GapMind for catabolism of small carbon sources

 

2'-deoxyinosine catabolism in Dyella japonica UNC79MFTsu3.2

Best path

nupG, deoD, deoB, deoC, adh, acs

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 (9 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
nupG deoxyinosine permease NupG/XapB N515DRAFT_2002 N515DRAFT_1323
deoD deoxyinosine phosphorylase N515DRAFT_0396
deoB phosphopentomutase N515DRAFT_1372
deoC deoxyribose-5-phosphate aldolase
adh acetaldehyde dehydrogenase (not acylating) N515DRAFT_0465 N515DRAFT_3729
acs acetyl-CoA synthetase, AMP-forming N515DRAFT_3075 N515DRAFT_0016
Alternative steps:
ackA acetate kinase N515DRAFT_2456
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 N515DRAFT_2413 N515DRAFT_3232
H281DRAFT_01114 deoxynucleoside transporter, substrate-binding component
H281DRAFT_01115 deoxynucleoside transporter, permease component 1
nupA deoxyinosine ABC transporter, ATPase component N515DRAFT_3232 N515DRAFT_2413
nupB deoxyinosine ABC transporter, permease component 1
nupC deoxyinosine:H+ symporter NupC
nupC' deoxyinosine ABC transporter, permease component 2
pta phosphate acetyltransferase N515DRAFT_2182

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.

Links

Downloads

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 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