Abstract
In a genome the set of proteins are formed by duplication and combination of domain superfamilies. P-loop containing nucleotide triphosphate (NTP) hydrolases superfamily is massively duplicated and has the most different partner superfamilies among archaea, bacteria and eukarya. Here, we study the distributions of duplication and combination of p-loop containing NTP hydrolases superfamily in 169 completed genomes. When the total number of domains in a genome is larger, duplication and combination partners of p-loop containing NTP hydrolases are more. This phenomenon is more obvious in metazoa. The distributions of abundance and combination of partners relate to the functions of the protein. Those distributions in metazoa are very different from those in other kingdoms because of complexity of metazoa. Finally the relationship between duplication and combination of p-loop containing NTP hydrolases superfamily in different genomes is described. It fits a power law.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Vogel C, Teichmann S A, Pereira L J. The Relationship between Domain Duplication and Recombination [J].J Mol Biol, 2005,346(1):355–365.
Chothia C, Gough J, Vogel C,et al. Evolution of the Protein Repertoire [J].Science, 2003,300:1701–1703.
Muller A, Maccallum R M, Stemberg M J. Structural Characterization of the Human Proteome [J].Genome Res, 2002,12:1625–1641.
Vogel C, Bashton M, Kerrison N D,et al. Structure, Function and Evolution of Multidomain Proteins [J].Curr Opin Struct Biol, 2004,14:208–216.
Qian J, Luscombe N M, Gerstein M. Protein Family and Fold Occurrence in Genomes: Power-Law Behaviour and Evolutionary Model [J].J Mol Biol, 2001,313:673–681.
Apic G, Gough J, Teichmann S A. Domain Combinations in Archael, Eubacterial and Eukaryotic Proteomes [J].J Mol Biol, 2001,310:311–325.
Murzin A, Brenner S E, Hubbard T,et al. SCOP: A Structural Classification of Proteins Database for the Investigation of Sequences and Structures [J].J Mol Biol, 1995,247: 536–540.
Madera M, Vogel C, Kummerfeld S K. The Superfamily Database in 2004: Addition and Improvements [J].Nucl Acids Res, 2004,32:D235-D239.
Gough J, Chothia C. Superfamily: HMMs Representing all Proteins of Known Structure. SCOP Sequence Searches, Alignments and Genome Assignments [J].Nucleic Acids Res, 2002,30:268–272.
Gough J, Karplus K, Hughey R,et al. Assignment of Homology to Genome Sequences Using a Library of Hidden Markov Models that Represent All Proteins of Known Structure [J].J Mol Biol, 2001,313:903–919.
Yang S, Doolittle R F, Bourne P. Phylogeny Determined by Protein Domain Conten [J].Proc Natl Acad Sci, 2005,102 (2):373–378.
Author information
Authors and Affiliations
Additional information
Foundation item: Supported by the National Natural Science Foundation of China (10374072)
Biography: SANG Jianping(1959-), male. Professor, Ph.D., research direction: soft condensed matter.
Rights and permissions
About this article
Cite this article
Jianping, S., Wei, G. & Xianwu, Z. Duplication and combination of P-loop containing nucleotide triphosphate hydrolases superfamily. Wuhan Univ. J. Nat. Sci. 11, 577–580 (2006). https://doi.org/10.1007/BF02836668
Received:
Issue Date:
DOI: https://doi.org/10.1007/BF02836668