GapMind for catabolism of small carbon sources


2-deoxy-D-ribose catabolism in Sphingomonas laterariae LNB2

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 (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit CHB74_RS19265 CHB74_RS19795
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit CHB74_RS19270 CHB74_RS07680
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component
deoxyribonate-transport 2-deoxy-D-ribonate transporter
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase CHB74_RS07330 CHB74_RS01195
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme CHB74_RS17780
garK glycerate 2-kinase
atoA acetoacetyl-CoA transferase, A subunit CHB74_RS04050 CHB74_RS04925
atoD acetoacetyl-CoA transferase, B subunit CHB74_RS04045
atoB acetyl-CoA C-acetyltransferase CHB74_RS13115 CHB74_RS09855
Alternative steps:
aacS acetoacetyl-CoA synthetase CHB74_RS05000 CHB74_RS03820
ackA acetate kinase CHB74_RS18125 CHB74_RS20060
acs acetyl-CoA synthetase, AMP-forming CHB74_RS04770 CHB74_RS05000
adh acetaldehyde dehydrogenase (not acylating) CHB74_RS04745 CHB74_RS12680
ald-dh-CoA acetaldehyde dehydrogenase, acylating CHB74_RS01220
deoC deoxyribose-5-phosphate aldolase CHB74_RS15415
deoK deoxyribokinase
deoP deoxyribose transporter
pta phosphate acetyltransferase CHB74_RS18130 CHB74_RS20065

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