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Conserved domains on  [gi|1167348381|gb|OQB68544|]
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CRISPR-associated endoribonuclease Cas2 [Spirochaetes bacterium ADurb.Bin133]

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 ...
 9-97 2.12e-25

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: 91.85  E-value: 2.12e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167348381   9 YKIMWLFVFFDLPVANKKDQKNAAKFRKNLLNDGFTMMQFSVYIRHCASKEAMKTHVQRIEAFIPPKGSVSMVSITDKQY 88
Cdd:COG3512     4 YKFMRMILMFDLPTDTAAERKAANKFRQFLLKDGYQMLQFSVYSRILKGRDSNQKHIGRLREHLPNEGNIRCLEVTEKQF 83


                  ....*....
gi 1167348381  89 GDIINFWGQ 97
Cdd:COG3512    84 ARMKLLLGE 92
 
Name Accession Description Interval E-value
Cas2 COG3512
CRISPR/Cas system-associated protein Cas2, endoribonuclease [Defense mechanisms];
9-97 2.12e-25

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


Pssm-ID: 226043  Cd Length: 116  Bit Score: 91.85  E-value: 2.12e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167348381   9 YKIMWLFVFFDLPVANKKDQKNAAKFRKNLLNDGFTMMQFSVYIRHCASKEAMKTHVQRIEAFIPPKGSVSMVSITDKQY 88
Cdd:COG3512     4 YKFMRMILMFDLPTDTAAERKAANKFRQFLLKDGYQMLQFSVYSRILKGRDSNQKHIGRLREHLPNEGNIRCLEVTEKQF 83


                  ....*....
gi 1167348381  89 GDIINFWGQ 97
Cdd:COG3512    84 ARMKLLLGE 92
CRISPR_Cas2 pfam09827
CRISPR associated protein Cas2; This entry represents members of the family of Cas2, one of ...
 12-89 1.69e-18

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: 72.91  E-value: 1.69e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1167348381  12 MWLFVFFDLpvankKDQKNAAKFRKNLLNDgFTMMQFSVYIRhCASKEAMKTHVQRIEAFIPP-KGSVSMVSITDKQYG 89
Cdd:pfam09827   1 MYVLVVYDI-----SDRKRRRKVAKILKKY-FQRVQNSVFEG-ELSEAQAEKLKKRLKKIIDPeEDSIRIYPLTDKQFS 72
cas2 TIGR01573
CRISPR-associated endonuclease Cas2; This model describes most members of the family of Cas2, ...
 12-92 3.69e-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: 3.69e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167348381  12 MWLFVFFDLPvaNKKDQKNAAKFRKNLLNDGFTMMQFSVYIRHCASKEAMKTHVQRIEAFIPPKGSVSMVSITDKQYGDI 91
Cdd:TIGR01573   1 MLVLVVYDIP--TDGERKRRRKLRKLLEKYGLQRVQYSVFEGILEPNQLARKLIERLKRIIPDEGSIRIYPLTEKQYAAA 78


                  .
gi 1167348381  92 I 92
Cdd:TIGR01573  79 I 79
Cas2_I_II_III cd09638
CRISPR/Cas system-associated protein Cas2; CRISPR (Clustered Regularly Interspaced Short ...
 12-88 1.89e-15

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: 65.86  E-value: 1.89e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1167348381  12 MWLFVFFDLPVanKKDQKNAAKFRKNLLNDGFTMMQFSVYIRHCaSKEAMKTHVQRIEAFIPPKGSVSMVSITDKQY 88
Cdd:cd09638     1 MLVLVVYDIPE--DTERKRRRKLRKLLEKYGLFRVQYSVFEGIL-EPNLLASLIERLKKIIPDEDSIRIYPLTEKQK 74
 
Name Accession Description Interval E-value
Cas2 COG3512
CRISPR/Cas system-associated protein Cas2, endoribonuclease [Defense mechanisms];
9-97 2.12e-25

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


Pssm-ID: 226043  Cd Length: 116  Bit Score: 91.85  E-value: 2.12e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167348381   9 YKIMWLFVFFDLPVANKKDQKNAAKFRKNLLNDGFTMMQFSVYIRHCASKEAMKTHVQRIEAFIPPKGSVSMVSITDKQY 88
Cdd:COG3512     4 YKFMRMILMFDLPTDTAAERKAANKFRQFLLKDGYQMLQFSVYSRILKGRDSNQKHIGRLREHLPNEGNIRCLEVTEKQF 83


                  ....*....
gi 1167348381  89 GDIINFWGQ 97
Cdd:COG3512    84 ARMKLLLGE 92
Cas2 COG1343
CRISPR/Cas system-associated endoribonuclease Cas2 [Defense mechanisms]; CRISPR/Cas ...
 12-103 7.26e-20

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: 76.79  E-value: 7.26e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167348381  12 MWLFVFFDLPvankkDQKNAAKFRKNLLNDGFTMmQFSVYIRHCASKEAMKtHVQRIEAFIPP-KGSVSMVSITDKQYGD 90
Cdd:COG1343     1 MWVLVVYDIP-----DDKRRRKVAKLLKKYGFRV-QYSVFEGELTEAELAE-LKKRLKKIIDPeEDSVRIYPLTDKQFGK 73

                          90
                  ....*....|...
gi 1167348381  91 IInFWGQKEAPKP 103
Cdd:COG1343    74 VE-VLGKKKDPEQ 85
CRISPR_Cas2 pfam09827
CRISPR associated protein Cas2; This entry represents members of the family of Cas2, one of ...
 12-89 1.69e-18

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: 72.91  E-value: 1.69e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1167348381  12 MWLFVFFDLpvankKDQKNAAKFRKNLLNDgFTMMQFSVYIRhCASKEAMKTHVQRIEAFIPP-KGSVSMVSITDKQYG 89
Cdd:pfam09827   1 MYVLVVYDI-----SDRKRRRKVAKILKKY-FQRVQNSVFEG-ELSEAQAEKLKKRLKKIIDPeEDSIRIYPLTDKQFS 72
cas2 TIGR01573
CRISPR-associated endonuclease Cas2; This model describes most members of the family of Cas2, ...
 12-92 3.69e-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: 3.69e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167348381  12 MWLFVFFDLPvaNKKDQKNAAKFRKNLLNDGFTMMQFSVYIRHCASKEAMKTHVQRIEAFIPPKGSVSMVSITDKQYGDI 91
Cdd:TIGR01573   1 MLVLVVYDIP--TDGERKRRRKLRKLLEKYGLQRVQYSVFEGILEPNQLARKLIERLKRIIPDEGSIRIYPLTEKQYAAA 78


                  .
gi 1167348381  92 I 92
Cdd:TIGR01573  79 I 79
Cas2_I_II_III cd09638
CRISPR/Cas system-associated protein Cas2; CRISPR (Clustered Regularly Interspaced Short ...
 12-88 1.89e-15

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: 65.86  E-value: 1.89e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1167348381  12 MWLFVFFDLPVanKKDQKNAAKFRKNLLNDGFTMMQFSVYIRHCaSKEAMKTHVQRIEAFIPPKGSVSMVSITDKQY 88
Cdd:cd09638     1 MLVLVVYDIPE--DTERKRRRKLRKLLEKYGLFRVQYSVFEGIL-EPNLLASLIERLKKIIPDEDSIRIYPLTEKQK 74
 
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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