GapMind for catabolism of small carbon sources

 

Protein GFF1302 in Phaeobacter inhibens BS107

Annotation: PGA1_c13180 ABC transporter, ATP binding protein

Length: 334 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-sorbitol (glucitol) catabolism mtlK hi ABC transporter for D-Sorbitol, ATPase component (characterized) 100% 100% 663.3 N-Acetyl-D-glucosamine ABC transport system, ATPase component 58% 385.2
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 74% 99% 482.3 ABC transporter for D-Sorbitol, ATPase component 100% 663.3
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 58% 95% 385.2 ABC transporter for D-Sorbitol, ATPase component 100% 663.3
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 58% 95% 385.2 ABC transporter for D-Sorbitol, ATPase component 100% 663.3
D-maltose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 57% 96% 374.8 ABC transporter for D-Sorbitol, ATPase component 100% 663.3
sucrose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 57% 96% 374.8 ABC transporter for D-Sorbitol, ATPase component 100% 663.3
trehalose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 57% 96% 374.8 ABC transporter for D-Sorbitol, ATPase component 100% 663.3
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 55% 100% 348.2 ABC transporter for D-Sorbitol, ATPase component 100% 663.3
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 52% 99% 347.1 ABC transporter for D-Sorbitol, ATPase component 100% 663.3
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 52% 99% 347.1 ABC transporter for D-Sorbitol, ATPase component 100% 663.3
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 52% 99% 347.1 ABC transporter for D-Sorbitol, ATPase component 100% 663.3
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 53% 100% 346.7 ABC transporter for D-Sorbitol, ATPase component 100% 663.3
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 45% 94% 251.9 ABC transporter for D-Sorbitol, ATPase component 100% 663.3
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 35% 98% 200.7 ABC transporter for D-Sorbitol, ATPase component 100% 663.3
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 38% 81% 153.7 ABC transporter for D-Sorbitol, ATPase component 100% 663.3

Sequence Analysis Tools

View GFF1302 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

MGQIKLESVTKNFGPVEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGTI
RIDGEDATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAAA
LNLTDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELH
KRLATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSPKMN
LLTGPQAAQHNAATIGIRPEHLSISETEGMWAGTIGVSEHLGSDTFFHVQCDAFDDPLTV
RASGELDLGYGERVFLTPDMTHLHRFGSDGLRIE

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

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 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