GapMind for Amino acid biosynthesis

 

L-tyrosine biosynthesis

Analysis of pathway tyr in 276 genomes

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

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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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