GapMind for catabolism of small carbon sources

 

2'-deoxyinosine catabolism in Algoriphagus machipongonensis PR1

Best path

nupC, 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 (9 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
nupC deoxyinosine:H+ symporter NupC ALPR1_RS10400
deoD deoxyinosine phosphorylase ALPR1_RS19070
deoB phosphopentomutase ALPR1_RS10665
deoC deoxyribose-5-phosphate aldolase ALPR1_RS01625
adh acetaldehyde dehydrogenase (not acylating) ALPR1_RS18135 ALPR1_RS00010
acs acetyl-CoA synthetase, AMP-forming ALPR1_RS02860 ALPR1_RS19255
Alternative steps:
ackA acetate kinase
ald-dh-CoA acetaldehyde dehydrogenase, acylating
bmpA deoxyinosine ABC transporter, substrate-binding component
H281DRAFT_01112 deoxynucleoside transporter, permease component 2
H281DRAFT_01113 deoxynucleoside transporter, ATPase component
H281DRAFT_01114 deoxynucleoside transporter, substrate-binding component
H281DRAFT_01115 deoxynucleoside transporter, permease component 1
nupA deoxyinosine ABC transporter, ATPase component ALPR1_RS06225 ALPR1_RS06390
nupB deoxyinosine ABC transporter, permease component 1
nupC' deoxyinosine ABC transporter, permease component 2
nupG deoxyinosine permease NupG/XapB ALPR1_RS17995
pta phosphate acetyltransferase ALPR1_RS16330

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 Sep 24 2021. 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