GapMind for Amino acid biosynthesis

 

Potential Gaps in Amino acid biosynthesis in Desulfovibrio vulgaris Hildenborough

Found 3 low-confidence and 1 medium-confidence steps on the best paths for 18 pathways. 4 of 4 gaps have been manually classified.

Pathway Step Best candidate 2nd candidate Class of gap
his hisN: histidinol-phosphate phosphatase DVU2490 DVU1040 diverged
ser serA: 3-phosphoglycerate dehydrogenase DVU0339 DVU1412 novel
ser serB: phosphoserine phosphatase DVU2935 novel
ser serC: 3-phosphoserine aminotransferase DVU0494 DVU3121 novel

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