As text, or see rules and steps
# Deoxyribose utilization in GapMind is based on MetaCyc pathways # 2-deoxy-D-ribose degradation I via deoxyribose 5-phosphate aldolase (metacyc:PWY-8060) # and pathway II via oxidation to 2-deoxy-3-dehydro-D-ribonate (metacyc:PWY-8058). # Salmonella deoP (Q8XEV7) is near deoK and can enhance growth of E. coli on deoxyribose, even # though it is not essential for deoxyribose utilization in Salmonella, see PMC94358. deoP deoxyribose transporter curated:TCDB::Q8XEV7 deoxyribose-transport: deoP # The best-known pathway for deoxyribose utilization involves a # kinase forming deoxyribose-5-phosphate, an aldolase, forming # glyceraldehyde 3-phosphate (an intermediate in glycolysis) # and acetaldehyde, and acetaldehyde dehydrogenase to acetyl-CoA. # EC 2.7.1.15 (ribose kinase) includes enzymes known to act on deoxyribose. deoK deoxyribokinase EC:2.7.1.229 EC:2.7.1.15 # Produces acetaldehyde and glyceraldehyde 3-phosphate deoC deoxyribose-5-phosphate aldolase EC:4.1.2.4 import ethanol.steps:acetaldehyde-degradation # Another pathway involves periplasmic oxidation to deoxyribonate, # cytoplasmic oxidation to 2-deoxy-3-ketoribonate, and a cleavage # enzyme that uses acetyl-CoA to yield glyceryl-CoA and acetoacetate. # The glyceryl-CoA is apparently hydrolyzed to glycerate and then # phosphorylated by a kinase, yielding 2-phospho-D-glycerate, an # intermediate in glycolysis. The acetoacetate is activated to # acetoacetyl-CoA and cleaved to two acetyl-CoA. # This three-component periplasmic (probably) dehydrogenase seems to be non-specific, but # it is the only known way to convert deoxyribose to deoxyribonate. # (Oxidative damage of DNA and archaeal glycolysis may also be sources of deoxyribonate.) # It probably forms 1,5-lactone, but since that is uncertain, # the lactonase is not included in this pathway definition drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit term:deoxy%ribose dehydrogenase%alpha ignore_other:vanillin dehydrogenase drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit term:deoxy%ribose dehydrogenase%beta ignore_other:vanillin dehydrogenase drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component term:cytochrome%deoxyribose dehydrogenase ignore_other:vanillin dehydrogenase deoxyribose-dehyd: drdehyd-alpha drdehyd-beta drdehyd-cytc import leucine.steps:acetoacetate-degradation # acetoacetate is an intermediate in deoxyribonate degradation import deoxyribonate.steps:deoxyribonate-transport deoxyribonate-degradation # The deoxyribose 5-phosphate pathway involves the kinase deoK and the aldolase deoC. all: deoxyribose-transport deoK deoC acetaldehyde-degradation # The oxidative pathway involves oxidation in the periplasm to deoxyribonate. all: deoxyribose-dehyd 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