GapMind for Amino acid biosynthesis

 

L-isoleucine biosynthesis in Dyella japonica UNC79MFTsu3.2

Best path

ilvA, ilvI?, ilvH, ilvC, ilvD, ilvE

Also see fitness data for the top candidates

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.

13 steps (11 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate Class of gap
ilvA threonine deaminase N515DRAFT_0565 N515DRAFT_0537  
ilvI? acetohydroxybutanoate synthase regulatory subunit N515DRAFT_0566 diverged
ilvH acetohydroxybutanoate synthase catalytic subunit N515DRAFT_0567 N515DRAFT_0378  
ilvC 2-hydroxy-3-ketol-acid reductoisomerase N515DRAFT_0568  
ilvD (R)-2,3-dihydroxy-3-methylpentanoate dehydratase N515DRAFT_0569 N515DRAFT_2409  
ilvE isoleucine transaminase N515DRAFT_2015 N515DRAFT_0573  
Alternative steps:
cimA (R)-citramalate synthase N515DRAFT_0574  
leuB 3-methylmalate dehydrogenase N515DRAFT_0570 N515DRAFT_1138  
leuC citramalate isomerase large subunit N515DRAFT_0572 N515DRAFT_0029  
leuD citramalate isomerase small subunit N515DRAFT_0571 N515DRAFT_1419  
ofoa 2-oxobutanoate:ferredoxin oxidoreductase, alpha subunit  
ofob 2-oxobutanoate:ferredoxin oxidoreductase, beta subunit  
prpE propionyl-CoA synthetase N515DRAFT_0016 N515DRAFT_3075  

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