GapMind for Amino acid biosynthesis

 

L-phenylalanine biosynthesis

Analysis of pathway phe in 150 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 cmutase, preph-dehydratase, PPYAT
Acidithiobacillus ferrooxidans ATCC 23270 cmutase, preph-dehydratase, PPYAT
Alicycliphilus denitrificans K601 cmutase, preph-dehydratase, PPYAT
Allochromatium vinosum DSM 180 cmutase, preph-dehydratase, PPYAT
Ammonifex degensii KC4 cmutase, preph-dehydratase, PPYAT
Archaeoglobus veneficus SNP6 cmutase, preph-dehydratase, PPYAT
Arcobacter nitrofigilis DSM 7299 cmutase, preph-dehydratase, PPYAT
Azoarcus sp. BH72 cmutase, preph-dehydratase, PPYAT
Azohydromonas australica DSM 1124 cmutase, preph-dehydratase, PPYAT
Azorhizobium caulinodans ORS 571 cmutase, ptransferase, aro-dehydratase
Azospirillum lipoferum B510 cmutase, ptransferase, aro-dehydratase
Bacillus alkalinitrilicus DSM 22532 cmutase, preph-dehydratase, PPYAT
Beijerinckia indica ATCC 9039 cmutase, preph-dehydratase, PPYAT
Beijerinckia mobilis UQM 1969 cmutase, preph-dehydratase, PPYAT
Bradyrhizobium sp. BTAi1 cmutase, ptransferase, aro-dehydratase
Burkholderia vietnamiensis G4 cmutase, preph-dehydratase, PPYAT
Calditerrivibrio nitroreducens DSM 19672 cmutase, preph-dehydratase, PPYAT
Caminibacter mediatlanticus TB-2 cmutase, preph-dehydratase, PPYAT
Chlorobaculum parvum NCIB 8327 cmutase, ptransferase, aro-dehydratase
Chlorobaculum tepidum TLS cmutase, ptransferase, aro-dehydratase
Chlorobium limicola DSM 245 cmutase, ptransferase, aro-dehydratase
Chlorobium phaeobacteroides BS1 cmutase, ptransferase, aro-dehydratase
Clostridium acetobutylicum ATCC 824 cmutase, preph-dehydratase, PPYAT
Clostridium kluyveri DSM 555 cmutase, preph-dehydratase, PPYAT
Crocosphaera subtropica ATCC 51142 cmutase, preph-dehydratase, PPYAT
Dechloromonas agitata is5 cmutase, preph-dehydratase, PPYAT
Dehalococcoides mccartyi 195 cmutase, preph-dehydratase, PPYAT
Denitrovibrio acetiphilus DSM 12809 cmutase, preph-dehydratase, PPYAT
Derxia gummosa DSM 723 cmutase, preph-dehydratase, PPYAT
Desulfacinum hydrothermale DSM 13146 cmutase, ptransferase, aro-dehydratase
Desulfacinum infernum DSM 9756 cmutase, preph-dehydratase, PPYAT
Desulfallas geothermicus DSM 3669 cmutase, preph-dehydratase, PPYAT
Desulfarculus baarsii DSM 2075 cmutase, preph-dehydratase, PPYAT
Desulfatibacillum aliphaticivorans DSM 15576 cmutase, preph-dehydratase, PPYAT
Desulfatiglans anilini DSM 4660 cmutase, preph-dehydratase, PPYAT
Desulfitobacterium hafniense DCB-2 cmutase, preph-dehydratase, PPYAT
Desulfobacca acetoxidans DSM 11109 cmutase, preph-dehydratase, PPYAT
Desulfobacter vibrioformis DSM 8776 cmutase, preph-dehydratase, PPYAT
Desulfobulbus mediterraneus DSM 13871 cmutase, ptransferase, aro-dehydratase
Desulfotalea psychrophila LSv54 cmutase, preph-dehydratase, PPYAT
Desulfotomaculum ruminis DSM 2154 cmutase, preph-dehydratase, PPYAT
Desulfovibrio bastinii DSM 16055 cmutase, preph-dehydratase, PPYAT
Desulfovibrio gracilis DSM 16080 cmutase, preph-dehydratase, PPYAT
Desulfovibrio oxyclinae DSM 11498 cmutase, ptransferase, aro-dehydratase
Desulfovibrio zosterae DSM 11974 cmutase, preph-dehydratase, PPYAT
Desulfurobacterium atlanticum DSM 15668 cmutase, preph-dehydratase, PPYAT
Desulfuromonas acetexigens cmutase, preph-dehydratase, PPYAT
Desulfuromusa kysingii DSM 7343 cmutase, preph-dehydratase, PPYAT
Ferroglobus placidus DSM 10642 cmutase, preph-dehydratase, PPYAT
Frankia alni ACN14A cmutase, preph-dehydratase, PPYAT
Geobacter lovleyi SZ cmutase, preph-dehydratase, PPYAT
Geobacter metallireducens GS-15 cmutase, preph-dehydratase, PPYAT
Geobacter uraniireducens Rf4 cmutase, preph-dehydratase, PPYAT
Haloechinothrix alba DSM 45207 cmutase, preph-dehydratase, PPYAT
Haloglycomyces albus DSM 45210 cmutase, preph-dehydratase, PPYAT
Halomonas desiderata SP1 cmutase, preph-dehydratase, PPYAT
Halorhodospira halophila SL1 cmutase, ptransferase, aro-dehydratase
Heliobacterium modesticaldum Ice1; ATCC 51547 cmutase, preph-dehydratase, PPYAT
Herbaspirillum autotrophicum IAM 14942 cmutase, ptransferase, aro-dehydratase
Hydrogenophaga taeniospiralis NBRC 102512 cmutase, preph-dehydratase, PPYAT
Hydrogenovibrio halophilus DSM 15072 cmutase, preph-dehydratase, PPYAT
Hydrogenovibrio kuenenii DSM 12350 cmutase, preph-dehydratase, PPYAT
Hydrogenovibrio marinus DSM 11271 cmutase, preph-dehydratase, PPYAT
Hyphomicrobium sulfonivorans WDL6 cmutase, preph-dehydratase, PPYAT
Klebsiella variicola At-22 cmutase, preph-dehydratase, PPYAT
Kyrpidia tusciae DSM 2912 cmutase, preph-dehydratase, PPYAT
Leptospirillum ferrooxidans C2-3 cmutase, preph-dehydratase, PPYAT
Malonomonas rubra DSM 5091 cmutase, preph-dehydratase, PPYAT
Mesorhizobium ciceri WSM1271 cmutase, preph-dehydratase, PPYAT
Methanobacterium lacus AL-21 cmutase, preph-dehydratase, PPYAT
Methanococcus aeolicus Nankai-3 cmutase, preph-dehydratase, PPYAT
Methanococcus maripaludis C5 cmutase, preph-dehydratase, PPYAT
Methanosarcina acetivorans C2A cmutase, ptransferase, aro-dehydratase?
Methanosarcina barkeri Fusaro cmutase, preph-dehydratase, PPYAT
Methanosarcina mazei Go1 cmutase, preph-dehydratase, PPYAT
Methanothermobacter thermautotrophicus Delta H cmutase, preph-dehydratase, PPYAT
Methylobacterium nodulans ORS 2060 cmutase, ptransferase, aro-dehydratase
Methylobacterium sp. 4-46 cmutase, ptransferase, aro-dehydratase
Methylocapsa acidiphila B2 cmutase, preph-dehydratase, PPYAT
Methylocapsa aurea KYG T cmutase, preph-dehydratase, PPYAT
Methylocella silvestris BL2 cmutase, preph-dehydratase, PPYAT
Methylococcus capsulatus Bath cmutase, preph-dehydratase, PPYAT
Methylocystis bryophila S285 cmutase, preph-dehydratase, PPYAT
Methyloferula stellata AR4T cmutase, ptransferase, aro-dehydratase
Methylohalobius crimeensis 10Ki cmutase, preph-dehydratase, PPYAT
Methylomicrobium alcaliphilum 20Z cmutase, preph-dehydratase, PPYAT
Methylomonas methanica MC09 cmutase, preph-dehydratase, PPYAT
Methylosarcina fibrata AML-C10 cmutase, preph-dehydratase, PPYAT
Methylovulum miyakonense HT12 cmutase, preph-dehydratase, PPYAT
Mycolicibacterium vanbaalenii PYR-1 cmutase, preph-dehydratase, PPYAT
Nitratifractor salsuginis DSM 16511 cmutase, preph-dehydratase, PPYAT
Nitratiruptor tergarcus DSM 16512 cmutase, preph-dehydratase, PPYAT
Nitriliruptor alkaliphilus DSM 45188 cmutase, preph-dehydratase, PPYAT
Nocardiopsis lucentensis DSM 44048 cmutase, preph-dehydratase, PPYAT
Nostoc punctiforme ATCC 29133; PCC 73102 cmutase, preph-dehydratase, PPYAT
Novosphingobium aromaticivorans DSM 12444 cmutase, preph-dehydratase, PPYAT
Oleispira antarctica cmutase, preph-dehydratase, PPYAT
Paraburkholderia phymatum STM815 cmutase, preph-dehydratase, PPYAT
Paraburkholderia sp. CCGE1002 cmutase, preph-dehydratase, PPYAT
Pelobacter propionicus DSM 2379 cmutase, preph-dehydratase, PPYAT
Persephonella marina EX-H1 cmutase, preph-dehydratase, PPYAT
Polaromonas naphthalenivorans CJ2 cmutase, preph-dehydratase, PPYAT
Prosthecochloris aestuarii DSM 271 cmutase, ptransferase, aro-dehydratase
Pseudarthrobacter sulfonivorans Ar51 cmutase, preph-dehydratase, PPYAT
Pseudomonas benzenivorans DSM 8628 cmutase, preph-dehydratase, PPYAT
Pseudomonas stutzeri A1501 cmutase, preph-dehydratase, PPYAT
Pyrolobus fumarii 1A cmutase, ptransferase, aro-dehydratase
Rhizobium etli CFN 42 cmutase, preph-dehydratase, PPYAT
Rhizobium leguminosarum 3841 cmutase, preph-dehydratase, PPYAT
Rhizobium leguminosarum WSM1325 cmutase, preph-dehydratase, PPYAT
Rhodobacter sphaeroides ATCC 17029 cmutase, preph-dehydratase, PPYAT
Rhodomicrobium vannielii ATCC 17100 cmutase, preph-dehydratase, PPYAT
Rhodopseudomonas palustris CGA009 cmutase, preph-dehydratase, PPYAT
Rhodospirillum centenum SW; ATCC 51521 cmutase, preph-dehydratase, PPYAT
Rhodospirillum rubrum ATCC 11170 cmutase, preph-dehydratase, PPYAT
Saccharomonospora cyanea NA-134 cmutase, preph-dehydratase, PPYAT
Sedimenticola selenatireducens DSM 17993 cmutase, preph-dehydratase, PPYAT
Sinorhizobium fredii NGR234 cmutase, preph-dehydratase, PPYAT
Sinorhizobium medicae WSM419 cmutase, preph-dehydratase, PPYAT
Sphingomonas wittichii RW1 cmutase, preph-dehydratase, PPYAT
Stenotrophomonas chelatiphaga DSM 21508 cmutase, preph-dehydratase, PPYAT
Steroidobacter denitrificans DSM 18526 cmutase, preph-dehydratase, PPYAT
Sulfuricurvum kujiense DSM 16994 cmutase, preph-dehydratase, PPYAT
Sulfurihydrogenibium azorense Az-Fu1 cmutase, preph-dehydratase, PPYAT
Sulfurihydrogenibium subterraneum DSM 15120 cmutase, preph-dehydratase, PPYAT
Sulfurimonas denitrificans DSM 1251 cmutase, preph-dehydratase, PPYAT
Sulfuritalea hydrogenivorans DSM 22779 cmutase, preph-dehydratase, PPYAT
Sulfurivirga caldicuralii DSM 17737 cmutase, preph-dehydratase, PPYAT
Teredinibacter turnerae T7901 cmutase, preph-dehydratase, PPYAT
Thauera aminoaromatica S2 cmutase, preph-dehydratase, PPYAT
Thermithiobacillus tepidarius DSM 3134 cmutase, preph-dehydratase, PPYAT
Thermocrinis albus DSM 14484 cmutase, preph-dehydratase, PPYAT
Thermodesulforhabdus norvegica DSM 9990 cmutase, ptransferase, aro-dehydratase
Thermomonospora curvata DSM 43183 cmutase, preph-dehydratase, PPYAT
Thermovibrio ammonificans HB-1 cmutase, preph-dehydratase, PPYAT
Thioalkalivibrio denitrificans ALJD cmutase, preph-dehydratase, PPYAT
Thioalkalivibrio halophilus HL17 cmutase, preph-dehydratase, PPYAT
Thioalkalivibrio paradoxus ARh 1 cmutase, preph-dehydratase, PPYAT
Thioalkalivibrio thiocyanodenitrificans ARhD 1 cmutase, preph-dehydratase, PPYAT
Thiohalomonas denitrificans HLD2 cmutase, preph-dehydratase, PPYAT
Thiomicrorhabdus arctica DSM 13458 cmutase, preph-dehydratase, PPYAT
Thiomicrorhabdus chilensis DSM 12352 cmutase, preph-dehydratase, PPYAT
Thiomicrospira cyclica ALM1 cmutase, preph-dehydratase, PPYAT
Thiomicrospira microaerophila ASL8-2 cmutase, preph-dehydratase, PPYAT
Thiomicrospira pelophila DSM 1534 cmutase, preph-dehydratase, PPYAT
Thiothrix lacustris DSM 21227 cmutase, preph-dehydratase, PPYAT
Trichodesmium erythraeum IMS101 cmutase, preph-dehydratase, PPYAT
Trichormus variabilis ATCC 29413 cmutase, preph-dehydratase, PPYAT
Xanthobacter autotrophicus Py2 cmutase, preph-dehydratase, PPYAT
Xenophilus azovorans DSM 13620 cmutase, preph-dehydratase, PPYAT

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 10 2024. The underlying query database was built on Apr 09 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