Pathways are sorted by name. Sort by completeness instead.
| Pathway | Steps |
|---|---|
| arg | argJ, argB, argC, argD, carA, carB, argI, argG, argH |
| asn | aspS2, gatA, gatB, gatC |
| chorismate | aroG, aroB, aroD, aroE, aroL, aroA, aroC |
| cys | serA, serC, PSSH |
| gln | glnA |
| gly | glyA |
| his | prs, hisG, hisI, hisE, hisA, hisF, hisH, hisB, hisC, hisN, hisD |
| ile | ilvA, ilvI, ilvH, ilvC, ilvD, ilvE |
| leu | ilvI, ilvH, 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 |
| phe | cmutase, preph-dehydratase, PPYAT |
| pro | proB, proA, proC |
| ser | serA, serC, serB |
| thr | asp-kinase, asd, hom, thrB, thrC |
| trp | trpED, trpD_2, PRAI, IGPS, trpA, trpB |
| tyr | cmutase, pre-dehydr, tyrB |
| val | ilvI, ilvH, 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 Sep 19 2024. The underlying query database was built on Jul 25 2024.
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:
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