Definition of 2'-deoxyinosine catabolism

GapMind for catabolism of small carbon sources

Definition of 2'-deoxyinosine catabolism

# In the known pathway for deoxyinosine utilization, a phosphorylase forms deoxyribose 1-phosphate,
# phosphopentomutase forms deoxyribose 5-phosphate, and an aldolase produces
# 3-phosphoglycerate (an intermediate in glycolysis) and acetaldehyde (metacyc:PWY-7179-1).
# MetaCyc also describes a purine deoxyribonucleosidase (EC 3.2.2.M2),
# yielding deoxyribose, but this enzyme has not been linked to
# sequence, so it is not included in GapMind.  This reaction might also
# occur non-specifically via ribonucleosidases. The fitness data for
# Paraburkholderia bryophila 376MFSha3.1 does suggest cytoplasmic
# hydrolysis of purine deoxynucleosides, but did not identify the
# deoxyribonucleosidase.

# These proteins are reported to transport inosine, and likely transport deoxyinosine as well.
# The specificity of E. coli nupX (P33021, also known as yeiJ) seems to be unknown.
nupC	deoxyinosine:H+ symporter NupC	curated:SwissProt::O25792	curated:SwissProt::P0AFF2	curated:SwissProt::P42312	curated:TCDB::Q9KPL5	ignore:SwissProt::P33021
deoxyinosine-transport: nupC

# These two proteins are reported to transport inosine and (deoxy)thymidine,
# and probably tranpsort deoxyinosine as well.
nupG	deoxyinosine permease NupG/XapB	curated:CharProtDB::CH_088596	curated:SwissProt::P45562
deoxyinosine-transport: nupG

# In  Paraburkholderia bryophila 376MFSha3.1,
# H281DRAFT_01115-01112 is a 4-component ABC transporter that is important for
# deoxyinosine utilization.
H281DRAFT_01115	deoxynucleoside transporter, permease component 1	curated:reanno::Burk376:H281DRAFT_01115
H281DRAFT_01114	deoxynucleoside transporter, substrate-binding component	curated:reanno::Burk376:H281DRAFT_01114
H281DRAFT_01113	deoxynucleoside transporter, ATPase component	curated:reanno::Burk376:H281DRAFT_01113
H281DRAFT_01112	deoxynucleoside transporter, permease component 2	curated:reanno::Burk376:H281DRAFT_01112
deoxyinosine-transport: H281DRAFT_01115 H281DRAFT_01114 H281DRAFT_01113 H281DRAFT_01112

# In Lactococcus lactis, a 4-component ABC transporter is active on deoxyinosine
# A related system, RnsBCDA from Streptococcus mutans, also probably transports deoxyinosine
nupA	deoxyinosine ABC transporter, ATPase component	curated:TCDB::A2RKA7	curated:TCDB::Q8DU37
nupB	deoxyinosine ABC transporter, permease component 1	curated:TCDB::A2RKA6	curated:TCDB::Q8DU38
nupC'	deoxyinosine ABC transporter, permease component 2	curated:TCDB::A2RKA5	curated:TCDB::Q8DU39
bmpA	deoxyinosine ABC transporter, substrate-binding component	curated:TCDB::D2BKA1	curated:TCDB::Q8DU36
deoxyinosine-transport: nupA nupB nupC' bmpA

# The phosphorylase produces 2-deoxy-alpha-D-ribose 1-phosphate
# (2.4.2.1 includes activity on purine nucleosides and deoxynucleosides)
# Ignore hits to guanosine phosphorylase (EC 2.4.2.15), which is a quite similar reaction
deoD	deoxyinosine phosphorylase	EC:2.4.2.1	ignore_other:2.4.2.15

# deoB converts 1-phosphate to 5-phosphate
deoB	phosphopentomutase	EC:5.4.2.7

import ethanol.steps:acetaldehyde-degradation

# deoC is deoxribose-phosphate aldolase
import deoxyribose.steps:deoC

all: deoxyinosine-transport deoD deoB deoC acetaldehyde-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 2024 update 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