GapMind for Amino acid biosynthesis


chorismate biosynthesis in Derxia gummosa DSM 723

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 (10 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate Class of gap
tpiA D-glyceraldehyde-3-phosphate phospholyase H566_RS0103365 H566_RS0102430  
fbp 6-deoxy-5-ketofructose 1-phosphate synthase H566_RS25615 H566_RS0102425  
asp-kinase aspartate kinase H566_RS0120680 H566_RS0109000  
asd aspartate semi-aldehyde dehydrogenase H566_RS0118875  
aroA'? 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase spurious
aroB'? dehydroquinate synthase II spurious
aroD 3-dehydroquinate dehydratase H566_RS0106880 H566_RS0106940  
aroE shikimate dehydrogenase H566_RS0106940 H566_RS0106895  
aroL shikimate kinase H566_RS0100705 H566_RS0113145  
aroA 3-phosphoshikimate 1-carboxyvinyltransferase H566_RS0107825  
aroC chorismate synthase H566_RS0118905  
Alternative steps:
aroB 3-dehydroquinate synthase  
aroG 3-deoxy-7-phosphoheptulonate synthase H566_RS0121835 H566_RS0110515  

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