ilvH, ilvI, ilvC, ilvD, leuA, leuC, leuD, leuB, ilvE
Overview: Leucine biosynthesis in GapMind is based on MetaCyc pathway L-leucine biosynthesis (link). This begins with the initial steps of valine biosynthesis (see link), up to 3-methyloxobutanoate.
Or see definitions of steps
| Step | Description | Best candidate | 2nd candidate |
|---|---|---|---|
| ilvH | acetolactate/acetohydroxybutanoate synthase regulatory subunit | PNAP_RS08585 | |
| ilvI | acetolactate/acetohydroxybutanoate synthase catalytic subunit | PNAP_RS08580 | PNAP_RS11090 |
| ilvC | 2-hydroxy-3-ketol-acid reductoisomerase | PNAP_RS08590 | |
| ilvD | dihydroxy-acid dehydratase | PNAP_RS14365 | PNAP_RS13320 |
| leuA | 2-isopropylmalate synthase | PNAP_RS08600 | PNAP_RS11555 |
| leuC | 3-isopropylmalate dehydratase / citramalate isomerase, large subunit | PNAP_RS15200 | PNAP_RS15140 |
| leuD | 3-isopropylmalate dehydaratase / citramalate isomerase, small subunit | PNAP_RS15205 | PNAP_RS15125 |
| leuB | 3-methylmalate dehydrogenase / 3-isopropylmalate dehydrogenase | PNAP_RS15210 | PNAP_RS08150 |
| ilvE | leucine transaminase | PNAP_RS01975 | PNAP_RS00730 |
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 10 2024. The underlying query database was built on Apr 09 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