GapMind for Amino acid biosynthesis

 

Amino acid biosynthesis in Shewanella oneidensis MR-1

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
his prs, hisG, hisI, hisE, hisA, hisF, hisH, hisB, hisC, hisN, hisD
arg argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
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, metA, metB, metC, metH, B12-reactivation-domain
trp trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
ile ilvA, ilvI, ilvH, ilvC, ilvD, ilvE
thr asp-kinase, asd, hom, thrB, thrC
val ilvH, ilvI, ilvC, ilvD, ilvE
phe cmutase, preph-dehydratase, ilvE
pro proB, proA, proC
ser serA, serC, serB
tyr cmutase, pre-dehydr, tyrB
cys cysE, cysK
asn asnB
gln glnA
gly glyA
chorismate aroG, aroB, aroD, aroE, aroL, aroA, aroC?

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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

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