GapMind for catabolism of small carbon sources

 

Protein GFF5095 in Pseudomonas simiae WCS417

Annotation: FitnessBrowser__WCS417:GFF5095

Length: 239 amino acids

Source: WCS417 in FitnessBrowser

Candidate for 2 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-lysine catabolism hisQ hi Amino acid ABC transporter, membrane protein (characterized, see rationale) 79% 100% 366.3 ABC transporter for L-Arginine and L-Citrulline, permease component 2 35% 152.1
L-histidine catabolism aapM lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized) 36% 62% 119.8 ABC transporter for L-Lysine, permease component 1 43% 165.2

Sequence Analysis Tools

View GFF5095 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

Fitness BLAST: loading...

Sequence

MLEQLSLLSFANGGWGSALLAGALVTITLALACIPLGLPLGLLVALAARSKRRWLRTGAT
VFSTVFRGLPELLTLLIIYYGCQIAAQRMLAAMGYQGEVTINTFVAAMIAFSLVFAAFSS
EVWLSAFKSLSKGQFEAATMLGLPKGTTLRKVVLPQLTRIALPGLSNNWLSLLKDTSLVS
TISLVDLMRQTSLAVSVTKEPMLFYAVACFGYLFFSALSGRVFNFLERYFSRHQLSAKP

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

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