GapMind for Amino acid biosynthesis


chorismate biosynthesis in Desulfobacca acetoxidans DSM 11109

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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
tpiA D-glyceraldehyde-3-phosphate phospholyase DESAC_RS16645 DESAC_RS16640
fbp 6-deoxy-5-ketofructose 1-phosphate synthase DESAC_RS06270 DESAC_RS10530
asp-kinase aspartate kinase DESAC_RS11615 DESAC_RS10105
asd aspartate semi-aldehyde dehydrogenase DESAC_RS14610
aroA' 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase DESAC_RS03235
aroB' dehydroquinate synthase II DESAC_RS03230
aroD 3-dehydroquinate dehydratase DESAC_RS03220 DESAC_RS03215
aroE shikimate dehydrogenase DESAC_RS03215
aroL shikimate kinase DESAC_RS13360
aroA 3-phosphoshikimate 1-carboxyvinyltransferase DESAC_RS03210
aroC chorismate synthase DESAC_RS13365
Alternative steps:
aroB 3-dehydroquinate synthase DESAC_RS04610
aroG 3-deoxy-7-phosphoheptulonate synthase DESAC_RS04605 DESAC_RS10410

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.



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