GapMind for catabolism of small carbon sources

 

Protein GFF725 in Phaeobacter inhibens BS107

Annotation: PGA1_c07400 binding protein dependent transport system permease

Length: 282 amino acids

Source: Phaeo in FitnessBrowser

Candidate for 15 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism gtsC med GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 35% 98% 176.8 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 33% 164.5
D-glucose catabolism gtsC med GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 35% 98% 176.8 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 33% 164.5
lactose catabolism gtsC med GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 35% 98% 176.8 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 33% 164.5
D-maltose catabolism gtsC med GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 35% 98% 176.8 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 33% 164.5
sucrose catabolism gtsC med GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 35% 98% 176.8 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 33% 164.5
trehalose catabolism gtsC med GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 35% 98% 176.8 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 33% 164.5
D-xylose catabolism gtsC med ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized) 35% 98% 171 ABC transporter for D-Galactose and D-Glucose, permease component 2 35% 168.3
D-galactose catabolism PfGW456L13_1896 med ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) 35% 94% 168.3 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 33% 164.5
D-cellobiose catabolism SMc04257 lo ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized) 33% 93% 164.5 GtsC (GLcG), component of Glucose porter, GtsABCD 35% 176.8
D-mannose catabolism TT_C0326 lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 34% 94% 159.5 GtsC (GLcG), component of Glucose porter, GtsABCD 35% 176.8
N-acetyl-D-glucosamine catabolism ngcG lo NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 32% 92% 156.4 GtsC (GLcG), component of Glucose porter, GtsABCD 35% 176.8
D-glucosamine (chitosamine) catabolism ngcG lo NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 32% 92% 156.4 GtsC (GLcG), component of Glucose porter, GtsABCD 35% 176.8
N-acetyl-D-glucosamine catabolism SMc02871 lo N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized) 31% 95% 136 GtsC (GLcG), component of Glucose porter, GtsABCD 35% 176.8
D-glucosamine (chitosamine) catabolism SMc02871 lo N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized) 31% 95% 136 GtsC (GLcG), component of Glucose porter, GtsABCD 35% 176.8
D-cellobiose catabolism cebG lo CBP protein aka CebG, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 32% 97% 127.1 GtsC (GLcG), component of Glucose porter, GtsABCD 35% 176.8

Sequence Analysis Tools

View GFF725 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MFPKPIQNSSRAWQTTYQALVPAALVMWLLPLIAVAIFSIKPEADFTTGNYWGVPSSFEG
LSNYGRVFFGSDMPRYLLNSVLITVPTVIGAVALSCMTGFALGVYKFRGNLLLFFMFVAG
NFVPFQILMVPVRDLTLDMGLYNTKTGLVLFHIAFQTGFCTLFMRNFIRALPFELIEAAR
VEGVAEWRIFWFVVLPLMKPAIAALSVLIFTFIWNDYFWAVVLTQGAESQPVTAGITSFN
AQYRAAYHLMSAGSIVAALPPVAMFFLMQRHFIAGLTLGAVK

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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