PMC

A representative selection of Cas1 protein sequences were aligned using ClustalW, and columns with greater than 20% gaps were removed. A neighbor-joining tree was calculated in Belvu using the Storm and Sonnhammer distance correction. Trees calculated using more computationally intensive methods showed insignificant differences.
^aFrom the preliminary annotation of the Haloferax volcanii genome, currently sequenced at The Institute for Genomic Research (http://www.tigr.org/tdb/mdb/mdbinprogress.html).

The taxonomy of each species/strain is indicated on the left side of the figure. The CRISPR/cas loci of a number of illustrative examples for the different CRISPR subtypes are displayed on the right side of the figure.
^a E. coli K12-MG1655, O157:H7 EDL933, and O157:H7 VT2-Sakai.
^b Salmonella enterica Paratyphi ATCC9150, serovar Typhi CT18, and Ty2; Salmonella typhimurium LT2 SGSC1412.
^c Y. pestis CO92, KIM, and biovar Mediaevalis 91001; Yersinia pseudotuberculosis IP32593.
^d“p” indicates a partial cluster lacking some of the genes usually associated with this subtype, the repeats, or both. Such clusters may represent autonomous functional units, degradation from the common subtype, or cases in which the missing components are supplied by distantly located CRISPR clusters within the same genome.