GapMind for catabolism of small carbon sources

 

Finding step MFS-glucose for D-glucose catabolism in Pedobacter sp. GW460-11-11-14-LB5

5 candidates for MFS-glucose: glucose transporter, MFS superfamily

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other-bits
med CA265_RS04675 L-fucose:H+ symporter permease Glucose/galactose porter (characterized) 41% 100% 317.4 L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease 43% 332.8
med CA265_RS08575 L-fucose:H+ symporter permease Glucose/galactose transporter (characterized, see rationale) 40% 98% 283.1 L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease 41% 311.2
lo CA265_RS23325 MFS transporter Glucose/fructose:H+ symporter, GlcP (characterized) 38% 99% 285.4 D-xylose-proton symporter 38% 320.5
lo CA265_RS01275 hypothetical protein Glucose/fructose:H+ symporter, GlcP (characterized) 36% 97% 272.7 Arabinose-proton symporter; Arabinose transporter 40% 330.5
lo CA265_RS08675 glucose/galactose MFS transporter Glucose/galactose porter (characterized) 33% 97% 236.1 N-acetylglucosamine transporter nagP 42% 343.6

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

Also see fitness data for the candidates

Definition of step MFS-glucose

Or cluster all characterized MFS-glucose proteins

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