GapMind for catabolism of small carbon sources

 

Definition of 2'-deoxyinosine catabolism

As text, or see rules and steps

# 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

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 (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:

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. 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:

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:

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