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Conserved domains on  [gi|61557082|ref|NP_001013161|]
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telomeric repeat-binding factor 2-interacting protein 1 [Rattus norvegicus]

Protein Classification

SANT/Myb-like DNA-binding domain-containing protein( domain architecture ID 11244296)

SANT (SWI3, ADA2, N-CoR and TFIIIB)/Myb-like DNA-binding domain-containing protein binds DNA and may function as a transcription factor

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Myb_DNA-bind_2 pfam08914
Rap1 Myb domain; The Rap1 Myb domain adopts a canonical three-helix bundle tertiary structure, ...
 129-193 2.31e-33

Rap1 Myb domain; The Rap1 Myb domain adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function of this domain is unclear: it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions.


:

Pssm-ID: 286058  Cd Length: 65  Bit Score: 119.16  E-value: 2.31e-33
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 61557082   129 GRIAYTDADDVAILTYVKENARSPSSVTGNALWKAMEKSSLTQHSWQSLKDRYLKHLQGQEHKYL 193
Cdd:pfam08914   1 GRLPYTPEEDAAILHYVLEKERSPASVRGNAIWKEMEKKHLTRHSWQSMKDRYLKHLRGQHREGL 65
rap1_RCT cd11653
C-terminal domain of RAP1 recruits proteins to telomeres; The RAP1 (repressor activator ...
 300-393 2.90e-21

C-terminal domain of RAP1 recruits proteins to telomeres; The RAP1 (repressor activator protein 1) C-terminal domain (RCT) mediates interactions with other proteins such as TRF2 (human), Rif1, Rif2, Sir3, Sir4 (Saccharomyces cerevisiae), and Taz1 (Schizosaccharomyces pombe) at telomeres and other loci. RAP1, identified in budding yeast as repressor/activator protein 1, is a well-conserved telomere binding protein, also found in fission yeast and mammals. In Saccharomyces cerevisiae, RAP1 directly binds DNA and is involved in transcriptional activation, gene silencing, as well as binding at numerous sites at each telemore, where it functions in telomere length regulation, telomeric position effect gene silencing and telomere end protection. Human RAP1 apparently does not bind telomeric DNA directly, but binds telomere repeat binding factor 2 (TRF2) via the RCT. RAP1 might act by suppressing nonhomologous end-joining. Yeast RAP1 has two myb-type DNA binding modules, and an RCT domain that recruits Sir proteins 3 and 4 (Sir3, Sir4) for gene silencing, and Rif1 and Rif2 for telomere length maintenance. Schizosaccharomyces pombe RAP1 (spRap1), like human RAP1, lacks direct DNA-binding activity and is localized to telomeres via Taz1, an ortholog of TRF1 and TRF2. The S. pompe RCT resembles the first 3-helix bundle of the yeast and human RCT forms, but is not included in this larger model.


:

Pssm-ID: 212167  Cd Length: 100  Bit Score: 87.77  E-value: 2.90e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61557082 300 VSTQEVGTAIKIIRQLMEKFNLDLSTVTQALLKNSGELEATSSFLESGRR------PDGFPIWCRQDDLDLQKDDDDTRN 373
Cdd:cd11653   1 SSSYEPEQAEKLVQDLDDEIGIRLVTVTQALLKASGCLSMDPRLALNVLRylvgipPDMPGIWTREDDECLQSDDPRTIE 80

                        90       100
                ....*....|....*....|
gi 61557082 374 ALVKKYGAQNVARRIEFRKK 393
Cdd:cd11653  81 RLIKKHGAENVARRWEFLEM 100
BRCT_2 pfam16589
BRCT domain, a BRCA1 C-terminus domain; This BRCT domain, a BRCA1 C-terminus region, is found ...
 17-99 2.89e-14

BRCT domain, a BRCA1 C-terminus domain; This BRCT domain, a BRCA1 C-terminus region, is found on many RAP1 proteins, usually at the very N-terminus. The function in human at least of a BRCT is to contribute to the heterogeneity of the telomere DNA length, but that may not be its general function, which remains unknown.


:

Pssm-ID: 465186 [Multi-domain]  Cd Length: 84  Bit Score: 67.78  E-value: 2.89e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61557082    17 SSTLFvredgSAMSFYV--RPSSAKRRLSTLILHGGGILCRVQKPGAVLLAQPGE----ALAEASGDFISTQYILDCVER 90
Cdd:pfam16589   1 LPNLF-----EPLRFYInaIPSPSRSKLKRLIEANGGTVVDNINPAVYIVIAPYNktdkLAENTKLGVVSPQWIFDCVKK 75


                  ....*....
gi 61557082    91 NEKLELEAY 99
Cdd:pfam16589  76 GKLLPLENY 84
 
Name Accession Description Interval E-value
Myb_DNA-bind_2 pfam08914
Rap1 Myb domain; The Rap1 Myb domain adopts a canonical three-helix bundle tertiary structure, ...
 129-193 2.31e-33

Rap1 Myb domain; The Rap1 Myb domain adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function of this domain is unclear: it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions.


Pssm-ID: 286058  Cd Length: 65  Bit Score: 119.16  E-value: 2.31e-33
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 61557082   129 GRIAYTDADDVAILTYVKENARSPSSVTGNALWKAMEKSSLTQHSWQSLKDRYLKHLQGQEHKYL 193
Cdd:pfam08914   1 GRLPYTPEEDAAILHYVLEKERSPASVRGNAIWKEMEKKHLTRHSWQSMKDRYLKHLRGQHREGL 65
rap1_RCT cd11653
C-terminal domain of RAP1 recruits proteins to telomeres; The RAP1 (repressor activator ...
 300-393 2.90e-21

C-terminal domain of RAP1 recruits proteins to telomeres; The RAP1 (repressor activator protein 1) C-terminal domain (RCT) mediates interactions with other proteins such as TRF2 (human), Rif1, Rif2, Sir3, Sir4 (Saccharomyces cerevisiae), and Taz1 (Schizosaccharomyces pombe) at telomeres and other loci. RAP1, identified in budding yeast as repressor/activator protein 1, is a well-conserved telomere binding protein, also found in fission yeast and mammals. In Saccharomyces cerevisiae, RAP1 directly binds DNA and is involved in transcriptional activation, gene silencing, as well as binding at numerous sites at each telemore, where it functions in telomere length regulation, telomeric position effect gene silencing and telomere end protection. Human RAP1 apparently does not bind telomeric DNA directly, but binds telomere repeat binding factor 2 (TRF2) via the RCT. RAP1 might act by suppressing nonhomologous end-joining. Yeast RAP1 has two myb-type DNA binding modules, and an RCT domain that recruits Sir proteins 3 and 4 (Sir3, Sir4) for gene silencing, and Rif1 and Rif2 for telomere length maintenance. Schizosaccharomyces pombe RAP1 (spRap1), like human RAP1, lacks direct DNA-binding activity and is localized to telomeres via Taz1, an ortholog of TRF1 and TRF2. The S. pompe RCT resembles the first 3-helix bundle of the yeast and human RCT forms, but is not included in this larger model.


Pssm-ID: 212167  Cd Length: 100  Bit Score: 87.77  E-value: 2.90e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61557082 300 VSTQEVGTAIKIIRQLMEKFNLDLSTVTQALLKNSGELEATSSFLESGRR------PDGFPIWCRQDDLDLQKDDDDTRN 373
Cdd:cd11653   1 SSSYEPEQAEKLVQDLDDEIGIRLVTVTQALLKASGCLSMDPRLALNVLRylvgipPDMPGIWTREDDECLQSDDPRTIE 80

                        90       100
                ....*....|....*....|
gi 61557082 374 ALVKKYGAQNVARRIEFRKK 393
Cdd:cd11653  81 RLIKKHGAENVARRWEFLEM 100
rap1_myb-like cd11655
DNA-binding modules of yeast Rap1 and related proteins; Yeast Rap1 DNA-binding activity is ...
 130-186 1.75e-14

DNA-binding modules of yeast Rap1 and related proteins; Yeast Rap1 DNA-binding activity is mediated by a pair of DNA-binding modules comprised of 2 3-helix bundles with an N-terminal arm, closely matching the structure of homeodomain and myb-type proteins. Human Rap1 has a single myb-like module, and may not bind DNA directly. Rap1, identified in budding yeast as repressor-activator protein 1, is a conserved telomere binding protein, also identified in fission yeast and mammals. In Saccharomyces cerevisiae, Rap1 directly binds DNA and is involved in transcriptional activation, gene silencing, as well as binding at numerous binding sites at each telomere, where it functions in telomere length regulation, telomeric position effect gene silencing and telomere end protection. Human Rap1 apparently does not bind telomeric DNA directly, but binds telomere repeat binding factor 2 (TRF2) via the Rap C-terminal domain (RCT). Rap1 may act by suppressing non-homologous end-joining. Yeast Rap1 has 2 myb-type DNA binding modules, a BRCT domain, and a RCT domain that recruits Sir3 and Sir4 proteins for gene silencing and Rif1 and Rif2 for telomere length maintenance. Human Rap1 has a similar domain architecture but has a single myb-like domain.


Pssm-ID: 212554  Cd Length: 57  Bit Score: 67.26  E-value: 1.75e-14
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 61557082 130 RIAYTDADDVAILTYVKENARSPSSVTGNALWKAMEKSSlTQHSWQSLKDRYLKHLQ 186
Cdd:cd11655   1 RTKFTAEDDYILCKYVAKYGRRGRGRLGNSFYKELAEEH-PRHTWQSWRDRYRKFLS 56
BRCT_2 pfam16589
BRCT domain, a BRCA1 C-terminus domain; This BRCT domain, a BRCA1 C-terminus region, is found ...
 17-99 2.89e-14

BRCT domain, a BRCA1 C-terminus domain; This BRCT domain, a BRCA1 C-terminus region, is found on many RAP1 proteins, usually at the very N-terminus. The function in human at least of a BRCT is to contribute to the heterogeneity of the telomere DNA length, but that may not be its general function, which remains unknown.


Pssm-ID: 465186 [Multi-domain]  Cd Length: 84  Bit Score: 67.78  E-value: 2.89e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61557082    17 SSTLFvredgSAMSFYV--RPSSAKRRLSTLILHGGGILCRVQKPGAVLLAQPGE----ALAEASGDFISTQYILDCVER 90
Cdd:pfam16589   1 LPNLF-----EPLRFYInaIPSPSRSKLKRLIEANGGTVVDNINPAVYIVIAPYNktdkLAENTKLGVVSPQWIFDCVKK 75


                  ....*....
gi 61557082    91 NEKLELEAY 99
Cdd:pfam16589  76 GKLLPLENY 84
Rap1_C pfam11626
TRF2-interacting telomeric protein/Rap1 - C terminal domain; This family of proteins ...
 315-391 4.20e-11

TRF2-interacting telomeric protein/Rap1 - C terminal domain; This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C terminal domain. Rap1 is otherwise known as TRF2-interacting protein, as it is one of the six subunit components of the Shelterin complex. Shelterin protects telomere ends from attack by DNA-repair mechanisms. Model doesn't capture Sch. pombe as it cuts this sequence into two.


Pssm-ID: 431966  Cd Length: 82  Bit Score: 58.80  E-value: 4.20e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61557082   315 LMEKFNLDLSTVTQALLKNSGELEATSSFLESGRRPDGFP-----IWCRQDDLDLQKDDDDTRNALVKKYGAQNVARRIE 389
Cdd:pfam11626   1 LYEELGYSREFVTHALKATSGDPGLAEYVLESLKRGKGIPdnvpgIWTEEDDEALRSGDERDLERLEKKHGEERIEARRK 80


                  ..
gi 61557082   390 FR 391
Cdd:pfam11626  81 FL 82
 
Name Accession Description Interval E-value
Myb_DNA-bind_2 pfam08914
Rap1 Myb domain; The Rap1 Myb domain adopts a canonical three-helix bundle tertiary structure, ...
 129-193 2.31e-33

Rap1 Myb domain; The Rap1 Myb domain adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function of this domain is unclear: it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions.


Pssm-ID: 286058  Cd Length: 65  Bit Score: 119.16  E-value: 2.31e-33
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 61557082   129 GRIAYTDADDVAILTYVKENARSPSSVTGNALWKAMEKSSLTQHSWQSLKDRYLKHLQGQEHKYL 193
Cdd:pfam08914   1 GRLPYTPEEDAAILHYVLEKERSPASVRGNAIWKEMEKKHLTRHSWQSMKDRYLKHLRGQHREGL 65
rap1_RCT cd11653
C-terminal domain of RAP1 recruits proteins to telomeres; The RAP1 (repressor activator ...
 300-393 2.90e-21

C-terminal domain of RAP1 recruits proteins to telomeres; The RAP1 (repressor activator protein 1) C-terminal domain (RCT) mediates interactions with other proteins such as TRF2 (human), Rif1, Rif2, Sir3, Sir4 (Saccharomyces cerevisiae), and Taz1 (Schizosaccharomyces pombe) at telomeres and other loci. RAP1, identified in budding yeast as repressor/activator protein 1, is a well-conserved telomere binding protein, also found in fission yeast and mammals. In Saccharomyces cerevisiae, RAP1 directly binds DNA and is involved in transcriptional activation, gene silencing, as well as binding at numerous sites at each telemore, where it functions in telomere length regulation, telomeric position effect gene silencing and telomere end protection. Human RAP1 apparently does not bind telomeric DNA directly, but binds telomere repeat binding factor 2 (TRF2) via the RCT. RAP1 might act by suppressing nonhomologous end-joining. Yeast RAP1 has two myb-type DNA binding modules, and an RCT domain that recruits Sir proteins 3 and 4 (Sir3, Sir4) for gene silencing, and Rif1 and Rif2 for telomere length maintenance. Schizosaccharomyces pombe RAP1 (spRap1), like human RAP1, lacks direct DNA-binding activity and is localized to telomeres via Taz1, an ortholog of TRF1 and TRF2. The S. pompe RCT resembles the first 3-helix bundle of the yeast and human RCT forms, but is not included in this larger model.


Pssm-ID: 212167  Cd Length: 100  Bit Score: 87.77  E-value: 2.90e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61557082 300 VSTQEVGTAIKIIRQLMEKFNLDLSTVTQALLKNSGELEATSSFLESGRR------PDGFPIWCRQDDLDLQKDDDDTRN 373
Cdd:cd11653   1 SSSYEPEQAEKLVQDLDDEIGIRLVTVTQALLKASGCLSMDPRLALNVLRylvgipPDMPGIWTREDDECLQSDDPRTIE 80

                        90       100
                ....*....|....*....|
gi 61557082 374 ALVKKYGAQNVARRIEFRKK 393
Cdd:cd11653  81 RLIKKHGAENVARRWEFLEM 100
rap1_myb-like cd11655
DNA-binding modules of yeast Rap1 and related proteins; Yeast Rap1 DNA-binding activity is ...
 130-186 1.75e-14

DNA-binding modules of yeast Rap1 and related proteins; Yeast Rap1 DNA-binding activity is mediated by a pair of DNA-binding modules comprised of 2 3-helix bundles with an N-terminal arm, closely matching the structure of homeodomain and myb-type proteins. Human Rap1 has a single myb-like module, and may not bind DNA directly. Rap1, identified in budding yeast as repressor-activator protein 1, is a conserved telomere binding protein, also identified in fission yeast and mammals. In Saccharomyces cerevisiae, Rap1 directly binds DNA and is involved in transcriptional activation, gene silencing, as well as binding at numerous binding sites at each telomere, where it functions in telomere length regulation, telomeric position effect gene silencing and telomere end protection. Human Rap1 apparently does not bind telomeric DNA directly, but binds telomere repeat binding factor 2 (TRF2) via the Rap C-terminal domain (RCT). Rap1 may act by suppressing non-homologous end-joining. Yeast Rap1 has 2 myb-type DNA binding modules, a BRCT domain, and a RCT domain that recruits Sir3 and Sir4 proteins for gene silencing and Rif1 and Rif2 for telomere length maintenance. Human Rap1 has a similar domain architecture but has a single myb-like domain.


Pssm-ID: 212554  Cd Length: 57  Bit Score: 67.26  E-value: 1.75e-14
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 61557082 130 RIAYTDADDVAILTYVKENARSPSSVTGNALWKAMEKSSlTQHSWQSLKDRYLKHLQ 186
Cdd:cd11655   1 RTKFTAEDDYILCKYVAKYGRRGRGRLGNSFYKELAEEH-PRHTWQSWRDRYRKFLS 56
BRCT_2 pfam16589
BRCT domain, a BRCA1 C-terminus domain; This BRCT domain, a BRCA1 C-terminus region, is found ...
 17-99 2.89e-14

BRCT domain, a BRCA1 C-terminus domain; This BRCT domain, a BRCA1 C-terminus region, is found on many RAP1 proteins, usually at the very N-terminus. The function in human at least of a BRCT is to contribute to the heterogeneity of the telomere DNA length, but that may not be its general function, which remains unknown.


Pssm-ID: 465186 [Multi-domain]  Cd Length: 84  Bit Score: 67.78  E-value: 2.89e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61557082    17 SSTLFvredgSAMSFYV--RPSSAKRRLSTLILHGGGILCRVQKPGAVLLAQPGE----ALAEASGDFISTQYILDCVER 90
Cdd:pfam16589   1 LPNLF-----EPLRFYInaIPSPSRSKLKRLIEANGGTVVDNINPAVYIVIAPYNktdkLAENTKLGVVSPQWIFDCVKK 75


                  ....*....
gi 61557082    91 NEKLELEAY 99
Cdd:pfam16589  76 GKLLPLENY 84
Rap1_C pfam11626
TRF2-interacting telomeric protein/Rap1 - C terminal domain; This family of proteins ...
 315-391 4.20e-11

TRF2-interacting telomeric protein/Rap1 - C terminal domain; This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C terminal domain. Rap1 is otherwise known as TRF2-interacting protein, as it is one of the six subunit components of the Shelterin complex. Shelterin protects telomere ends from attack by DNA-repair mechanisms. Model doesn't capture Sch. pombe as it cuts this sequence into two.


Pssm-ID: 431966  Cd Length: 82  Bit Score: 58.80  E-value: 4.20e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61557082   315 LMEKFNLDLSTVTQALLKNSGELEATSSFLESGRRPDGFP-----IWCRQDDLDLQKDDDDTRNALVKKYGAQNVARRIE 389
Cdd:pfam11626   1 LYEELGYSREFVTHALKATSGDPGLAEYVLESLKRGKGIPdnvpgIWTEEDDEALRSGDERDLERLEKKHGEERIEARRK 80


                  ..
gi 61557082   390 FR 391
Cdd:pfam11626  81 FL 82
 
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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