GapMind for catabolism of small carbon sources


Finding step proV for L-proline catabolism in Synechococcus elongatus PCC 7942

3 candidates for proV: proline ABC transporter, ATPase component ProV

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
lo Synpcc7942_1680 Sulphate transport system permease protein 1 glycine betaine/l-proline transport atp-binding protein prov (characterized) 40% 66% 193.4 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 Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 40% 57% 161 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
lo Synpcc7942_1236 nitrate transport ATP-binding subunits C and D Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 36% 55% 154.8 Nitrate import ATP-binding protein NrtD; EC 100% 549.7

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 proV

Or cluster all characterized proV 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, 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