GapMind for catabolism of small carbon sources


Protein BPHYT_RS19500 in Burkholderia phytofirmans PsJN

Annotation: FitnessBrowser__BFirm:BPHYT_RS19500

Length: 512 amino acids

Source: BFirm in FitnessBrowser

Candidate for 6 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC (characterized) 73% 100% 758.8
myo-inositol catabolism mmsA hi malonate-semialdehyde dehydrogenase (acetylating) (EC (characterized) 73% 100% 758.8
propionate catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC (characterized) 73% 100% 758.8
L-threonine catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC (characterized) 73% 100% 758.8
L-valine catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC (characterized) 73% 100% 758.8
L-valine catabolism mmsA med malonate-semialdehyde dehydrogenase (EC; malonate-semialdehyde dehydrogenase (acetylating) (EC; methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC (characterized) 63% 99% 630.6 malonate-semialdehyde dehydrogenase (acetylating) (EC 73% 758.8
L-valine catabolism mmsA med mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC (TIGR01722) 100% 729 malonate-semialdehyde dehydrogenase (acetylating) (EC 73% 758.8

Sequence Analysis Tools

View BPHYT_RS19500 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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

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