GapMind for Amino acid biosynthesis

 

L-valine biosynthesis in Bacteroides thetaiotaomicron VPI-5482

Best path

ilvH, ilvI, ilvC, ilvD, ilvE

Also see fitness data for the top candidates

Rules

Overview: Valine biosynthesis in GapMind is based on MetaCyc pathway L-valine biosynthesis (link).

5 steps (5 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ilvH acetohydroxybutanoate synthase catalytic subunit BT2077
ilvI acetohydroxybutanoate synthase regulatory subunit BT2076
ilvC ketol-acid reductoisomerase BT2074
ilvD (R)-2,3-dihydroxy-3-methylbutanoate dehydratase BT2078
ilvE valine transaminase BT3892

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