GapMind for Amino acid biosynthesis

 

L-tryptophan biosynthesis

Analysis of pathway trp in 276 genomes

Genome Best path
Acidovorax caeni R-24608 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Actinokineospora bangkokensis 44EHW trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Actinomyces timonensis 7400942 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Algiphilus aromaticivorans DG1253 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Algoriphagus aquaeductus T4 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Algoriphagus machipongonensis PR1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Alicyclobacillus ferrooxydans TC-34 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Alishewanella agri BL06 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Alistipes indistinctus YIT 12060 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Alistipes shahii WAL 8301 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Alkalitalea saponilacus SC/BZ-SP2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Amantichitinum ursilacus IGB-41 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Amphibacillus jilinensis Y1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Amphritea japonica JAMM 1866 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Amycolatopsis halophila YIM 93223 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Amycolatopsis xylanica CPCC 202699 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Aquimarina agarilytica ZC1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Aquimarina longa SW024 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Aquimarina macrocephali JAMB N27 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Archaeoglobus sulfaticallidus PM70-1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Arcticibacter svalbardensis MN12-7 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Ardenticatena maritima 110S trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Arenimonas metalli CF5-1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Arenitalea lutea P7-3-5 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Azospirillum humicireducens SgZ-5 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Azospirillum thiophilum BV-S trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Bacillus altitudinis 41KF2b trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Bacillus coahuilensis m4-4 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Bacillus cytotoxicus NVH 391-98 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Bacillus horneckiae 1P01SC trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Bacillus okhensis Kh10-101 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Bacillus safensis FO-36b trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Bacillus velezensis CBMB205 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Bacteroides clarus YIT 12056 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Bacteroides faecis MAJ27 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Bacteroides fluxus YIT 12057 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Bacteroides oleiciplenus YIT 12058 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Barnesiella intestinihominis YIT 11860 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Belnapia rosea CPCC 100156 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Bizionia argentinensis JUB59 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Bradyrhizobium diazoefficiens USDA110 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Brevibacterium jeotgali SJ5-8 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Brucella inopinata BO1 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Brucella microti CCM 4915 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Bryobacter aggregatus MPL3 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Caldicellulosiruptor hydrothermalis 108 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Caldicellulosiruptor kronotskyensis 2002 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Carboxydothermus pertinax Ug1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Catellicoccus marimammalium M35/04/3 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Chromobacterium vaccinii MWU205 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Chryseobacterium angstadtii KM trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Chryseobacterium arthrosphaerae CC-VM-7 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Chryseobacterium viscerum 687B-08 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Cloacibacillus porcorum CL-84 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Cobetia crustatorum JO1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Collimonas arenae Ter10 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Collimonas pratensis Ter91 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Collinsella tanakaei YIT 12063 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Coprobacter fastidiosus NSB1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Corynebacterium deserti GIMN1.010 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Corynebacterium frankenforstense ST18 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Corynebacterium lactis RW2-5 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Croceitalea dokdonensis DOKDO 023 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Cronobacter condimenti 1330 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Cronobacter muytjensii ATCC 51329 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Cronobacter universalis NCTC 9529 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulfatitalea tepidiphila S28bF trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulfotomaculum hydrothermale Lam5 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Dethiosulfovibrio salsuginis USBA 82 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Devosia chinhatensis IPL18 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Devriesea agamarum IMP2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Dialister succinatiphilus YIT 11850 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Dietzia timorensis ID05-A0528 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Dokdonella koreensis DS-123 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Domibacillus robiginosus WS 4628 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Duganella sacchari Sac-22 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Dyadobacter tibetensis Y620-1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Dyella jiangningensis SBZ3-12 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Endozoicomonas montiporae CL-33 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Enterococcus termitis LMG 8895 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Enterorhabdus caecimuris B7 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Epibacterium ulvae U95 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Erythrobacter gangjinensis K7-2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Erythrobacter marinus HWDM-33 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Ethanoligenens harbinense YUAN-3 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Fervidicella metallireducens AeB trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Fibrella aestuarina BUZ 2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Flammeovirga pacifica WPAGA1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Flaviramulus ichthyoenteri Th78 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Flavobacterium beibuense F44-8 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Flavobacterium glycines Gm-149 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Flavobacterium sp. LM5 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Flavobacterium ummariense DS-12 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Frischella perrara PEB0191 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Galbibacter marinus ck-I2-15 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Gallaecimonas xiamenensis 3-C-1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Geobacter daltonii FRC-32 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Gillisia marina CBA3202 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Gracilibacillus halophilus YIM-C55.5 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Granulicella mallensis MP5ACTX8 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Granulicella tundricola MP5ACTX9 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Hafnia paralvei ATCC 29927 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Haladaptatus cibarius D43 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Halioglobus japonicus S1-36 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Halobacillus alkaliphilus FP5 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Halococcus hamelinensis 100A6 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Halomonas salina B6 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Halomonas smyrnensis AAD6 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Halomonas stevensii S18214 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Halomonas titanicae BH1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Halomonas xinjiangensis TRM 0175 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Halopiger salifodinae KCY07-B2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Halostagnicola larsenii XH-48 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Haloterrigena daqingensis JX313 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Herbaspirillum aquaticum IEH 4430 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Hippea alviniae EP5-r trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Hippea jasoniae Mar08-272r trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Hoeflea phototrophica DFL-43 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Hyphomicrobium nitrativorans NL23 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Imtechella halotolerans K1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Indibacter alkaliphilus LW1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Jannaschia aquimarina GSW-M26 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Jeotgalibacillus soli P9 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Kangiella geojedonensis YCS-5 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Knoellia flava TL1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Kocuria flava HO-9041 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Kocuria turfanensis HO-9042 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Laceyella sediminis RHA1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Lacinutrix algicola AKS293 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Lacinutrix himadriensis E4-9a trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Lacinutrix mariniflava AKS432 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Lactobacillus curieae CCTCC M 2011381 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Lactobacillus delbrueckii ZN7a-9 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Lactobacillus hokkaidonensis LOOC260 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Lactobacillus oryzae SG293 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Lactobacillus pobuzihii E100301 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Lactobacillus shenzhenensis LY-73 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Lactobacillus silagei IWT126 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Leeuwenhoekiella blandensis MED217 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Lentibacillus jeotgali Grbi trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Limnohabitans curvus MWH-C5 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Limnohabitans parvus II-B4 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Listeria fleischmannii LU2006-1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Luteimonas huabeiensis HB2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Luteipulveratus mongoliensis MN07-A0370 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Lutibaculum baratangense AMV1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Lysobacter daejeonensis GH1-9 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Magnetovibrio blakemorei MV-1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Marinicella litoralis KMM 3900 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Mariniradius saccharolyticus AK6 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Marinobacter algicola DG893 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Marinobacter guineae M3B trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Marinobacter psychrophilus 20041 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Marinomonas arctica 328 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Marivita geojedonensis DPG-138 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Martelella endophytica YC6887 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Megamonas funiformis YIT 11815 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Mesorhizobium ciceri WSM1271 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Methanobacterium arcticum M2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methanobacterium veterum MK4 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methanocella arvoryzae MRE50 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methanococcus aeolicus Nankai-3 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methanoculleus horonobensis T10 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methanolinea tarda NOBI-1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methanosarcina soligelidi SMA-21 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methanospirillum lacunae Ki8-1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methanospirillum stamsii Pt1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methylibium petroleiphilum PM1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methylobacterium gossipiicola Gh-105 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methylocapsa aurea KYG trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Methylotenera versatilis 301 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Microbacterium profundi Shh49 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Microvirga lotononidis WSM3557 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Moritella dasanensis ArB 0140 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Mucilaginibacter gossypii Gh-67 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Mucilaginibacter gossypiicola Gh-48 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Mucilaginibacter mallensis MP1X4 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Nafulsella turpanensis ZLM-10 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Natronomonas moolapensis 8.8.11 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Nautilia profundicola AmH trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Neiella marina J221 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Neptunomonas antarctica S3-22 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Nocardioides daejeonensis MJ31 trpE?, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Nocardioides dokdonensis FR1436 trpE?, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Nocardiopsis baichengensis YIM 90130 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Nocardiopsis gilva YIM 90087 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Novosphingobium barchaimii LL02 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Novosphingobium fuchskuhlense FNE08-7 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Novosphingobium lindaniclasticum LE124 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Oceanisphaera arctica V1-41 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Ochrobactrum rhizosphaerae PR17 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Ochrobactrum thiophenivorans DSM 7216 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Oscillibacter ruminantium GH1 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Paenisporosarcina indica PN2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Palaeococcus pacificus DY20341 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Paludibacter propionicigenes WB4 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pandoraea thiooxydans ATSB16 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pantoea rwandensis LMG 26275 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pedobacter arcticus A12 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Photobacterium gaetbulicola Gung47 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Photobacterium jeanii R-40508 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Phyllobacterium brassicacearum STM 196 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Phyllobacterium endophyticum PEPV15 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Phyllobacterium leguminum ORS 1419 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Planktomarina temperata RCA23 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Planococcus halocryophilus Or1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pleomorphomonas diazotrophica R5-392 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Polaribacter dokdonensis DSW-5 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pontibacillus litoralis JSM 072002 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pontibacter lucknowensis DM9 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pontibacter ramchanderi LP43 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pontimonas salivibrio CL-TW6 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Porphyrobacter dokdonensis DSW-74 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pseudoalteromonas arctica A 37-1-2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pseudomonas baetica a390 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pseudomonas litoralis 2SM5 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pseudomonas taeanensis MS-3 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pseudovibrio axinellae Ad2 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Psychrobacter arcticus 273-4 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Psychrobacter cryohalolentis K5 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Psychromonas ingrahamii 37 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Psychromonas ossibalaenae JAMM 0738 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Rhizobium freirei PRF 81 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Rhizobium grahamii CCGE 502 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Rhizobium subbaraonis JC85 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Rhodanobacter denitrificans 2APBS1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Rhodobacter johrii JA192 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Rhodobacter maris JA276 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Rhodobacter ovatus JA234 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Rhodobacter viridis JA737 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Rhodococcus qingshengii djl-6-2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Rhodopseudomonas pseudopalustris DSM 123 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Roseateles aquatilis CCUG 48205 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Roseivirga spongicola UST030701-084 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Rubrivirga marina SAORIC-28 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Ruegeria conchae TW15 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Saccharomonospora marina XMU15 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Salinicoccus carnicancri Crm trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Serinicoccus profundi MCCC 1A05965 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Shewanella halifaxensis HAW-EB4 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Skermanella stibiiresistens SB22 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Snodgrassella alvi wkB2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Sphaerochaeta globosa Buddy trpED, trpD_2, PRAI, IGPS, trpA, trpB
Sphaerochaeta pleomorpha Grapes trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Sphingobium baderi LL03 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Sphingobium czechense LL01 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Sphingobium quisquiliarum P25 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Sphingomonas histidinilytica UM2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Sphingomonas indica Dd16 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Sphingomonas laterariae LNB2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Sphingopyxis indica DS15 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Sphingopyxis terrae UI2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Sporolactobacillus vineae SL153 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Streptacidiphilus oryzae TH49 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Streptococcus anginosus CCUG 39159 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Streptococcus massiliensis 4401825 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Streptococcus oralis 7747 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Streptococcus oralis AZ_3a trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Streptomyces kebangsaanensis SUK12 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Succinatimonas hippei YIT 12066 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Sulfurimonas gotlandica GD1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Tatumella morbirosei LMG 23360 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thauera humireducens SgZ-1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thermoactinomyces daqus H-18 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thermobifida halotolerans YIM 90462 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Thermodesulfovibrio aggregans TGE-P1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thermophagus xiamenensis HS1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thermovenabulum gondwanense R270 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Thioclava dalianensis DLFJ1-1 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Thiohalospira halophila HL 3 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Tistlia consotensis USBA 355 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Vagococcus penaei CD276 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Verminephrobacter eiseniae EF01-2 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Weissella oryzae SG25 trpED, trpD_2, PRAI, IGPS, trpA, trpB
Williamsia sterculiae CPCC 203464 trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Yersinia intermedia Y228 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 26 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