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Conserved domains on  [gi|2227679239|ref|NP_001392093|]
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pogo transposable element with KRAB domain isoform 5 [Mus musculus]

Protein Classification

BrkDBD and DDE_1 domain-containing protein( domain architecture ID 10560312)

protein containing domains BrkDBD, CENPB, and DDE_1

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DDE_1 pfam03184
DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are ...
 277-449 1.10e-63

DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Interestingly this family also includes the CENP-B protein. This domain in that protein appears to have lost the metal binding residues and is unlikely to have endonuclease activity. Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere.


:

Pssm-ID: 367380  Cd Length: 177  Bit Score: 204.55  E-value: 1.10e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2227679239 277 KLRITAMLG-VLADGRKLPPYIILRGTYIPPGKF-----PSGMEIRCHRYGWMTEDLMQDWLEVVWRRRTGAVPRQRGML 350
Cdd:pfam03184   1 KERLTVMLCcNAAGSEKLPPLVIGKGKNPRAFKNektpkPLPVEYKSNGKAWMTTSIFEEWLQKWFDPRMRESPGRKVLL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2227679239 351 ILNGFRCHATDSVKSSMENMNTDMVIIPGGLTSQLQVLDVVVYKPLNDSVRAQYSNWLLAGNLALSPtgNAKKPPLGLFL 430
Cdd:pfam03184  81 LLDGSGSHPTVELIRSCGLQNIFLVFLPANSTSILQPLDQGVVSTFKANYRRQWLQYLLAGNNLLSP--PWKKLTLLDAL 158

                         170
                  ....*....|....*....
gi 2227679239 431 EWIMVAWNSISSESIVQGF 449
Cdd:pfam03184 159 KWIAKAWNAVSPSTITSGF 177
BrkDBD pfam09607
Brinker DNA-binding domain; This DNA-binding domain is the first approx. 100 residues of the ...
 77-129 1.75e-26

Brinker DNA-binding domain; This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway.


:

Pssm-ID: 462838 [Multi-domain]  Cd Length: 58  Bit Score: 101.74  E-value: 1.75e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2227679239  77 GMRRSYDAGFKLMVVEYAESTNNCQ-----AAKQFGVLEKNVRDWRKVKPQLQNAHAM 129
Cdd:pfam09607   1 GMRHIFDAGFKLMVLESAENDNDCKgnqraAAKKFGIHEKNIQDWLKCEPNLQNAHAM 58
CENPB smart00674
Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;
138-205 2.54e-17

Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;


:

Pssm-ID: 197828  Cd Length: 66  Bit Score: 76.18  E-value: 2.54e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2227679239  138 NGRFALVDQRVAEYVRYMQAKGDPITREAMQLKALEIAQEMNIPekGFKASLGWCRRMMRRYDLSLRH 205
Cdd:smart00674   1 RRLYPLLEKALYEWILRQEALGIPISGEDIREKALEILQRLGLE--NFKASKGWLTRFKKRHNIVKTK 66
 
Name Accession Description Interval E-value
DDE_1 pfam03184
DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are ...
 277-449 1.10e-63

DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Interestingly this family also includes the CENP-B protein. This domain in that protein appears to have lost the metal binding residues and is unlikely to have endonuclease activity. Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere.


Pssm-ID: 367380  Cd Length: 177  Bit Score: 204.55  E-value: 1.10e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2227679239 277 KLRITAMLG-VLADGRKLPPYIILRGTYIPPGKF-----PSGMEIRCHRYGWMTEDLMQDWLEVVWRRRTGAVPRQRGML 350
Cdd:pfam03184   1 KERLTVMLCcNAAGSEKLPPLVIGKGKNPRAFKNektpkPLPVEYKSNGKAWMTTSIFEEWLQKWFDPRMRESPGRKVLL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2227679239 351 ILNGFRCHATDSVKSSMENMNTDMVIIPGGLTSQLQVLDVVVYKPLNDSVRAQYSNWLLAGNLALSPtgNAKKPPLGLFL 430
Cdd:pfam03184  81 LLDGSGSHPTVELIRSCGLQNIFLVFLPANSTSILQPLDQGVVSTFKANYRRQWLQYLLAGNNLLSP--PWKKLTLLDAL 158

                         170
                  ....*....|....*....
gi 2227679239 431 EWIMVAWNSISSESIVQGF 449
Cdd:pfam03184 159 KWIAKAWNAVSPSTITSGF 177
BrkDBD pfam09607
Brinker DNA-binding domain; This DNA-binding domain is the first approx. 100 residues of the ...
 77-129 1.75e-26

Brinker DNA-binding domain; This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway.


Pssm-ID: 462838 [Multi-domain]  Cd Length: 58  Bit Score: 101.74  E-value: 1.75e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2227679239  77 GMRRSYDAGFKLMVVEYAESTNNCQ-----AAKQFGVLEKNVRDWRKVKPQLQNAHAM 129
Cdd:pfam09607   1 GMRHIFDAGFKLMVLESAENDNDCKgnqraAAKKFGIHEKNIQDWLKCEPNLQNAHAM 58
CENPB smart00674
Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;
138-205 2.54e-17

Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;


Pssm-ID: 197828  Cd Length: 66  Bit Score: 76.18  E-value: 2.54e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2227679239  138 NGRFALVDQRVAEYVRYMQAKGDPITREAMQLKALEIAQEMNIPekGFKASLGWCRRMMRRYDLSLRH 205
Cdd:smart00674   1 RRLYPLLEKALYEWILRQEALGIPISGEDIREKALEILQRLGLE--NFKASKGWLTRFKKRHNIVKTK 66
HTH_Tnp_Tc5 pfam03221
Tc5 transposase DNA-binding domain;
141-202 1.87e-13

Tc5 transposase DNA-binding domain;


Pssm-ID: 460850  Cd Length: 63  Bit Score: 64.96  E-value: 1.87e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2227679239 141 FALVDQRVAEYVRYMQAKGDPITREAMQLKALEIAQE-MNIPEKGFKASLGWCRRMMRRYDLS 202
Cdd:pfam03221   1 YPDLEKALYEWILQLRARGIPITGPMIREKALELAQLaADLGEPDFKASKGWLDRFKKRHGIK 63
 
Name Accession Description Interval E-value
DDE_1 pfam03184
DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are ...
 277-449 1.10e-63

DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Interestingly this family also includes the CENP-B protein. This domain in that protein appears to have lost the metal binding residues and is unlikely to have endonuclease activity. Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere.


Pssm-ID: 367380  Cd Length: 177  Bit Score: 204.55  E-value: 1.10e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2227679239 277 KLRITAMLG-VLADGRKLPPYIILRGTYIPPGKF-----PSGMEIRCHRYGWMTEDLMQDWLEVVWRRRTGAVPRQRGML 350
Cdd:pfam03184   1 KERLTVMLCcNAAGSEKLPPLVIGKGKNPRAFKNektpkPLPVEYKSNGKAWMTTSIFEEWLQKWFDPRMRESPGRKVLL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2227679239 351 ILNGFRCHATDSVKSSMENMNTDMVIIPGGLTSQLQVLDVVVYKPLNDSVRAQYSNWLLAGNLALSPtgNAKKPPLGLFL 430
Cdd:pfam03184  81 LLDGSGSHPTVELIRSCGLQNIFLVFLPANSTSILQPLDQGVVSTFKANYRRQWLQYLLAGNNLLSP--PWKKLTLLDAL 158

                         170
                  ....*....|....*....
gi 2227679239 431 EWIMVAWNSISSESIVQGF 449
Cdd:pfam03184 159 KWIAKAWNAVSPSTITSGF 177
BrkDBD pfam09607
Brinker DNA-binding domain; This DNA-binding domain is the first approx. 100 residues of the ...
 77-129 1.75e-26

Brinker DNA-binding domain; This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway.


Pssm-ID: 462838 [Multi-domain]  Cd Length: 58  Bit Score: 101.74  E-value: 1.75e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2227679239  77 GMRRSYDAGFKLMVVEYAESTNNCQ-----AAKQFGVLEKNVRDWRKVKPQLQNAHAM 129
Cdd:pfam09607   1 GMRHIFDAGFKLMVLESAENDNDCKgnqraAAKKFGIHEKNIQDWLKCEPNLQNAHAM 58
CENPB smart00674
Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;
138-205 2.54e-17

Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;


Pssm-ID: 197828  Cd Length: 66  Bit Score: 76.18  E-value: 2.54e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2227679239  138 NGRFALVDQRVAEYVRYMQAKGDPITREAMQLKALEIAQEMNIPekGFKASLGWCRRMMRRYDLSLRH 205
Cdd:smart00674   1 RRLYPLLEKALYEWILRQEALGIPISGEDIREKALEILQRLGLE--NFKASKGWLTRFKKRHNIVKTK 66
HTH_Tnp_Tc5 pfam03221
Tc5 transposase DNA-binding domain;
141-202 1.87e-13

Tc5 transposase DNA-binding domain;


Pssm-ID: 460850  Cd Length: 63  Bit Score: 64.96  E-value: 1.87e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2227679239 141 FALVDQRVAEYVRYMQAKGDPITREAMQLKALEIAQE-MNIPEKGFKASLGWCRRMMRRYDLS 202
Cdd:pfam03221   1 YPDLEKALYEWILQLRARGIPITGPMIREKALELAQLaADLGEPDFKASKGWLDRFKKRHGIK 63
 
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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