GapMind for catabolism of small carbon sources

 

L-tyrosine catabolism

Analysis of pathway tyrosine in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Acidithiobacillus ferrooxidans ATCC 23270 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Acidovorax sp. GW101-3H11 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Algiphilus aromaticivorans DG1253 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Alicycliphilus denitrificans K601 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Alkalihalobacterium alkalinitrilicum DSM 22532 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Allochromatium vinosum DSM 180 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Ammonifex degensii KC4 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Anaerobutyricum hallii DSM 3353 tyt1, HPD, hmgA, maiA, fahA, aacS, atoB
Aquimarina longa SW024 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Archaeoglobus veneficus SNP6 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Arcobacter nitrofigilis DSM 7299 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Azoarcus olearius BH72 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
Azohydromonas australica DSM 1124 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Azorhizobium caulinodans ORS 571 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
Azospirillum brasilense Sp245 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
Azospirillum sp. B510 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Bacteroides thetaiotaomicron VPI-5482 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Beijerinckia indica ATCC 9039 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Beijerinckia mobilis UQM 1969 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Billgrantia desiderata SP1 aroP, HPD, hmgA, maiA, fahA, atoA*, atoD, atoB
Bradyrhizobium sp. BTAi1 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Brevundimonas sp. GW460-12-10-14-LB2 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Burkholderia phytofirmans PsJN Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Burkholderia vietnamiensis G4 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Calditerrivibrio nitroreducens DSM 19672 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Caminibacter mediatlanticus TB-2 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Carboxydothermus pertinax Ug1 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Caulobacter crescentus NA1000 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Cereibacter sphaeroides ATCC 17029 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Chlorobaculum parvum NCIB 8327 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Chlorobaculum tepidum TLS aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Chlorobium limicola DSM 245 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Chlorobium phaeobacteroides BS1 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Clostridium acetobutylicum ATCC 824 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Clostridium kluyveri DSM 555 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Clostridium tyrobutyricum FAM22553 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Crocosphaera subtropica ATCC 51142 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Cupriavidus basilensis FW507-4G11 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Dechloromonas agitata is5 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
Dechlorosoma suillum PS Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
Dehalococcoides mccartyi 195 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Denitrovibrio acetiphilus DSM 12809 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Derxia gummosa DSM 723 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Desulfacinum hydrothermale DSM 13146 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Desulfacinum infernum DSM 9756 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Desulfarculus baarsii DSM 2075 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Desulfatibacillum aliphaticivorans DSM 15576 tyt1, HPD, hmgA, maiA, fahA, aacS, atoB
Desulfatiglans anilini DSM 4660 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
Desulfitobacterium hafniense DCB-2 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Desulfobacca acetoxidans DSM 11109 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Desulfobacter vibrioformis DSM 8776 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Desulfogranum mediterraneum DSM 13871 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
Desulforamulus ruminis DSM 2154 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Desulfoscipio geothermicus DSM 3669 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Desulfotalea psychrophila LSv54 tyrP, HPD, hmgA, maiA, fahA, aacS, atoB
Desulfovibrio oxyclinae DSM 11498 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Desulfovibrio vulgaris Hildenborough JW710 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Desulfovibrio vulgaris Miyazaki F aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Desulfurobacterium atlanticum DSM 15668 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Desulfuromonas acetexigens aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Desulfuromusa kysingii DSM 7343 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Dinoroseobacter shibae DFL-12 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Dyella japonica UNC79MFTsu3.2 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Echinicola vietnamensis KMM 6221, DSM 17526 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Escherichia coli BW25113 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Ferroglobus placidus DSM 10642 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Frankia alni ACN14a Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Geobacter metallireducens GS-15 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Geotalea uraniireducens Rf4 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Halococcus hamelinensis 100A6 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Haloechinothrix alba DSM 45207 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Haloferax volcanii DS2 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Haloglycomyces albus DSM 45210 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Halorhodospira halophila SL1 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Heliomicrobium modesticaldum Ice1; ATCC 51547 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Herbaspirillum autotrophicum IAM 14942 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Herbaspirillum seropedicae SmR1 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Hippea alviniae EP5-r aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Hydrogenophaga taeniospiralis NBRC 102512 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Hydrogenovibrio halophilus DSM 15072 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Hydrogenovibrio kuenenii DSM 12350 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Hydrogenovibrio marinus DSM 11271 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Hyphomicrobium sulfonivorans WDL6 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Klebsiella michiganensis M5al Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Klebsiella variicola At-22 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Kyrpidia tusciae DSM 2912 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
Leptospirillum ferrooxidans C2-3 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Magnetospirillum magneticum AMB-1 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
Malonomonas rubra DSM 5091 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
Maridesulfovibrio bastinii DSM 16055 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Maridesulfovibrio zosterae DSM 11974 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
Marinobacter adhaerens HP15 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
Mesorhizobium ciceri WSM1271 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Methanobacterium lacus AL-21 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Methanococcus aeolicus Nankai-3 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Methanococcus maripaludis C5 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Methanosarcina acetivorans C2A aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Methanosarcina mazei Go1 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Methanospirillum lacunae Ki8-1 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Methanothermobacter thermautotrophicus Delta H aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Methylobacterium nodulans ORS 2060 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Methylobacterium sp. 4-46 Apr-46 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Methylocapsa acidiphila B2 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Methylocapsa aurea KYG aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Methylocella silvestris BL2 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Methylococcus capsulatus Bath aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Methylocystis bryophila S285 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Methyloferula stellata AR4T aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Methylohalobius crimeensis 10Ki aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Methylomonas methanica MC09 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Methylosarcina fibrata AML-C10 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Methylotuvimicrobium alcaliphilum 20Z aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Methylovulum miyakonense HT12 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Mycolicibacterium vanbaalenii PYR-1 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Nitratifractor salsuginis DSM 16511 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Nitratiruptor tergarcus DSM 16512 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Nitriliruptor alkaliphilus DSM 45188 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Nocardioides dokdonensis FR1436 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Nocardiopsis lucentensis DSM 44048 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Nostoc punctiforme ATCC 29133; PCC 73102 tyrP, HPD, hmgA, maiA, fahA, aacS, atoB
Novosphingobium aromaticivorans DSM 12444 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Oleispira antarctica aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Paraburkholderia atlantica CCGE1002 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Paraburkholderia bryophila 376MFSha3.1 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Paraburkholderia phymatum STM815 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Paucidesulfovibrio gracilis DSM 16080 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
Pedobacter sp. GW460-11-11-14-LB5 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Pelobacter propionicus DSM 2379 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Persephonella marina EX-H1 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Phaeacidiphilus oryzae TH49 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Phaeobacter inhibens BS107 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Polaromonas naphthalenivorans CJ2 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Prosthecochloris aestuarii DSM 271 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Pseudarthrobacter sulfonivorans Ar51 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Pseudomonas benzenivorans DSM 8628 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Pseudomonas fluorescens FW300-N1B4 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Pseudomonas fluorescens FW300-N2C3 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Pseudomonas fluorescens FW300-N2E2 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Pseudomonas fluorescens FW300-N2E3 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Pseudomonas fluorescens GW456-L13 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Pseudomonas putida KT2440 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Pseudomonas simiae WCS417 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Pseudomonas stutzeri RCH2 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Pyrolobus fumarii 1A aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Rhizobium etli CFN 42 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Rhizobium johnstonii 3841 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Rhizobium leguminosarum WSM1325 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Rhizorhabdus wittichii RW1 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Rhodanobacter denitrificans FW104-10B01 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Rhodomicrobium vannielii ATCC 17100 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
Rhodopseudomonas palustris CGA009 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Rhodospirillum centenum SW; ATCC 51521 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Rhodospirillum rubrum ATCC 11170 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Roseburia faecis M72 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Saccharomonospora cyanea NA-134 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Sedimenticola selenatireducens DSM 17993 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
Shewanella amazonensis SB2B tyrP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Shewanella loihica PV-4 tyrP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Shewanella oneidensis MR-1 tyrP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Shewanella sp. ANA-3 tyrP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Sinorhizobium fredii NGR234 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Sinorhizobium medicae WSM419 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Sinorhizobium meliloti 1021 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Sphingomonas koreensis DSMZ 15582 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Stenotrophomonas chelatiphaga DSM 21508 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Steroidobacter denitrificans DSM 18526 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Stutzerimonas stutzeri A1501 aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Sulfuricurvum kujiense DSM 16994 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Sulfurihydrogenibium azorense Az-Fu1 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Sulfurihydrogenibium subterraneum DSM 15120 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Sulfurimonas denitrificans DSM 1251 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Sulfuritalea hydrogenivorans DSM 22779 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
Sulfurivirga caldicuralii DSM 17737 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Synechococcus elongatus PCC 7942 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Teredinibacter turnerae T7901 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Thauera aminoaromatica S2 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
Thermithiobacillus tepidarius DSM 3134 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Thermocrinis albus DSM 14484 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Thermodesulforhabdus norvegica DSM 9990 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Thermomonospora curvata DSM 43183 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Thermovibrio ammonificans HB-1 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Thermus aquaticus YT-1 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
Thioalkalivibrio denitrificans ALJD aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Thioalkalivibrio halophilus HL17 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Thioalkalivibrio paradoxus ARh 1 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Thioalkalivibrio thiocyanodenitrificans ARhD 1 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Thiohalomonas denitrificans HLD2 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Thiohalospira halophila HL 3 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Thiomicrorhabdus arctica DSM 13458 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Thiomicrorhabdus chilensis DSM 12352 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Thiomicrospira cyclica ALM1 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Thiomicrospira microaerophila ASL8-2 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Thiomicrospira pelophila DSM 1534 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Thiothrix lacustris DSM 21227 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
Tistlia consotensis USBA 355 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
Trichlorobacter lovleyi SZ aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Trichormus variabilis ATCC 29413 aroP, HPD, hmgA, maiA, fahA, aacS, atoB
Xanthobacter autotrophicus Py2 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Xenophilus azovorans DSM 13620 Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, 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