GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Cronobacter condimenti 1330

Best path

deoP, deoK, deoC, adh, ackA, pta

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 BN137_RS10460
deoK deoxyribokinase BN137_RS17445 BN137_RS14165
deoC deoxyribose-5-phosphate aldolase BN137_RS11395
adh acetaldehyde dehydrogenase (not acylating) BN137_RS07500 BN137_RS04415
ackA acetate kinase BN137_RS04835
pta phosphate acetyltransferase BN137_RS15910 BN137_RS10155
Alternative steps:
aacS acetoacetyl-CoA synthetase BN137_RS13680
acs acetyl-CoA synthetase, AMP-forming BN137_RS07225
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoA acetoacetyl-CoA transferase, A subunit
atoB acetyl-CoA C-acetyltransferase BN137_RS18035 BN137_RS11135
atoD acetoacetyl-CoA transferase, B subunit
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase BN137_RS14795 BN137_RS10485
deoxyribonate-transport 2-deoxy-D-ribonate transporter BN137_RS08130
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit BN137_RS01840
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component BN137_RS16385
garK glycerate 2-kinase BN137_RS08885
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme

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