GapMind for catabolism of small carbon sources

 

Protein GFF3014 in Marinobacter adhaerens HP15

Annotation: HP15_2958 extracellular solute-binding protein family 1

Length: 416 amino acids

Source: Marino in FitnessBrowser

Candidate for 10 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism gtsA hi Sugar ABC transporter substrate-binding protein (characterized, see rationale) 54% 99% 453.8 ABC transporter for D-Cellobiose and D-Salicin, periplasmic substrate-binding protein 38% 261.9
D-glucose catabolism gtsA hi Sugar ABC transporter substrate-binding protein (characterized, see rationale) 54% 99% 453.8 ABC transporter for D-Cellobiose and D-Salicin, periplasmic substrate-binding protein 38% 261.9
lactose catabolism gtsA hi Sugar ABC transporter substrate-binding protein (characterized, see rationale) 54% 99% 453.8 ABC transporter for D-Cellobiose and D-Salicin, periplasmic substrate-binding protein 38% 261.9
D-maltose catabolism gtsA hi Sugar ABC transporter substrate-binding protein (characterized, see rationale) 54% 99% 453.8 ABC transporter for D-Cellobiose and D-Salicin, periplasmic substrate-binding protein 38% 261.9
sucrose catabolism gtsA hi Sugar ABC transporter substrate-binding protein (characterized, see rationale) 54% 99% 453.8 ABC transporter for D-Cellobiose and D-Salicin, periplasmic substrate-binding protein 38% 261.9
trehalose catabolism gtsA hi Sugar ABC transporter substrate-binding protein (characterized, see rationale) 54% 99% 453.8 ABC transporter for D-Cellobiose and D-Salicin, periplasmic substrate-binding protein 38% 261.9
D-galactose catabolism PfGW456L13_1894 hi ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component (characterized) 53% 98% 438.3 ABC transporter for D-Cellobiose and D-Salicin, periplasmic substrate-binding protein 38% 261.9
D-xylose catabolism gtsA med ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized) 52% 98% 432.2 ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component 53% 438.3
D-cellobiose catabolism SMc04259 lo ABC transporter for D-Cellobiose and D-Salicin, periplasmic substrate-binding protein (characterized) 38% 99% 261.9 ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component 53% 438.3
D-mannose catabolism TT_C0328 lo Glucose-binding protein aka TT_C0328, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 32% 97% 189.5 ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component 53% 438.3

Sequence Analysis Tools

View GFF3014 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MTMTTFKKTLTAAAVSAALLPAQALQAGEVEVLHWWTAGGEARAAVALKEMMEDQGHTWK
DFAVAGGGGEAAMTVLKTRAVSGNPPAAAQIKGLDIREWAKLGFLTSLDDVAEANNWGQL
IPPVIADVMQYEDSYVAVPVNVHRVNWLWANPETLNKVGVGVPKTLDEFYQAAEKLKAAG
ITPLAHGGQPWQDATVFEAVALAVMGPDDFASAFVEHDMDVINSAQMEEVFAEFAKVMSY
VDDNAAGRDWNTATGMVIRGEAAMQIMGDWAKGEFTAAGLTPGEDYVCAAAPGTGGQFTF
NVDSFAMFSLSDEDNTKAQKDLARTIMEPEFQAVFNKAKGSIPVRTDFDTCAQASMDTFK
SSAEDGGLVPSFAHGLATTSYVQGQIFDVVTNFVNSDNKDPARATDQLAAAIQAAL

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, the preprint on GapMind for carbon sources, 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