GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_595 in Pseudomonas fluorescens FW300-N1B4

Annotation: Glucose ABC transport system, inner membrane component 1

Length: 314 amino acids

Source: pseudo1_N1B4 in FitnessBrowser

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism gtsB hi ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized) 97% 100% 595.5 ABC transporter for D-Cellobiose and D-Salicin, permease component 2 44% 255.4
D-galactose catabolism PfGW456L13_1895 hi ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized) 97% 100% 595.5 ABC transporter for D-Cellobiose and D-Salicin, permease component 2 44% 255.4
D-glucose catabolism gtsB hi ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized) 97% 100% 595.5 ABC transporter for D-Cellobiose and D-Salicin, permease component 2 44% 255.4
lactose catabolism gtsB hi ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized) 97% 100% 595.5 ABC transporter for D-Cellobiose and D-Salicin, permease component 2 44% 255.4
D-maltose catabolism gtsB hi ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized) 97% 100% 595.5 ABC transporter for D-Cellobiose and D-Salicin, permease component 2 44% 255.4
sucrose catabolism gtsB hi ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized) 97% 100% 595.5 ABC transporter for D-Cellobiose and D-Salicin, permease component 2 44% 255.4
trehalose catabolism gtsB hi ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized) 97% 100% 595.5 ABC transporter for D-Cellobiose and D-Salicin, permease component 2 44% 255.4
D-xylose catabolism gtsB med ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized) 88% 100% 553.9 ABC transporter for D-Galactose and D-Glucose, permease component 1 97% 595.5
D-cellobiose catabolism SMc04258 med ABC transporter for D-Cellobiose and D-Salicin, permease component 2 (characterized) 44% 97% 255.4 ABC transporter for D-Galactose and D-Glucose, permease component 1 97% 595.5
L-arabinose catabolism xacH lo Xylose/arabinose import permease protein XacH (characterized, see rationale) 34% 89% 157.5 ABC transporter for D-Galactose and D-Glucose, permease component 1 97% 595.5
D-mannose catabolism TT_C0327 lo Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 32% 58% 120.2 ABC transporter for D-Galactose and D-Glucose, permease component 1 97% 595.5

Sequence Analysis Tools

View Pf1N1B4_595 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

VPISFLFTWIIPMSSVAVFSKASPFDALQRWLPKLVLAPSMLIVLVGFYGYIIWTFVLSF
TNSSFMPSYKWVGLQQYIRLMDNDRWWVASKNLAVFGGMFIGISLVLGVFLAVLLDQRIR
KEGFIRTVYLYPMALSMIVTGTAWKWLLNPGLGLDKMLRDWGWEGFRLDWLVDQDRVVYC
LVIAAVWQASGFVMAMFLAGLRGVDQSIIRAAQVDGASLPTIYLKIVLPSLRPVFFSAFM
ILAHIAIKSFDLVAAMTAGGPGYSSDLPAMFMYSFTFSRGQMGIGSASAMMMLGAILAIL
VPYLYSELRGKRHE

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