GapMind for catabolism of small carbon sources


2-deoxy-D-ribose catabolism in Bacillus horneckiae 1P01SC

Best path

deoP, deoK, deoC, adh, ackA, pta


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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase CWS20_RS04510
deoC deoxyribose-5-phosphate aldolase CWS20_RS11410 CWS20_RS22180
adh acetaldehyde dehydrogenase (not acylating) CWS20_RS10330 CWS20_RS13150
ackA acetate kinase CWS20_RS01815 CWS20_RS25205
pta phosphate acetyltransferase CWS20_RS14775 CWS20_RS25195
Alternative steps:
aacS acetoacetyl-CoA synthetase CWS20_RS04900 CWS20_RS10170
acs acetyl-CoA synthetase, AMP-forming CWS20_RS23850 CWS20_RS10745
ald-dh-CoA acetaldehyde dehydrogenase, acylating CWS20_RS13130
atoA acetoacetyl-CoA transferase, A subunit CWS20_RS18535 CWS20_RS01255
atoB acetyl-CoA C-acetyltransferase CWS20_RS27420 CWS20_RS14695
atoD acetoacetyl-CoA transferase, B subunit CWS20_RS18530 CWS20_RS01260
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase CWS20_RS27195 CWS20_RS01530
deoxyribonate-transport 2-deoxy-D-ribonate transporter
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 CWS20_RS08285 CWS20_RS21505
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 24 2021. The underlying query database was built on Sep 17 2021.



Related tools

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