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 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