Supplemental Material

This article contains the following supporting material:

• Supplemental Data 1 - ARP containing chromatin modulating complexes.
• Supplemental Data 2 - Selected query protein sequences for each ARP subfamily. The 37 identification (ID) and/or accession (AC) numbers are from the Uniprot database.
• Supplemental Data 3 - List of sequences present in ARP-MACS with identification, accession number, description and organism designation from Uniprot database.
• Supplemental Data 4 - List of equivalent positions in ARP-MACS and in conventional actin, with secondary structure positions.
• Supplemental Data 5 - List of insertions and deletions for ARP subfamilies. Positions are given according to the reference actin sequence (P02568). Conserved insertions or deletions in an ARP subfamily are highlighted in green and bold.
• Supplemental Data 6 - Summary of the presence/absence searches. Black dots (·) represent the presence and minus signs (-) the absence (or lack of detection) of a gene or a protein in a given organism. The grey columns, marked P (at the bottom) are obtained using BlastP similarity searches in protein databases, whereas the white columns, marked G, represent genomic sequence searches with the TBlastN program.
• Supplemental Figure 1 - The phylogenetic tree was built with Phylo_win (Galtier et al., 1996) on complete ARP sequences (excluding orphans) available in ARP-MACS. The program was used with parameters set to pairwise gap removal using the neighbor joining method. Branches were tested by bootstrapping (500 replicates) and the tree was edited and displayed with ATV (Zmasek and Eddy, 2001).

  Galtier, N., Gouy, M., and Gautier, C. (1996). SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12, 543-548.

  Zmasek, C.M., and Eddy, S.R. (2001). ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics 17, 383-384.