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Conserved domains on  [gi|1827625822|ref|NP_001366348|]
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DNA-binding protein RFX5 isoform 2 [Homo sapiens]

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 ...
 367-574 2.45e-115

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


:

Pssm-ID: 464220  Cd Length: 219  Bit Score: 341.50  E-value: 2.45e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827625822 367 TQPRGTENREVGIGGDQGPHDKGVKRTAEVPVSEASGQAPPAKAAKQDIEDTASDAKRKRGRPRKKSGGSGERNSTPLKS 446
Cdd:pfam14621  12 IQPQGTENREVGIGGDPGPHDKGVKRTAEVPVSEASGQDPPAKAAKQDTEDTGSDAKRKRGRPRKKSGGSGERNSTPEKS 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827625822 447 AAAMESAQSSRLPWETWGSGGEGNSAGGAERPGPMGEAEKGAVLAQGQGDGTVSKGGRGPGSQHTKEAEDKIPLVPSKVS 526
Cdd:pfam14621  92 AAAMDSAQSSRLPWETWGSGRESNSAGGSERPGPVGEAEKGVVLAQGQEDGAVSKGGRGPSSRHAKEAEDKIPLVTSKVS 171

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1827625822 527 VIKGSRSQKEAFPLAKGEVDTAPQGNKDLKEHVLQSSLSQEHKDPKAT 574
Cdd:pfam14621 172 VIKGSRSQKEALQLVKGEVDTAAQGNKDLKGHVLQSSLFHEHKDPKAT 219
RFX5_N super family cl39672
RFX5 N-terminal domain; This is the N-terminal domain of regulatory factor X (RFX)-5 protein ...
 28-78 1.69e-26

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: 101.94  E-value: 1.69e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1827625822  28 TTLLQRLRGTISKAVQNKVEGILQDVQKFSDNDKLYLYLQLPSGPTTGDKR 78
Cdd:pfam18326   1 NALQQKIKNSICKAVQSKVDGILQDVEKFTDNEKLYLYLQLPSGPSSGDKS 51
RFX_DNA_binding super family cl03504
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 80-128 1.70e-21

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).


The actual alignment was detected with superfamily member pfam02257:

Pssm-ID: 460512  Cd Length: 79  Bit Score: 88.38  E-value: 1.70e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1827625822  80 YCESLACcRPLSTANFGKIIREIFPDIKARRLGGRGQSKYCYSGIRRKT 128
Cdd:pfam02257  32 FCSKLGI-KPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
 
Name Accession Description Interval E-value
RFX5_DNA_bdg pfam14621
RFX5 DNA-binding domain; RFX5 and RFXAP reveals molecular details associated with MHCII gene ...
 367-574 2.45e-115

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


Pssm-ID: 464220  Cd Length: 219  Bit Score: 341.50  E-value: 2.45e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827625822 367 TQPRGTENREVGIGGDQGPHDKGVKRTAEVPVSEASGQAPPAKAAKQDIEDTASDAKRKRGRPRKKSGGSGERNSTPLKS 446
Cdd:pfam14621  12 IQPQGTENREVGIGGDPGPHDKGVKRTAEVPVSEASGQDPPAKAAKQDTEDTGSDAKRKRGRPRKKSGGSGERNSTPEKS 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827625822 447 AAAMESAQSSRLPWETWGSGGEGNSAGGAERPGPMGEAEKGAVLAQGQGDGTVSKGGRGPGSQHTKEAEDKIPLVPSKVS 526
Cdd:pfam14621  92 AAAMDSAQSSRLPWETWGSGRESNSAGGSERPGPVGEAEKGVVLAQGQEDGAVSKGGRGPSSRHAKEAEDKIPLVTSKVS 171

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1827625822 527 VIKGSRSQKEAFPLAKGEVDTAPQGNKDLKEHVLQSSLSQEHKDPKAT 574
Cdd:pfam14621 172 VIKGSRSQKEALQLVKGEVDTAAQGNKDLKGHVLQSSLFHEHKDPKAT 219
RFX5_N pfam18326
RFX5 N-terminal domain; This is the N-terminal domain of regulatory factor X (RFX)-5 protein ...
 28-78 1.69e-26

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: 101.94  E-value: 1.69e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1827625822  28 TTLLQRLRGTISKAVQNKVEGILQDVQKFSDNDKLYLYLQLPSGPTTGDKR 78
Cdd:pfam18326   1 NALQQKIKNSICKAVQSKVDGILQDVEKFTDNEKLYLYLQLPSGPSSGDKS 51
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 80-128 1.70e-21

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: 88.38  E-value: 1.70e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1827625822  80 YCESLACcRPLSTANFGKIIREIFPDIKARRLGGRGQSKYCYSGIRRKT 128
Cdd:pfam02257  32 FCSKLGI-KPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
 
Name Accession Description Interval E-value
RFX5_DNA_bdg pfam14621
RFX5 DNA-binding domain; RFX5 and RFXAP reveals molecular details associated with MHCII gene ...
 367-574 2.45e-115

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


Pssm-ID: 464220  Cd Length: 219  Bit Score: 341.50  E-value: 2.45e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827625822 367 TQPRGTENREVGIGGDQGPHDKGVKRTAEVPVSEASGQAPPAKAAKQDIEDTASDAKRKRGRPRKKSGGSGERNSTPLKS 446
Cdd:pfam14621  12 IQPQGTENREVGIGGDPGPHDKGVKRTAEVPVSEASGQDPPAKAAKQDTEDTGSDAKRKRGRPRKKSGGSGERNSTPEKS 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827625822 447 AAAMESAQSSRLPWETWGSGGEGNSAGGAERPGPMGEAEKGAVLAQGQGDGTVSKGGRGPGSQHTKEAEDKIPLVPSKVS 526
Cdd:pfam14621  92 AAAMDSAQSSRLPWETWGSGRESNSAGGSERPGPVGEAEKGVVLAQGQEDGAVSKGGRGPSSRHAKEAEDKIPLVTSKVS 171

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1827625822 527 VIKGSRSQKEAFPLAKGEVDTAPQGNKDLKEHVLQSSLSQEHKDPKAT 574
Cdd:pfam14621 172 VIKGSRSQKEALQLVKGEVDTAAQGNKDLKGHVLQSSLFHEHKDPKAT 219
RFX5_N pfam18326
RFX5 N-terminal domain; This is the N-terminal domain of regulatory factor X (RFX)-5 protein ...
 28-78 1.69e-26

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: 101.94  E-value: 1.69e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1827625822  28 TTLLQRLRGTISKAVQNKVEGILQDVQKFSDNDKLYLYLQLPSGPTTGDKR 78
Cdd:pfam18326   1 NALQQKIKNSICKAVQSKVDGILQDVEKFTDNEKLYLYLQLPSGPSSGDKS 51
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 80-128 1.70e-21

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: 88.38  E-value: 1.70e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1827625822  80 YCESLACcRPLSTANFGKIIREIFPDIKARRLGGRGQSKYCYSGIRRKT 128
Cdd:pfam02257  32 FCSKLGI-KPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
 
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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