GapMind for Amino acid biosynthesis


Potential Gaps in Amino acid biosynthesis in Desulfovibrio oxyclinae DSM 11498

Found 6 low-confidence and 4 medium-confidence steps on the best paths for 18 pathways. 1 of 10 gaps have been classified.

Pathway Step Best candidate 2nd candidate Class of gap
chorismate fbp: 6-deoxy-5-ketofructose 1-phosphate synthase B149_RS0107855 B149_RS0103015  
gln glnA: glutamine synthetase B149_RS0106590  
gln gltX: glutamyl-tRNA(Glx) synthetase B149_RS0103595  
his hisN: histidinol-phosphate phosphatase B149_RS0104715 B149_RS0111010  
ile ilvD: dihydroxy-acid dehydratase  
leu ilvD: dihydroxy-acid dehydratase  
phe aro-dehydratase: arogenate dehydratase B149_RS16240 B149_RS0112780  
ser serA: 3-phosphoglycerate dehydrogenase B149_RS0109925 spurious
ser serC: 3-phosphoserine aminotransferase B149_RS0100570  
val ilvD: dihydroxy-acid dehydratase  

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