GapMind for catabolism of small carbon sources

 

2'-deoxyinosine catabolism in Burkholderia phytofirmans PsJN

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 BPHYT_RS25800 BPHYT_RS28205
H281DRAFT_01114 deoxynucleoside transporter, substrate-binding component BPHYT_RS25795
H281DRAFT_01113 deoxynucleoside transporter, ATPase component BPHYT_RS25790 BPHYT_RS27185
H281DRAFT_01112 deoxynucleoside transporter, permease component 2 BPHYT_RS25785 BPHYT_RS22740
deoD deoxyinosine phosphorylase
deoB phosphopentomutase BPHYT_RS14155
deoC deoxyribose-5-phosphate aldolase BPHYT_RS25815
adh acetaldehyde dehydrogenase (not acylating) BPHYT_RS25810 BPHYT_RS00120
ackA acetate kinase BPHYT_RS06125 BPHYT_RS26200
pta phosphate acetyltransferase BPHYT_RS21700 BPHYT_RS27695
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming BPHYT_RS07000 BPHYT_RS27780
ald-dh-CoA acetaldehyde dehydrogenase, acylating BPHYT_RS07245 BPHYT_RS21770
bmpA deoxyinosine ABC transporter, substrate-binding component
nupA deoxyinosine ABC transporter, ATPase component BPHYT_RS26080 BPHYT_RS21030
nupB deoxyinosine ABC transporter, permease component 1 BPHYT_RS26075
nupC deoxyinosine:H+ symporter NupC BPHYT_RS21960
nupC' deoxyinosine ABC transporter, permease component 2 BPHYT_RS11500 BPHYT_RS26070
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 Sep 17 2021. The underlying query database was built on Sep 17 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