D-ribose catabolism in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

D-ribose catabolism in Pseudomonas fluorescens FW300-N2E2

Best path

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.

all:

ribose-transport and rbsK
or ribose-PTS
Comment: Besides the kinase rbsK, the MetaCyc pathway includes D-ribose pyranase (rbsD). RbsD appears to be absent or not important for fitness in many bacteria that grow with ribose as the sole carbon source, so rbsD is not included in GapMind. Alternatively, uptake by a phosphotransferase (PTS) system can form D-ribofuranose 5-phosphate.

ribose-PTS: fru2-IIA, fru2-IIB and fru2-IIC

Comment: This PTS system probably forms ribose 5-phosphate

ribose-transport:

rbsA, rbsB and rbsC
or frcA, frcB and frcC
or rbsU
or BT2809
or LmGT2
or PLT5
Comment: Transporters and PTS systems were identified using: query: transporter:ribose:D-ribose:D-ribofuranose:CPD-10330:CPD0-1108:D-ribopyranose:CPD-15829:CPD0-1110:CPD-15818

14 steps (9 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
rbsA	D-ribose ABC transporter, ATPase component RbsA	Pf6N2E2_162	Pf6N2E2_523
rbsB	D-ribose ABC transporter, substrate-binding component RbsB	Pf6N2E2_161	Pf6N2E2_1793
rbsC	D-ribose ABC transporter, permease component RbsC	Pf6N2E2_163	Pf6N2E2_524
rbsK	ribokinase	Pf6N2E2_165
Alternative steps:
BT2809	D-ribose transporter
frcA	D-ribose ABC transporter, ATPase component FrcA	Pf6N2E2_993	Pf6N2E2_523
frcB	D-ribose ABC transporter, substrate-binding component FrcB
frcC	D-ribose ABC transporter, permease component FrcC	Pf6N2E2_524	Pf6N2E2_5970
fru2-IIA	D-ribose PTS, IIA component
fru2-IIB	D-ribose PTS, IIB component	Pf6N2E2_3337
fru2-IIC	D-ribose PTS, IIC component	Pf6N2E2_3337
LmGT2	D-ribose transporter LmGT2
PLT5	D-ribose transporter PLT5	Pf6N2E2_883
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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 (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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources