GapMind for catabolism of small carbon sources

 

D-ribose catabolism in Dinoroseobacter shibae DFL-12

Best path

frcA, frcB, frcC, rbsK

Also see fitness data for the top candidates

Rules

Overview: Ribose degradation in GapMind is based on the MetaCyc pathway ribose phosphorylation (link), which yields the central metabolic intermediate D-ribofuranose 5-phosphate, or on uptake by a phosphotransferase system.

14 steps (7 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
frcA D-ribose ABC transporter, ATPase component FrcA Dshi_0388 Dshi_1276
frcB D-ribose ABC transporter, substrate-binding component FrcB Dshi_0390
frcC D-ribose ABC transporter, permease component FrcC Dshi_0389 Dshi_2431
rbsK ribokinase Dshi_1976 Dshi_1621
Alternative steps:
BT2809 D-ribose transporter
fru2-IIA D-ribose PTS, IIA component
fru2-IIB D-ribose PTS, IIB component
fru2-IIC D-ribose PTS, IIC component
LmGT2 D-ribose transporter LmGT2
PLT5 D-ribose transporter PLT5
rbsA D-ribose ABC transporter, ATPase component RbsA Dshi_2433 Dshi_0519
rbsB D-ribose ABC transporter, substrate-binding component RbsB Dshi_2029
rbsC D-ribose ABC transporter, permease component RbsC Dshi_0389 Dshi_2432
rbsU probable D-ribose transporter RbsU

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

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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