GapMind for Amino acid biosynthesis


chorismate biosynthesis in Halococcus hamelinensis 100A6

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 (11 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate Class of gap
tpiA D-glyceraldehyde-3-phosphate phospholyase C447_RS06860 C447_RS09435  
fbp 6-deoxy-5-ketofructose 1-phosphate synthase C447_RS06675 C447_RS11620  
asp-kinase aspartate kinase C447_RS02970  
asd aspartate semi-aldehyde dehydrogenase C447_RS07535  
aroA' 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase C447_RS07450 C447_RS06675  
aroB' dehydroquinate synthase II C447_RS07460  
aroD? 3-dehydroquinate dehydratase C447_RS11795 spurious
aroE shikimate dehydrogenase C447_RS11795  
aroL shikimate kinase C447_RS11825  
aroA 3-phosphoshikimate 1-carboxyvinyltransferase C447_RS09560  
aroC chorismate synthase C447_RS09545  
Alternative steps:
aroB 3-dehydroquinate synthase  
aroG 3-deoxy-7-phosphoheptulonate synthase  

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