GapMind for Amino acid biosynthesis


chorismate biosynthesis in Persephonella marina EX-H1

Best path

tpiA, fbp?, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC


Overview: Chorismate is the starting point for the biosynthesis of the aromatic amino acids phenylalanine, tryptophan, and tyrosine. Chorismate biosynthesis in GapMind is based on MetaCyc pathways chorismate biosynthesis I (link), from D-erythrose-4-phosphate and phosphoenolpyruvate, or II (link), from D-glyceraldeyde-3-phosphate and L-asparatate. Both pathways are identical after they reach 3-dehydroquinate.

13 steps (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate Known gap?
tpiA D-glyceraldehyde-3-phosphate phospholyase PERMA_RS05205 PERMA_RS01115  
fbp? 6-deoxy-5-ketofructose 1-phosphate synthase PERMA_RS08670 known gap
asp-kinase aspartate kinase PERMA_RS08105  
asd aspartate semi-aldehyde dehydrogenase PERMA_RS01855  
aroA' 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase PERMA_RS08670  
aroB' dehydroquinate synthase II PERMA_RS07315  
aroD 3-dehydroquinate dehydratase PERMA_RS01595 PERMA_RS05330  
aroE shikimate dehydrogenase PERMA_RS05330  
aroL shikimate kinase PERMA_RS06960  
aroA 3-phosphoshikimate 1-carboxyvinyltransferase PERMA_RS08540  
aroC chorismate synthase PERMA_RS00945  
Alternative steps:
aroB 3-dehydroquinate synthase  
aroG 3-deoxy-7-phosphoheptulonate synthase PERMA_RS02070  

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.



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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