GapMind for catabolism of small carbon sources

 

Protein AZOBR_RS25585 in Azospirillum brasilense Sp245

Annotation: AZOBR_RS25585 ABC transporter permease

Length: 301 amino acids

Source: azobra in FitnessBrowser

Candidate for 14 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism thuF hi ABC transporter for D-Trehalose, permease component 1 (characterized) 61% 93% 380.9 PalF, component of Platinose (isomaltulose) (6-O-α-D-glucopyranosyl-D-fructofuranose) porter 59% 368.6
sucrose catabolism thuF hi ABC transporter for D-Trehalose, permease component 1 (characterized) 61% 93% 380.9 PalF, component of Platinose (isomaltulose) (6-O-α-D-glucopyranosyl-D-fructofuranose) porter 59% 368.6
trehalose catabolism thuF hi ABC transporter for D-Trehalose, permease component 1 (characterized) 61% 93% 380.9 PalF, component of Platinose (isomaltulose) (6-O-α-D-glucopyranosyl-D-fructofuranose) porter 59% 368.6
D-glucosamine (chitosamine) catabolism SM_b21220 med ABC transporter for D-Glucosamine, permease component 2 (characterized) 43% 93% 216.5 ABC transporter for D-Trehalose, permease component 1 61% 380.9
lactose catabolism lacF lo LacF, component of Lactose porter (characterized) 32% 97% 149.1 ABC transporter for D-Trehalose, permease component 1 61% 380.9
xylitol catabolism Dshi_0548 lo ABC transporter for Xylitol, permease component 1 (characterized) 33% 96% 145.2 ABC transporter for D-Trehalose, permease component 1 61% 380.9
L-fucose catabolism SM_b21104 lo ABC transporter for L-Fucose, permease component 1 (characterized) 33% 92% 140.6 ABC transporter for D-Trehalose, permease component 1 61% 380.9
D-maltose catabolism malF_Aa lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 31% 93% 134.8 ABC transporter for D-Trehalose, permease component 1 61% 380.9
N-acetyl-D-glucosamine catabolism ngcF lo NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 30% 94% 133.3 ABC transporter for D-Trehalose, permease component 1 61% 380.9
D-glucosamine (chitosamine) catabolism ngcF lo NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 30% 94% 133.3 ABC transporter for D-Trehalose, permease component 1 61% 380.9
D-sorbitol (glucitol) catabolism mtlF lo ABC transporter for D-Sorbitol, permease component 2 (characterized) 31% 90% 132.1 ABC transporter for D-Trehalose, permease component 1 61% 380.9
trehalose catabolism treT lo TreT, component of Trehalose porter (characterized) 31% 100% 129 ABC transporter for D-Trehalose, permease component 1 61% 380.9
glycerol catabolism glpP lo ABC transporter for Glycerol, permease component 1 (characterized) 30% 94% 120.9 ABC transporter for D-Trehalose, permease component 1 61% 380.9
xylitol catabolism HSERO_RS17005 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 30% 98% 113.2 ABC transporter for D-Trehalose, permease component 1 61% 380.9

Sequence Analysis Tools

View AZOBR_RS25585 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

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

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

LVSDPRAPSLMRQRRRAAWLFLLPMLIVLAGVAGWPLFRTVFFSFTDATLATLEGFQGVG
LDNYLWLMRDPVWWRAVWNTLVFTVVSVGIETALGLGIALILNAHLPGRGLLRAAVLIPW
AIPTVVSAQMWGWMFHDLYGVVNAILMGLGLIAEPRAWTADPDLALPVVIAVDVWKSTPF
MALLILAALQMLPRDLYEAARVDGVHPVKVFVRITLPLIRPALMVAVLFRTLDALRVFDL
MYVLTGNSRSTMSMSVYARQYLIDFQDVGYGSAAATLLVLVLAVATVLAVTLGRVRVDAG
R

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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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 paper from 2022 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