GapMind for Amino acid biosynthesis

 

L-leucine biosynthesis in Azospirillum brasilense Sp245

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 AZOBR_RS06560 AZOBR_RS23050
ilvI acetohydroxybutanoate synthase regulatory subunit AZOBR_RS06565
ilvC ketol-acid reductoisomerase AZOBR_RS06570
ilvD (R)-2,3-dihydroxy-3-methylbutanoate dehydratase AZOBR_RS15015 AZOBR_RS31260
leuA 2-isopropylmalate synthase AZOBR_RS12155 AZOBR_RS05495
leuC 3-isopropylmalate dehydratase, large subunit AZOBR_RS03545 AZOBR_RS27815
leuD 3-isopropylmalate dehydaratase, small subunit AZOBR_RS14135 AZOBR_RS27810
leuB 3-isopropylmalate dehydrogenase AZOBR_RS14130 AZOBR_RS11025
ilvE leucine transaminase AZOBR_RS06555 AZOBR_RS16425

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