GapMind for catabolism of small carbon sources


Protein PfGW456L13_2421 in Pseudomonas fluorescens GW456-L13

Annotation: FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2421

Length: 548 amino acids

Source: pseudo13_GW456_L13 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
phenylacetate catabolism ppa hi Phenylacetate permease, Ppa (characterized) 89% 100% 915.2 Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP 67% 740.3
acetate catabolism actP med Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized) 67% 100% 740.3 Phenylacetate permease, Ppa 89% 915.2
pyruvate catabolism actP med Acetate permease; SubName: Full=Actetate permease; SubName: Full=Cation acetate symporter; SubName: Full=Cation/acetate symporter (characterized, see rationale) 67% 100% 732.3 Phenylacetate permease, Ppa 89% 915.2
propionate catabolism mctC med Monocarboxylic acid transporter (characterized) 45% 98% 439.1 Phenylacetate permease, Ppa 89% 915.2
pyruvate catabolism mctC med Monocarboxylic acid transporter (characterized) 45% 98% 439.1 Phenylacetate permease, Ppa 89% 915.2
L-lactate catabolism Shew_2731 lo actP-like component of L-lactate and L-malate uptake system (characterized) 30% 54% 147.5 Phenylacetate permease, Ppa 89% 915.2

Sequence Analysis Tools

View PfGW456L13_2421 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