GapMind for Amino acid biosynthesis

 

L-leucine biosynthesis in Synechococcus elongatus PCC 7942

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 Synpcc7942_0139
ilvI acetohydroxybutanoate synthase regulatory subunit Synpcc7942_2434
ilvC ketol-acid reductoisomerase Synpcc7942_1552
ilvD (R)-2,3-dihydroxy-3-methylbutanoate dehydratase Synpcc7942_0626
leuA 2-isopropylmalate synthase Synpcc7942_1410 Synpcc7942_0428
leuC 3-isopropylmalate dehydratase, large subunit Synpcc7942_1898 Synpcc7942_0903
leuD 3-isopropylmalate dehydaratase, small subunit Synpcc7942_2548
leuB 3-isopropylmalate dehydrogenase Synpcc7942_1505 Synpcc7942_1719
ilvE leucine transaminase Synpcc7942_1029 Synpcc7942_1335

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, 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