GapMind for Amino acid biosynthesis

 

Potential Gaps in Amino acid biosynthesis in Dyella japonica UNC79MFTsu3.2

Found 1 low-confidence and 4 medium-confidence steps on the best paths for 18 pathways. 5 of 5 gaps have been manually classified.

Pathway Step Best candidate 2nd candidate Class of gap
ile ilvI: acetohydroxybutanoate synthase regulatory subunit N515DRAFT_0566 diverged
leu ilvI: acetohydroxybutanoate synthase regulatory subunit N515DRAFT_0566 diverged
met metC: cystathionine beta-lyase N515DRAFT_4305 N515DRAFT_4363 diverged
ser serB: phosphoserine phosphatase N515DRAFT_3581 N515DRAFT_0975 novel
val ilvI: acetohydroxybutanoate synthase regulatory subunit N515DRAFT_0566 diverged

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