bioRxiv preprint doi: https://doi.org/10.1101/2021.05.03.442417; this version posted May 16, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Open issues for protein function assignment in Haloferax volcanii and other halophilic archaea. Friedhelm Pfeiffer1# and Mike Dyall-Smith1,2 1Computational Biology Group, Max-Planck-Institute of Biochemistry, Martinsried, Germany 2Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Australia Corresponding authors addresses: Dr. Friedhelm Pfeiffer Computational Biology Group, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany e-mail:
[email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.05.03.442417; this version posted May 16, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Abstract 2 3 Background: Annotation ambiguities and annotation errors are a general challenge in 4 genomics. While a reliable protein function assignment can be obtained by 5 experimental characterization, this is expensive and time-consuming, and the number 6 of such Gold Standard Proteins (GSP) with experimental support remains very low 7 compared to proteins annotated by sequence homology, usually through automated 8 pipelines. Even a GSP may give a misleading assignment when used as a reference: 9 the homolog may be close enough to support isofunctionality, but the substrate of the 10 GSP is absent from the species being annotated.