GapMind for catabolism of small carbon sources


Protein GFF1261 in Pseudomonas simiae WCS417

Annotation: FitnessBrowser__WCS417:GFF1261

Length: 236 amino acids

Source: WCS417 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
L-lysine catabolism hisM hi ABC transporter for L-Lysine, permease component 2 (characterized) 91% 100% 438.3 ABC transporter for L-Arginine, permease component 1 67% 330.1
L-arginine catabolism artM hi ABC transporter for L-Arginine, permease component 1 (characterized) 67% 98% 330.1
L-citrulline catabolism PS417_17600 med ABC transporter permease; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine ABC transporter permease HisM; SubName: Full=Histidine transport system permease protein; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM (characterized, see rationale) 67% 100% 337.4 ABC transporter for L-Lysine, permease component 2 91% 438.3
L-histidine catabolism hisM med Histidine transport system permease protein HisM (characterized) 60% 97% 304.3 ABC transporter for L-Lysine, permease component 2 91% 438.3
L-citrulline catabolism AO353_03045 med ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized) 45% 93% 196.8 ABC transporter for L-Lysine, permease component 2 91% 438.3

Sequence Analysis Tools

View GFF1261 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