GapMind for catabolism of small carbon sources


Protein H281DRAFT_04160 in Paraburkholderia bryophila 376MFSha3.1

Annotation: FitnessBrowser__Burk376:H281DRAFT_04160

Length: 260 amino acids

Source: Burk376 in FitnessBrowser

Candidate for 4 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-sorbitol (glucitol) catabolism sdh hi sorbitol dehydrogenase, D-fructose forming (EC (characterized) 94% 100% 486.9 diacetyl reductase ((S)-acetoin forming); EC 37% 171.8
L-rhamnose catabolism LRA1 lo NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC; EC (characterized) 39% 98% 171 sorbitol dehydrogenase, D-fructose forming (EC 94% 486.9
glycerol catabolism dhaD lo NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC (characterized) 38% 94% 165.2 sorbitol dehydrogenase, D-fructose forming (EC 94% 486.9
D-sorbitol (glucitol) catabolism srlD lo Sorbitol-6-phosphate 2-dehydrogenase; EC; Glucitol-6-phosphate dehydrogenase; Ketosephosphate reductase (uncharacterized) 34% 97% 141.4 sorbitol dehydrogenase, D-fructose forming (EC 94% 486.9

Sequence Analysis Tools

View H281DRAFT_04160 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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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 (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