GapMind for catabolism of small carbon sources


2-deoxy-D-ribose catabolism in Azospirillum thiophilum BV-S

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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase AL072_RS27100
deoC deoxyribose-5-phosphate aldolase AL072_RS27130 AL072_RS21370
adh acetaldehyde dehydrogenase (not acylating) AL072_RS23920 AL072_RS26875
acs acetyl-CoA synthetase, AMP-forming AL072_RS06780 AL072_RS08155
Alternative steps:
aacS acetoacetyl-CoA synthetase AL072_RS12540 AL072_RS21625
ackA acetate kinase AL072_RS27185 AL072_RS00850
ald-dh-CoA acetaldehyde dehydrogenase, acylating AL072_RS26875
atoA acetoacetyl-CoA transferase, A subunit AL072_RS23380 AL072_RS21860
atoB acetyl-CoA C-acetyltransferase AL072_RS07385 AL072_RS27145
atoD acetoacetyl-CoA transferase, B subunit AL072_RS23385 AL072_RS21865
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase AL072_RS28085 AL072_RS25045
deoxyribonate-transport 2-deoxy-D-ribonate transporter
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit AL072_RS28560 AL072_RS17215
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit AL072_RS28555
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component AL072_RS29735
garK glycerate 2-kinase AL072_RS24725 AL072_RS26395
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme AL072_RS16520
pta phosphate acetyltransferase AL072_RS27180 AL072_RS00855

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