GapMind for catabolism of small carbon sources


2-deoxy-D-ribose catabolism in Pandoraea thiooxydans ATSB16

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 PATSB16_RS15835 PATSB16_RS09835
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit PATSB16_RS15840 PATSB16_RS09830
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component
deoxyribonate-transport 2-deoxy-D-ribonate transporter PATSB16_RS03885 PATSB16_RS06950
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase PATSB16_RS13335 PATSB16_RS14520
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme
garK glycerate 2-kinase PATSB16_RS10630 PATSB16_RS04105
atoA acetoacetyl-CoA transferase, A subunit PATSB16_RS12320 PATSB16_RS11255
atoD acetoacetyl-CoA transferase, B subunit PATSB16_RS12315 PATSB16_RS11250
atoB acetyl-CoA C-acetyltransferase PATSB16_RS05650 PATSB16_RS05675
Alternative steps:
aacS acetoacetyl-CoA synthetase PATSB16_RS19185 PATSB16_RS00745
ackA acetate kinase PATSB16_RS09135
acs acetyl-CoA synthetase, AMP-forming PATSB16_RS02175 PATSB16_RS15885
adh acetaldehyde dehydrogenase (not acylating) PATSB16_RS15895 PATSB16_RS16135
ald-dh-CoA acetaldehyde dehydrogenase, acylating PATSB16_RS14005
deoC deoxyribose-5-phosphate aldolase
deoK deoxyribokinase
deoP deoxyribose transporter
pta phosphate acetyltransferase PATSB16_RS09130 PATSB16_RS13940

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