GapMind for Amino acid biosynthesis


chorismate biosynthesis in Thioalkalivibrio halophilus HL17

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 B1A74_RS12405 B1A74_RS12840  
aroB 3-dehydroquinate synthase B1A74_RS10960  
aroD 3-dehydroquinate dehydratase B1A74_RS13425  
aroE shikimate dehydrogenase B1A74_RS01755  
aroL shikimate kinase B1A74_RS11020  
aroA 3-phosphoshikimate 1-carboxyvinyltransferase B1A74_RS01060  
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 B1A74_RS00505  
asp-kinase aspartate kinase B1A74_RS00670 B1A74_RS05210  
fbp 6-deoxy-5-ketofructose 1-phosphate synthase B1A74_RS11970  
tpiA D-glyceraldehyde-3-phosphate phospholyase B1A74_RS02505 B1A74_RS11980  

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