GapMind for Amino acid biosynthesis


Potential Gaps in Amino acid biosynthesis in Pelobacter propionicus DSM 2379

Found 2 low-confidence and 4 medium-confidence steps on the best paths for 18 pathways. 1 of 6 gaps have been classified.

Pathway Step Best candidate 2nd candidate Class of gap
chorismate aroE: shikimate dehydrogenase PPRO_RS11690  
his hisE: phosphoribosyl-AMP cyclohydrolase PPRO_RS15095 spurious
his hisN: histidinol-phosphate phosphatase PPRO_RS15085 PPRO_RS00085  
lys lysA: diaminopimelate decarboxylase PPRO_RS09900  
ser serB: phosphoserine phosphatase PPRO_RS13955 PPRO_RS03595  
thr homK: putative homoserine phosphotransferase PPRO_RS03790  

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.



Related tools

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