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Conserved domains on  [gi|564333325|ref|XP_006231297|]
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transcription factor RFX3 isoform X5 [Rattus norvegicus]

Protein Classification

RFX family transcription factor( domain architecture ID 11759140)

RFX family transcription factor activates transcription by binding to the X-box in the promoter of target genes; similar to human transcription factor RFX3

CATH:  1.10.10.10
Gene Ontology:  GO:0003700
PubMed:  8754849

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 ...
 184-258 1.08e-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: 151.93  E-value: 1.08e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564333325  184 LQWLLDNYETAEGVSLPRSTLYNHYLRHCQEHKLDPVNAASFGKLIRSIFMGLRTRRLGTRGNSKYHYYGIRVKP 258
Cdd:pfam02257   5 LQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGIKPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
RFX1_trans_act super family cl25722
RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding ...
 51-138 1.10e-27

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.


The actual alignment was detected with superfamily member pfam04589:

Pssm-ID: 461362 [Multi-domain]  Cd Length: 163  Bit Score: 109.63  E-value: 1.10e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333325   51 HVYPAQVQYVEGSDTVYTNGAIRTTTYPYTETQMYSQNTGGNYFDTQGSSAQVTTVVSSHSMV---GTGGIQMGVTGGQL 127
Cdd:pfam04589  74 HVYPNQVQYVEGGDAVYTTSTIRSSAYPYTETPLYTQGSGASYYEAQGGGAQVSTPATSLAVAvssSSVGIPMDVGGSQI 153

                          90
                  ....*....|.
gi 564333325  128 ISSSgGTYLIG 138
Cdd:pfam04589 154 VASS-SAASGG 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 ...
 184-258 1.08e-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: 151.93  E-value: 1.08e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564333325  184 LQWLLDNYETAEGVSLPRSTLYNHYLRHCQEHKLDPVNAASFGKLIRSIFMGLRTRRLGTRGNSKYHYYGIRVKP 258
Cdd:pfam02257   5 LQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGIKPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
RFX1_trans_act pfam04589
RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding ...
 51-138 1.10e-27

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: 109.63  E-value: 1.10e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333325   51 HVYPAQVQYVEGSDTVYTNGAIRTTTYPYTETQMYSQNTGGNYFDTQGSSAQVTTVVSSHSMV---GTGGIQMGVTGGQL 127
Cdd:pfam04589  74 HVYPNQVQYVEGGDAVYTTSTIRSSAYPYTETPLYTQGSGASYYEAQGGGAQVSTPATSLAVAvssSSVGIPMDVGGSQI 153

                          90
                  ....*....|.
gi 564333325  128 ISSSgGTYLIG 138
Cdd:pfam04589 154 VASS-SAASGG 163
COG3378 COG3378
DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];
159-260 2.78e-09

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


Pssm-ID: 442605 [Multi-domain]  Cd Length: 403  Bit Score: 59.95  E-value: 2.78e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333325 159 IEMAIEtLQKSDGLSTHRSSLL---------NSHLQWLLDNYETAEGVSLPRSTLYNHYLRHCQEHKLDPVNAASFGKLI 229
Cdd:COG3378  294 LEGLLR-LLENGGLTEPESVKEateeyreesDPLGAFLEECCELDPGARVPKKDLYEAYREWCEDNGEKPLSKRTFGKEL 372

                         90       100       110
                 ....*....|....*....|....*....|.
gi 564333325 230 RSIFMGLRTRRlgTRGNSKYHYYGIRVKPDS 260
Cdd:COG3378  373 KKLGFEYEKRR--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 ...
 184-258 1.08e-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: 151.93  E-value: 1.08e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564333325  184 LQWLLDNYETAEGVSLPRSTLYNHYLRHCQEHKLDPVNAASFGKLIRSIFMGLRTRRLGTRGNSKYHYYGIRVKP 258
Cdd:pfam02257   5 LQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGIKPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
RFX1_trans_act pfam04589
RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding ...
 51-138 1.10e-27

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: 109.63  E-value: 1.10e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333325   51 HVYPAQVQYVEGSDTVYTNGAIRTTTYPYTETQMYSQNTGGNYFDTQGSSAQVTTVVSSHSMV---GTGGIQMGVTGGQL 127
Cdd:pfam04589  74 HVYPNQVQYVEGGDAVYTTSTIRSSAYPYTETPLYTQGSGASYYEAQGGGAQVSTPATSLAVAvssSSVGIPMDVGGSQI 153

                          90
                  ....*....|.
gi 564333325  128 ISSSgGTYLIG 138
Cdd:pfam04589 154 VASS-SAASGG 163
COG3378 COG3378
DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];
159-260 2.78e-09

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


Pssm-ID: 442605 [Multi-domain]  Cd Length: 403  Bit Score: 59.95  E-value: 2.78e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333325 159 IEMAIEtLQKSDGLSTHRSSLL---------NSHLQWLLDNYETAEGVSLPRSTLYNHYLRHCQEHKLDPVNAASFGKLI 229
Cdd:COG3378  294 LEGLLR-LLENGGLTEPESVKEateeyreesDPLGAFLEECCELDPGARVPKKDLYEAYREWCEDNGEKPLSKRTFGKEL 372

                         90       100       110
                 ....*....|....*....|....*....|.
gi 564333325 230 RSIFMGLRTRRlgTRGNSKYHYYGIRVKPDS 260
Cdd:COG3378  373 KKLGFEYEKRR--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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