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:2.7.1.165 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
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:
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