GapMind for catabolism of small carbon sources


2-deoxy-D-ribose catabolism in Amycolatopsis xylanica CPCC 202699

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 BLV57_RS12630 BLV57_RS23565
deoC deoxyribose-5-phosphate aldolase BLV57_RS28720
adh acetaldehyde dehydrogenase (not acylating) BLV57_RS05155 BLV57_RS28715
acs acetyl-CoA synthetase, AMP-forming BLV57_RS09725 BLV57_RS31585
Alternative steps:
aacS acetoacetyl-CoA synthetase BLV57_RS42120 BLV57_RS08285
ackA acetate kinase BLV57_RS03855
ald-dh-CoA acetaldehyde dehydrogenase, acylating BLV57_RS32000
atoA acetoacetyl-CoA transferase, A subunit BLV57_RS07065 BLV57_RS23380
atoB acetyl-CoA C-acetyltransferase BLV57_RS25480 BLV57_RS23280
atoD acetoacetyl-CoA transferase, B subunit BLV57_RS07060
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase BLV57_RS37895 BLV57_RS35695
deoxyribonate-transport 2-deoxy-D-ribonate transporter BLV57_RS42095 BLV57_RS01370
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit BLV57_RS19515 BLV57_RS31390
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component
garK glycerate 2-kinase BLV57_RS35780 BLV57_RS04475
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme
pta phosphate acetyltransferase

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