nupA, nupB, nupC', bmpA, deoD, deoB, deoC, adh, acs
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.
Or see definitions of steps
| Step | Description | Best candidate | 2nd candidate |
|---|---|---|---|
| nupA | deoxyinosine ABC transporter, ATPase component | EDD55_RS02650 | EDD55_RS04935 |
| nupB | deoxyinosine ABC transporter, permease component 1 | EDD55_RS02655 | |
| nupC' | deoxyinosine ABC transporter, permease component 2 | EDD55_RS02660 | |
| bmpA | deoxyinosine ABC transporter, substrate-binding component | EDD55_RS02645 | |
| deoD | deoxyinosine phosphorylase | EDD55_RS02670 | EDD55_RS11905 |
| deoB | phosphopentomutase | EDD55_RS02680 | EDD55_RS11005 |
| deoC | deoxyribose-5-phosphate aldolase | EDD55_RS02635 | |
| adh | acetaldehyde dehydrogenase (not acylating) | EDD55_RS02640 | EDD55_RS12665 |
| acs | acetyl-CoA synthetase, AMP-forming | EDD55_RS00740 | EDD55_RS07400 |
| Alternative steps: | |||
| ackA | acetate kinase | ||
| ald-dh-CoA | acetaldehyde dehydrogenase, acylating | ||
| H281DRAFT_01112 | deoxynucleoside transporter, permease component 2 | ||
| H281DRAFT_01113 | deoxynucleoside transporter, ATPase component | EDD55_RS02650 | EDD55_RS03640 |
| 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 | EDD55_RS01270 | EDD55_RS07190 |
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 May 12 2024. The underlying query database was built on Sep 17 2021.
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:
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