GapMind for catabolism of small carbon sources

 

Finding step rbsA for D-ribose catabolism in Sinorhizobium meliloti 1021

5 candidates for rbsA: D-ribose ABC transporter, ATPase component RbsA

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi SM_b20673 sugar uptake ABC transporter ATP-binding protein Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) 46% 98% 442.2 m-Inositol ABC transporter, ATPase component (itaA) 48% 432.2
med SM_b20713 sugar uptake ABC transporter ATP-binding protein Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) 45% 96% 444.1 Inositol transport system ATP-binding protein 64% 630.6
med SMc02325 ABC transporter ATP-binding protein ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized) 46% 98% 441.4 RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) 68% 641.7
med SM_b21376 sugar uptake ABC transporter ATP-binding protein ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized) 46% 98% 424.9 Inositol transport system ATP-binding protein 46% 425.6
med SM_b20503 sugar ABC transporter ATP-binding protein ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized) 42% 99% 393.7 Inositol transport system ATP-binding protein 45% 425.6

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 rbsA

Or cluster all characterized rbsA 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