GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Duganella sacchari Sac-22

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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter BUA36_RS02040 BUA36_RS22585
deoK deoxyribokinase
deoC deoxyribose-5-phosphate aldolase BUA36_RS13010
adh acetaldehyde dehydrogenase (not acylating) BUA36_RS13005 BUA36_RS02795
acs acetyl-CoA synthetase, AMP-forming BUA36_RS11840 BUA36_RS28615
Alternative steps:
aacS acetoacetyl-CoA synthetase BUA36_RS29590 BUA36_RS10130
ackA acetate kinase BUA36_RS04825 BUA36_RS05735
ald-dh-CoA acetaldehyde dehydrogenase, acylating BUA36_RS24730
atoA acetoacetyl-CoA transferase, A subunit BUA36_RS10730
atoB acetyl-CoA C-acetyltransferase BUA36_RS06615 BUA36_RS07910
atoD acetoacetyl-CoA transferase, B subunit BUA36_RS10735
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase BUA36_RS18290 BUA36_RS17920
deoxyribonate-transport 2-deoxy-D-ribonate transporter BUA36_RS08325 BUA36_RS06120
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit BUA36_RS19880 BUA36_RS16595
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit BUA36_RS19885 BUA36_RS17795
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component BUA36_RS17110
garK glycerate 2-kinase BUA36_RS06115
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme
pta phosphate acetyltransferase BUA36_RS04820 BUA36_RS15335

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