GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Moritella dasanensis ArB 0140

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 (10 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase A923_RS0107865
deoC deoxyribose-5-phosphate aldolase A923_RS0106075 A923_RS0107260
adh acetaldehyde dehydrogenase (not acylating) A923_RS0109940 A923_RS0109685
ackA acetate kinase A923_RS0105270 A923_RS0113805
pta phosphate acetyltransferase A923_RS0105275
Alternative steps:
aacS acetoacetyl-CoA synthetase A923_RS0100990 A923_RS0104565
acs acetyl-CoA synthetase, AMP-forming A923_RS0118350 A923_RS0102085
ald-dh-CoA acetaldehyde dehydrogenase, acylating A923_RS0118180
atoA acetoacetyl-CoA transferase, A subunit
atoB acetyl-CoA C-acetyltransferase A923_RS0119275 A923_RS0119825
atoD acetoacetyl-CoA transferase, B subunit
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase A923_RS0108875
deoxyribonate-transport 2-deoxy-D-ribonate transporter
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component
garK glycerate 2-kinase
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