Pathways are sorted by name. Sort by completeness instead.
| Pathway | Steps |
|---|---|
| arg | lysW, argX, lysZ, lysY, lysJ, lysK, carA, carB, argI, argG*, argH |
| asn | aspS2, gatA, gatB, gatC |
| chorismate | tpiA, fbp, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC |
| cys | serA, serC, sepS, pscS |
| gln | gltX, glnA, gatA, gatB, gatC |
| gly | glyA |
| his | prs, hisG, hisI, hisE, hisA, hisF, hisH, hisB, hisC, hisN, hisD |
| ile | cimA, leuC, leuD, leuB, ilvI, ilvH, ilvC, ilvD, ilvE |
| leu | ilvI, ilvH, ilvC, ilvD, leuA, leuC, leuD, leuB, ilvE |
| lys | hcs, lysT, lysU, hicdh, lysN, lysW, lysX, lysZ, lysY, lysJ, lysK |
| met | asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesA |
| phe | cmutase, ptransferase, aro-dehydratase |
| pro | lysW, argX, lysZ, lysY, lysJ, lysK, OAT, proC |
| ser | serA, serC, serB |
| thr | asp-kinase, asd, hom, homK, thrC* |
| trp | trpED, trpD_2, PRAI, IGPS, trpA, trpB* |
| tyr | PAH |
| 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 Dec 26 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