GapMind for Amino acid biosynthesis


chorismate biosynthesis in Phaeacidiphilus oryzae TH49

Best path

aroG, 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
aroG 3-deoxy-7-phosphoheptulonate synthase BS73_RS28515 BS73_RS18005  
aroB 3-dehydroquinate synthase BS73_RS08495  
aroD 3-dehydroquinate dehydratase BS73_RS27260  
aroE shikimate dehydrogenase BS73_RS05680 BS73_RS08510  
aroL shikimate kinase BS73_RS08500  
aroA 3-phosphoshikimate 1-carboxyvinyltransferase BS73_RS15900 BS73_RS33985  
aroC? chorismate synthase spurious
Alternative steps:
aroA' 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase  
aroB' dehydroquinate synthase II  
asd aspartate semi-aldehyde dehydrogenase BS73_RS02665 BS73_RS20475  
asp-kinase aspartate kinase BS73_RS20470  
fbp 6-deoxy-5-ketofructose 1-phosphate synthase BS73_RS18945 BS73_RS16635  
tpiA D-glyceraldehyde-3-phosphate phospholyase BS73_RS12430 BS73_RS16890  

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