GapMind for Amino acid biosynthesis


L-isoleucine biosynthesis in Azospirillum brasilense Sp245

Best path

cimA, leuC, leuD, leuB, ilvI, ilvH, ilvC, ilvD, ilvE

Also see fitness data for the top candidates


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 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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
cimA (R)-citramalate synthase AZOBR_RS04265 AZOBR_RS05495
leuC citramalate isomerase large subunit AZOBR_RS03545 AZOBR_RS27815
leuD citramalate isomerase small subunit AZOBR_RS14135 AZOBR_RS27810
leuB 3-methylmalate dehydrogenase AZOBR_RS14130 AZOBR_RS11025
ilvI acetohydroxybutanoate synthase regulatory subunit AZOBR_RS06565
ilvH acetohydroxybutanoate synthase catalytic subunit AZOBR_RS06560 AZOBR_RS23050
ilvC 2-hydroxy-3-ketol-acid reductoisomerase AZOBR_RS06570
ilvD (R)-2,3-dihydroxy-3-methylpentanoate dehydratase AZOBR_RS15015 AZOBR_RS31260
ilvE isoleucine transaminase AZOBR_RS06555 AZOBR_RS16425
Alternative steps:
ilvA threonine deaminase AZOBR_RS06795
ofoa 2-oxobutanoate:ferredoxin oxidoreductase, alpha subunit AZOBR_RS02385
ofob 2-oxobutanoate:ferredoxin oxidoreductase, beta subunit AZOBR_RS02380
prpE propionyl-CoA synthetase AZOBR_RS06340 AZOBR_RS00270

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.



Related tools

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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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 paper from 2022 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