title: A survey of orphan enzyme activities.
abstract: BACKGROUND
  Using computational database searches, we have demonstrated previously that no gene sequences could be found for at least 36% of enzyme activities that have been assigned an Enzyme Commission number. Here we present a follow-up literature-based survey involving a statistically significant sample of such "orphan" activities. The survey was intended to determine whether sequences for these enzyme activities are truly unknown, or whether these sequences are absent from the public sequence databases but can be found in the literature.
  
  
  RESULTS
  We demonstrate that for ~80% of sampled orphans, the absence of sequence data is bona fide. Our analyses further substantiate the notion that many of these enzyme activities play biologically important roles.
  
  
  CONCLUSIONS
  This survey points toward significant scientific cost of having such a large fraction of characterized enzyme activities disconnected from sequence data. It also suggests that a larger effort, beginning with a comprehensive survey of all putative orphan activities, would resolve nearly 300 artifactual orphans and reconnect a wealth of enzyme research with modern genomics. For these reasons, we propose that a systematic effort to identify the cognate genes of orphan enzymes be undertaken.
authors.affiliation: Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, California 94025-3493, USA. ypouliot@stanford.edu <ypouliot@stanford.edu>
authors.forename: Yannick
authors.initials: Y
authors.lastname: Pouliot
authors.forename: Peter D
authors.initials: PD
authors.lastname: Karp
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003625:Data Collection; D016208:Databases, Factual; D030541:Databases, Genetic; D030562:Databases, Protein; D004798:Enzymes / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D023281:Genomics; D040901:Proteomics; D015203:Reproducibility of Results; D013045:Species Specificity
chemical_list: D004798:Enzymes