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Conserved domains on  [gi|1046856504|ref|XP_017454317|]
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pogo transposable element with KRAB domain isoform X2 [Rattus norvegicus]

Protein Classification

DNA-binding domain-containing protein( domain architecture ID 12204791)

DNA-binding domain-containing protein containing a Tc5 transposase-like DNA-binding domain; similar to Chaetomium globosum chaetoglobosin A biosynthesis cluster protein C

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 ...
 395-567 2.96e-64

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: 208.78  E-value: 2.96e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046856504 395 KLRITAMLG-VLADGRKLPPYIILRGTYIPPGKF-----PSGMEIRCHRYGWMTEDLMQDWLEVVWRRRTGAVPKQRGML 468
Cdd:pfam03184   1 KERLTVMLCcNAAGSEKLPPLVIGKGKNPRAFKNektpkPLPVEYKSNGKAWMTTSIFEEWLQKWFDPRMRESPGRKVLL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046856504 469 ILNGFRCHATDSVKTSMESMNTDMVIIPGGLTSQLQVLDVVVYKPLNDSVRAQYSNWLLAGNLALSPtgNAKKPPLGLFL 548
Cdd:pfam03184  81 LLDGSGSHPTVELIRSCGLQNIFLVFLPANSTSILQPLDQGVVSTFKANYRRQWLQYLLAGNNLLSP--PWKKLTLLDAL 158

                         170
                  ....*....|....*....
gi 1046856504 549 EWIMVAWNSISSESIVQGF 567
Cdd:pfam03184 159 KWIAKAWNAVSPSTITSGF 177
BrkDBD pfam09607
Brinker DNA-binding domain; This DNA-binding domain is the first approx. 100 residues of the ...
 195-247 2.43e-25

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: 99.04  E-value: 2.43e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1046856504 195 GMRRSYDAGFKLMVVEHAESTNNCQ-----AAKQFGVLEKNVRDWRKVKPQLQNAHAM 247
Cdd:pfam09607   1 GMRHIFDAGFKLMVLESAENDNDCKgnqraAAKKFGIHEKNIQDWLKCEPNLQNAHAM 58
KRAB smart00349
krueppel associated box;
49-104 7.51e-21

krueppel associated box;


:

Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 86.11  E-value: 7.51e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1046856504   49 FDEVAIYFSDEEWEVLTEQQKALYREVMRMNYETVLSLEFPFPKPDMINRLEREEE 104
Cdd:smart00349   3 FEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEE 58
CENPB smart00674
Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;
256-323 6.52e-17

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


:

Pssm-ID: 197828  Cd Length: 66  Bit Score: 75.02  E-value: 6.52e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1046856504  256 NGRFALVDQRVAEYVRYMQAKGDPITREAMQLKALEIAQEMNIPekGFKASLGWCRRMMRRYDLSLRH 323
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 ...
 395-567 2.96e-64

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: 208.78  E-value: 2.96e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046856504 395 KLRITAMLG-VLADGRKLPPYIILRGTYIPPGKF-----PSGMEIRCHRYGWMTEDLMQDWLEVVWRRRTGAVPKQRGML 468
Cdd:pfam03184   1 KERLTVMLCcNAAGSEKLPPLVIGKGKNPRAFKNektpkPLPVEYKSNGKAWMTTSIFEEWLQKWFDPRMRESPGRKVLL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046856504 469 ILNGFRCHATDSVKTSMESMNTDMVIIPGGLTSQLQVLDVVVYKPLNDSVRAQYSNWLLAGNLALSPtgNAKKPPLGLFL 548
Cdd:pfam03184  81 LLDGSGSHPTVELIRSCGLQNIFLVFLPANSTSILQPLDQGVVSTFKANYRRQWLQYLLAGNNLLSP--PWKKLTLLDAL 158

                         170
                  ....*....|....*....
gi 1046856504 549 EWIMVAWNSISSESIVQGF 567
Cdd:pfam03184 159 KWIAKAWNAVSPSTITSGF 177
BrkDBD pfam09607
Brinker DNA-binding domain; This DNA-binding domain is the first approx. 100 residues of the ...
 195-247 2.43e-25

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: 99.04  E-value: 2.43e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1046856504 195 GMRRSYDAGFKLMVVEHAESTNNCQ-----AAKQFGVLEKNVRDWRKVKPQLQNAHAM 247
Cdd:pfam09607   1 GMRHIFDAGFKLMVLESAENDNDCKgnqraAAKKFGIHEKNIQDWLKCEPNLQNAHAM 58
KRAB smart00349
krueppel associated box;
49-104 7.51e-21

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 86.11  E-value: 7.51e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1046856504   49 FDEVAIYFSDEEWEVLTEQQKALYREVMRMNYETVLSLEFPFPKPDMINRLEREEE 104
Cdd:smart00349   3 FEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEE 58
CENPB smart00674
Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;
256-323 6.52e-17

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


Pssm-ID: 197828  Cd Length: 66  Bit Score: 75.02  E-value: 6.52e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1046856504  256 NGRFALVDQRVAEYVRYMQAKGDPITREAMQLKALEIAQEMNIPekGFKASLGWCRRMMRRYDLSLRH 323
Cdd:smart00674   1 RRLYPLLEKALYEWILRQEALGIPISGEDIREKALEILQRLGLE--NFKASKGWLTRFKKRHNIVKTK 66
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 49-86 1.37e-13

KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression module, found in a subgroup of the zinc finger proteins (ZFPs) of the C2H2 family, KRAB-ZFPs. KRAB-ZFPs comprise the largest group of transcriptional regulators in mammals, and are only found in tetrapods. These proteins have been shown to play important roles in cell differentiation and organ development, and in regulating viral replication and transcription. A KRAB domain may consist of an A-box, or of an A-box plus either a B-box, a divergent B-box (b), or a C-box. Only the A-box is included in this model. The A-box is needed for repression, the B- and C- boxes are not. KRAB-ZFPs have one or two KRAB domains at their amino-terminal end, and multiple C2H2 zinc finger motifs at their C-termini. Some KRAB-ZFPs also contain a SCAN domain which mediates homo- and hetero-oligomerization. The KRAB domain is a protein-protein interaction module which represses transcription through recruiting corepressors. A key mechanism appears to be the following: KRAB-AFPs tethered to DNA recruit, via their KRAB domain, the repressor KAP1 (KRAB-associated protein-1, also known as transcription intermediary factor 1 beta , KRAB-A interacting protein , and tripartite motif protein 28). The KAP1/ KRAB-AFP complex in turn recruits the heterochromatin protein 1 (HP1) family, and other chromatin modulating proteins, leading to transcriptional repression through heterochromatin formation.


Pssm-ID: 143639  Cd Length: 40  Bit Score: 64.88  E-value: 1.37e-13
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1046856504  49 FDEVAIYFSDEEWEVLTEQQKALYREVMRMNYETVLSL 86
Cdd:cd07765     3 FEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLVSL 40
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 49-86 2.42e-13

KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.


Pssm-ID: 460171  Cd Length: 42  Bit Score: 64.41  E-value: 2.42e-13
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1046856504  49 FDEVAIYFSDEEWEVLTEQQKALYREVMRMNYETVLSL 86
Cdd:pfam01352   4 FEDVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSL 41
HTH_Tnp_Tc5 pfam03221
Tc5 transposase DNA-binding domain;
259-320 4.38e-13

Tc5 transposase DNA-binding domain;


Pssm-ID: 460850  Cd Length: 63  Bit Score: 64.19  E-value: 4.38e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1046856504 259 FALVDQRVAEYVRYMQAKGDPITREAMQLKALEIAQE-MNIPEKGFKASLGWCRRMMRRYDLS 320
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 ...
 395-567 2.96e-64

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: 208.78  E-value: 2.96e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046856504 395 KLRITAMLG-VLADGRKLPPYIILRGTYIPPGKF-----PSGMEIRCHRYGWMTEDLMQDWLEVVWRRRTGAVPKQRGML 468
Cdd:pfam03184   1 KERLTVMLCcNAAGSEKLPPLVIGKGKNPRAFKNektpkPLPVEYKSNGKAWMTTSIFEEWLQKWFDPRMRESPGRKVLL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046856504 469 ILNGFRCHATDSVKTSMESMNTDMVIIPGGLTSQLQVLDVVVYKPLNDSVRAQYSNWLLAGNLALSPtgNAKKPPLGLFL 548
Cdd:pfam03184  81 LLDGSGSHPTVELIRSCGLQNIFLVFLPANSTSILQPLDQGVVSTFKANYRRQWLQYLLAGNNLLSP--PWKKLTLLDAL 158

                         170
                  ....*....|....*....
gi 1046856504 549 EWIMVAWNSISSESIVQGF 567
Cdd:pfam03184 159 KWIAKAWNAVSPSTITSGF 177
BrkDBD pfam09607
Brinker DNA-binding domain; This DNA-binding domain is the first approx. 100 residues of the ...
 195-247 2.43e-25

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: 99.04  E-value: 2.43e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1046856504 195 GMRRSYDAGFKLMVVEHAESTNNCQ-----AAKQFGVLEKNVRDWRKVKPQLQNAHAM 247
Cdd:pfam09607   1 GMRHIFDAGFKLMVLESAENDNDCKgnqraAAKKFGIHEKNIQDWLKCEPNLQNAHAM 58
KRAB smart00349
krueppel associated box;
49-104 7.51e-21

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 86.11  E-value: 7.51e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1046856504   49 FDEVAIYFSDEEWEVLTEQQKALYREVMRMNYETVLSLEFPFPKPDMINRLEREEE 104
Cdd:smart00349   3 FEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEE 58
CENPB smart00674
Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;
256-323 6.52e-17

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


Pssm-ID: 197828  Cd Length: 66  Bit Score: 75.02  E-value: 6.52e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1046856504  256 NGRFALVDQRVAEYVRYMQAKGDPITREAMQLKALEIAQEMNIPekGFKASLGWCRRMMRRYDLSLRH 323
Cdd:smart00674   1 RRLYPLLEKALYEWILRQEALGIPISGEDIREKALEILQRLGLE--NFKASKGWLTRFKKRHNIVKTK 66
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 49-86 1.37e-13

KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression module, found in a subgroup of the zinc finger proteins (ZFPs) of the C2H2 family, KRAB-ZFPs. KRAB-ZFPs comprise the largest group of transcriptional regulators in mammals, and are only found in tetrapods. These proteins have been shown to play important roles in cell differentiation and organ development, and in regulating viral replication and transcription. A KRAB domain may consist of an A-box, or of an A-box plus either a B-box, a divergent B-box (b), or a C-box. Only the A-box is included in this model. The A-box is needed for repression, the B- and C- boxes are not. KRAB-ZFPs have one or two KRAB domains at their amino-terminal end, and multiple C2H2 zinc finger motifs at their C-termini. Some KRAB-ZFPs also contain a SCAN domain which mediates homo- and hetero-oligomerization. The KRAB domain is a protein-protein interaction module which represses transcription through recruiting corepressors. A key mechanism appears to be the following: KRAB-AFPs tethered to DNA recruit, via their KRAB domain, the repressor KAP1 (KRAB-associated protein-1, also known as transcription intermediary factor 1 beta , KRAB-A interacting protein , and tripartite motif protein 28). The KAP1/ KRAB-AFP complex in turn recruits the heterochromatin protein 1 (HP1) family, and other chromatin modulating proteins, leading to transcriptional repression through heterochromatin formation.


Pssm-ID: 143639  Cd Length: 40  Bit Score: 64.88  E-value: 1.37e-13
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1046856504  49 FDEVAIYFSDEEWEVLTEQQKALYREVMRMNYETVLSL 86
Cdd:cd07765     3 FEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLVSL 40
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 49-86 2.42e-13

KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.


Pssm-ID: 460171  Cd Length: 42  Bit Score: 64.41  E-value: 2.42e-13
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1046856504  49 FDEVAIYFSDEEWEVLTEQQKALYREVMRMNYETVLSL 86
Cdd:pfam01352   4 FEDVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSL 41
HTH_Tnp_Tc5 pfam03221
Tc5 transposase DNA-binding domain;
259-320 4.38e-13

Tc5 transposase DNA-binding domain;


Pssm-ID: 460850  Cd Length: 63  Bit Score: 64.19  E-value: 4.38e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1046856504 259 FALVDQRVAEYVRYMQAKGDPITREAMQLKALEIAQE-MNIPEKGFKASLGWCRRMMRRYDLS 320
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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