title: Unassigned MURF1 of kinetoplastids codes for NADH dehydrogenase subunit 2.
abstract: BACKGROUND
  In a previous study, we conducted a large-scale similarity-free function prediction of mitochondrion-encoded hypothetical proteins, by which the hypothetical gene murf1 (maxicircle unidentified reading frame 1) was assigned as nad2, encoding subunit 2 of NADH dehydrogenase (Complex I of the respiratory chain). This hypothetical gene occurs in the mitochondrial genome of kinetoplastids, a group of unicellular eukaryotes including the causative agents of African sleeping sickness and leishmaniasis. In the present study, we test this assignment by using bioinformatics methods that are highly sensitive in identifying remote homologs and confront the prediction with available biological knowledge.
  
  
  RESULTS
  Comparison of MURF1 profile Hidden Markov Model (HMM) against function-known profile HMMs in Pfam, Panther and TIGR shows that MURF1 is a Complex I protein, but without specifying the exact subunit. Therefore, we constructed profile HMMs for each individual subunit, using all available sequences clustered at various identity thresholds. HMM-HMM comparison of these individual NADH subunits against MURF1 clearly identifies this hypothetical protein as NAD2. Further, we collected the relevant experimental information about kinetoplastids, which provides additional evidence in support of this prediction.
  
  
  CONCLUSIONS
  Our in silico analyses provide convincing evidence for MURF1 being a highly divergent member of NAD2.
authors.affiliation: Robert Cedergren Research Center for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, Québec, H3T 1J4, Canada. sivakumar.kannan@umontreal.ca
authors.forename: Sivakumar
authors.initials: S
authors.lastname: Kannan
authors.forename: Gertraud
authors.initials: G
authors.lastname: Burger
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001185:Artificial Intelligence; D019295:Computational Biology / Q000379:methods*; D054629:Genome, Mitochondrial; D016830:Kinetoplastida / Q000201:enzymology / Q000235:genetics*; D008390:Markov Chains; D008969:Molecular Sequence Data; D009245:NADH Dehydrogenase / Q000235:genetics*; D016366:Open Reading Frames; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein
chemical_list: D009245:NADH Dehydrogenase