GapMind for catabolism of small carbon sources


2'-deoxyinosine catabolism in Phaeobacter inhibens BS107

Best path

nupA, nupB, nupC', bmpA, deoD, deoB, deoC, adh, acs

Also see fitness data for the top candidates


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 (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
nupA deoxyinosine ABC transporter, ATPase component PGA1_c03960 PGA1_c26910
nupB deoxyinosine ABC transporter, permease component 1 PGA1_c03950 PGA1_c26920
nupC' deoxyinosine ABC transporter, permease component 2 PGA1_c28160 PGA1_c03940
bmpA deoxyinosine ABC transporter, substrate-binding component PGA1_c03970
deoD deoxyinosine phosphorylase PGA1_c03820 PGA1_c06380
deoB phosphopentomutase PGA1_c11950
deoC deoxyribose-5-phosphate aldolase PGA1_c32790
adh acetaldehyde dehydrogenase (not acylating) PGA1_c32800 PGA1_c29650
acs acetyl-CoA synthetase, AMP-forming PGA1_c12950 PGA1_c11900
Alternative steps:
ackA acetate kinase PGA1_c28840
ald-dh-CoA acetaldehyde dehydrogenase, acylating PGA1_c19350
H281DRAFT_01112 deoxynucleoside transporter, permease component 2 PGA1_c23080
H281DRAFT_01113 deoxynucleoside transporter, ATPase component PGA1_c23060 PGA1_c28130
H281DRAFT_01114 deoxynucleoside transporter, substrate-binding component
H281DRAFT_01115 deoxynucleoside transporter, permease component 1
nupC deoxyinosine:H+ symporter NupC
nupG deoxyinosine permease NupG/XapB
pta phosphate acetyltransferase PGA1_c28850

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



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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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