GapMind for catabolism of small carbon sources


2-deoxy-D-ribose catabolism in Rhizobium grahamii CCGE 502

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 RGCCGE502_RS12300
deoK deoxyribokinase RGCCGE502_RS02210
deoC deoxyribose-5-phosphate aldolase RGCCGE502_RS01060
adh acetaldehyde dehydrogenase (not acylating) RGCCGE502_RS23535 RGCCGE502_RS00735
acs acetyl-CoA synthetase, AMP-forming RGCCGE502_RS24205 RGCCGE502_RS24215
Alternative steps:
aacS acetoacetyl-CoA synthetase RGCCGE502_RS03670 RGCCGE502_RS02470
ackA acetate kinase RGCCGE502_RS11645
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoA acetoacetyl-CoA transferase, A subunit RGCCGE502_RS33970
atoB acetyl-CoA C-acetyltransferase RGCCGE502_RS33960 RGCCGE502_RS23710
atoD acetoacetyl-CoA transferase, B subunit RGCCGE502_RS33965
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase RGCCGE502_RS31680 RGCCGE502_RS20770
deoxyribonate-transport 2-deoxy-D-ribonate transporter
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit RGCCGE502_RS13610 RGCCGE502_RS26530
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit RGCCGE502_RS13605
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component RGCCGE502_RS25475 RGCCGE502_RS05735
garK glycerate 2-kinase RGCCGE502_RS19565 RGCCGE502_RS11730
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme RGCCGE502_RS15375
pta phosphate acetyltransferase RGCCGE502_RS02115 RGCCGE502_RS10690

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