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Conserved domains on  [gi|528487120|ref|XP_005166895|]
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DNA-binding protein RFX2 isoform X2 [Danio rerio]

Protein Classification

RFX1_trans_act and RFX_DNA_binding domain-containing protein( domain architecture ID 12054117)

RFX1_trans_act and RFX_DNA_binding domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 175-249 1.83e-43

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: 150.78  E-value: 1.83e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528487120  175 LQWLLDNYETAEGVSLPRSSLYNHYLRHCQEQKLDPVNAASFGKLIRSVFMGLRTRRLGTRGNSKYHYYGIRLKP 249
Cdd:pfam02257   5 LQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGIKPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
RFX1_trans_act pfam04589
RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding ...
 10-129 3.82e-32

RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding proteins. RFX1 is a regulatory factor essential for expression of MHC class II genes. This region is to found N terminal to the RFX DNA binding region (pfam02257) in some mammalian RFX proteins, and is thought to activate transcription when associated with DNA. Deletion analysis has identified the region 233-351 in human RFX1 as being required for maximal activation.


:

Pssm-ID: 461362 [Multi-domain]  Cd Length: 163  Bit Score: 122.35  E-value: 3.82e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528487120   10 TPSTVALRTSTSAQAPVVQPVPASQQVQQVQ-----HYHSQQVQYVEGAEAVYPNGTIR-AAYSYnPESQLYGQGSGSAY 83
Cdd:pfam04589  38 TPSAPKGGHVQQLSVPRLQQVHVTQEVQQLQqvpvqHVYPNQVQYVEGGDAVYTTSTIRsSAYPY-TETPLYTQGSGASY 116

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 528487120   84 FDSQAGGAQVTTVVSSGGV-PTHGMVGIAMDVGGSQIISSGSAYLIH 129
Cdd:pfam04589 117 YEAQGGGAQVSTPATSLAVaVSSSSVGIPMDVGGSQIVASSSAASGG 163
 
Name Accession Description Interval E-value
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 175-249 1.83e-43

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: 150.78  E-value: 1.83e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528487120  175 LQWLLDNYETAEGVSLPRSSLYNHYLRHCQEQKLDPVNAASFGKLIRSVFMGLRTRRLGTRGNSKYHYYGIRLKP 249
Cdd:pfam02257   5 LQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGIKPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
RFX1_trans_act pfam04589
RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding ...
 10-129 3.82e-32

RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding proteins. RFX1 is a regulatory factor essential for expression of MHC class II genes. This region is to found N terminal to the RFX DNA binding region (pfam02257) in some mammalian RFX proteins, and is thought to activate transcription when associated with DNA. Deletion analysis has identified the region 233-351 in human RFX1 as being required for maximal activation.


Pssm-ID: 461362 [Multi-domain]  Cd Length: 163  Bit Score: 122.35  E-value: 3.82e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528487120   10 TPSTVALRTSTSAQAPVVQPVPASQQVQQVQ-----HYHSQQVQYVEGAEAVYPNGTIR-AAYSYnPESQLYGQGSGSAY 83
Cdd:pfam04589  38 TPSAPKGGHVQQLSVPRLQQVHVTQEVQQLQqvpvqHVYPNQVQYVEGGDAVYTTSTIRsSAYPY-TETPLYTQGSGASY 116

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 528487120   84 FDSQAGGAQVTTVVSSGGV-PTHGMVGIAMDVGGSQIISSGSAYLIH 129
Cdd:pfam04589 117 YEAQGGGAQVSTPATSLAVaVSSSSVGIPMDVGGSQIVASSSAASGG 163
COG3378 COG3378
DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];
172-251 1.92e-09

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


Pssm-ID: 442605 [Multi-domain]  Cd Length: 403  Bit Score: 60.34  E-value: 1.92e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528487120 172 NSHLQWLLDNYETAEGVSLPRSSLYNHYLRHCQEQKLDPVNAASFGKLIRSVFMGLRTRRlgTRGNSKYHYYGIRLKPDS 251
Cdd:COG3378  324 DPLGAFLEECCELDPGARVPKKDLYEAYREWCEDNGEKPLSKRTFGKELKKLGFEYEKRR--TNGGKRRGYRGIRLKDDS 401
 
Name Accession Description Interval E-value
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 175-249 1.83e-43

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: 150.78  E-value: 1.83e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528487120  175 LQWLLDNYETAEGVSLPRSSLYNHYLRHCQEQKLDPVNAASFGKLIRSVFMGLRTRRLGTRGNSKYHYYGIRLKP 249
Cdd:pfam02257   5 LQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGIKPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
RFX1_trans_act pfam04589
RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding ...
 10-129 3.82e-32

RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding proteins. RFX1 is a regulatory factor essential for expression of MHC class II genes. This region is to found N terminal to the RFX DNA binding region (pfam02257) in some mammalian RFX proteins, and is thought to activate transcription when associated with DNA. Deletion analysis has identified the region 233-351 in human RFX1 as being required for maximal activation.


Pssm-ID: 461362 [Multi-domain]  Cd Length: 163  Bit Score: 122.35  E-value: 3.82e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528487120   10 TPSTVALRTSTSAQAPVVQPVPASQQVQQVQ-----HYHSQQVQYVEGAEAVYPNGTIR-AAYSYnPESQLYGQGSGSAY 83
Cdd:pfam04589  38 TPSAPKGGHVQQLSVPRLQQVHVTQEVQQLQqvpvqHVYPNQVQYVEGGDAVYTTSTIRsSAYPY-TETPLYTQGSGASY 116

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 528487120   84 FDSQAGGAQVTTVVSSGGV-PTHGMVGIAMDVGGSQIISSGSAYLIH 129
Cdd:pfam04589 117 YEAQGGGAQVSTPATSLAVaVSSSSVGIPMDVGGSQIVASSSAASGG 163
COG3378 COG3378
DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];
172-251 1.92e-09

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


Pssm-ID: 442605 [Multi-domain]  Cd Length: 403  Bit Score: 60.34  E-value: 1.92e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528487120 172 NSHLQWLLDNYETAEGVSLPRSSLYNHYLRHCQEQKLDPVNAASFGKLIRSVFMGLRTRRlgTRGNSKYHYYGIRLKPDS 251
Cdd:COG3378  324 DPLGAFLEECCELDPGARVPKKDLYEAYREWCEDNGEKPLSKRTFGKELKKLGFEYEKRR--TNGGKRRGYRGIRLKDDS 401
 
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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