GapMind for Amino acid biosynthesis

 

Amino acid biosynthesis in Belnapia rosea CPCC 100156

Pathways are sorted by name. Sort by completeness instead.

Pathway Steps
arg argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
asn aspS2, gatA, gatB, gatC
chorismate aroG, aroB, aroD, aroE, aroL, aroA, aroC
cys cysE, cysK
gln gltX, glnA, gatA, gatB, gatC
gly glyA
his prs, hisG, hisI, hisE, hisA, hisF, hisH, hisB, hisC, hisN, hisD
ile ilvA, ilvI, ilvH, ilvC, ilvD, ilvE
leu ilvH, ilvI, ilvC, ilvD, leuA, leuC, leuD, leuB, ilvE
lys asp-kinase, asd, dapA, dapB, dapD, dapC, dapE, dapF, lysA
met asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
phe cmutase, preph-dehydratase, PPYAT
pro proB, proA, proC
ser serA, serC, serB
thr asp-kinase, asd, hom, thrB, thrC
trp trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
tyr cmutase, pre-dehydr, tyrB
val ilvH, ilvI, ilvC, ilvD, ilvE

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