GapMind for Amino acid biosynthesis


chorismate biosynthesis in Maridesulfovibrio zosterae DSM 11974

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 H589_RS0114465 H589_RS0114460
fbp 6-deoxy-5-ketofructose 1-phosphate synthase H589_RS0115820 H589_RS0105345
asp-kinase aspartate kinase H589_RS0114245 H589_RS0113380
asd aspartate semi-aldehyde dehydrogenase H589_RS0110325
aroA' 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase H589_RS0105345 H589_RS0118440
aroB' dehydroquinate synthase II H589_RS0105340
aroD 3-dehydroquinate dehydratase H589_RS0115265 H589_RS0102675
aroE shikimate dehydrogenase H589_RS0102675
aroL shikimate kinase H589_RS0104475 H589_RS0117045
aroA 3-phosphoshikimate 1-carboxyvinyltransferase H589_RS0105330
aroC chorismate synthase H589_RS0104470
Alternative steps:
aroB 3-dehydroquinate synthase H589_RS0106415
aroG 3-deoxy-7-phosphoheptulonate synthase H589_RS0106420 H589_RS0110200

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