GapMind for Amino acid biosynthesis


Potential Gaps in Amino acid biosynthesis in Persephonella marina EX-H1

Found 4 low-confidence and 4 medium-confidence steps on the best paths for 18 pathways.

Pathway Step Best candidate 2nd candidate
chorismate fbp: 6-deoxy-5-ketofructose 1-phosphate synthase PERMA_RS08670
cys serC: 3-phosphoserine aminotransferase PERMA_RS01695
his hisN: histidinol-phosphate phosphatase PERMA_RS02725 PERMA_RS01120
met metB: cystathionine gamma-synthase
met metC: cystathionine beta-lyase
ser serC: 3-phosphoserine aminotransferase PERMA_RS01695
trp IGPS: indole-3-glycerol phosphate synthase PERMA_RS04655
trp PRAI: phosphoribosylanthranilate isomerase PERMA_RS02510 PERMA_RS08165

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 Apr 09 2024. The underlying query database was built on Apr 09 2024.



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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 (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:

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. 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:

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:

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