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

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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