Table 1.

Classification of Cas protein subtypes

subtype name*	Reference organism	core genes	subtype-specific genes
Ecoli	Escherichia coli	cas1–cas3	cse1–cse4 and cas5e‡
Ypest	Yersinia pestis	cas1–cas3	csy1–csy4
Nmeni	Neisseria meningitidis	cas1-cas2	csn1–csn2
Dvulg	Desulfovibrio vulgaris	cas1-cas4	csd1–csd2 and cas5d‡
Tneap	Thermotoga neapolitana	cas1–cas4 and cas6	cst1–cst2 and cas5t‡
Hmari	Haloarcula marismortui	cas1–cas4 and cas6	csh1–csh2 and cas5h‡
Apern	Aeropyrum pernix	cas1–cas6	csa1–csa5
Mtube	Mycobacterium tuberculosis	cas1–cas2 and cas6	csm1–csm5
RAMP module§	-	None	cmr1–cmr6

^*As described in Haft et al.²⁸ and adopted by the Integrated Microbial Genomes data management system (http://img.jgi.doe.gov). Each CRISPR subtype is named after a reference genome in which there is only one CRISPR locus.

^‡Many members of the Cas5 family contain a conserved amino-terminal domain, but the rest of the sequence seems to be subtype-specific with no conservation across other subtypes. Therefore, cas5 gene names are followed by a letter denoting the subtype to which they belong.

^§The RAMP superfamily was found to be linked to CRISPR loci by Makarova et al.³¹. The Cas module RAMP — which contains six genes, cmr1–cmr6 — is present in a range of bacteria and archaea and does not seem to exist as an autonomous functional unit; instead it is always associated with one of the other eight CRISPR subtypes. Cas, CRISPR-associated; CRISPR, clustered, regularly interspaced short palindromic repeat; RAMP, repeat-associated mysterious protein.