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Conserved domains on  [gi|2279656847|ref|WP_256335429|]
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MULTISPECIES: CRISPR-associated endonuclease Cas2 [Listeria]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Cas2_I_II_III super family cl11442
CRISPR/Cas system-associated protein Cas2; CRISPR (Clustered Regularly Interspaced Short ...
 1-98 2.06e-28

CRISPR/Cas system-associated protein Cas2; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas2 is present in majority of CRISPR/Cas systems along with Cas1; RNAse specific to U-rich regions; Possesses an RRM/ferredoxin fold


The actual alignment was detected with superfamily member COG3512:

Pssm-ID: 472181  Cd Length: 116  Bit Score: 99.17  E-value: 2.06e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2279656847   1 MLFFDLPMNTKHERKVYTRFRKYLINNGFTMVQFSVYSKIFPNRSSLDSYLIGLRASVPKNGSVRAMAVTEKQYGKMMIL 80
Cdd:COG3512    10 ILMFDLPTDTAAERKAANKFRQFLLKDGYQMLQFSVYSRILKGRDSNQKHIGRLREHLPNEGNIRCLEVTEKQFARMKLL 89

                          90
                  ....*....|....*...
gi 2279656847  81 VGGKTLQEENITDDPLVI 98
Cdd:COG3512    90 LGELVFNEKKVNSDQLLL 107
 
Name Accession Description Interval E-value
Cas2 COG3512
CRISPR/Cas system-associated protein Cas2, endoribonuclease [Defense mechanisms];
1-98 2.06e-28

CRISPR/Cas system-associated protein Cas2, endoribonuclease [Defense mechanisms];


Pssm-ID: 226043  Cd Length: 116  Bit Score: 99.17  E-value: 2.06e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2279656847   1 MLFFDLPMNTKHERKVYTRFRKYLINNGFTMVQFSVYSKIFPNRSSLDSYLIGLRASVPKNGSVRAMAVTEKQYGKMMIL 80
Cdd:COG3512    10 ILMFDLPTDTAAERKAANKFRQFLLKDGYQMLQFSVYSRILKGRDSNQKHIGRLREHLPNEGNIRCLEVTEKQFARMKLL 89

                          90
                  ....*....|....*...
gi 2279656847  81 VGGKTLQEENITDDPLVI 98
Cdd:COG3512    90 LGELVFNEKKVNSDQLLL 107
cas2 TIGR01573
CRISPR-associated endonuclease Cas2; This model describes most members of the family of Cas2, ...
 1-98 1.86e-16

CRISPR-associated endonuclease Cas2; This model describes most members of the family of Cas2, one of the first four protein families found to mark prokaryotic genomes that contain multiple CRISPR elements. CRISPR systems protect against invasive nucleic acid sequences, including phage. Cas2 proteins have been characterized as either endoribonuclease (for ssRNA) or endodeoxyribonuclease (for dsDNA), depending on the system to which the Cas2 belongs. CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats. The cas genes usually are found near the repeats. A distinct branch of the Cas2 family shows a very low level of sequence identity and is modeled by TIGR01873 instead of by this model (TIGR01573).


Pssm-ID: 273699  Cd Length: 95  Bit Score: 67.77  E-value: 1.86e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2279656847  1 MLFFDLPmnTKHERKVYTRFRKYLINNGFTMVQFSVYSKIFPNRSSLDSYLIGLRASVPKNGSVRAMAVTEKQYGKMMIL 80
Cdd:TIGR01573  4 LVVYDIP--TDGERKRRRKLRKLLEKYGLQRVQYSVFEGILEPNQLARKLIERLKRIIPDEGSIRIYPLTEKQYAAAIVI 81

                         90
                 ....*....|....*...
gi 2279656847 81 VGGKTLQEEnitdDPLVI 98
Cdd:TIGR01573 82 GGEPVTSAE----DNLLL 95
Cas2_I_II_III cd09638
CRISPR/Cas system-associated protein Cas2; CRISPR (Clustered Regularly Interspaced Short ...
 1-84 2.15e-16

CRISPR/Cas system-associated protein Cas2; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas2 is present in majority of CRISPR/Cas systems along with Cas1; RNAse specific to U-rich regions; Possesses an RRM/ferredoxin fold


Pssm-ID: 187769  Cd Length: 90  Bit Score: 67.79  E-value: 2.15e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2279656847  1 MLFFDLPmnTKHERKVYTRFRKYLINNGFTMVQFSVYSKIFpNRSSLDSYLIGLRASVPKNGSVRAMAVTEKQYGKMMIL 80
Cdd:cd09638    4 LVVYDIP--EDTERKRRRKLRKLLEKYGLFRVQYSVFEGIL-EPNLLASLIERLKKIIPDEDSIRIYPLTEKQKTAIRIL 80


                 ....
gi 2279656847 81 VGGK 84
Cdd:cd09638   81 GGEA 84
CRISPR_Cas2 pfam09827
CRISPR associated protein Cas2; This entry represents members of the family of Cas2, one of ...
 1-75 2.67e-09

CRISPR associated protein Cas2; This entry represents members of the family of Cas2, one of the first four protein families found to be associated with prokaryotic genomes containing multiple CRISPR elements. CRISPR systems protect against invasive nucleic acid sequences, including phage. Cas2 proteins have been characterized as either endoribonuclease (for ssRNA) or endodeoxyribonuclease (for dsDNA), depending on the system to which the Cas2 belongs. The cas genes usually are found near the palindromic repeats. The structural subunit of Cas2, belongs to the VapD family of interferases. The interferase catalytic site is intact in the majority of the Cas2 proteins but is disrupted in some, and is not required for spacer acquisition. This entry also includes the endoribonuclease VapD.


Pssm-ID: 462916  Cd Length: 72  Bit Score: 49.02  E-value: 2.67e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2279656847  1 MLFFDLPmntkhERKVYTRFRKYLINNgFTMVQFSVYSKiFPNRSSLDSYLIGLRASVPKN-GSVRAMAVTEKQYG 75
Cdd:pfam09827  4 LVVYDIS-----DRKRRRKVAKILKKY-FQRVQNSVFEG-ELSEAQAEKLKKRLKKIIDPEeDSIRIYPLTDKQFS 72
 
Name Accession Description Interval E-value
Cas2 COG3512
CRISPR/Cas system-associated protein Cas2, endoribonuclease [Defense mechanisms];
1-98 2.06e-28

CRISPR/Cas system-associated protein Cas2, endoribonuclease [Defense mechanisms];


Pssm-ID: 226043  Cd Length: 116  Bit Score: 99.17  E-value: 2.06e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2279656847   1 MLFFDLPMNTKHERKVYTRFRKYLINNGFTMVQFSVYSKIFPNRSSLDSYLIGLRASVPKNGSVRAMAVTEKQYGKMMIL 80
Cdd:COG3512    10 ILMFDLPTDTAAERKAANKFRQFLLKDGYQMLQFSVYSRILKGRDSNQKHIGRLREHLPNEGNIRCLEVTEKQFARMKLL 89

                          90
                  ....*....|....*...
gi 2279656847  81 VGGKTLQEENITDDPLVI 98
Cdd:COG3512    90 LGELVFNEKKVNSDQLLL 107
cas2 TIGR01573
CRISPR-associated endonuclease Cas2; This model describes most members of the family of Cas2, ...
 1-98 1.86e-16

CRISPR-associated endonuclease Cas2; This model describes most members of the family of Cas2, one of the first four protein families found to mark prokaryotic genomes that contain multiple CRISPR elements. CRISPR systems protect against invasive nucleic acid sequences, including phage. Cas2 proteins have been characterized as either endoribonuclease (for ssRNA) or endodeoxyribonuclease (for dsDNA), depending on the system to which the Cas2 belongs. CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats. The cas genes usually are found near the repeats. A distinct branch of the Cas2 family shows a very low level of sequence identity and is modeled by TIGR01873 instead of by this model (TIGR01573).


Pssm-ID: 273699  Cd Length: 95  Bit Score: 67.77  E-value: 1.86e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2279656847  1 MLFFDLPmnTKHERKVYTRFRKYLINNGFTMVQFSVYSKIFPNRSSLDSYLIGLRASVPKNGSVRAMAVTEKQYGKMMIL 80
Cdd:TIGR01573  4 LVVYDIP--TDGERKRRRKLRKLLEKYGLQRVQYSVFEGILEPNQLARKLIERLKRIIPDEGSIRIYPLTEKQYAAAIVI 81

                         90
                 ....*....|....*...
gi 2279656847 81 VGGKTLQEEnitdDPLVI 98
Cdd:TIGR01573 82 GGEPVTSAE----DNLLL 95
Cas2_I_II_III cd09638
CRISPR/Cas system-associated protein Cas2; CRISPR (Clustered Regularly Interspaced Short ...
 1-84 2.15e-16

CRISPR/Cas system-associated protein Cas2; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas2 is present in majority of CRISPR/Cas systems along with Cas1; RNAse specific to U-rich regions; Possesses an RRM/ferredoxin fold


Pssm-ID: 187769  Cd Length: 90  Bit Score: 67.79  E-value: 2.15e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2279656847  1 MLFFDLPmnTKHERKVYTRFRKYLINNGFTMVQFSVYSKIFpNRSSLDSYLIGLRASVPKNGSVRAMAVTEKQYGKMMIL 80
Cdd:cd09638    4 LVVYDIP--EDTERKRRRKLRKLLEKYGLFRVQYSVFEGIL-EPNLLASLIERLKKIIPDEDSIRIYPLTEKQKTAIRIL 80


                 ....
gi 2279656847 81 VGGK 84
Cdd:cd09638   81 GGEA 84
Cas2 COG1343
CRISPR/Cas system-associated endoribonuclease Cas2 [Defense mechanisms]; CRISPR/Cas ...
 1-89 1.77e-09

CRISPR/Cas system-associated endoribonuclease Cas2 [Defense mechanisms]; CRISPR/Cas system-associated endoribonuclease Cas2 is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 440954  Cd Length: 89  Bit Score: 49.82  E-value: 1.77e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2279656847  1 MLFFDLPmntkhERKVYTRFRKYLINNGFTmVQFSVYSKIFPNRsSLDSYLIGLRASVPKN-GSVRAMAVTEKQYGKMMI 79
Cdd:COG1343    4 LVVYDIP-----DDKRRRKVAKLLKKYGFR-VQYSVFEGELTEA-ELAELKKRLKKIIDPEeDSVRIYPLTDKQFGKVEV 76

                         90
                 ....*....|
gi 2279656847 80 LvGGKTLQEE 89
Cdd:COG1343   77 L-GKKKDPEQ 85
CRISPR_Cas2 pfam09827
CRISPR associated protein Cas2; This entry represents members of the family of Cas2, one of ...
 1-75 2.67e-09

CRISPR associated protein Cas2; This entry represents members of the family of Cas2, one of the first four protein families found to be associated with prokaryotic genomes containing multiple CRISPR elements. CRISPR systems protect against invasive nucleic acid sequences, including phage. Cas2 proteins have been characterized as either endoribonuclease (for ssRNA) or endodeoxyribonuclease (for dsDNA), depending on the system to which the Cas2 belongs. The cas genes usually are found near the palindromic repeats. The structural subunit of Cas2, belongs to the VapD family of interferases. The interferase catalytic site is intact in the majority of the Cas2 proteins but is disrupted in some, and is not required for spacer acquisition. This entry also includes the endoribonuclease VapD.


Pssm-ID: 462916  Cd Length: 72  Bit Score: 49.02  E-value: 2.67e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2279656847  1 MLFFDLPmntkhERKVYTRFRKYLINNgFTMVQFSVYSKiFPNRSSLDSYLIGLRASVPKN-GSVRAMAVTEKQYG 75
Cdd:pfam09827  4 LVVYDIS-----DRKRRRKVAKILKKY-FQRVQNSVFEG-ELSEAQAEKLKKRLKKIIDPEeDSIRIYPLTDKQFS 72
 
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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