GapMind for catabolism of small carbon sources


Protein PP_4484 in Pseudomonas putida KT2440

Annotation: FitnessBrowser__Putida:PP_4484

Length: 232 amino acids

Source: Putida 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
L-arginine catabolism artM hi ABC transporter for L-Arginine, permease component 2 (characterized) 93% 100% 431
L-citrulline catabolism AO353_03045 hi ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized) 91% 100% 430.3 ABC transporter for L-Lysine, permease component 2 52% 219.9
L-lysine catabolism hisM med ABC transporter for L-Lysine, permease component 2 (characterized) 52% 97% 219.9 ABC transporter for L-Arginine, permease component 2 93% 431.0
L-histidine catabolism hisM med Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, 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) 46% 96% 201.8 ABC transporter for L-Arginine, permease component 2 93% 431.0
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) 44% 92% 184.5 ABC transporter for L-Arginine, permease component 2 93% 431.0
L-histidine catabolism BPHYT_RS24010 med Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale) 41% 91% 181.8 ABC transporter for L-Arginine, permease component 2 93% 431.0

Sequence Analysis Tools

View PP_4484 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.



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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