GapMind for catabolism of small carbon sources

 

2'-deoxyinosine catabolism in Azospirillum brasilense Sp245

Best path

nupC, 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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
nupC deoxyinosine:H+ symporter NupC
deoD deoxyinosine phosphorylase AZOBR_RS06645 AZOBR_RS09940
deoB phosphopentomutase AZOBR_RS33725 AZOBR_RS07040
deoC deoxyribose-5-phosphate aldolase
adh acetaldehyde dehydrogenase (not acylating) AZOBR_RS22315 AZOBR_RS26825
acs acetyl-CoA synthetase, AMP-forming AZOBR_RS00270 AZOBR_RS06340
Alternative steps:
ackA acetate kinase AZOBR_RS12495 AZOBR_RS04605
ald-dh-CoA acetaldehyde dehydrogenase, acylating AZOBR_RS32240 AZOBR_RS32475
bmpA deoxyinosine ABC transporter, substrate-binding component AZOBR_RS06620
H281DRAFT_01112 deoxynucleoside transporter, permease component 2 AZOBR_RS31200
H281DRAFT_01113 deoxynucleoside transporter, ATPase component AZOBR_RS31210 AZOBR_RS31245
H281DRAFT_01114 deoxynucleoside transporter, substrate-binding component
H281DRAFT_01115 deoxynucleoside transporter, permease component 1
nupA deoxyinosine ABC transporter, ATPase component AZOBR_RS06625 AZOBR_RS31880
nupB deoxyinosine ABC transporter, permease component 1 AZOBR_RS06630 AZOBR_RS06955
nupC' deoxyinosine ABC transporter, permease component 2 AZOBR_RS06635 AZOBR_RS06960
nupG deoxyinosine permease NupG/XapB
pta phosphate acetyltransferase AZOBR_RS04600 AZOBR_RS12500

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