GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Shewanella oneidensis MR-1

Best path

deoP, deoK, deoC, adh, ackA, pta

Also see fitness data for the top candidates

Rules

Overview: Deoxyribose utilization in GapMind is based on MetaCyc pathways 2-deoxy-D-ribose degradation I via deoxyribose 5-phosphate aldolase (link) and pathway II via oxidation to 2-deoxy-3-dehydro-D-ribonate (link).

19 steps (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase SO0810
deoC deoxyribose-5-phosphate aldolase SO1217
adh acetaldehyde dehydrogenase (not acylating) SO4480 SO2136
ackA acetate kinase SO2915 SO3613
pta phosphate acetyltransferase SO2916
Alternative steps:
aacS acetoacetyl-CoA synthetase SO1971 SO3664
acs acetyl-CoA synthetase, AMP-forming SO2743 SO3664
ald-dh-CoA acetaldehyde dehydrogenase, acylating SO2136
atoA acetoacetyl-CoA transferase, A subunit SO1892
atoB acetyl-CoA C-acetyltransferase SO1677 SO0020
atoD acetoacetyl-CoA transferase, B subunit SO1891
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase SO0438
deoxyribonate-transport 2-deoxy-D-ribonate transporter
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit SO3049
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit SO3048
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component
garK glycerate 2-kinase SO1770
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme

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, the preprint on GapMind for carbon sources, 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