GapMind for catabolism of small carbon sources

 

Finding step gtsB for D-cellobiose catabolism in Paraburkholderia atlantica CCGE1002

5 candidates for gtsB: glucose ABC transporter, permease component 1 (GtsB)

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi BC1002_RS03670 sugar ABC transporter permease GtsB (GLcF), component of Glucose porter, GtsABCD (characterized) 59% 99% 376.3 ABC transporter for D-Cellobiose and D-Salicin, permease component 2 44% 238.0
med BC1002_RS17610 sugar ABC transporter permease ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized) 45% 92% 271.9 ABC transporter for D-Cellobiose and D-Salicin, permease component 2 45% 283.5
lo BC1002_RS21740 sugar ABC transporter permease ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized) 30% 96% 146 Putative sugar-transporter integral membrane protein, component of α-glucoside uptake permease, Agl3E/Agl3F/Agl3G. Plays a role in normal morphogenesis and antibiotic production. Strongly induced by trehalose and melibiose, and weakly induced by lactose and glycerol but not glucose (Hillerich and Westpheling 2006).The operon is controlled by a GntR homologue, Agl3R, and downstream of the gntR 34% 151.4
lo BC1002_RS31125 sugar ABC transporter permease ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized) 30% 94% 139.4 NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) 37% 199.9
lo BC1002_RS13855 sn-glycerol-3-phosphate ABC transporter permease UgpA ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized) 30% 92% 119.4 ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) 68% 406.0

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.

Definition of step gtsB

Or cluster all characterized gtsB proteins

This GapMind analysis is from Apr 09 2024. 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:

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