GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Williamsia sterculiae CPCC 203464

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 (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase BW971_RS14065
deoC deoxyribose-5-phosphate aldolase BW971_RS07940
ald-dh-CoA acetaldehyde dehydrogenase, acylating BW971_RS01140 BW971_RS03540
Alternative steps:
aacS acetoacetyl-CoA synthetase BW971_RS03270 BW971_RS03265
ackA acetate kinase BW971_RS08540 BW971_RS01390
acs acetyl-CoA synthetase, AMP-forming BW971_RS08810 BW971_RS18805
adh acetaldehyde dehydrogenase (not acylating) BW971_RS18685 BW971_RS10750
atoA acetoacetyl-CoA transferase, A subunit
atoB acetyl-CoA C-acetyltransferase BW971_RS20375 BW971_RS04170
atoD acetoacetyl-CoA transferase, B subunit
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase BW971_RS03935 BW971_RS08115
deoxyribonate-transport 2-deoxy-D-ribonate transporter
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit BW971_RS05055
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component
garK glycerate 2-kinase BW971_RS13175
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme
pta phosphate acetyltransferase BW971_RS08545

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