GapMind for Amino acid biosynthesis

 

L-leucine biosynthesis in Maridesulfovibrio zosterae DSM 11974

Best path

ilvH, ilvI, ilvC, ilvD, leuA, leuC, leuD, leuB, ilvE

Rules

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.

9 steps (9 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ilvH acetolactate/acetohydroxybutanoate synthase regulatory subunit H589_RS0113595 H589_RS0112015
ilvI acetolactate/acetohydroxybutanoate synthase catalytic subunit H589_RS0113590 H589_RS0113925
ilvC 2-hydroxy-3-ketol-acid reductoisomerase H589_RS0113600 H589_RS0116415
ilvD dihydroxy-acid dehydratase H589_RS0102910
leuA 2-isopropylmalate synthase H589_RS0111930 H589_RS0116575
leuC 3-isopropylmalate dehydratase / citramalate isomerase, large subunit H589_RS0111935 H589_RS0101690
leuD 3-isopropylmalate dehydaratase / citramalate isomerase, small subunit H589_RS0111940 H589_RS0101690
leuB 3-methylmalate dehydrogenase / 3-isopropylmalate dehydrogenase H589_RS0111950 H589_RS0107940
ilvE leucine transaminase H589_RS0113395 H589_RS0105035

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.

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