GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Azohydromonas australica DSM 1124

Best path

drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit H537_RS0124510 H537_RS0130925
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit H537_RS0125530 H537_RS0131415
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component
deoxyribonate-transport 2-deoxy-D-ribonate transporter H537_RS0132785 H537_RS0124480
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase H537_RS0132795 H537_RS0124925
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme H537_RS0132790
garK glycerate 2-kinase H537_RS0107580
atoA acetoacetyl-CoA transferase, A subunit H537_RS0111095 H537_RS0113245
atoD acetoacetyl-CoA transferase, B subunit H537_RS0111100 H537_RS0103575
atoB acetyl-CoA C-acetyltransferase H537_RS0122115 H537_RS0129600
Alternative steps:
aacS acetoacetyl-CoA synthetase H537_RS0139785 H537_RS0135265
ackA acetate kinase H537_RS0124355 H537_RS0122965
acs acetyl-CoA synthetase, AMP-forming H537_RS0109260 H537_RS0102685
adh acetaldehyde dehydrogenase (not acylating) H537_RS0138370 H537_RS0137335
ald-dh-CoA acetaldehyde dehydrogenase, acylating H537_RS0138815
deoC deoxyribose-5-phosphate aldolase
deoK deoxyribokinase H537_RS0126345
deoP deoxyribose transporter
pta phosphate acetyltransferase H537_RS0133805 H537_RS0124360

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 Apr 09 2024. 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