GapMind for catabolism of small carbon sources


2-deoxy-D-ribose catabolism in Microvirga lotononidis WSM3557

Best path

deoP, deoK, deoC, adh, acs


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 (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase MICLODRAFT_RS26160 MICLODRAFT_RS25570
deoC deoxyribose-5-phosphate aldolase MICLODRAFT_RS31620
adh acetaldehyde dehydrogenase (not acylating) MICLODRAFT_RS21540 MICLODRAFT_RS17515
acs acetyl-CoA synthetase, AMP-forming MICLODRAFT_RS29080 MICLODRAFT_RS22300
Alternative steps:
aacS acetoacetyl-CoA synthetase MICLODRAFT_RS32190 MICLODRAFT_RS22300
ackA acetate kinase MICLODRAFT_RS09085 MICLODRAFT_RS12250
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoA acetoacetyl-CoA transferase, A subunit MICLODRAFT_RS23795 MICLODRAFT_RS09110
atoB acetyl-CoA C-acetyltransferase MICLODRAFT_RS27925 MICLODRAFT_RS10820
atoD acetoacetyl-CoA transferase, B subunit MICLODRAFT_RS23800 MICLODRAFT_RS09115
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase MICLODRAFT_RS19270 MICLODRAFT_RS09215
deoxyribonate-transport 2-deoxy-D-ribonate transporter
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit MICLODRAFT_RS07510 MICLODRAFT_RS06735
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component MICLODRAFT_RS23090
garK glycerate 2-kinase MICLODRAFT_RS20190
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme
pta phosphate acetyltransferase MICLODRAFT_RS09080 MICLODRAFT_RS19205

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 24 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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