GapMind for catabolism of small carbon sources


Definition of 2-deoxy-D-ribonate catabolism

As text, or see rules and steps

# 2-deoxy-D-ribonate degradation is based on an oxidative pathway for
# deoxyribose degradation (metacyc:PWY-8058). 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.

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

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

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

# GarK produces 2-phospho-D-glycerate, an intermediate in glycolysis.
# psRCH2:GFF1145 is believed to do this reaction but was not annotated with this EC number.
garK	glycerate 2-kinase	EC:	curated:reanno::psRCH2:GFF1145

import leucine.steps:acetoacetate-degradation

# After oxidation of deoxyribonate to 2-deoxy-3-ketoribonate, a
# cleavage enzyme produces glyceroyl-CoA and acetoacetate; the enzyme
# for the conversion of glyceroyl-CoA to glycerate is not known; and
# garK phosphorylates glycerate to 2-phospho-D-glycerate, an
# intermediate in glycolysis.
deoxyribonate-degradation: deoxyribonate-dehyd ketodeoxyribonate-cleavage garK acetoacetate-degradation

all: deoxyribonate-transport deoxyribonate-degradation



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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 paper from 2022 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