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Conserved domains on  [gi|157821255|ref|NP_001101164|]
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DNA-binding protein RFX5 [Rattus norvegicus]

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 ...
 466-679 1.79e-110

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


:

Pssm-ID: 464220  Cd Length: 219  Bit Score: 332.64  E-value: 1.79e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821255  466 RVPPRAPILPRGTESREVGISGDPRPHDKGVKRTAEVPLSEASGQDPPVKEMKHETEDTVSEAKRKRGRPRKKTGGSGER 545
Cdd:pfam14621   5 RAPPGGLIQPQGTENREVGIGGDPGPHDKGVKRTAEVPVSEASGQDPPAKAAKQDTEDTGSDAKRKRGRPRKKSGGSGER 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821255  546 NATPEKSAAAVNSPRSPRLLWETWGSKRENNLVGRPERPGAVGEAQRETVLAQGQEDGAVSKGEKSLSSQEAKEAEDKIP 625
Cdd:pfam14621  85 NSTPEKSAAAMDSAQSSRLPWETWGSGRESNSAGGSERPGPVGEAEKGVVLAQGQEDGAVSKGGRGPSSRHAKEAEDKIP 164

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 157821255  626 PVTSKVSVIKG-RIQKEALQLVKGEADAATQGNKGLKGRVLQSSLTHEHKDPKAT 679
Cdd:pfam14621 165 LVTSKVSVIKGsRSQKEALQLVKGEVDTAAQGNKDLKGHVLQSSLFHEHKDPKAT 219
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 94-167 1.93e-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: 1.93e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157821255   94 WIRNHLEEHMDTCLPKQSVYDAYRKYCESLACcRPLSTANFGKIIREIFPDIKARRLGGRGQSKYCYSGIRRKT 167
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 ...
 27-85 3.17e-30

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: 113.12  E-value: 3.17e-30
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 157821255   27 TTLLQRLRGTISKAVQNKVEGILQEVQKFSDNDKLYLYLQLPSGPSTGDKSSEPSILSN 85
Cdd:pfam18326   1 NALQQKIKNSICKAVQSKVDGILQDVEKFTDNEKLYLYLQLPSGPSSGDKSSDQSTMSS 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 ...
 466-679 1.79e-110

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


Pssm-ID: 464220  Cd Length: 219  Bit Score: 332.64  E-value: 1.79e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821255  466 RVPPRAPILPRGTESREVGISGDPRPHDKGVKRTAEVPLSEASGQDPPVKEMKHETEDTVSEAKRKRGRPRKKTGGSGER 545
Cdd:pfam14621   5 RAPPGGLIQPQGTENREVGIGGDPGPHDKGVKRTAEVPVSEASGQDPPAKAAKQDTEDTGSDAKRKRGRPRKKSGGSGER 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821255  546 NATPEKSAAAVNSPRSPRLLWETWGSKRENNLVGRPERPGAVGEAQRETVLAQGQEDGAVSKGEKSLSSQEAKEAEDKIP 625
Cdd:pfam14621  85 NSTPEKSAAAMDSAQSSRLPWETWGSGRESNSAGGSERPGPVGEAEKGVVLAQGQEDGAVSKGGRGPSSRHAKEAEDKIP 164

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 157821255  626 PVTSKVSVIKG-RIQKEALQLVKGEADAATQGNKGLKGRVLQSSLTHEHKDPKAT 679
Cdd:pfam14621 165 LVTSKVSVIKGsRSQKEALQLVKGEVDTAAQGNKDLKGHVLQSSLFHEHKDPKAT 219
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 94-167 1.93e-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: 1.93e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157821255   94 WIRNHLEEHMDTCLPKQSVYDAYRKYCESLACcRPLSTANFGKIIREIFPDIKARRLGGRGQSKYCYSGIRRKT 167
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 ...
 27-85 3.17e-30

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: 113.12  E-value: 3.17e-30
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 157821255   27 TTLLQRLRGTISKAVQNKVEGILQEVQKFSDNDKLYLYLQLPSGPSTGDKSSEPSILSN 85
Cdd:pfam18326   1 NALQQKIKNSICKAVQSKVDGILQDVEKFTDNEKLYLYLQLPSGPSSGDKSSDQSTMSS 59
COG3378 COG3378
DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];
86-167 4.79e-07

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


Pssm-ID: 442605 [Multi-domain]  Cd Length: 403  Bit Score: 52.64  E-value: 4.79e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821255  86 EEYMYA----YRWIRNHLEEHMDTCLPKQSVYDAYRKYCESLAcCRPLSTANFGKIIREIFPDIKARRLGGRgqSKYCYS 161
Cdd:COG3378  317 EEYREEsdplGAFLEECCELDPGARVPKKDLYEAYREWCEDNG-EKPLSKRTFGKELKKLGFEYEKRRTNGG--KRRGYR 393


                 ....*.
gi 157821255 162 GIRRKT 167
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 ...
 466-679 1.79e-110

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


Pssm-ID: 464220  Cd Length: 219  Bit Score: 332.64  E-value: 1.79e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821255  466 RVPPRAPILPRGTESREVGISGDPRPHDKGVKRTAEVPLSEASGQDPPVKEMKHETEDTVSEAKRKRGRPRKKTGGSGER 545
Cdd:pfam14621   5 RAPPGGLIQPQGTENREVGIGGDPGPHDKGVKRTAEVPVSEASGQDPPAKAAKQDTEDTGSDAKRKRGRPRKKSGGSGER 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821255  546 NATPEKSAAAVNSPRSPRLLWETWGSKRENNLVGRPERPGAVGEAQRETVLAQGQEDGAVSKGEKSLSSQEAKEAEDKIP 625
Cdd:pfam14621  85 NSTPEKSAAAMDSAQSSRLPWETWGSGRESNSAGGSERPGPVGEAEKGVVLAQGQEDGAVSKGGRGPSSRHAKEAEDKIP 164

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 157821255  626 PVTSKVSVIKG-RIQKEALQLVKGEADAATQGNKGLKGRVLQSSLTHEHKDPKAT 679
Cdd:pfam14621 165 LVTSKVSVIKGsRSQKEALQLVKGEVDTAAQGNKDLKGHVLQSSLFHEHKDPKAT 219
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 94-167 1.93e-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: 1.93e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157821255   94 WIRNHLEEHMDTCLPKQSVYDAYRKYCESLACcRPLSTANFGKIIREIFPDIKARRLGGRGQSKYCYSGIRRKT 167
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 ...
 27-85 3.17e-30

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: 113.12  E-value: 3.17e-30
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 157821255   27 TTLLQRLRGTISKAVQNKVEGILQEVQKFSDNDKLYLYLQLPSGPSTGDKSSEPSILSN 85
Cdd:pfam18326   1 NALQQKIKNSICKAVQSKVDGILQDVEKFTDNEKLYLYLQLPSGPSSGDKSSDQSTMSS 59
COG3378 COG3378
DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];
86-167 4.79e-07

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


Pssm-ID: 442605 [Multi-domain]  Cd Length: 403  Bit Score: 52.64  E-value: 4.79e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821255  86 EEYMYA----YRWIRNHLEEHMDTCLPKQSVYDAYRKYCESLAcCRPLSTANFGKIIREIFPDIKARRLGGRgqSKYCYS 161
Cdd:COG3378  317 EEYREEsdplGAFLEECCELDPGARVPKKDLYEAYREWCEDNG-EKPLSKRTFGKELKKLGFEYEKRRTNGG--KRRGYR 393


                 ....*.
gi 157821255 162 GIRRKT 167
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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