GapMind for Amino acid biosynthesis

 

L-tryptophan biosynthesis

Analysis of pathway trp in 206 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Acidithiobacillus ferrooxidans ATCC 23270 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Acidovorax sp. GW101-3H11 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Algiphilus aromaticivorans DG1253 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Alicycliphilus denitrificans K601 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Alkalihalobacterium alkalinitrilicum DSM 22532 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Allochromatium vinosum DSM 180 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Ammonifex degensii KC4 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Anaerobutyricum hallii DSM 3353 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Aquimarina longa SW024 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Archaeoglobus veneficus SNP6 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Arcobacter nitrofigilis DSM 7299 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Azoarcus olearius BH72 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Azohydromonas australica DSM 1124 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Azorhizobium caulinodans ORS 571 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Azospirillum brasilense Sp245 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Azospirillum sp. B510 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Bacteroides thetaiotaomicron VPI-5482 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Beijerinckia indica subsp. indica ATCC 9039 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Beijerinckia mobilis UQM 1969 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Bradyrhizobium sp. BTAi1 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Brevundimonas sp. GW460-12-10-14-LB2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Burkholderia phytofirmans PsJN trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Burkholderia vietnamiensis G4 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Calditerrivibrio nitroreducens DSM 19672 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Caminibacter mediatlanticus TB-2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Carboxydothermus pertinax Ug1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Caulobacter crescentus NA1000 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Cereibacter sphaeroides ATCC 17029 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Chlorobaculum parvum NCIB 8327 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Chlorobaculum tepidum TLS trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Chlorobium limicola DSM 245 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Chlorobium phaeobacteroides BS1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Clostridium acetobutylicum ATCC 824 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Clostridium kluyveri DSM 555 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Clostridium tyrobutyricum FAM22553 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Crocosphaera subtropica ATCC 51142 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Cupriavidus basilensis FW507-4G11 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Dechloromonas agitata is5 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Dechlorosoma suillum PS trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Dehalococcoides mccartyi 195 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Denitrovibrio acetiphilus DSM 12809 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Derxia gummosa DSM 723 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulfacinum hydrothermale DSM 13146 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulfacinum infernum DSM 9756 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulfarculus baarsii DSM 2075 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulfatibacillum aliphaticivorans DSM 15576 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulfatiglans anilini DSM 4660 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulfitobacterium hafniense DCB-2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulfobacca acetoxidans DSM 11109 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulfobacter vibrioformis DSM 8776 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulfogranum mediterraneum DSM 13871 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulforamulus ruminis DSM 2154 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulfoscipio geothermicus DSM 3669 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulfotalea psychrophila LSv54 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulfovibrio oxyclinae DSM 11498 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulfovibrio vulgaris Hildenborough JW710 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulfovibrio vulgaris Miyazaki F trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulfurobacterium atlanticum DSM 15668 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulfuromonas acetexigens DSM 1397 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulfuromusa kysingii DSM 7343 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Dinoroseobacter shibae DFL-12 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Dyella japonica UNC79MFTsu3.2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Echinicola vietnamensis KMM 6221, DSM 17526 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Escherichia coli BW25113 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Ferroglobus placidus DSM 10642 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Frankia alni ACN14a trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Geobacter metallireducens GS-15 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Geotalea uraniireducens Rf4 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Halococcus hamelinensis 100A6 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Haloechinothrix alba DSM 45207 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Haloferax volcanii DS2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Haloglycomyces albus DSM 45210 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Halomonas desiderata SP1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Halorhodospira halophila SL1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Heliomicrobium modesticaldum Ice1 Ice1; ATCC 51547 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Herbaspirillum autotrophicum IAM 14942 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Herbaspirillum seropedicae SmR1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Hippea alviniae EP5-r trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Hydrogenovibrio halophilus DSM 15072 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Hydrogenovibrio kuenenii DSM 12350 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Hydrogenovibrio marinus DSM 11271 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Hyphomicrobium sulfonivorans WDL6 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Klebsiella michiganensis M5al trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Klebsiella variicola At-22 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Kyrpidia tusciae DSM 2912 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Leptospirillum ferrooxidans C2-3 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Lysobacter soli OAE881 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Magnetospirillum magneticum AMB-1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Malonomonas rubra DSM 5091 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Maridesulfovibrio bastinii DSM 16055 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Maridesulfovibrio zosterae DSM 11974 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Marinobacter adhaerens HP15 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Mesorhizobium ciceri biovar biserrulae WSM1271 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Methanobacterium lacus AL-21 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methanococcus aeolicus Nankai-3 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methanococcus maripaludis C5 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methanosarcina acetivorans C2A trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methanosarcina mazei Go1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methanospirillum lacunae Ki8-1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methanothermobacter thermautotrophicus str. Delta H trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methylobacterium nodulans ORS 2060 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methylobacterium sp. 4-46 Apr-46 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methylocapsa acidiphila B2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methylocapsa aurea KYG trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methylocella silvestris BL2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methylococcus capsulatus str. Bath trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methylocystis bryophila S285 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methyloferula stellata AR4 AR4T trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methylohalobius crimeensis 10Ki trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methylomonas methanica MC09 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methylosarcina fibrata AML-C10 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methylotuvimicrobium alcaliphilum 20Z trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methylovulum miyakonense HT12 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Mucilaginibacter yixingensis DSM 26809 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Mycolicibacterium vanbaalenii PYR-1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Nitratifractor salsuginis DSM 16511 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Nitratiruptor tergarcus DSM 16512 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Nitriliruptor alkaliphilus DSM 45188 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Nitrosopumilus maritimus SCM1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Nocardioides dokdonensis FR1436 trpE?, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Nocardiopsis lucentensis DSM 44048 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Novosphingobium aromaticivorans DSM 12444 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Oleispira antarctica RB-8 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Paraburkholderia atlantica CCGE1002 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Paraburkholderia bryophila 376MFSha3.1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Paraburkholderia phymatum STM815 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Paucidesulfovibrio gracilis DSM 16080 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pedobacter sp. GW460-11-11-14-LB5 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pelobacter propionicus DSM 2379 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Persephonella marina EX-H1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Phaeacidiphilus oryzae TH49 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Phaeobacter inhibens BS107 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Polaromonas naphthalenivorans CJ2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Prosthecochloris aestuarii DSM 271 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pseudarthrobacter sulfonivorans Ar51 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pseudomonas benzenivorans DSM 8628 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pseudomonas fluorescens FW300-N1B4 trpE, trpD_1, trpD_2, PRAI*, IGPS, trpA, trpB
Pseudomonas fluorescens FW300-N2C3 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pseudomonas fluorescens FW300-N2E2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pseudomonas fluorescens FW300-N2E3 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pseudomonas fluorescens GW456-L13 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pseudomonas putida KT2440 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pseudomonas simiae WCS417 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pseudomonas stutzeri RCH2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pyrolobus fumarii 1A trpE, trpD_1, trpD_2, PRAI, IGPS, trpA?, trpB
Rhizobium etli CFN 42 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Rhizobium johnstonii 3841 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Rhizobium leguminosarum bv. trifolii WSM1325 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Rhizorhabdus wittichii RW1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Rhodanobacter denitrificans FW104-10B01 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Rhodomicrobium vannielii ATCC 17100 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Rhodopseudomonas palustris CGA009 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Rhodospirillum centenum SW SW; ATCC 51521 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Rhodospirillum rubrum ATCC 11170 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Roseburia faecis M72 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Saccharomonospora cyanea NA-134 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Sedimenticola selenatireducens DSM 17993 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Shewanella amazonensis SB2B trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Shewanella loihica PV-4 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Shewanella oneidensis MR-1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Shewanella sp. ANA-3 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Sinorhizobium fredii NGR234 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Sinorhizobium medicae WSM419 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Sinorhizobium meliloti 1021 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Sphingomonas koreensis DSMZ 15582 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Stenotrophomonas chelatiphaga DSM 21508 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Steroidobacter denitrificans DSM 18526 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Stutzerimonas stutzeri A1501 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Sulfuricurvum kujiense DSM 16994 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Sulfurihydrogenibium azorense Az-Fu1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Sulfurihydrogenibium subterraneum DSM 15120 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Sulfurimonas denitrificans DSM 1251 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Sulfuritalea hydrogenivorans sk43H DSM 22779 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Sulfurivirga caldicuralii DSM 17737 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Synechococcus elongatus PCC 7942 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Teredinibacter turnerae T7901 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thauera aminoaromatica S2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thermithiobacillus tepidarius DSM 3134 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thermoanaerobacter kivui LKT-1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thermocrinis albus DSM 14484 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thermodesulforhabdus norvegica DSM 9990 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thermomonospora curvata DSM 43183 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Thermovibrio ammonificans HB-1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thermus aquaticus YT-1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thioalkalivibrio denitrificans ALJD trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thioalkalivibrio halophilus HL17 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thioalkalivibrio paradoxus ARh 1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thioalkalivibrio thiocyanodenitrificans ARhD 1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thiohalomonas denitrificans HLD2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thiohalospira halophila DSM 15071 HL 3 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thiomicrorhabdus arctica DSM 13458 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thiomicrorhabdus chilensis DSM 12352 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thiomicrospira cyclica ALM1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thiomicrospira microaerophila ASL8-2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thiomicrospira pelophila DSM 1534 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thiothrix lacustris DSM 21227 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Tistlia consotensis USBA 355 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Trichlorobacter lovleyi SZ trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Trichormus variabilis ATCC 29413 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Xanthobacter autotrophicus Py2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Xanthomonas campestris pv. campestris strain 8004 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Xenophilus azovorans DSM 13620 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB

Confidence: high confidence medium confidence low confidence
? – known gap: despite the lack of a good candidate for this step, this organism (or a related organism) performs the pathway

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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