GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribonate catabolism in Shewanella sp. ANA-3

Best path

deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB

Also see fitness data for the top candidates

Rules

Overview: 2-deoxy-D-ribonate degradation is based on an oxidative pathway for deoxyribose degradation (link). 2-deoxyribonate is thought to be the primary natural substrate for this pathway (PMC6365646). Alternatively, Klebsiella michiganensis appears to consume deoxyribonate via a deoxyribonyl-CoA dehydrogenase (PMC6365646), but this pathway is less established and is not included in GapMind.

8 steps (6 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoxyribonate-transport 2-deoxy-D-ribonate transporter
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase Shewana3_2690 Shewana3_0437
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme
garK glycerate 2-kinase Shewana3_2685
atoA acetoacetyl-CoA transferase, A subunit Shewana3_3467 Shewana3_1667
atoD acetoacetyl-CoA transferase, B subunit Shewana3_1666 Shewana3_3468
atoB acetyl-CoA C-acetyltransferase Shewana3_2771 Shewana3_0023
Alternative steps:
aacS acetoacetyl-CoA synthetase Shewana3_2475 Shewana3_2386

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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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