GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Cobetia crustatorum JO1

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 (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase BF12_RS0114555
deoC deoxyribose-5-phosphate aldolase
adh acetaldehyde dehydrogenase (not acylating) BF12_RS0101560 BF12_RS0106720
acs acetyl-CoA synthetase, AMP-forming BF12_RS0102090 BF12_RS0100005
Alternative steps:
aacS acetoacetyl-CoA synthetase BF12_RS0108370 BF12_RS0114500
ackA acetate kinase
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoA acetoacetyl-CoA transferase, A subunit BF12_RS0106855
atoB acetyl-CoA C-acetyltransferase BF12_RS0110000 BF12_RS0111470
atoD acetoacetyl-CoA transferase, B subunit BF12_RS0106860
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase BF12_RS0111880 BF12_RS0116955
deoxyribonate-transport 2-deoxy-D-ribonate transporter
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit BF12_RS19050 BF12_RS0102355
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit BF12_RS0106775
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component BF12_RS0112680 BF12_RS0112075
garK glycerate 2-kinase BF12_RS0107560
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme BF12_RS0110205
pta phosphate acetyltransferase BF12_RS0112365

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.

Links

Downloads

Related tools

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