GapMind for Amino acid biosynthesis


chorismate biosynthesis in Sulfurihydrogenibium subterraneum DSM 15120

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 (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate Known gap?
tpiA D-glyceraldehyde-3-phosphate phospholyase Q385_RS0104030 Q385_RS0102690  
fbp? 6-deoxy-5-ketofructose 1-phosphate synthase Q385_RS0101975 known gap
asp-kinase aspartate kinase Q385_RS0104175  
asd aspartate semi-aldehyde dehydrogenase Q385_RS0103220  
aroA' 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase Q385_RS0101975  
aroB' dehydroquinate synthase II Q385_RS0102630  
aroD 3-dehydroquinate dehydratase Q385_RS0100825 Q385_RS0104370  
aroE shikimate dehydrogenase Q385_RS0104370  
aroL shikimate kinase Q385_RS0105865  
aroA 3-phosphoshikimate 1-carboxyvinyltransferase Q385_RS0107205  
aroC chorismate synthase Q385_RS0105705  
Alternative steps:
aroB 3-dehydroquinate synthase  
aroG 3-deoxy-7-phosphoheptulonate synthase Q385_RS0106720  

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