2'-deoxyinosine catabolism in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

2'-deoxyinosine catabolism in Cereibacter sphaeroides ATCC 17029

Best path

H281DRAFT_01115, H281DRAFT_01114, H281DRAFT_01113, H281DRAFT_01112, deoD, deoB, deoC, adh, acs

Rules

Overview: 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 (link). 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.

all: deoxyinosine-transport, deoD, deoB, deoC and acetaldehyde-degradation
acetaldehyde-degradation:

ald-dh-CoA
or adh and acs
or adh, ackA and pta
Comment: Acetaldehyde can be oxidized to acetyl-CoA, or oxidized to acetate and activated to acetyl-CoA by either acetyl-CoA synthetase (acs) or by acetate kinase (ackA) and phosphate acetyltransferase (pta).

deoxyinosine-transport:

nupC
or nupG
or H281DRAFT_01115, H281DRAFT_01114, H281DRAFT_01113 and H281DRAFT_01112
or nupA, nupB, nupC' and bmpA

18 steps (15 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
H281DRAFT_01115	deoxynucleoside transporter, permease component 1	RSPH17029_RS17470
H281DRAFT_01114	deoxynucleoside transporter, substrate-binding component	RSPH17029_RS17455
H281DRAFT_01113	deoxynucleoside transporter, ATPase component	RSPH17029_RS17460	RSPH17029_RS05240
H281DRAFT_01112	deoxynucleoside transporter, permease component 2	RSPH17029_RS17465
deoD	deoxyinosine phosphorylase	RSPH17029_RS04490	RSPH17029_RS02465
deoB	phosphopentomutase	RSPH17029_RS01270	RSPH17029_RS02595
deoC	deoxyribose-5-phosphate aldolase	RSPH17029_RS17485
adh	acetaldehyde dehydrogenase (not acylating)	RSPH17029_RS17490	RSPH17029_RS13480
acs	acetyl-CoA synthetase, AMP-forming	RSPH17029_RS11250	RSPH17029_RS01250
Alternative steps:
ackA	acetate kinase	RSPH17029_RS14695
ald-dh-CoA	acetaldehyde dehydrogenase, acylating
bmpA	deoxyinosine ABC transporter, substrate-binding component	RSPH17029_RS04510
nupA	deoxyinosine ABC transporter, ATPase component	RSPH17029_RS04505	RSPH17029_RS10035
nupB	deoxyinosine ABC transporter, permease component 1	RSPH17029_RS04500	RSPH17029_RS16320
nupC	deoxyinosine:H+ symporter NupC
nupC'	deoxyinosine ABC transporter, permease component 2	RSPH17029_RS04495	RSPH17029_RS10025
nupG	deoxyinosine permease NupG/XapB
pta	phosphate acetyltransferase	RSPH17029_RS14700	RSPH17029_RS14510

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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