GapMind for catabolism of small carbon sources

 

2'-deoxyinosine catabolism in Dinoroseobacter shibae DFL-12

Best path

H281DRAFT_01115, H281DRAFT_01114, H281DRAFT_01113, H281DRAFT_01112, deoD, deoB, deoC, adh, ackA, pta

Also see fitness data for the top candidates

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 Dshi_0528
H281DRAFT_01114 deoxynucleoside transporter, substrate-binding component Dshi_0531 Dshi_2434
H281DRAFT_01113 deoxynucleoside transporter, ATPase component Dshi_0530 Dshi_2433
H281DRAFT_01112 deoxynucleoside transporter, permease component 2 Dshi_0529 Dshi_2432
deoD deoxyinosine phosphorylase Dshi_2858 Dshi_2068
deoB phosphopentomutase Dshi_0829 Dshi_2397
deoC deoxyribose-5-phosphate aldolase Dshi_3016
adh acetaldehyde dehydrogenase (not acylating) Dshi_3017 Dshi_1095
ackA acetate kinase Dshi_0632 Dshi_5006
pta phosphate acetyltransferase Dshi_1825 Dshi_0633
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming Dshi_3553 Dshi_1399
ald-dh-CoA acetaldehyde dehydrogenase, acylating
bmpA deoxyinosine ABC transporter, substrate-binding component Dshi_2842
nupA deoxyinosine ABC transporter, ATPase component Dshi_2843 Dshi_1947
nupB deoxyinosine ABC transporter, permease component 1 Dshi_2844 Dshi_1946
nupC deoxyinosine:H+ symporter NupC
nupC' deoxyinosine ABC transporter, permease component 2 Dshi_2846 Dshi_1945
nupG deoxyinosine permease NupG/XapB

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 Aug 02 2021. The underlying query database was built on Aug 02 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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