GapMind for catabolism of small carbon sources


Finding step rbsC for D-ribose catabolism in Dinoroseobacter shibae DFL-12

5 candidates for rbsC: D-ribose ABC transporter, permease component RbsC

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
lo Dshi_0389 Monosaccharide-transporting ATPase (RefSeq) Ribose import permease protein RbsC (characterized) 35% 97% 183 Fructose import permease protein FrcC 71% 493.8
lo Dshi_2432 Monosaccharide-transporting ATPase (RefSeq) Ribose import permease protein RbsC (characterized) 34% 96% 179.9 RhaP, 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!) 61% 400.6
lo Dshi_2431 Monosaccharide-transporting ATPase (RefSeq) ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) 31% 98% 168.7 Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR 35% 186.0
lo Dshi_0528 Monosaccharide-transporting ATPase (RefSeq) ABC transporter permease (characterized, see rationale) 30% 89% 144.4 deoxynucleoside transporter, permease component 1 44% 244.2
lo Dshi_0529 Monosaccharide-transporting ATPase (RefSeq) ABC transporter permease (characterized, see rationale) 31% 93% 134 deoxynucleoside transporter, permease component 2 45% 275.8

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 rbsC

Or cluster all characterized rbsC 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