GapMind for catabolism of small carbon sources

 

Protein AO356_09905 in Pseudomonas fluorescens FW300-N2C3

Annotation: FitnessBrowser__pseudo5_N2C3_1:AO356_09905

Length: 231 amino acids

Source: pseudo5_N2C3_1 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 hisQ hi ABC transporter for L-Lysine, permease component 1 (characterized) 100% 100% 454.1 ABC transporter for L-Arginine, permease component 1 45% 206.5
L-arginine catabolism artQ hi Probable permease of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 67% 99% 324.7
L-histidine catabolism hisQ hi Probable permease of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 67% 99% 324.7 ABC transporter for L-Arginine, permease component 1 45% 206.5
L-histidine catabolism BPHYT_RS24005 lo Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale) 39% 98% 171 ABC transporter for L-Lysine, permease component 1 100% 454.1
D-glucosamine (chitosamine) catabolism AO353_21715 lo ABC transporter for D-glucosamine, permease component 1 (characterized) 38% 93% 131.7 ABC transporter for L-Lysine, permease component 1 100% 454.1

Sequence Analysis Tools

View AO356_09905 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

MMIDLHGFGPALAAGALMTVKLALSALCLGLVLGLLGALAKTSPYKPLQWLGGTYSTLVR
GIPELLWVLLIYFGTVNLMRALGEYLGMPDLALNAFAAGVIALGLCFGAYATEVFRGAIL
AIPKGHREAGVALGLSKWRIFTRLIMPQMWRIALPGLGNLFMILMKDTALVSVIGLEEIM
RHAQIGVTVSKQPFTFYMVAALMYLGLTVLAMLGMHLLERRAARGFARSTQ

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