GapMind for Amino acid biosynthesis

 

L-leucine biosynthesis in Dyella japonica UNC79MFTsu3.2

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 Class of gap
ilvH acetohydroxybutanoate synthase catalytic subunit N515DRAFT_0567 N515DRAFT_0378  
ilvI? acetohydroxybutanoate synthase regulatory subunit N515DRAFT_0566 diverged
ilvC ketol-acid reductoisomerase N515DRAFT_0568  
ilvD (R)-2,3-dihydroxy-3-methylbutanoate dehydratase N515DRAFT_0569 N515DRAFT_2409  
leuA 2-isopropylmalate synthase N515DRAFT_0574  
leuC 3-isopropylmalate dehydratase, large subunit N515DRAFT_0572 N515DRAFT_0029  
leuD 3-isopropylmalate dehydaratase, small subunit N515DRAFT_0571 N515DRAFT_1419  
leuB 3-isopropylmalate dehydrogenase N515DRAFT_0570 N515DRAFT_1138  
ilvE leucine transaminase N515DRAFT_2015 N515DRAFT_0573  

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