Open Access Highly Accessed Research article

Molecular evolution of cyclin proteins in animals and fungi

Konstantin V Gunbin1*, Valentin V Suslov1, Igor I Turnaev1, Dmitry A Afonnikov12 and Nikolay A Kolchanov12

  • * Corresponding author: Konstantin V Gunbin genkvg@gmail.com

  • † Equal contributors

Author Affiliations

1 Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev ave., 10, Novosibirsk, Russia

2 Novosibirsk state University, Pirogova, 2, Novosibirsk, Russia

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BMC Evolutionary Biology 2011, 11:224  doi:10.1186/1471-2148-11-224

Published: 28 July 2011

Additional files

Additional file 1:

The packed archive contains files with multiple alignments of A-, B-, D-, and E- cyclin protein sequences in FASTA format.

Format: GZ Size: 52KB Download file

Open Data

Additional file 2:

The packed archive contains files with gapless multiple alignments of A-, B-, D-, and E- cyclin proteins with reconstructed ancestors in FASTA format.

Format: GZ Size: 42KB Download file

Open Data

Additional file 3:

The packed archive contains FASTA-like text files. Each text file contains space delimited numbers representing reconstruction probabilities of ancestral amino acids in internal tree nodes of A-, B-, D-, and E- cyclin phylogenetic trees for each ancestral sequence.

Format: GZ Size: 154KB Download file

Open Data

Additional file 4:

The packed archive contains amino acid replacement matrices (in PAML format) for A-, B-, D-, and E- cyclin protein families. Each matrix file contains additional information for INDELIBLE simulations: the proportion of invariable sites; the shape parameter for the gamma distribution; the number of categories for use in the discrete gamma approximation.

Format: GZ Size: 3KB Download file

Open Data

Additional file 5:

The packed archive contains MS Excel 2007 files. Each file represents the data on expected and observed number of amino acid replacements on each branch of the A-, B-, D-, and E- cyclin protein trees with probabilities p of its observation according to the stationary and homogeneous Markov model of protein evolution. These Excel files also contain the phylogenetic trees with ancestral node labels.

Format: GZ Size: 3.2MB Download file

Open Data

Additional file 6:

The packed archive contains MS Excel 2007 files. Each file represents the following data: (1) the expected and observed numbers of amino acid replacements for each secondary structure element of animal A-, B-, B3-, D- and E-cyclins and fungal B-cyclins; (2) the probabilities p of its observation under the assumption that fixed replacements are distributed evenly in the protein.

Format: GZ Size: 364KB Download file

Open Data

Additional file 7:

The packed archive contains Accelrys Discovery Studio *msv files. Each file contains 3D protein structure with mapped sites containing atypical amino acid replacements (in blue).

Format: GZ Size: 639KB Download file

Open Data

Additional file 8:

MS Excel 2007 file contains the number of protein-protein interactions for different paralogs of the A-, B- D-, and E- cyclin proteins according to data deposited in the I2D (Version 1.72), HPRD (Release 8) and DroID (Version 5.0) databases.

Format: XLSX Size: 47KB Download file

Open Data