GapMind for Amino acid biosynthesis

 

Finding step ilvI for L-valine biosynthesis in Dyella japonica UNC79MFTsu3.2

Manual classification of gap: diverged
Rationale: This genome and others of its species (Dyella japonica) have a short IlvI (regulatory subunit of acetolactate synthase), i.e. N515DRAFT_0566. The conservation suggests that it is functional.

1 candidates for ilvI: acetohydroxybutanoate synthase regulatory subunit

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
lo N515DRAFT_0566 acetolactate synthase, small subunit Probable acetolactate synthase small subunit; EC 2.2.1.6; Acetohydroxy-acid synthase small subunit; AHAS; ALS (uncharacterized) 48% 52% 85.5
med N515DRAFT_0566 acetolactate synthase, small subunit ilvN: acetolactate synthase, small subunit (EC 2.2.1.6) (TIGR00119) 47% 96.5

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

Also see fitness data for the candidates

Definition of step ilvI

Or cluster all characterized ilvI proteins

Known gaps in related organisms

This GapMind analysis is from Mar 30 2021. The underlying query database was built on Mar 30 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