GapMind for catabolism of small carbon sources


Protein Pf6N2E2_5660 in Pseudomonas fluorescens FW300-N2E2

Annotation: FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5660

Length: 257 amino acids

Source: pseudo6_N2E2 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 artJ hi L-Arginine ABC transporter, periplasmic substrate-binding component (characterized) 100% 100% 510
L-citrulline catabolism AO353_03055 hi ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized) 97% 100% 496.9 ABC transporter for L-Arginine, periplasmic substrate-binding component 47% 235.3
L-lysine catabolism argT med lysine/arginine/ornithine ABC transporter, periplasmic lysine/arginine/ornithine-binding protein ArgT (characterized) 44% 100% 232.6 L-Arginine ABC transporter, periplasmic substrate-binding component 100% 510.0
L-histidine catabolism hisJ med histidine ABC transporter, periplasmic histidine-binding protein HisJ (characterized) 43% 100% 214.9 L-Arginine ABC transporter, periplasmic substrate-binding component 100% 510.0
L-citrulline catabolism PS417_17590 med ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale) 43% 97% 202.2 L-Arginine ABC transporter, periplasmic substrate-binding component 100% 510.0
L-histidine catabolism BPHYT_RS24000 lo Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale) 31% 96% 127.5 L-Arginine ABC transporter, periplasmic substrate-binding component 100% 510.0

Sequence Analysis Tools

View Pf6N2E2_5660 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