GapMind for catabolism of small carbon sources

 

Protein 5208608 in Shewanella loihica PV-4

Annotation: FitnessBrowser__PV4:5208608

Length: 418 amino acids

Source: PV4 in FitnessBrowser

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
N-acetyl-D-glucosamine catabolism nagP hi N-acetylglucosamine transporter nagP (characterized) 89% 97% 728.8 Glucose/galactose porter 32% 198.0
D-glucosamine (chitosamine) catabolism nagP hi N-acetylglucosamine transporter nagP (characterized) 89% 97% 728.8 Glucose/galactose porter 32% 198.0
D-fructose catabolism fruP lo MFS transporter, FHS family, L-fucose permease (characterized, see rationale) 33% 92% 204.9 N-acetylglucosamine transporter nagP 89% 728.8
sucrose catabolism fruP lo MFS transporter, FHS family, L-fucose permease (characterized, see rationale) 33% 92% 204.9 N-acetylglucosamine transporter nagP 89% 728.8
D-cellobiose catabolism MFS-glucose lo Glucose/galactose porter (characterized) 32% 92% 198 N-acetylglucosamine transporter nagP 89% 728.8
D-galactose catabolism HP1174 lo Glucose/galactose porter (characterized) 32% 92% 198 N-acetylglucosamine transporter nagP 89% 728.8
D-glucose catabolism MFS-glucose lo Glucose/galactose porter (characterized) 32% 92% 198 N-acetylglucosamine transporter nagP 89% 728.8
lactose catabolism MFS-glucose lo Glucose/galactose porter (characterized) 32% 92% 198 N-acetylglucosamine transporter nagP 89% 728.8
D-maltose catabolism MFS-glucose lo Glucose/galactose porter (characterized) 32% 92% 198 N-acetylglucosamine transporter nagP 89% 728.8
sucrose catabolism MFS-glucose lo Glucose/galactose porter (characterized) 32% 92% 198 N-acetylglucosamine transporter nagP 89% 728.8
trehalose catabolism MFS-glucose lo Glucose/galactose porter (characterized) 32% 92% 198 N-acetylglucosamine transporter nagP 89% 728.8
D-mannose catabolism gluP lo D-mannitol and D-mannose transporter (MFS superfamily) (characterized) 33% 90% 178.3 N-acetylglucosamine transporter nagP 89% 728.8

Sequence Analysis Tools

View 5208608 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

MAIVAGLFFILGFATWLNGSLMPYLKQILQLTPLQASLILFSFYIAVTFTALPSAWVIRK
VGYKTGMAMGMGIMMIAGLLFIPAAKTQVFALFLFAQLVMGTGQTLLQTAVNPYVVRIGP
EESAAARVSVMGILNKGAGVIAPLVFTALILDSFKDRVGVELTQAQIDEMANGLVFPYLG
MAIFIGVLALLVKKSPLPELENEDEQEEGTKGHTREALSHPNLALGVVALFFYVAVEVIA
GDTIGTFALSLGVENYGVMTSYTMICMVIGYSLGILTIPRFISQPKALMISAILGLMLTL
GILFGDNESYAIANALLVPFGGAMLPDTLLMIAFLGLANAIVWPAVWPLALSGMGKLTST
GSALLVMGIAGGAFGPLFWGLTSSATSLGQQGGYMVMLPCYLFILFYAVKGYKMRSWK

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