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Conserved domains on  [gi|568908728|ref|XP_006529486|]
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R3H domain-containing protein 1 isoform X11 [Mus musculus]

Protein Classification

R3H domain-containing protein( domain architecture ID 11552619)

R3H domain-containing protein with SUZ and Med15 domains, may bind ssDNA or ssRNA in a sequence-specific manner; similar to Mus musculus R3H domain-containing protein 2

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
R3H_encore_like cd02642
R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the ...
 167-228 2.44e-26

R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H domain is a potential regulator of DBF1 activity in stress responses. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


:

Pssm-ID: 100071  Cd Length: 63  Bit Score: 102.68  E-value: 2.44e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568908728  167 DRMMLLKLEQEILDFIGNNESPRKKFPPMTSYHRMLLHRVAAYFGLDHNVDQSG-KSVIVNKT 228
Cdd:cd02642     1 DRLFVLKLEKDLLAFIKDSTRQSLELPPMNSYYRLLAHRVAQYYGLDHNVDNSGgKCVIVNKT 63
SUZ pfam12752
SUZ domain; The SUZ domain is a conserved RNA-binding domain found in eukaryotes and enriched ...
 251-302 3.28e-12

SUZ domain; The SUZ domain is a conserved RNA-binding domain found in eukaryotes and enriched in positively charged amino acids. It was first characterized in the C.elegans protein Szy-20 where it has been shown to bind RNA and allow their localization to the centrosome. Warning- the domain has a compositionally biased character.


:

Pssm-ID: 463689 [Multi-domain]  Cd Length: 56  Bit Score: 62.34  E-value: 3.28e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 568908728   251 QKRYILKRDNSSFD--KDDSQMRIRLKDDRRSKSIEEREEEYQRARDRIFSQDS 302
Cdd:pfam12752    3 PKMKILRRPSSGSSssSSAGSSGASSSSGSDSKTLEEREAEYAEARARIFGSSE 56
Med15 super family cl26621
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 553-874 2.39e-03

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


The actual alignment was detected with superfamily member pfam09606:

Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 41.92  E-value: 2.39e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568908728   553 PSPQMPACYCAPGHyhSSQPQYRPIPSVHHSSHLNQPLPQPAQHTGYQVMPNQQQnyQGIVGVQSPQS--QSLMGG---- 626
Cdd:pfam09606  140 PSQMSRVGRMQPGG--QAGGMMQPSSGQPGSGTPNQMGPNGGPGQGQAGGMNGGQ--QGPMGGQMPPQmgVPGMPGpada 215

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568908728   627 -------QPNSTGPHIQGVVIPYPSVPSYQV-SLPQGSQGIAHQTYQQPVVFPnQSNQGSLPtTGMPVyYSVIPPGQQSN 698
Cdd:pfam09606  216 gaqmgqqAQANGGMNPQQMGGAPNQVAMQQQqPQQQGQQSQLGMGINQMQQMP-QGVGGGAG-QGGPG-QPMGPPGQQPG 292

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568908728   699 LSSAVGYLQHPGSEQVQFPRTtspcSSQQLQGHQCAAVPQQPpgggmvmmqlNLPNNPQSRTHSPPQwkQNKHYCDHQRG 778
Cdd:pfam09606  293 AMPNVMSIGDQNNYQQQQTRQ----QQQQQGGNHPAAHQQQM----------NQSVGQGGQVVALGG--LNHLETWNPGN 356

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568908728   779 QkcmDFSNMDNIVQPSP-QLSSPilSPVQSPAPAQLSTLKTIRPSGPPlsimsQFARPFVPGQGDARYPlLGQPLQynPP 857
Cdd:pfam09606  357 F---GGLGANPMQRGQPgMMSSP--SPVPGQQVRQVTPNQFMRQSPQP-----SVPSPQGPGSQPPQSH-PGGMIP--SP 423

                          330
                   ....*....|....*...
gi 568908728   858 TLLHGHIPH-QQGQSGSR 874
Cdd:pfam09606  424 ALIPSPSPQmSQQPAQQR 441
 
Name Accession Description Interval E-value
R3H_encore_like cd02642
R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the ...
 167-228 2.44e-26

R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H domain is a potential regulator of DBF1 activity in stress responses. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100071  Cd Length: 63  Bit Score: 102.68  E-value: 2.44e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568908728  167 DRMMLLKLEQEILDFIGNNESPRKKFPPMTSYHRMLLHRVAAYFGLDHNVDQSG-KSVIVNKT 228
Cdd:cd02642     1 DRLFVLKLEKDLLAFIKDSTRQSLELPPMNSYYRLLAHRVAQYYGLDHNVDNSGgKCVIVNKT 63
R3H smart00393
Putative single-stranded nucleic acids-binding domain;
151-228 1.59e-17

Putative single-stranded nucleic acids-binding domain;


Pssm-ID: 214647  Cd Length: 79  Bit Score: 78.11  E-value: 1.59e-17
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568908728    151 IDLHEFLVNTLKNNPRDRMMLLKLEQEILDFIgNNESPRKKFPPMTSYHRMLLHRVAAYFGLDHNVDQSG--KSVIVNKT 228
Cdd:smart00393    1 ADFLPVTLDALSYRPRRREELIELELEIARFV-KSTKESVELPPMNSYERKIVHELAEKYGLESESFGEGpkRRVVISKK 79
SUZ pfam12752
SUZ domain; The SUZ domain is a conserved RNA-binding domain found in eukaryotes and enriched ...
 251-302 3.28e-12

SUZ domain; The SUZ domain is a conserved RNA-binding domain found in eukaryotes and enriched in positively charged amino acids. It was first characterized in the C.elegans protein Szy-20 where it has been shown to bind RNA and allow their localization to the centrosome. Warning- the domain has a compositionally biased character.


Pssm-ID: 463689 [Multi-domain]  Cd Length: 56  Bit Score: 62.34  E-value: 3.28e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 568908728   251 QKRYILKRDNSSFD--KDDSQMRIRLKDDRRSKSIEEREEEYQRARDRIFSQDS 302
Cdd:pfam12752    3 PKMKILRRPSSGSSssSSAGSSGASSSSGSDSKTLEEREAEYAEARARIFGSSE 56
R3H pfam01424
R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most ...
 169-227 2.16e-11

R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA.


Pssm-ID: 460206  Cd Length: 60  Bit Score: 59.81  E-value: 2.16e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568908728   169 MMLLKLEQEILDFIGNNESPrKKFPPMTSYHRMLLHRVAAYFGLDHNV--DQSGKSVIVNK 227
Cdd:pfam01424    1 EFLEQLAEKLAEFVKDTGKS-LELPPMSSYERRIIHELAQKYGLESESegEEPNRRVVVYK 60
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 553-874 2.39e-03

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 41.92  E-value: 2.39e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568908728   553 PSPQMPACYCAPGHyhSSQPQYRPIPSVHHSSHLNQPLPQPAQHTGYQVMPNQQQnyQGIVGVQSPQS--QSLMGG---- 626
Cdd:pfam09606  140 PSQMSRVGRMQPGG--QAGGMMQPSSGQPGSGTPNQMGPNGGPGQGQAGGMNGGQ--QGPMGGQMPPQmgVPGMPGpada 215

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568908728   627 -------QPNSTGPHIQGVVIPYPSVPSYQV-SLPQGSQGIAHQTYQQPVVFPnQSNQGSLPtTGMPVyYSVIPPGQQSN 698
Cdd:pfam09606  216 gaqmgqqAQANGGMNPQQMGGAPNQVAMQQQqPQQQGQQSQLGMGINQMQQMP-QGVGGGAG-QGGPG-QPMGPPGQQPG 292

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568908728   699 LSSAVGYLQHPGSEQVQFPRTtspcSSQQLQGHQCAAVPQQPpgggmvmmqlNLPNNPQSRTHSPPQwkQNKHYCDHQRG 778
Cdd:pfam09606  293 AMPNVMSIGDQNNYQQQQTRQ----QQQQQGGNHPAAHQQQM----------NQSVGQGGQVVALGG--LNHLETWNPGN 356

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568908728   779 QkcmDFSNMDNIVQPSP-QLSSPilSPVQSPAPAQLSTLKTIRPSGPPlsimsQFARPFVPGQGDARYPlLGQPLQynPP 857
Cdd:pfam09606  357 F---GGLGANPMQRGQPgMMSSP--SPVPGQQVRQVTPNQFMRQSPQP-----SVPSPQGPGSQPPQSH-PGGMIP--SP 423

                          330
                   ....*....|....*...
gi 568908728   858 TLLHGHIPH-QQGQSGSR 874
Cdd:pfam09606  424 ALIPSPSPQmSQQPAQQR 441
 
Name Accession Description Interval E-value
R3H_encore_like cd02642
R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the ...
 167-228 2.44e-26

R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H domain is a potential regulator of DBF1 activity in stress responses. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100071  Cd Length: 63  Bit Score: 102.68  E-value: 2.44e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568908728  167 DRMMLLKLEQEILDFIGNNESPRKKFPPMTSYHRMLLHRVAAYFGLDHNVDQSG-KSVIVNKT 228
Cdd:cd02642     1 DRLFVLKLEKDLLAFIKDSTRQSLELPPMNSYYRLLAHRVAQYYGLDHNVDNSGgKCVIVNKT 63
R3H smart00393
Putative single-stranded nucleic acids-binding domain;
151-228 1.59e-17

Putative single-stranded nucleic acids-binding domain;


Pssm-ID: 214647  Cd Length: 79  Bit Score: 78.11  E-value: 1.59e-17
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568908728    151 IDLHEFLVNTLKNNPRDRMMLLKLEQEILDFIgNNESPRKKFPPMTSYHRMLLHRVAAYFGLDHNVDQSG--KSVIVNKT 228
Cdd:smart00393    1 ADFLPVTLDALSYRPRRREELIELELEIARFV-KSTKESVELPPMNSYERKIVHELAEKYGLESESFGEGpkRRVVISKK 79
SUZ pfam12752
SUZ domain; The SUZ domain is a conserved RNA-binding domain found in eukaryotes and enriched ...
 251-302 3.28e-12

SUZ domain; The SUZ domain is a conserved RNA-binding domain found in eukaryotes and enriched in positively charged amino acids. It was first characterized in the C.elegans protein Szy-20 where it has been shown to bind RNA and allow their localization to the centrosome. Warning- the domain has a compositionally biased character.


Pssm-ID: 463689 [Multi-domain]  Cd Length: 56  Bit Score: 62.34  E-value: 3.28e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 568908728   251 QKRYILKRDNSSFD--KDDSQMRIRLKDDRRSKSIEEREEEYQRARDRIFSQDS 302
Cdd:pfam12752    3 PKMKILRRPSSGSSssSSAGSSGASSSSGSDSKTLEEREAEYAEARARIFGSSE 56
R3H pfam01424
R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most ...
 169-227 2.16e-11

R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA.


Pssm-ID: 460206  Cd Length: 60  Bit Score: 59.81  E-value: 2.16e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568908728   169 MMLLKLEQEILDFIGNNESPrKKFPPMTSYHRMLLHRVAAYFGLDHNV--DQSGKSVIVNK 227
Cdd:pfam01424    1 EFLEQLAEKLAEFVKDTGKS-LELPPMSSYERRIIHELAQKYGLESESegEEPNRRVVVYK 60
R3H cd02325
R3H domain. The name of the R3H domain comes from the characteristic spacing of the most ...
 171-227 6.06e-11

R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100064  Cd Length: 59  Bit Score: 58.78  E-value: 6.06e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 568908728  171 LLKLEQEILDFIGNNESPRKKFPPMTSYHRMLLHRVAAYFGLDHNVDQSG--KSVIVNK 227
Cdd:cd02325     1 REEREEELEAFAKDAAGKSLELPPMNSYERKLIHDLAEYYGLKSESEGEGpnRRVVITK 59
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 553-874 2.39e-03

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 41.92  E-value: 2.39e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568908728   553 PSPQMPACYCAPGHyhSSQPQYRPIPSVHHSSHLNQPLPQPAQHTGYQVMPNQQQnyQGIVGVQSPQS--QSLMGG---- 626
Cdd:pfam09606  140 PSQMSRVGRMQPGG--QAGGMMQPSSGQPGSGTPNQMGPNGGPGQGQAGGMNGGQ--QGPMGGQMPPQmgVPGMPGpada 215

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568908728   627 -------QPNSTGPHIQGVVIPYPSVPSYQV-SLPQGSQGIAHQTYQQPVVFPnQSNQGSLPtTGMPVyYSVIPPGQQSN 698
Cdd:pfam09606  216 gaqmgqqAQANGGMNPQQMGGAPNQVAMQQQqPQQQGQQSQLGMGINQMQQMP-QGVGGGAG-QGGPG-QPMGPPGQQPG 292

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568908728   699 LSSAVGYLQHPGSEQVQFPRTtspcSSQQLQGHQCAAVPQQPpgggmvmmqlNLPNNPQSRTHSPPQwkQNKHYCDHQRG 778
Cdd:pfam09606  293 AMPNVMSIGDQNNYQQQQTRQ----QQQQQGGNHPAAHQQQM----------NQSVGQGGQVVALGG--LNHLETWNPGN 356

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568908728   779 QkcmDFSNMDNIVQPSP-QLSSPilSPVQSPAPAQLSTLKTIRPSGPPlsimsQFARPFVPGQGDARYPlLGQPLQynPP 857
Cdd:pfam09606  357 F---GGLGANPMQRGQPgMMSSP--SPVPGQQVRQVTPNQFMRQSPQP-----SVPSPQGPGSQPPQSH-PGGMIP--SP 423

                          330
                   ....*....|....*...
gi 568908728   858 TLLHGHIPH-QQGQSGSR 874
Cdd:pfam09606  424 ALIPSPSPQmSQQPAQQR 441
 
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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