GapMind for Amino acid biosynthesis


chorismate biosynthesis in Heliomicrobium modesticaldum Ice1; ATCC 51547

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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroG 3-deoxy-7-phosphoheptulonate synthase HM1_RS08650 HM1_RS08950
aroB 3-dehydroquinate synthase HM1_RS02465
aroD 3-dehydroquinate dehydratase HM1_RS02360 HM1_RS02480
aroE shikimate dehydrogenase HM1_RS02480
aroL shikimate kinase HM1_RS02470
aroA 3-phosphoshikimate 1-carboxyvinyltransferase HM1_RS08665
aroC chorismate synthase HM1_RS02475
Alternative steps:
aroA' 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase HM1_RS08040
aroB' dehydroquinate synthase II HM1_RS08045
asd aspartate semi-aldehyde dehydrogenase HM1_RS10580
asp-kinase aspartate kinase HM1_RS08725 HM1_RS10585
fbp 6-deoxy-5-ketofructose 1-phosphate synthase HM1_RS04085 HM1_RS08040
tpiA D-glyceraldehyde-3-phosphate phospholyase HM1_RS07270 HM1_RS03000

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