BMC Genomics 2008, 9:308 http://www.biomedcentral.com/1471-2164/9/308 36. Brunk BP, Martin EC, Adler PN: Drosophila genes Posterior Sex Combs and Suppressor two of zeste encode proteins with homology to the murine bmi-1 oncogene. Nature 1991, 353:351-3. 37. van Lohuizen M, Frasch M, Wientjens E, Berns A: Sequence simi- larity between the mammalian bmi-1 proto-oncogene and the Drosophila regulatory genes Psc and Su(z)2. Nature 1991, 353:353-5. 38. Kyba M, Brock HW: The Drosophila polycomb group protein Psc contacts ph and Pc through specific conserved domains. Mol Cell Biol 1998, 18:2712-20. 39. Alkema MJ, Bronk M, Verhoeven E, Otte A, van 't Veer LJ, Berns A, van Lohuizen M: Identification of Bmi1-interacting proteins as constituents of a multimeric mammalian polycomb com- plex. Genes Dev 1997, 11:226-40. 40. Satijn DP, Otte AP: Polycomb group protein complexes: do dif- ferent complexes regulate distinct target genes? Biochim Bio- phys Acta 1999, 1447:1-16. 41. Altschul S, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lip- man DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-402. 42. UniProt [http://www.ebi.uniprot.org/] 43. NBCI [http://www.ncbi.nlm.nih.gov] 44. ENSEMBL [http://www.ensembl.org] 45. JGI [http://www.jgi.doe.gov/] 46. Notredame C, Higgins D, Heringa J: T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000, 302:205-17. 47. Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O'Donovan C, Redaschi N, Suzek B: The Universal Protein Resource (UniProt): an expanding universe of pro- tein information. Nucleic Acids Res 2006, 34:D187-91. 48. Eddy SR: Hidden Markov models. Curr Opin Struct Biol 1996, 6:361-365. 49. Soding J: Protein homology detection by HMM-HMM compar- ison. Bioinformatics 2005, 21:951-60. 50. Cho N, Kingston D, Chang H, Kwon EK, Kim JM, Lee JH, Chu H, Choi MS, Kim IS, Jung JU: Association of herpesvirus saimiri tip with lipid raft is essential for downregulation of T-cell receptor and CD4 coreceptor. J Virol 2006, 80:108-18. 51. Park J, Lee BS, Choi JK, Means RE, Choe J, Jung JU: Herpesviral pro- tein targets a cellular WD repeat endosomal protein to downregulate T lymphocyte receptor expression. Immunity 2002, 17:221-33. 52. Park J, Cho NH, Choi JK, Feng P, Choe J, Jung JU: Distinct roles of cellular Lck and p80 proteins in herpesvirus saimiri Tip func- tion on lipid rafts. J Virol 2003, 77:9041-51. 53. Vijay-Kumar S, Bugg CE, Wilkinson KD, Vierstra RD, Hatfield PM, Cook WJ: Comparison of the three-dimensional structures of human, yeast and oat ubiquitin. J Biol Chem 1987, 262:6396-9. 54. Kiel C, Serrano L: The ubiquitin domain superfold: structure- based sequence alignments and characterization of binding epitopes. J Mol Biol 2006, 355:821-44. 55. Rost B: PHD: predicting one-dimensional protein structure by profile-based neural networks. Methods Enzymol 1996, 266:525-539. 56. McGuffin L, Jones D: Benchmarking secondary structure pre- diction for fold recognition. Proteins 2003, 52:166-75. 57. Melo F, Sanchez R, Sali A: Statistical potentials for fold assess- ment. Protein Sci 2002, 11:430-48. 58. Bork P, Holm L, Sander C: The immunoglobulin fold. Structural classification, sequence patterns and common core. J Mol Biol 1994, 242:309-20. 59. Scalley-Kim M, Minard P, Baker D: Low free energy cost of very long loop insertions in proteins. Protein Sci 2003, 12:197-206. 60. Czypionka A, de los Paños OR, Mateu MG, Barrera FN, Hurtado- Gómez E, Gómez J, Vidal M, Neira JL: The isolated C-Terminal domain of Ring1B is a dimer made od stable, well-structured monomers. Biochemistry 2007, 46:12764-12776. 61. Jentsch S, Pyrowolakis G: Ubiquitin and its kin: how close are the family ties? Trends Cell Biol 2000, 10:335-42. 62. Buchberger A: From UBA to UBX: new words in the ubiquitin vocabulary. Trends Cell Biol 2002, 12:216-21. 63. Buchberger A, Howard M, Proctor M, Bycroft M: The UBX domain: a widespread ubiquitin-like module. J Mol Biol 2001, 307:17-24. 64. Yuan X, Shaw A, Zhang X, Kondo H, Lally J, Freemont PS, Matthews S: Solution structure and interaction surface of the C-termi- nal domain from p47: a major p97-cofactor involved in SNARE disassembly. J Mol Biol 2001, 311:255-263. 65. Safadi SS, Shaw GS: A Disease State Mutation Unfolds the Par- kin Ubiquitin-like Domain. Biochemistry 2007, 46:14162-14169. 66. Fallon L, Bélanger CM, Corera AT, Kontogiannea M, Regan-Klapisz E, Moreau F, Voortman J, Haber M, Rouleau G, Thorarinsdottir T, Brice A, En Henegouwen PM van Bergen, Fon EA: A regulated interac- tion with the UIM protein Eps15 implicates parkin in EGF receptor trafficking and PI(3)K-Akt signalling. Nat Cell Biol 2006, 8:834-42. 67. Dreveny I, Kondo H, Uchiyama K, Shaw A, Zhang X, Freemont PS: Structural basis of the interaction between the AAA ATPase p97/VCP and its adaptor protein p47. EMBO J 2004, 23:1030-1039. 68. Park S, Rancour DM, Bednarek SY: Protein Domain-Domain Interactions and Requirements for the Negative Regulation of Arabidopsis CDC48/p97 by the Plant Ubiquitin Regulatory X (UBX) Domain-containing Protein, PUX1. J Biol Chem 2007, 282:5217-5224. 69. Andrade M, Perez-Iratxeta C, Ponting C: Protein repeats: struc- tures, functions, and evolution. J Struct Biol 2001, 134:117-131. 70. Higa L, Zhang H: Stealing the spotlight: CUL4-DDB1 ubiquitin ligase docks WD40-repeat proteins to destroy. Cell Div 2007, 6:2-5. 71. Zhu X, Menard R, Sulea T: High incidence of ubiquitin-like domains in human ubiquitin-specific proteases. Proteins 2007, 69:1-7. 72. Bronner C, Achour M, Arima Y, Chataigneau T, Saya H, Schini-Kerth VB: The UHRF family: Oncogenes that are drugable targets for cancer therapy in the near future? Pharmacol Ther 2007, 115:419-434. 73. Stone SL, Hauksdóttir H, Troy A, Herschleb J, Kraft E, Callis J: Func- tional analysis of the RING-type ubiquitin ligase family of Arabidopsis. Plant Physiol 2005, 137:13-30. 74. TAIR [http://www.arabidopsis.org/] 75. Whitcomb S, Basu A, Allis C, Bernstein E: Polycomb Group pro- teins: an evolutionary perspective. Trends Genet 2007, 23:494-502. 76. Gough J: Convergent evolution of domain architectures (is rare). Bioinformatics 2005, 21:1464-71. 77. Fong Y, Bender L, Wang W, Strome S: Regulation of the different chromatin states of autosomes and X chromosomes in the germ line of C. elegans. Science 2002, 296:2235-2238. 78. Sonnhammer EL, Hollich V: Scoredist: a simple and robust pro- tein sequence distance estimator. BMC Bioinformatics 2005, 6:108. 79. Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4:406-25. 80. Higgins DG, Thompson JD, Gibson TJ: Using CLUSTAL for mul- tiple sequence alignments. Methods Enzymol 1996, 266:383-402. 81. Maciukenas M: Treetool 2.0.2. 1994 [http://iubio.bio.indiana.edu/ soft/molbio/unix/treetool]. 82. Felsenstein J: Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791. 83. Sali A, Blundell TL: Comparative protein modelling by satisfac- tion of spatial restraints. J Mol Biol 1993, 234:779-815. 84. Knight D, Harris R, McAlister MS, Phelan JP, Geddes S, Moss SJ, Dris- coll PC, Keep NH: The X-ray crystal structure and putative lig- and-derived peptide binding properties of gamma- aminobutyric acid receptor type A receptor-associated pro- tein. J Biol Chem 2002, 277:5556-61. 85. DeLano WL: Unraveling hot spots in binding interfaces: progress and challenges. Curr Opin Struct Biol 2002, 12:14-20. 86. Holm L, Sander C: Dali: a network tool for protein structure comparison. Trends Biochem Sci 1995, 20:478-80. 87. Ramelot T, Cort JR, Yee AA, Semesi A, Edwards AM, Arrowsmith CH, Kennedy MA: Solution structure of the yeast ubiquitin-like modifier protein Hub1. J Struct Funct Genomics 2003, 4:25-30. Page 10 of 11 (page number not for citation purposes)