ilvH, ilvI, ilvC, ilvD, leuA, leuC, leuD, leuB, ilvE
Also see fitness data for the top candidates
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 | PGA1_c20220 | |
| ilvI | acetolactate/acetohydroxybutanoate synthase catalytic subunit | PGA1_c20210 | PGA1_c19360 |
| ilvC | 2-hydroxy-3-ketol-acid reductoisomerase | PGA1_c06580 | |
| ilvD | dihydroxy-acid dehydratase | PGA1_c29490 | PGA1_c07380 |
| leuA | 2-isopropylmalate synthase | PGA1_c26470 | PGA1_c16460 |
| leuC | 3-isopropylmalate dehydratase / citramalate isomerase, large subunit | PGA1_c29780 | |
| leuD | 3-isopropylmalate dehydaratase / citramalate isomerase, small subunit | PGA1_c29790 | PGA1_c18830 |
| leuB | 3-methylmalate dehydrogenase / 3-isopropylmalate dehydrogenase | PGA1_c29830 | PGA1_c17990 |
| ilvE | leucine transaminase | PGA1_c34110 | PGA1_c34960 |
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.
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