GapMind for Amino acid biosynthesis

 

Potential Gaps in Amino acid biosynthesis in Trichlorobacter lovleyi SZ

Found 1 low-confidence and 6 medium-confidence steps on the best paths for 18 pathways.

Pathway Step Best candidate 2nd candidate
chorismate aroL: shikimate kinase GLOV_RS07865 GLOV_RS15295
his hisN: histidinol-phosphate phosphatase GLOV_RS04040 GLOV_RS01995
leu leuD: 3-isopropylmalate dehydaratase / citramalate isomerase, small subunit GLOV_RS15655 GLOV_RS07970
lys lysA: diaminopimelate decarboxylase GLOV_RS14990
ser serB: phosphoserine phosphatase GLOV_RS13540 GLOV_RS10410
ser serC: 3-phosphoserine aminotransferase GLOV_RS16555
thr thrB: homoserine kinase GLOV_RS15295 GLOV_RS07865

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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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