GapMind for catabolism of small carbon sources


Finding step mtlK for D-sorbitol (glucitol) catabolism in Synechococcus elongatus PCC 7942

4 candidates for mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med Synpcc7942_0960 ATPase ABC transporter for D-Sorbitol, ATPase component (characterized) 46% 98% 296.2 Trehalose/maltose import ATP-binding protein MalK; EC 50% 337.8
med Synpcc7942_0947 ATPase ABC transporter for D-sorbitol, ATPase component (characterized) 42% 96% 280 MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] 44% 290.0
med Synpcc7942_1680 Sulphate transport system permease protein 1 ABC transporter for D-sorbitol, ATPase component (characterized) 41% 89% 228.4 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 53% 336.7
lo Synpcc7942_1406 ATPase ABC transporter for D-Sorbitol, ATPase component (characterized) 36% 95% 195.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4

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.

Also see fitness data for the candidates

Definition of step mtlK

Or cluster all characterized mtlK 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 (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