GapMind for catabolism of small carbon sources

 

2'-deoxyinosine catabolism in Klebsiella michiganensis M5al

Best path

nupC, 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
nupC deoxyinosine:H+ symporter NupC BWI76_RS20540 BWI76_RS04125
deoD deoxyinosine phosphorylase BWI76_RS20605 BWI76_RS04145
deoB phosphopentomutase BWI76_RS04140 BWI76_RS25130
deoC deoxyribose-5-phosphate aldolase BWI76_RS04130 BWI76_RS23665
adh acetaldehyde dehydrogenase (not acylating) BWI76_RS21985 BWI76_RS15205
ackA acetate kinase BWI76_RS20235 BWI76_RS23200
pta phosphate acetyltransferase BWI76_RS20240 BWI76_RS20805
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming BWI76_RS02095 BWI76_RS17800
ald-dh-CoA acetaldehyde dehydrogenase, acylating BWI76_RS17250 BWI76_RS20790
bmpA deoxyinosine ABC transporter, substrate-binding component
H281DRAFT_01112 deoxynucleoside transporter, permease component 2 BWI76_RS00280 BWI76_RS00655
H281DRAFT_01113 deoxynucleoside transporter, ATPase component BWI76_RS07240 BWI76_RS00660
H281DRAFT_01114 deoxynucleoside transporter, substrate-binding component BWI76_RS00665
H281DRAFT_01115 deoxynucleoside transporter, permease component 1 BWI76_RS14865 BWI76_RS00280
nupA deoxyinosine ABC transporter, ATPase component BWI76_RS07240 BWI76_RS02160
nupB deoxyinosine ABC transporter, permease component 1
nupC' deoxyinosine ABC transporter, permease component 2
nupG deoxyinosine permease NupG/XapB BWI76_RS24170 BWI76_RS20600

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