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87  structures 6413  species 3  interactions 16907  sequences 28  architectures

Clan: RAMPS-Cas5-like (CL0362)


CRISPR-associated (Cas) Repair Associated Mysterious Proteins Add an annotation

This group of families is one of several protein families that are always found associated with prokaryotic CRISPRs, themselves a family of clustered regularly interspaced short palindromic repeats, DNA repeats found in nearly half of all bacterial and archaeal genomes. These DNA repeat regions have a remarkably regular structure: unique sequences of constant size, called spacers, sit between each pair of repeats [1]. It has been shown that the CRISPRs are virus-derived sequences acquired by the host to enable them to resist viral infection. The Cas proteins from the host use the CRISPRs to mediate an antiviral response. After transcription of the CRISPR, a complex of Cas proteins termed Cascade cleaves a CRISPR RNA precursor in each repeat and retains the cleavage products containing the virus-derived sequence. Assisted by the helicase Cas3, these mature CRISPR RNAs then serve as small guide RNAs that enable Cascade to interfere with virus proliferation [2]. Cas5 contains an endonuclease motif, whose inactivation leads to loss of resistance, even in the presence of phage-derived spacers [3].

This clan contains 7 families and the total number of domains in the clan is 16907. The clan was built by A Bateman and P Coggill.

Literature references

  1. Haft DH, Selengut J, Mongodin EF, Nelson KE; , PLoS Comput Biol. 2005;1:e60.: A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PUBMED:16292354 EPMC:16292354
  2. Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, Dickman MJ, Makarova KS, Koonin EV, van der Oost J;, Science. 2008;321:960-964.: Small CRISPR RNAs guide antiviral defense in prokaryotes. PUBMED:18703739 EPMC:18703739
  3. Sorek R, Kunin V, Hugenholtz P;, Nat Rev Microbiol. 2008;6:181-186.: CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea. PUBMED:18157154 EPMC:18157154


This clan contains the following 7 member families:

Cas6 Cas_Cas5d Cas_Cas6 Cas_Cmr3 CRISPR_assoc DUF2276 RAMPs

Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

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The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
RAMPs (PF03787) 5395 (31.9%) View
Cas_Cas5d (PF09704) 4682 (27.7%) View
CRISPR_assoc (PF08798) 2803 (16.6%) View
DUF2276 (PF10040) 2256 (13.3%) View
Cas_Cas6 (PF01881) 1211 (7.2%) View
Cas_Cmr3 (PF09700) 387 (2.3%) View
Cas6 (PF09559) 173 (1.0%) View
Total: 7 Total: 16907 Clan alignment

Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.

Family relationships

This diagram shows the relationships between members of this clan. More...

Species distribution

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This tree shows the occurrence of the domains in this clan across different species. More...



There are 3 interactions for this clan. More...

Interacting families
Cas_Cas6 Cas_Cas6
Cas_Cmr3 DUF3692
CRISPR_assoc CRISPR_assoc


For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

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