GapMind for Amino acid biosynthesis

 

L-leucine biosynthesis in Dinoroseobacter shibae DFL-12

Best path

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

Also see fitness data for the top candidates

Rules

Overview: Leucine biosynthesis in GapMind is based on MetaCyc pathway L-leucine biosynthesis (link). This begins with 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 acetohydroxybutanoate synthase catalytic subunit Dshi_1779 Dshi_3840
ilvI acetohydroxybutanoate synthase regulatory subunit Dshi_1781
ilvC ketol-acid reductoisomerase Dshi_2396
ilvD (R)-2,3-dihydroxy-3-methylbutanoate dehydratase Dshi_0129 Dshi_1244
leuA 2-isopropylmalate synthase Dshi_0596 Dshi_1696
leuC 3-isopropylmalate dehydratase, large subunit Dshi_0085 Dshi_0695
leuD 3-isopropylmalate dehydaratase, small subunit Dshi_0083 Dshi_0696
leuB 3-isopropylmalate dehydrogenase Dshi_0775 Dshi_0081
ilvE leucine transaminase Dshi_3301 Dshi_3150

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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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