GapMind for catabolism of small carbon sources


2-deoxy-D-ribose catabolism in Yersinia intermedia Y228

Best path

deoP, deoK, deoC, ald-dh-CoA


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 CH53_RS19800 CH53_RS04195
deoK deoxyribokinase CH53_RS08880 CH53_RS19805
deoC deoxyribose-5-phosphate aldolase CH53_RS05555 CH53_RS01050
ald-dh-CoA acetaldehyde dehydrogenase, acylating CH53_RS19095 CH53_RS12405
Alternative steps:
aacS acetoacetyl-CoA synthetase CH53_RS13215
ackA acetate kinase CH53_RS01940 CH53_RS21405
acs acetyl-CoA synthetase, AMP-forming CH53_RS07140
adh acetaldehyde dehydrogenase (not acylating) CH53_RS19095 CH53_RS18425
atoA acetoacetyl-CoA transferase, A subunit CH53_RS10535
atoB acetyl-CoA C-acetyltransferase CH53_RS10520 CH53_RS10255
atoD acetoacetyl-CoA transferase, B subunit CH53_RS10530
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase CH53_RS04400
deoxyribonate-transport 2-deoxy-D-ribonate transporter CH53_RS11075 CH53_RS01795
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component
garK glycerate 2-kinase CH53_RS06835 CH53_RS00320
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme
pta phosphate acetyltransferase CH53_RS01945 CH53_RS12390

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