GapMind for catabolism of small carbon sources


Finding step pimD for phenylacetate catabolism in Burkholderia phytofirmans PsJN

4 candidates for pimD: pimeloyl-CoA dehydrogenase, large subunit

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi BPHYT_RS06715 acyl-CoA dehydrogenase pimeloyl-CoA dehydrogenase large subunit (EC (characterized) 56% 100% 464.2 5-hydroxy-3-[(3aS,4S,5R,7aS)-7a-methyl-1,5-dioxo-octahydro-1H-inden-4-yl]propanoyl-CoA dehydrogenase 37% 233.0
hi BPHYT_RS13550 acyl-CoA dehydrogenase pimeloyl-CoA dehydrogenase large subunit (EC (characterized) 52% 100% 424.9 Putative acyl-CoA dehydrogenase FadE17; EC 1.3.99.- 38% 240.4
hi BPHYT_RS25380 acyl-CoA dehydrogenase pimeloyl-CoA dehydrogenase large subunit (EC (characterized) 44% 97% 330.1 Putative acyl-CoA dehydrogenase FadE17; EC 1.3.99.- 36% 213.4
lo BPHYT_RS32685 acyl-CoA dehydrogenase pimeloyl-CoA dehydrogenase large subunit (EC (characterized) 31% 92% 161 butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC; short-chain acyl-CoA dehydrogenase (EC 36% 221.5

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

Also see fitness data for the candidates

Definition of step pimD

Or cluster all characterized pimD proteins

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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.

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