GapMind for Amino acid biosynthesis

 

Definition of L-isoleucine biosynthesis

As rules and steps, or see full text

Rules

Overview: Isoleucine biosynthesis in GapMind is based on MetaCyc pathways L-isoleucine biosynthesis I (from threonine) (link), II via citramalate (link), or IV from propanoate (link). These pathways share a common intermediate, 2-oxobutanoate, but vary in how the 2-oxobutanoate is formed. Pathway IV is included because propanoate is a common fermentative end product and need not be a nutrient requirement, but it is not always clear if it could be the main pathway to isoleucine. Pathway III (link), via glutamate mutase, is not included because the first step (glutamate mutase, EC 5.4.99.1) has not been linked to sequence and because no organism has been demonstrated to rely on this pathway to form oxobutanoate. Pathway V, from 2-methylbutanoate (link), is not included.

Steps

ilvA: threonine deaminase

ilvH: acetohydroxybutanoate synthase catalytic subunit

ilvI: acetohydroxybutanoate synthase regulatory subunit

ilvC: 2-hydroxy-3-ketol-acid reductoisomerase

ilvD: (R)-2,3-dihydroxy-3-methylpentanoate dehydratase

ilvE: isoleucine transaminase

cimA: (R)-citramalate synthase

leuC: citramalate isomerase large subunit

leuD: citramalate isomerase small subunit

leuB: 3-methylmalate dehydrogenase

prpE: propionyl-CoA synthetase

ofoa: 2-oxobutanoate:ferredoxin oxidoreductase, alpha subunit

ofob: 2-oxobutanoate:ferredoxin oxidoreductase, beta subunit

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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