GapMind for Amino acid biosynthesis

 

chorismate biosynthesis in Desulfovibrio vulgaris Hildenborough

Best path

tpiA, fbp, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC

Rules

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
tpiA D-glyceraldehyde-3-phosphate phospholyase DVU1677 DVU2529
fbp 6-deoxy-5-ketofructose 1-phosphate synthase DVU2143 DVU0460
asp-kinase aspartate kinase DVU1913
asd aspartate semi-aldehyde dehydrogenase DVU3048
aroA' 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase DVU0460
aroB' dehydroquinate synthase II DVU0461
aroD 3-dehydroquinate dehydratase DVU1665
aroE shikimate dehydrogenase DVU0115
aroL shikimate kinase DVU0892 DVU2521
aroA 3-phosphoshikimate 1-carboxyvinyltransferase DVU0463
aroC chorismate synthase DVU0894
Alternative steps:
aroB 3-dehydroquinate synthase
aroG 3-deoxy-7-phosphoheptulonate synthase DVU1624

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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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