacca acetoxidans DSM 11109 braC, braD, braE, braF, braG, tdcB, tdcE, pccA, pccB, epi, mcm-large, mcm-small
Desulfobacter vibrioformis DSM 8776 tdcC, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Desulfogranum mediterraneum DSM 13871 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Desulforamulus ruminis DSM 2154 RR42_RS28305, ltaE, ald-dh-CoA, gcvP, gcvT, gcvH, lpd
Desulfoscipio geothermicus DSM 3669 tdcC, tdcB, tdcE, pccA, pccB, epi, mcm-large, mcm-small
Desulfotalea psychrophila LSv54 sstT, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Desulfovibrio oxyclinae DSM 11498 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Desulfovibrio vulgaris Hildenborough JW710 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Desulfovibrio vulgaris Miyazaki F braC, braD, braE, braF, braG, ltaE, ald-dh-CoA, gcvP, gcvT, gcvH, lpd
Desulfurobacterium atlanticum DSM 15668 braC, braD, braE, braF, braG, tdh, tynA, yvgN, aldA, L-LDH
Desulfuromonas acetexigens snatA, tdcB, tdcE, pccA, pccB, epi, mcm-large, mcm-small
Desulfuromusa kysingii DSM 7343 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Dinoroseobacter shibae DFL-12 snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Dyella japonica UNC79MFTsu3.2 RR42_RS28305, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Echinicola vietnamensis KMM 6221, DSM 17526 tdcC, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Escherichia coli BW25113 tdcC, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Ferroglobus placidus DSM 10642 tdcC, tdcB, tdcE, pccA, pccB, epi, mcm-large, mcm-small
Frankia alni ACN14a tdcC, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Geobacter metallireducens GS-15 tdcC, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Geotalea uraniireducens Rf4 snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Halococcus hamelinensis 100A6 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Haloechinothrix alba DSM 45207 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Haloferax volcanii DS2 tdcC, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Haloglycomyces albus DSM 45210 tdcC, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Halorhodospira halophila SL1 tdcC, tdcB, tdcE, prpC, prpD, acn, prpB
Heliomicrobium modesticaldum Ice1; ATCC 51547 tdcC, tdcB, tdcE, pccA, pccB, epi, mcmA
Herbaspirillum autotrophicum IAM 14942 braC, braD, braE, braF, braG, tdcB, tdcE, prpC, acnD, prpF, acn, prpB
Herbaspirillum seropedicae SmR1 braC, braD, braE, braF, braG, tdcB, tdcE, prpC, acnD, prpF, acn, prpB
Hippea alviniae EP5-r tdcC, tdcB, tdcE, pccA, pccB, epi, mcm-large, mcm-small
Hydrogenophaga taeniospiralis NBRC 102512 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Hydrogenovibrio halophilus DSM 15072 tdcC, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Hydrogenovibrio kuenenii DSM 12350 snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Hydrogenovibrio marinus DSM 11271 snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Hyphomicrobium sulfonivorans WDL6 braC, braD, braE, braF, braG, tdcB, tdcE, pccA, pccB, epi, mcm-large, mcm-small
Klebsiella michiganensis M5al sstT, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Klebsiella variicola At-22 tdcC, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Kyrpidia tusciae DSM 2912 RR42_RS28305, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Leptospirillum ferrooxidans C2-3 tdcC, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Magnetospirillum magneticum AMB-1 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Malonomonas rubra DSM 5091 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Maridesulfovibrio bastinii DSM 16055 sstT, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Maridesulfovibrio zosterae DSM 11974 sstT, tdh, kbl, gcvP, gcvT, gcvH, lpd
Marinobacter adhaerens HP15 braC, braD, braE, braF, braG, tdcB, tdcE, prpC, acnD, prpF, acn, prpB
Mesorhizobium ciceri WSM1271 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Methanobacterium lacus AL-21 tdcC, tdh, tynA, yvgN, aldA, lctO, acs
Methanococcus aeolicus Nankai-3 snatA, tdh, tynA, yvgN, aldA, L-LDH
Methanococcus maripaludis C5 snatA, tdh, tynA, yvgN, aldA, L-LDH
Methanosarcina acetivorans C2A snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Methanosarcina mazei Go1 snatA, tdh, tynA, yvgN, aldA, L-LDH
Methanospirillum lacunae Ki8-1 snatA, tdh, tynA, gloA, gloB, D-LDH
Methanothermobacter thermautotrophicus Delta H tdcC, tdh, tynA, gloA, gloB, D-LDH
Methylobacterium nodulans ORS 2060 RR42_RS28305, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Methylobacterium sp. 4-46 Apr-46 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Methylocapsa acidiphila B2 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Methylocapsa aurea KYG braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Methylocella silvestris BL2 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Methylococcus capsulatus Bath snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Methylocystis bryophila S285 tdcC, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Methyloferula stellata AR4T braC, braD, braE, braF, braG, tdh, tynA, gloA, gloB, glcD, glcE, glcF
Methylohalobius crimeensis 10Ki snatA, tdh, tynA, gloA, gloB, glcD, glcE, glcF
Methylomonas methanica MC09 snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Methylosarcina fibrata AML-C10 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Methylotuvimicrobium alcaliphilum 20Z snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Methylovulum miyakonense HT12 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Mycolicibacterium vanbaalenii PYR-1 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Nitratifractor salsuginis DSM 16511 snatA, tdh, tynA, yvgN, aldA, lldE, lldF, lldG
Nitratiruptor tergarcus DSM 16512 snatA, tdh, tynA, yvgN, aldA, L-LDH
Nitriliruptor alkaliphilus DSM 45188 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Nocardioides dokdonensis FR1436 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Nocardiopsis lucentensis DSM 44048 braC, braD, braE, braF, braG, ltaE, adh, acs*, gcvP, gcvT, gcvH, lpd
Nostoc punctiforme ATCC 29133; PCC 73102 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Novosphingobium aromaticivorans DSM 12444 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Oleispira antarctica tdcC, ltaE, ald-dh-CoA, gcvP, gcvT, gcvH, lpd
Paraburkholderia atlantica CCGE1002 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Paraburkholderia bryophila 376MFSha3.1 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Paraburkholderia phymatum STM815 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Paucidesulfovibrio gracilis DSM 16080 braC, braD, braE, braF, braG, tdh, kbl, gcvP, gcvT, gcvH, lpd
Pedobacter sp. GW460-11-11-14-LB5 tdcC, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Pelobacter propionicus DSM 2379 tdcC, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Persephonella marina EX-H1 tdcC, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Phaeacidiphilus oryzae TH49 braC, braD, braE, braF, braG, tdcB, tdcE, pccA, pccB, epi, mcm-large, mcm-small
Phaeobacter inhibens BS107 snatA, tdh, kbl, gcvP, gcvT, gcvH, lpd
Polaromonas naphthalenivorans CJ2 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Prosthecochloris aestuarii DSM 271 tdcC, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Pseudarthrobacter sulfonivorans Ar51 RR42_RS28305, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Pseudomonas benzenivorans DSM 8628 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Pseudomonas fluorescens FW300-N1B4 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Pseudomonas fluorescens FW300-N2C3 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Pseudomonas fluorescens FW300-N2E2 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Pseudomonas fluorescens FW300-N2E3 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Pseudomonas fluorescens GW456-L13 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Pseudomonas putida KT2440 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Pseudomonas simiae WCS417 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Pseudomonas stutzeri RCH2 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Pyrolobus fumarii 1A snatA, ltaE, ald-dh-CoA, gcvP, gcvT, gcvH, lpd
Rhizobium etli CFN 42 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Rhizobium johnstonii 3841 braC, braD, braE, braF, braG, tdh, tynA, gloA, gloB, glcD, glcE, glcF
Rhizobium leguminosarum WSM1325 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Rhizorhabdus wittichii RW1 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Rhodanobacter denitrificans FW104-10B01 serP1, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Rhodomicrobium vannielii ATCC 17100 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Rhodopseudomonas palustris CGA009 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Rhodospirillum centenum SW; ATCC 51521 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Rhodospirillum rubrum ATCC 11170 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Roseburia faecis M72 tdcC, tdcB, tdcE, pco, hpcD, dddA, iolA
Saccharomonospora cyanea NA-134 RR42_RS28305, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Sedimenticola selenatireducens DSM 17993 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Shewanella amazonensis SB2B sstT, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Shewanella loihica PV-4 sstT, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Shewanella oneidensis MR-1 sstT, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Shewanella sp. ANA-3 sstT, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Sinorhizobium fredii NGR234 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Sinorhizobium medicae WSM419 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Sinorhizobium meliloti 1021 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Sphingomonas koreensis DSMZ 15582 snatA, tdh, kbl, gcvP, gcvT, gcvH, lpd
Stenotrophomonas chelatiphaga DSM 21508 tdcC, tdh, kbl, gcvP, gcvT, gcvH, lpd
Steroidobacter denitrificans DSM 18526 snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Stutzerimonas stutzeri A1501 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Sulfuricurvum kujiense DSM 16994 tdcC, tdh, tynA, yvgN, aldA, L-LDH
Sulfurihydrogenibium azorense Az-Fu1 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Sulfurihydrogenibium subterraneum DSM 15120 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Sulfurimonas denitrificans DSM 1251 tdcC, tdh, tynA, yvgN, aldA, L-LDH
Sulfuritalea hydrogenivorans DSM 22779 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Sulfurivirga caldicuralii DSM 17737 tdcC, tdh, tynA, gloA, gloB, D-LDH
Synechococcus elongatus PCC 7942 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Teredinibacter turnerae T7901 snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Thauera aminoaromatica S2 sstT, tdh, kbl, gcvP, gcvT, gcvH, lpd
Thermithiobacillus tepidarius DSM 3134 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Thermocrinis albus DSM 14484 tdcC, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Thermodesulforhabdus norvegica DSM 9990 snatA, tdcB, tdcE, pccA, pccB, epi, mcm-large, mcm-small
Thermomonospora curvata DSM 43183 tdcC, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Thermovibrio ammonificans HB-1 tdcC, tdh, tynA, gloA, gloB, D-LDH
Thermus aquaticus YT-1 snatA, tdh, kbl, gcvP*, gcvT, gcvH, lpd
Thioalkalivibrio denitrificans ALJD snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Thioalkalivibrio halophilus HL17 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Thioalkalivibrio paradoxus ARh 1 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Thioalkalivibrio thiocyanodenitrificans ARhD 1 snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Thiohalomonas denitrificans HLD2 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Thiohalospira halophila HL 3 tdcC, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Thiomicrorhabdus arctica DSM 13458 snatA, ltaE, ald-dh-CoA, gcvP, gcvT, gcvH, lpd
Thiomicrorhabdus chilensis DSM 12352 snatA, tdh, tynA, gloA, gloB, D-LDH
Thiomicrospira cyclica ALM1 tdcC, tdh, tynA, gloA, gloB, D-LDH
Thiomicrospira microaerophila ASL8-2 tdcC, tdh, tynA, gloA, gloB, D-LDH
Thiomicrospira pelophila DSM 1534 tdcC, tdh, tynA, gloA, gloB, D-LDH
Thiothrix lacustris DSM 21227 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Tistlia consotensis USBA 355 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Trichlorobacter lovleyi SZ tdcC, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome tdcC, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Trichormus variabilis ATCC 29413 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Xanthobacter autotrophicus Py2 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Xenophilus azovorans DSM 13620 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd

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