Definition of D-ribose catabolism

GapMind for catabolism of small carbon sources

Definition of D-ribose catabolism

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

# ABC transporters:

# E. coli rbsABC and the related system from T. maritima.
# The fitness data also identified a related system in Herbaspirillum:
#   rbsBAC = HSERO_RS11480 (D8IUD0), HSERO_RS11485 (D8IUD1), HSERO_RS11490 (D8IUD2);
# and in various Pseudomonas:
#   rbsBAC = PS417_18405 (A0A1N7UEH6) PS417_18400 (A0A1N7TZ92) PS417_18395 (A0A1N7UNQ5)
#     or Pf1N1B4_6035 (A0A161ZH48), Pf1N1B4_6034 (A0A166R419), Pf1N1B4_6033  (A0A166R405).
rbsA	D-ribose ABC transporter, ATPase component RbsA	curated:CharProtDB::CH_003578	curated:TCDB::Q9X051	uniprot:D8IUD1	uniprot:A0A1N7TZ92	uniprot:A0A166R419
rbsB	D-ribose ABC transporter, substrate-binding component RbsB	curated:CharProtDB::CH_003593	curated:TCDB::Q9X053	uniprot:D8IUD0	uniprot:A0A1N7UEH6	uniprot:A0A161ZH48
rbsC	D-ribose ABC transporter, permease component RbsC	curated:SwissProt::P0AGI1	curated:TCDB::Q9X050	uniprot:D8IUD2	uniprot:A0A1N7UNQ5	uniprot:A0A166R405

# 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
ribose-transport: rbsA rbsB rbsC

# FrcABC from S. meliloti
frcA	D-ribose ABC transporter, ATPase component FrcA	curated:SwissProt::Q9F9B0
frcB	D-ribose ABC transporter, substrate-binding component FrcB	curated:SwissProt::Q9F9B2
frcC	D-ribose ABC transporter, permease component FrcC	curated:SwissProt::Q9F9B1
ribose-transport: frcA frcB frcC

# The fru2 PTS system in Streptococcus agalactiae is thought to transport ribose (TC 4.A.2.1.22); it is not
# proven that this is coupled to phosphorylation to form ribose 5-phosphate, but it seems likely
fru2-IIA	D-ribose PTS, IIA component	curated:TCDB::Q3JZE3
fru2-IIB	D-ribose PTS, IIB component	curated:TCDB::Q3JZE2
fru2-IIC	D-ribose PTS, IIC component	curated:TCDB::Q3JZE4

# This PTS system probably forms ribose 5-phosphate
ribose-PTS: fru2-IIA fru2-IIB fru2-IIC

# Homomeric transporters

rbsU	probable D-ribose transporter RbsU	curated:TCDB::Q9X4M3
ribose-transport: rbsU

BT2809	D-ribose transporter	curated:reanno::Btheta:352336
ribose-transport: BT2809

LmGT2	D-ribose transporter LmGT2	curated:TCDB::O61059
ribose-transport: LmGT2

PLT5	D-ribose transporter PLT5	curated:CharProtDB::CH_091483
ribose-transport: PLT5

# deoxyribose kinases are sometimes annotated with the same EC number; most of these
# sequences are thought to be ribokinases as well
rbsK	ribokinase	EC:2.7.1.15

# 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.
all: ribose-transport rbsK
all: ribose-PTS

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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 (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