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.
Or see definitions of steps
| Step | Description | Best candidate | 2nd candidate | Class of gap |
|---|---|---|---|---|
| tpiA | D-glyceraldehyde-3-phosphate phospholyase | B5D49_RS06130 | B5D49_RS06125 | |
| fbp? | 6-deoxy-5-ketofructose 1-phosphate synthase | B5D49_RS08675 | B5D49_RS01240 | spurious |
| asp-kinase | aspartate kinase | B5D49_RS06950 | ||
| asd | aspartate semi-aldehyde dehydrogenase | B5D49_RS04345 | ||
| aroA' | 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase | B5D49_RS01240 | B5D49_RS09460 | |
| aroB' | dehydroquinate synthase II | B5D49_RS01235 | ||
| aroD | 3-dehydroquinate dehydratase | B5D49_RS06055 | B5D49_RS11430 | |
| aroE | shikimate dehydrogenase | B5D49_RS11430 | ||
| aroL | shikimate kinase | B5D49_RS08835 | B5D49_RS08205 | |
| aroA | 3-phosphoshikimate 1-carboxyvinyltransferase | B5D49_RS01225 | ||
| aroC | chorismate synthase | B5D49_RS08820 | ||
| Alternative steps: | ||||
| aroB | 3-dehydroquinate synthase | |||
| aroG | 3-deoxy-7-phosphoheptulonate synthase | B5D49_RS05600 | ||
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 10 2024. The underlying query database was built on Apr 09 2024.
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:
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