GapMind for catabolism of small carbon sources

 

2'-deoxyinosine catabolism in Sinorhizobium fredii NGR234

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.

18 steps (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
H281DRAFT_01115 deoxynucleoside transporter, permease component 1 NGR_RS05505 NGR_RS02105
H281DRAFT_01114 deoxynucleoside transporter, substrate-binding component NGR_RS05490 NGR_RS12580
H281DRAFT_01113 deoxynucleoside transporter, ATPase component NGR_RS19930 NGR_RS05495
H281DRAFT_01112 deoxynucleoside transporter, permease component 2 NGR_RS05500 NGR_RS00535
deoD deoxyinosine phosphorylase NGR_RS28385
deoB phosphopentomutase NGR_RS28415 NGR_RS25025
deoC deoxyribose-5-phosphate aldolase NGR_RS06130
adh acetaldehyde dehydrogenase (not acylating) NGR_RS06135 NGR_RS22740
acs acetyl-CoA synthetase, AMP-forming NGR_RS27780 NGR_RS27800
Alternative steps:
ackA acetate kinase NGR_RS06510
ald-dh-CoA acetaldehyde dehydrogenase, acylating
bmpA deoxyinosine ABC transporter, substrate-binding component NGR_RS28805
nupA deoxyinosine ABC transporter, ATPase component NGR_RS28365 NGR_RS01145
nupB deoxyinosine ABC transporter, permease component 1 NGR_RS28370 NGR_RS01140
nupC deoxyinosine:H+ symporter NupC
nupC' deoxyinosine ABC transporter, permease component 2 NGR_RS28375 NGR_RS01135
nupG deoxyinosine permease NupG/XapB
pta phosphate acetyltransferase NGR_RS06505 NGR_RS11510

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 09 2024. The underlying query database was built on Sep 17 2021.

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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:

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