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Conserved domains on  [gi|2077348319|ref|WP_220095130|]
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Cas9 endonuclease PAM-interacting domain-containing protein [Ligilactobacillus salivarius]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Cas9_PI super family cl24973
PAM-interacting domain of CRISPR-associated endonuclease Cas9; Cas9_PI is a family found at ...
 2-167 6.58e-18

PAM-interacting domain of CRISPR-associated endonuclease Cas9; Cas9_PI is a family found at the C-terminal of bacterial type II CRISPR system Cas9 endonuclease. This domain adopts a novel protein fold that is unique to the Cas9 family. It is positioned in the structure-DNA-complex to recognize the PAM sequence on the non-complementary DNA strand of the crRNA. PAM sequence is protospacer-adjacent motifs on DNA. See family CRISPR-DR2, Rfam:RF01315. Cas9 carries two nuclease domains, HNH and RuvC, which cleave the DNA strands that are complementary and non-complementary to the 20 nucleotide guide sequence in crRNAs, respectively.


The actual alignment was detected with superfamily member pfam16595:

Pssm-ID: 435449  Cd Length: 264  Bit Score: 78.13  E-value: 6.58e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077348319   2 LDKVYYGQLIIDGGQKYTLGSSEYK---YNAMQLHLSERALKILAK-----EKIKDAKVTDK------ELVDVYEEILSV 67
Cdd:pfam16595  96 LPKIKKNSLIKIDGFRMLLTGKTENrllKNAVQLVLSNDDEKYIKKiekfvKKNKDDIIEEKdglteeKNIKLYDELLDK 175

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077348319  68 VNKHFELYDISKFRQKLNEGLELFKELPIYNvyesnkikqvgKFEVLNRILIGLHANAMRTDLKVLGIKVNLGQMQVKGG 147
Cdd:pfam16595 176 MKNTIYYKRPSNQGEKLEKLKEKFIKLSLEE-----------KCKVLIEILKLTHANPTSADLKLIGGSKHAGRIKISNN 244

                         170       180
                  ....*....|....*....|
gi 2077348319 148 IKLSPDAKLIYQSPTGIFSR 167
Cdd:pfam16595 245 ISKASNIKLINQSVTGLYEK 264
 
Name Accession Description Interval E-value
Cas9_PI pfam16595
PAM-interacting domain of CRISPR-associated endonuclease Cas9; Cas9_PI is a family found at ...
 2-167 6.58e-18

PAM-interacting domain of CRISPR-associated endonuclease Cas9; Cas9_PI is a family found at the C-terminal of bacterial type II CRISPR system Cas9 endonuclease. This domain adopts a novel protein fold that is unique to the Cas9 family. It is positioned in the structure-DNA-complex to recognize the PAM sequence on the non-complementary DNA strand of the crRNA. PAM sequence is protospacer-adjacent motifs on DNA. See family CRISPR-DR2, Rfam:RF01315. Cas9 carries two nuclease domains, HNH and RuvC, which cleave the DNA strands that are complementary and non-complementary to the 20 nucleotide guide sequence in crRNAs, respectively.


Pssm-ID: 435449  Cd Length: 264  Bit Score: 78.13  E-value: 6.58e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077348319   2 LDKVYYGQLIIDGGQKYTLGSSEYK---YNAMQLHLSERALKILAK-----EKIKDAKVTDK------ELVDVYEEILSV 67
Cdd:pfam16595  96 LPKIKKNSLIKIDGFRMLLTGKTENrllKNAVQLVLSNDDEKYIKKiekfvKKNKDDIIEEKdglteeKNIKLYDELLDK 175

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077348319  68 VNKHFELYDISKFRQKLNEGLELFKELPIYNvyesnkikqvgKFEVLNRILIGLHANAMRTDLKVLGIKVNLGQMQVKGG 147
Cdd:pfam16595 176 MKNTIYYKRPSNQGEKLEKLKEKFIKLSLEE-----------KCKVLIEILKLTHANPTSADLKLIGGSKHAGRIKISNN 244

                         170       180
                  ....*....|....*....|
gi 2077348319 148 IKLSPDAKLIYQSPTGIFSR 167
Cdd:pfam16595 245 ISKASNIKLINQSVTGLYEK 264
 
Name Accession Description Interval E-value
Cas9_PI pfam16595
PAM-interacting domain of CRISPR-associated endonuclease Cas9; Cas9_PI is a family found at ...
 2-167 6.58e-18

PAM-interacting domain of CRISPR-associated endonuclease Cas9; Cas9_PI is a family found at the C-terminal of bacterial type II CRISPR system Cas9 endonuclease. This domain adopts a novel protein fold that is unique to the Cas9 family. It is positioned in the structure-DNA-complex to recognize the PAM sequence on the non-complementary DNA strand of the crRNA. PAM sequence is protospacer-adjacent motifs on DNA. See family CRISPR-DR2, Rfam:RF01315. Cas9 carries two nuclease domains, HNH and RuvC, which cleave the DNA strands that are complementary and non-complementary to the 20 nucleotide guide sequence in crRNAs, respectively.


Pssm-ID: 435449  Cd Length: 264  Bit Score: 78.13  E-value: 6.58e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077348319   2 LDKVYYGQLIIDGGQKYTLGSSEYK---YNAMQLHLSERALKILAK-----EKIKDAKVTDK------ELVDVYEEILSV 67
Cdd:pfam16595  96 LPKIKKNSLIKIDGFRMLLTGKTENrllKNAVQLVLSNDDEKYIKKiekfvKKNKDDIIEEKdglteeKNIKLYDELLDK 175

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2077348319  68 VNKHFELYDISKFRQKLNEGLELFKELPIYNvyesnkikqvgKFEVLNRILIGLHANAMRTDLKVLGIKVNLGQMQVKGG 147
Cdd:pfam16595 176 MKNTIYYKRPSNQGEKLEKLKEKFIKLSLEE-----------KCKVLIEILKLTHANPTSADLKLIGGSKHAGRIKISNN 244

                         170       180
                  ....*....|....*....|
gi 2077348319 148 IKLSPDAKLIYQSPTGIFSR 167
Cdd:pfam16595 245 ISKASNIKLINQSVTGLYEK 264
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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