GapMind for catabolism of small carbon sources

 

Protein GFF3855 in Phaeobacter inhibens BS107

Annotation: PGA1_78p00190 sn-glycerol-3-phosphate import ATP-binding protein UgbC

Length: 361 amino acids

Source: Phaeo in FitnessBrowser

Candidate for 9 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism SMc04256 hi ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 63% 100% 439.1 ABC transporter for D-Glucosamine, ATPase component 51% 325.1
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 51% 99% 325.1 ABC transporter for D-Cellobiose and D-Salicin, ATPase component 63% 439.1
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 49% 99% 312.4 ABC transporter for D-Cellobiose and D-Salicin, ATPase component 63% 439.1
D-maltose catabolism malK med Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 48% 96% 311.2 ABC transporter for D-Cellobiose and D-Salicin, ATPase component 63% 439.1
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 47% 94% 309.7 ABC transporter for D-Cellobiose and D-Salicin, ATPase component 63% 439.1
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 46% 94% 307.4 ABC transporter for D-Cellobiose and D-Salicin, ATPase component 63% 439.1
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 47% 98% 302.4 ABC transporter for D-Cellobiose and D-Salicin, ATPase component 63% 439.1
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 47% 89% 300.8 ABC transporter for D-Cellobiose and D-Salicin, ATPase component 63% 439.1
glycerol catabolism glpT lo ABC transporter for Glycerol, ATPase component 2 (characterized) 39% 88% 216.5 ABC transporter for D-Cellobiose and D-Salicin, ATPase component 63% 439.1

Sequence Analysis Tools

View GFF3855 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

MTLMTHSVEIRDLDLHFGELQVLHQLNLDIEQGEFLVLLGSSGCGKSTLLNCIAGLLDIS
DGQIFIQGQNVTWAEPSERGIGMVFQSYALYPQMTVEGNLSFGLKNARLPKAEIAKRVAR
AAEVLQIEPLLKRKPAALSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRADLRVEL
KRLHQQLANTMIYVTHDQVEAMTLADRIAIMKGGRIMQLSSPDEIYNRPQNLYVAGFIGS
PAMNLIEGVLIDGVFHAGSLALPMQRYDYRNGPHHGAAVIGIRPEHILTGEQITRADATA
EVLVDLVEGLGSDTLVYATHGAQNLRLRMDGASRVSAGDRLRIGFDTGRASLFDPNTEAR
L

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