GapMind for catabolism of small carbon sources

 

Definition of 2-deoxy-D-ribonate catabolism

As rules and steps, or see full text

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.

Steps

deoxyribonate-transport: 2-deoxy-D-ribonate transporter

deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase

ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme

garK: glycerate 2-kinase

atoA: acetoacetyl-CoA transferase, A subunit

atoD: acetoacetyl-CoA transferase, B subunit

aacS: acetoacetyl-CoA synthetase

atoB: acetyl-CoA C-acetyltransferase

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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