GapMind for catabolism of small carbon sources


2-deoxy-D-ribose catabolism in Skermanella stibiiresistens SB22

Best path

drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB


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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit N825_RS21035 N825_RS25785
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit N825_RS21040 N825_RS15305
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component N825_RS18835 N825_RS17715
deoxyribonate-transport 2-deoxy-D-ribonate transporter N825_RS13450 N825_RS17750
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase N825_RS02230 N825_RS21440
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme N825_RS02220 N825_RS25125
garK glycerate 2-kinase N825_RS15075
atoA acetoacetyl-CoA transferase, A subunit N825_RS01845 N825_RS12900
atoD acetoacetyl-CoA transferase, B subunit N825_RS01850 N825_RS12895
atoB acetyl-CoA C-acetyltransferase N825_RS19860 N825_RS25015
Alternative steps:
aacS acetoacetyl-CoA synthetase N825_RS03700 N825_RS21445
ackA acetate kinase N825_RS32490 N825_RS20750
acs acetyl-CoA synthetase, AMP-forming N825_RS11705 N825_RS11835
adh acetaldehyde dehydrogenase (not acylating) N825_RS20855 N825_RS19970
ald-dh-CoA acetaldehyde dehydrogenase, acylating
deoC deoxyribose-5-phosphate aldolase N825_RS21770
deoK deoxyribokinase N825_RS14445 N825_RS21250
deoP deoxyribose transporter
pta phosphate acetyltransferase N825_RS32495 N825_RS20745

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