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Conserved domains on  [gi|568923247|ref|XP_006501761|]
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DNA-binding protein Rfx5 isoform X2 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RFX5_DNA_bdg pfam14621
RFX5 DNA-binding domain; RFX5 and RFXAP reveals molecular details associated with MHCII gene ...
 417-631 3.83e-96

RFX5 DNA-binding domain; RFX5 and RFXAP reveals molecular details associated with MHCII gene expression.


:

Pssm-ID: 464220  Cd Length: 219  Bit Score: 294.12  E-value: 3.83e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568923247  417 RVPPRAPILPRGAENREVGISSDPRPHDKGIKRTAEVPLSEASGQDPPVKEMKHETQDTtVSEAKRKRGRPRKKPGGSGE 496
Cdd:pfam14621   5 RAPPGGLIQPQGTENREVGIGGDPGPHDKGVKRTAEVPVSEASGQDPPAKAAKQDTEDT-GSDAKRKRGRPRKKSGGSGE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568923247  497 RNATPEKSAAIVNSPRSPRLLWETWGSKRENNFIGRPEGPGPGGEAERETVLVQGQQDGAVSKGERSLSSQEAKEAEDKI 576
Cdd:pfam14621  84 RNSTPEKSAAAMDSAQSSRLPWETWGSGRESNSAGGSERPGPVGEAEKGVVLAQGQEDGAVSKGGRGPSSRHAKEAEDKI 163

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 568923247  577 PPVTSKVSVIKG-RIQKEALQLVKGEADAATQGNKGLKGRVLQSSLTPEHKDPKAT 631
Cdd:pfam14621 164 PLVTSKVSVIKGsRSQKEALQLVKGEVDTAAQGNKDLKGHVLQSSLFHEHKDPKAT 219
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 69-142 1.62e-32

RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer. It recognize X-boxes (DNA of the sequence 5'-GTNRCC(0-3N)RGYAAC-3', where N is any nucleotide, R is a purine and Y is a pyrimidine) using a highly conserved 76-residue DNA-binding domain (DBD).


:

Pssm-ID: 460512  Cd Length: 79  Bit Score: 119.96  E-value: 1.62e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568923247   69 WIRNHLEEHMDTCLPKQSVYDAYRKYCESLACcRPLSTANFGKIIREIFPDIKARRLGGRGQSKYCYSGIRRKT 142
Cdd:pfam02257   7 WLNANYEVAEGSSVPRSRVYAHYLSFCSKLGI-KPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
RFX5_N super family cl39672
RFX5 N-terminal domain; This is the N-terminal domain of regulatory factor X (RFX)-5 protein ...
 25-60 1.42e-15

RFX5 N-terminal domain; This is the N-terminal domain of regulatory factor X (RFX)-5 protein of the RFX complex present in Homo sapiens. The RFX complex is made up of RFX5, RFXAP and RFXB. The complex is involved in the regulation of the expression of the major histocompatibility complex class II (MHCII) gene products. These gene products are essential for the initiation and regulation of the mammalian immune response. The N-terminal domain of RFX5 is responsible for homodimerization of RFX5 which promotes folding of the C-terminal domain of RFXAP. The folding of RFXAP results in the formation of a potential binding site for RFXB to bind to the MHCII promoter.


The actual alignment was detected with superfamily member pfam18326:

Pssm-ID: 375753  Cd Length: 59  Bit Score: 71.13  E-value: 1.42e-15
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 568923247   25 QEVQKFSDNDKLYLYLQLPSGPSVGEKSSEPSLLSN 60
Cdd:pfam18326  24 QDVEKFTDNEKLYLYLQLPSGPSSGDKSSDQSTMSS 59
 
Name Accession Description Interval E-value
RFX5_DNA_bdg pfam14621
RFX5 DNA-binding domain; RFX5 and RFXAP reveals molecular details associated with MHCII gene ...
 417-631 3.83e-96

RFX5 DNA-binding domain; RFX5 and RFXAP reveals molecular details associated with MHCII gene expression.


Pssm-ID: 464220  Cd Length: 219  Bit Score: 294.12  E-value: 3.83e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568923247  417 RVPPRAPILPRGAENREVGISSDPRPHDKGIKRTAEVPLSEASGQDPPVKEMKHETQDTtVSEAKRKRGRPRKKPGGSGE 496
Cdd:pfam14621   5 RAPPGGLIQPQGTENREVGIGGDPGPHDKGVKRTAEVPVSEASGQDPPAKAAKQDTEDT-GSDAKRKRGRPRKKSGGSGE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568923247  497 RNATPEKSAAIVNSPRSPRLLWETWGSKRENNFIGRPEGPGPGGEAERETVLVQGQQDGAVSKGERSLSSQEAKEAEDKI 576
Cdd:pfam14621  84 RNSTPEKSAAAMDSAQSSRLPWETWGSGRESNSAGGSERPGPVGEAEKGVVLAQGQEDGAVSKGGRGPSSRHAKEAEDKI 163

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 568923247  577 PPVTSKVSVIKG-RIQKEALQLVKGEADAATQGNKGLKGRVLQSSLTPEHKDPKAT 631
Cdd:pfam14621 164 PLVTSKVSVIKGsRSQKEALQLVKGEVDTAAQGNKDLKGHVLQSSLFHEHKDPKAT 219
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 69-142 1.62e-32

RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer. It recognize X-boxes (DNA of the sequence 5'-GTNRCC(0-3N)RGYAAC-3', where N is any nucleotide, R is a purine and Y is a pyrimidine) using a highly conserved 76-residue DNA-binding domain (DBD).


Pssm-ID: 460512  Cd Length: 79  Bit Score: 119.96  E-value: 1.62e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568923247   69 WIRNHLEEHMDTCLPKQSVYDAYRKYCESLACcRPLSTANFGKIIREIFPDIKARRLGGRGQSKYCYSGIRRKT 142
Cdd:pfam02257   7 WLNANYEVAEGSSVPRSRVYAHYLSFCSKLGI-KPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
RFX5_N pfam18326
RFX5 N-terminal domain; This is the N-terminal domain of regulatory factor X (RFX)-5 protein ...
 25-60 1.42e-15

RFX5 N-terminal domain; This is the N-terminal domain of regulatory factor X (RFX)-5 protein of the RFX complex present in Homo sapiens. The RFX complex is made up of RFX5, RFXAP and RFXB. The complex is involved in the regulation of the expression of the major histocompatibility complex class II (MHCII) gene products. These gene products are essential for the initiation and regulation of the mammalian immune response. The N-terminal domain of RFX5 is responsible for homodimerization of RFX5 which promotes folding of the C-terminal domain of RFXAP. The folding of RFXAP results in the formation of a potential binding site for RFXB to bind to the MHCII promoter.


Pssm-ID: 375753  Cd Length: 59  Bit Score: 71.13  E-value: 1.42e-15
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 568923247   25 QEVQKFSDNDKLYLYLQLPSGPSVGEKSSEPSLLSN 60
Cdd:pfam18326  24 QDVEKFTDNEKLYLYLQLPSGPSSGDKSSDQSTMSS 59
COG3378 COG3378
DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];
61-142 4.32e-07

DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];


Pssm-ID: 442605 [Multi-domain]  Cd Length: 403  Bit Score: 52.64  E-value: 4.32e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568923247  61 EEYMYA----YRWIRNHLEEHMDTCLPKQSVYDAYRKYCESLAcCRPLSTANFGKIIREIFPDIKARRLGGRgqSKYCYS 136
Cdd:COG3378  317 EEYREEsdplGAFLEECCELDPGARVPKKDLYEAYREWCEDNG-EKPLSKRTFGKELKKLGFEYEKRRTNGG--KRRGYR 393


                 ....*.
gi 568923247 137 GIRRKT 142
Cdd:COG3378  394 GIRLKD 399
 
Name Accession Description Interval E-value
RFX5_DNA_bdg pfam14621
RFX5 DNA-binding domain; RFX5 and RFXAP reveals molecular details associated with MHCII gene ...
 417-631 3.83e-96

RFX5 DNA-binding domain; RFX5 and RFXAP reveals molecular details associated with MHCII gene expression.


Pssm-ID: 464220  Cd Length: 219  Bit Score: 294.12  E-value: 3.83e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568923247  417 RVPPRAPILPRGAENREVGISSDPRPHDKGIKRTAEVPLSEASGQDPPVKEMKHETQDTtVSEAKRKRGRPRKKPGGSGE 496
Cdd:pfam14621   5 RAPPGGLIQPQGTENREVGIGGDPGPHDKGVKRTAEVPVSEASGQDPPAKAAKQDTEDT-GSDAKRKRGRPRKKSGGSGE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568923247  497 RNATPEKSAAIVNSPRSPRLLWETWGSKRENNFIGRPEGPGPGGEAERETVLVQGQQDGAVSKGERSLSSQEAKEAEDKI 576
Cdd:pfam14621  84 RNSTPEKSAAAMDSAQSSRLPWETWGSGRESNSAGGSERPGPVGEAEKGVVLAQGQEDGAVSKGGRGPSSRHAKEAEDKI 163

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 568923247  577 PPVTSKVSVIKG-RIQKEALQLVKGEADAATQGNKGLKGRVLQSSLTPEHKDPKAT 631
Cdd:pfam14621 164 PLVTSKVSVIKGsRSQKEALQLVKGEVDTAAQGNKDLKGHVLQSSLFHEHKDPKAT 219
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 69-142 1.62e-32

RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer. It recognize X-boxes (DNA of the sequence 5'-GTNRCC(0-3N)RGYAAC-3', where N is any nucleotide, R is a purine and Y is a pyrimidine) using a highly conserved 76-residue DNA-binding domain (DBD).


Pssm-ID: 460512  Cd Length: 79  Bit Score: 119.96  E-value: 1.62e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568923247   69 WIRNHLEEHMDTCLPKQSVYDAYRKYCESLACcRPLSTANFGKIIREIFPDIKARRLGGRGQSKYCYSGIRRKT 142
Cdd:pfam02257   7 WLNANYEVAEGSSVPRSRVYAHYLSFCSKLGI-KPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
RFX5_N pfam18326
RFX5 N-terminal domain; This is the N-terminal domain of regulatory factor X (RFX)-5 protein ...
 25-60 1.42e-15

RFX5 N-terminal domain; This is the N-terminal domain of regulatory factor X (RFX)-5 protein of the RFX complex present in Homo sapiens. The RFX complex is made up of RFX5, RFXAP and RFXB. The complex is involved in the regulation of the expression of the major histocompatibility complex class II (MHCII) gene products. These gene products are essential for the initiation and regulation of the mammalian immune response. The N-terminal domain of RFX5 is responsible for homodimerization of RFX5 which promotes folding of the C-terminal domain of RFXAP. The folding of RFXAP results in the formation of a potential binding site for RFXB to bind to the MHCII promoter.


Pssm-ID: 375753  Cd Length: 59  Bit Score: 71.13  E-value: 1.42e-15
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 568923247   25 QEVQKFSDNDKLYLYLQLPSGPSVGEKSSEPSLLSN 60
Cdd:pfam18326  24 QDVEKFTDNEKLYLYLQLPSGPSSGDKSSDQSTMSS 59
COG3378 COG3378
DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];
61-142 4.32e-07

DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];


Pssm-ID: 442605 [Multi-domain]  Cd Length: 403  Bit Score: 52.64  E-value: 4.32e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568923247  61 EEYMYA----YRWIRNHLEEHMDTCLPKQSVYDAYRKYCESLAcCRPLSTANFGKIIREIFPDIKARRLGGRgqSKYCYS 136
Cdd:COG3378  317 EEYREEsdplGAFLEECCELDPGARVPKKDLYEAYREWCEDNG-EKPLSKRTFGKELKKLGFEYEKRRTNGG--KRRGYR 393


                 ....*.
gi 568923247 137 GIRRKT 142
Cdd:COG3378  394 GIRLKD 399
 
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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