GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Collimonas pratensis Ter91

Best path

deoP, deoK, deoC, adh, acs

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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase CPter91_RS23405 CPter91_RS17385
deoC deoxyribose-5-phosphate aldolase
adh acetaldehyde dehydrogenase (not acylating) CPter91_RS03500 CPter91_RS20805
acs acetyl-CoA synthetase, AMP-forming CPter91_RS18980 CPter91_RS16700
Alternative steps:
aacS acetoacetyl-CoA synthetase CPter91_RS24510 CPter91_RS16700
ackA acetate kinase CPter91_RS16575
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoA acetoacetyl-CoA transferase, A subunit CPter91_RS09800 CPter91_RS00700
atoB acetyl-CoA C-acetyltransferase CPter91_RS02625 CPter91_RS24525
atoD acetoacetyl-CoA transferase, B subunit CPter91_RS09805 CPter91_RS00705
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase CPter91_RS07315 CPter91_RS24970
deoxyribonate-transport 2-deoxy-D-ribonate transporter CPter91_RS19920 CPter91_RS09345
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit CPter91_RS13525
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit CPter91_RS13530
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component CPter91_RS19240 CPter91_RS25320
garK glycerate 2-kinase CPter91_RS19750
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme
pta phosphate acetyltransferase CPter91_RS04625 CPter91_RS06765

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