Definition of 2-deoxy-D-ribose catabolism

GapMind for catabolism of small carbon sources

Definition of 2-deoxy-D-ribose catabolism

# Deoxyribose utilization in GapMind is based on MetaCyc pathways
# 2-deoxy-D-ribose degradation I via deoxyribose 5-phosphate aldolase (metacyc:PWY-8060) 
# and pathway II via oxidation to 2-deoxy-3-dehydro-D-ribonate (metacyc:PWY-8058).

# Salmonella deoP (Q8XEV7) is near deoK and can enhance growth of E. coli on deoxyribose, even
# though it is not essential for deoxyribose utilization in Salmonella, see PMC94358.
deoP	deoxyribose transporter	curated:TCDB::Q8XEV7
deoxyribose-transport: deoP

# The best-known pathway for deoxyribose utilization involves a
# kinase forming deoxyribose-5-phosphate, an aldolase, forming
# glyceraldehyde 3-phosphate (an intermediate in glycolysis)
# and acetaldehyde, and acetaldehyde dehydrogenase to acetyl-CoA.

# EC 2.7.1.15 (ribose kinase) includes enzymes known to act on deoxyribose.
deoK	deoxyribokinase	EC:2.7.1.229	EC:2.7.1.15

# Produces acetaldehyde and glyceraldehyde 3-phosphate
deoC	deoxyribose-5-phosphate aldolase	EC:4.1.2.4

import ethanol.steps:acetaldehyde-degradation

# Another pathway involves periplasmic oxidation to deoxyribonate,
# cytoplasmic oxidation to 2-deoxy-3-ketoribonate, and a cleavage
# enzyme that uses acetyl-CoA to yield glyceryl-CoA and acetoacetate.
# The glyceryl-CoA is apparently hydrolyzed to glycerate and then
# phosphorylated by a kinase, yielding 2-phospho-D-glycerate, an
# intermediate in glycolysis. The acetoacetate is activated to
# acetoacetyl-CoA and cleaved to two acetyl-CoA.

# This three-component periplasmic (probably) dehydrogenase seems to be non-specific, but
# it is the only known way to convert deoxyribose to deoxyribonate.
# (Oxidative damage of DNA and archaeal glycolysis may also be sources of deoxyribonate.)
# It probably forms 1,5-lactone, but since that is uncertain,
# the lactonase is not included in this pathway definition
drdehyd-alpha	2-deoxy-D-ribose dehydrogenase, alpha subunit	term:deoxy%ribose dehydrogenase%alpha	ignore_other:vanillin dehydrogenase
drdehyd-beta	2-deoxy-D-ribose dehydrogenase, beta subunit	term:deoxy%ribose dehydrogenase%beta	ignore_other:vanillin dehydrogenase
drdehyd-cytc	2-deoxyribose-D dehydrogenase, cytochrome c component	term:cytochrome%deoxyribose dehydrogenase	ignore_other:vanillin dehydrogenase
deoxyribose-dehyd: drdehyd-alpha drdehyd-beta drdehyd-cytc

import leucine.steps:acetoacetate-degradation # acetoacetate is an intermediate in deoxyribonate degradation
import deoxyribonate.steps:deoxyribonate-transport deoxyribonate-degradation

# The deoxyribose 5-phosphate pathway involves the kinase deoK and the aldolase deoC.
all: deoxyribose-transport deoK deoC acetaldehyde-degradation

# The oxidative pathway involves oxidation in the periplasm to deoxyribonate.
all: deoxyribose-dehyd deoxyribonate-transport deoxyribonate-degradation

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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