GapMind for Amino acid biosynthesis

 

L-tyrosine biosynthesis

Analysis of pathway tyr in 206 genomes

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