GapMind for catabolism of small carbon sources


2-deoxy-D-ribose catabolism in Bacillus okhensis Kh10-101

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 (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase LQ50_RS17500
deoC deoxyribose-5-phosphate aldolase LQ50_RS00945
adh acetaldehyde dehydrogenase (not acylating) LQ50_RS09680 LQ50_RS02455
ackA acetate kinase LQ50_RS15465 LQ50_RS04310
pta phosphate acetyltransferase LQ50_RS18055
Alternative steps:
aacS acetoacetyl-CoA synthetase LQ50_RS19555 LQ50_RS19520
acs acetyl-CoA synthetase, AMP-forming LQ50_RS12660 LQ50_RS00925
ald-dh-CoA acetaldehyde dehydrogenase, acylating LQ50_RS09970 LQ50_RS23465
atoA acetoacetyl-CoA transferase, A subunit LQ50_RS07090 LQ50_RS17370
atoB acetyl-CoA C-acetyltransferase LQ50_RS11705 LQ50_RS17975
atoD acetoacetyl-CoA transferase, B subunit LQ50_RS07085 LQ50_RS17365
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase LQ50_RS07860 LQ50_RS14895
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 LQ50_RS16040
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme LQ50_RS14880 LQ50_RS05305

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