GapMind for catabolism of small carbon sources


Protein GFF3716 in Pseudomonas stutzeri RCH2

Annotation: FitnessBrowser__psRCH2:GFF3716

Length: 511 amino acids

Source: psRCH2 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-maltose catabolism susB med alpha-glucosidase (EC (characterized) 46% 99% 443 oligo-α-1,6-glucosidase (EC 46% 442.2
trehalose catabolism treF med α,α-trehalase / α-glucosidase (TTC0107) (EC| (characterized) 45% 99% 438.3 alpha-glucosidase (EC 46% 443.0
sucrose catabolism ams med Alpha-glucosidase; EC (characterized, see rationale) 43% 94% 406.8 alpha-glucosidase (EC 46% 443.0
trehalose catabolism treC lo trehalose-6-phosphate hydrolase (TreC) (EC (characterized) 38% 99% 349.4 alpha-glucosidase (EC 46% 443.0

Sequence Analysis Tools

View GFF3716 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