GapMind for catabolism of small carbon sources

 

2'-deoxyinosine catabolism in Herbaspirillum seropedicae SmR1

Best path

H281DRAFT_01115, H281DRAFT_01114, H281DRAFT_01113, H281DRAFT_01112, 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 (11 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
H281DRAFT_01115 deoxynucleoside transporter, permease component 1 HSERO_RS05100 HSERO_RS20095
H281DRAFT_01114 deoxynucleoside transporter, substrate-binding component HSERO_RS05095 HSERO_RS22225
H281DRAFT_01113 deoxynucleoside transporter, ATPase component HSERO_RS05090 HSERO_RS03640
H281DRAFT_01112 deoxynucleoside transporter, permease component 2 HSERO_RS05085 HSERO_RS05325
deoD deoxyinosine phosphorylase
deoB phosphopentomutase
deoC deoxyribose-5-phosphate aldolase HSERO_RS05120
adh acetaldehyde dehydrogenase (not acylating) HSERO_RS05115 HSERO_RS09465
acs acetyl-CoA synthetase, AMP-forming HSERO_RS07770 HSERO_RS23535
Alternative steps:
ackA acetate kinase HSERO_RS01305 HSERO_RS11090
ald-dh-CoA acetaldehyde dehydrogenase, acylating
bmpA deoxyinosine ABC transporter, substrate-binding component
nupA deoxyinosine ABC transporter, ATPase component HSERO_RS21310 HSERO_RS07080
nupB deoxyinosine ABC transporter, permease component 1
nupC deoxyinosine:H+ symporter NupC
nupC' deoxyinosine ABC transporter, permease component 2 HSERO_RS21320 HSERO_RS07090
nupG deoxyinosine permease NupG/XapB
pta phosphate acetyltransferase HSERO_RS12030 HSERO_RS01300

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