GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Cloacibacillus porcorum CL-84

Best path

deoP, deoK, deoC, ald-dh-CoA

Rules

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 BED41_RS05600
deoC deoxyribose-5-phosphate aldolase BED41_RS12255
ald-dh-CoA acetaldehyde dehydrogenase, acylating BED41_RS11335 BED41_RS04145
Alternative steps:
aacS acetoacetyl-CoA synthetase BED41_RS01515 BED41_RS14140
ackA acetate kinase BED41_RS06145 BED41_RS04200
acs acetyl-CoA synthetase, AMP-forming BED41_RS15085 BED41_RS12210
adh acetaldehyde dehydrogenase (not acylating) BED41_RS11335 BED41_RS08950
atoA acetoacetyl-CoA transferase, A subunit BED41_RS01550 BED41_RS12320
atoB acetyl-CoA C-acetyltransferase BED41_RS01560 BED41_RS10190
atoD acetoacetyl-CoA transferase, B subunit BED41_RS01555 BED41_RS12325
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase BED41_RS15695 BED41_RS00875
deoxyribonate-transport 2-deoxy-D-ribonate transporter
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit BED41_RS01915 BED41_RS04870
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component
garK glycerate 2-kinase BED41_RS04765
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme
pta phosphate acetyltransferase BED41_RS08975 BED41_RS04165

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