chorismate biosynthesis in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

chorismate biosynthesis in Desulfovibrio vulgaris Miyazaki F

Best path

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

Also see fitness data for the top candidates

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.

all: 3-dehydroquinate, aroD, aroE, aroL, aroA and aroC
3-dehydroquinate:

aroG and aroB
or tpiA, fbp, aspartate-semialdehyde, aroA' and aroB'
Comment: Pathway I uses aroG and aroB, while pathway II uses non-canonical activities of triose-phosphate isomerase (tpiA) and fructose-bisphosphate aldolase (fbp) to form 6-deoxy-5-ketofructose 1-phosphate. AroA' condenses this with asparate semialdehyde to 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate, and AroB' cyclizes it to 3-dehydroquinate.

aspartate-semialdehyde: asp-kinase and asd

13 steps (12 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
tpiA	D-glyceraldehyde-3-phosphate phospholyase	DvMF_0348	DvMF_0975
fbp	6-deoxy-5-ketofructose 1-phosphate synthase	DvMF_0013	DvMF_1751
asp-kinase	aspartate kinase	DvMF_0276
asd	aspartate semi-aldehyde dehydrogenase	DvMF_2382
aroA'	2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase	DvMF_1751
aroB'	dehydroquinate synthase II	DvMF_1750
aroD	3-dehydroquinate dehydratase	DvMF_0373
aroE	shikimate dehydrogenase	DvMF_1962
aroL	shikimate kinase	DvMF_1410	DvMF_0971
aroA	3-phosphoshikimate 1-carboxyvinyltransferase	DvMF_1748
aroC	chorismate synthase	DvMF_1408
Alternative steps:
aroB	3-dehydroquinate synthase
aroG	3-deoxy-7-phosphoheptulonate synthase	DvMF_0432

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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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, the paper from 2022 on GapMind for carbon sources, 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

GapMind for Amino acid biosynthesis