Open Access Highly Accessed Research article

Structural and evolutionary divergence of eukaryotic protein kinases in Apicomplexa

Eric Talevich1, Amar Mirza2 and Natarajan Kannan12*

Author Affiliations

1 Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA

2 Department of Biochemistry, University of Georgia, Athens, GA 30602, USA

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BMC Evolutionary Biology 2011, 11:321  doi:10.1186/1471-2148-11-321

Published: 2 November 2011

Additional files

Additional file 1:

Kinome annotations. Zip archive of hierarchical kinase classifications for each gene in the kinomes of each apicomplexan, plus P. marinus and T. pseudonana. Each file contains two tab-separated columns listing each gene's accession and kinase family assignment. Accessions are taken from the sources listed in Table 2.

Format: ZIP Size: 16KB Download file

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Additional file 2:

CMGC kinase family sizes. Number of copies of each conserved CMGC kinase family in each of the surveyed genomes.

Format: CSV Size: 1KB Download file

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Additional file 3:

CDK-SCTTLRE subfamily FASTA alignment. Plain-text alignment of the kinase domains of the 14 sequences belonging to proposed CDK subfamily ("SCTTLRE"), in FASTA format.

Format: FASTA Size: 10KB Download file

Open Data

Additional file 4:

CDK-SCTTLRE subfamily CHAIN alignment versus the CDK family. Colorized sequence alignment and partition generated by the CHAIN program, comparing the apicomplexan-specific subfamily of CDKs to a diverse set of eukaryotic CDKs. CHAIN compares a given "query" set (here, members of the putative subfamily) to a larger "main" set (here, a diverse set of eukaryotic CDKs) and divides the main set into 3 partitions based on contrasting levels of residue conservation: a "foreground" set of sequences with residue motifs matching the query, a "background" which does not conserve the distinguishing motifs of the foreground, and an "intermediate" which contains sequences that may partially match both the foreground and background sequence motifs. The alignment summary generated by CHAIN displays only the aligned sequences in the query, but highlights the alignment columns according to the conservation patterns defining each partition. The alignment appears as three blocks, labeled "Intermediate", "Background" and "Foreground", corresponding to those partitions. Above each block is a histogram indicating residue conservation patterns unique to that sequence set; dots above each column indicate which columns form the distinguishing pattern. Thus, tall red bars above columns in the "Foreground" block indicate residues that are strikingly conserved in the foreground, but not in the background. The rows below each "Background" and "Foreground" block indicate the conserved residue types and their conservation levels within those sequence sets, in units of 10%.

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Additional file 5:

CDK-SCTTLRE subfamily CHAIN alignment versus the CDC2 subfamily. Colorized sequence alignment and partition generated by the CHAIN program, comparing the apicomplexan-specific subfamily of CDKs to eukaryotic CDC2 subfamily members.

Format: PDF Size: 220KB Download file

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Additional file 6:

CDPK subfamily FASTA alignment. Plain-text alignment of the 76 kinase domain sequences belonging to the proposed CDPK subfamily, in FASTA format.

Format: FASTA Size: 37KB Download file

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Additional file 7:

CDPK subfamily CHAIN alignment. Colorized sequence alignment and partition generated by the CHAIN program, comparing the lineage-specific subfamily of CDPKs to a large set of chromalveolate CDPKs.

Format: PDF Size: 152KB Download file

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Additional file 8:

CpCDPK2 and MAPK structure alignment for PyMOL. PyMOL script to superimpose structures of CpCDPK2 and phosphorylated mammalian p38α, a MAP kinase. The structures are automatically downloaded from the wwPDB server and aligned within PyMOL. Constrastingly conserved CpCDPK2 residues identified by CHAIN, and the equivalents in p38α, are highlighted as sticks. The reader is encouraged to explore nearby side chains and other features using the built-in capabilities of PyMOL.

Format: PML Size: 2KB Download file

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Additional file 9:

Alignment of selected CDPK subfamily and MAPK sequences. Annotated alignment of CDPK subfamily representatives CpCDPK2 and PfCDPK5 with human MAPK sequences p38, JNK1 and ERK1. GUIDANCE [100] was used to align the sequence segments, calculate reliability scores, and generate the initial version of the figure, to which we added further annotations.

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Additional file 10:

CLK family FASTA alignment. Plain-text alignment of the kinase domains of 33 sequences belonging to a divergent clade of CLK, in FASTA format.

Format: FASTA Size: 19KB Download file

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Additional file 11:

CLK family CHAIN alignment. Colorized sequence alignment and partition generated by the CHAIN program, comparing the apicomplexan-specific subfamily of CLKs to a diverse set of eukaryotic CLKs.

Format: PDF Size: 180KB Download file

This file can be viewed with: Adobe Acrobat Reader

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Additional file 12:

CLK family structure alignment for PyMOL. PyMOL script to superimpose structures of PfLAMMER and human Clk2 and Clk3. Constrastingly conserved PfLAMMER residues identified by CHAIN, and the equivalents in the human CLKs, are highlighted as sticks.

Format: PML Size: 4KB Download file

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