Additional file 3: Information File S1. of Phylogenomics of Cas4 family nucleases

Complete tree for Cas4-like set in Newick format. Cas4 assignments are included in the leaf name. (TXT 463 kb

Additional file 7: Table S1 of Phylogenomics of Cas4 family nucleases

Worksheet “loci” provides detailed information on all cas4 loci in completely sequenced and draft genomes of archaea and bacteria. Annotation for the proteins encoded in the loci is based on Cas protein and CDD assignments using PSI-BLAST program (see Methods for details). Worksheet “tree order and assignments” provides information of the order of the Cas4 in the tree (Supplementary file 1), Cas4 assignments to distinct groups of CAS-Cas4, solo-Cas4 and others. (TXT 28 kb

Additional file 2: Figure S2. of Phylogenomics of Cas4 family nucleases

Nucleotide sequence comparisons of CRISPR-Cas loci encoded in closely related strains. On the axes, the labels contain the name of the source genome, contig ID and the coordinates of the respective loci. The annotations for CRISPR-Cas loci were taken from the Additional file 7: Table S1, “Loci” worksheet. The cartoons on the axes represent the genes and CRISPR repeats encoded in these loci. The sizes of the cartoons are proportional to the actual sizes of these genes. Colors: black are CRISPR arrays, blue are cas genes, green - cas4 gene, shaded area are the regions which have >70% sequence identity level. Left: Comparison of two I-C systems from Marinobacter strains. Right: Comparison of two I-B systems from Campylobacter strains. (DOCX 606 kb

Additional file 1: Figure S1. of Phylogenomics of Cas4 family nucleases

Schematic representation of the maximum likelihood phylogenetic tree of Cas4 (7060 sequences all together), available in the Supplementary File 1. Support values are calculated by FastTRee program only for the confidently aligned groups, all other values were assigned to zero automatically. Major well-supported distinct branches are shown by rectangles which are color-coded according to Cas4 assignments. Assignments and other comments are shown next to the each collapsed branch. Individual sequences in the tree are described by a local numeric ID, species name and color-coded according to Cas4 assignment (also provided in the Additional file 7: Table S1). Blue shading shows tree clades that belong to pfam12705 family. (PDF 694 kb

Additional file 6: Information File S4. of Phylogenomics of Cas4 family nucleases

Complete tree for selected representatives of UvrD family in Newick format. The tree is based on the helicase domain alignment. Protein linked to Cas4 are indicated in the respective leaf names. (DOCX 51 kb

Additional file 4: Information File S2. of Phylogenomics of Cas4 family nucleases

Breakdown of CAS-Cas4 and solo-Cas4 presence in completely sequenced genomes. (XLSX 248 kb

Additional file 5: Information File S3. of Phylogenomics of Cas4 family nucleases

Detailed description of the Cas4 dN/dS analysis, table with results. (DOCX 51 kb