GapMind for catabolism of small carbon sources


Protein 3607560 in Dinoroseobacter shibae DFL-12

Annotation: FitnessBrowser__Dino:3607560

Length: 276 amino acids

Source: Dino in FitnessBrowser

Candidate for 5 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 mtlG hi ABC transporter for D-Sorbitol, permease component 1 (characterized) 88% 100% 489.6
D-mannitol catabolism mtlG med SmoG, component of Hexitol (glucitol; mannitol) porter (characterized) 72% 100% 406 ABC transporter for D-Sorbitol, permease component 1 88% 489.6
xylitol catabolism Dshi_0549 lo ABC transporter for Xylitol, permease component 2 (characterized) 36% 100% 186 ABC transporter for D-Sorbitol, permease component 1 88% 489.6
xylitol catabolism HSERO_RS17010 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 34% 96% 146.4 ABC transporter for D-Sorbitol, permease component 1 88% 489.6
D-glucosamine (chitosamine) catabolism SM_b21219 lo ABC transporter for D-Glucosamine, permease component 1 (characterized) 34% 93% 142.1 ABC transporter for D-Sorbitol, permease component 1 88% 489.6

Sequence Analysis Tools

View 3607560 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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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