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Conserved domains on  [gi|1958746005|ref|XP_038953458|]
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MHC class II regulatory factor RFX1 isoform X2 [Rattus norvegicus]

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 ...
 523-600 2.00e-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: 2.00e-43
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958746005  523 PATVQWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRSVFMGLRTRRLGTRGNSKYHYYGLRIKA 600
Cdd:pfam02257    2 VFALQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGIKPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
RFX1_trans_act pfam04589
RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding ...
 214-458 2.91e-37

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: 137.75  E-value: 2.91e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958746005  214 AGTPAGTVQQLQVHSVQQSVPVTQERSVVQATPQ-TKAGPVQQLTVQGLQPVHVAQEssgsqfparkaeqqetrptpppe 292
Cdd:pfam04589    7 SAPPAAVLQQLAPTQVVQPVPASQQRSVVQATPSaPKGGHVQQLSVPRLQQVHVTQE----------------------- 63

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958746005  293 ppprppgpgpaccgealqlgseqqpphyepgveqwvelvgvlpphlllpqqrvvfepqpglsaraspdlrvrihrmpqVQ 372
Cdd:pfam04589   64 ------------------------------------------------------------------------------VQ 65

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958746005  373 QLPQVPVPHVYSSQVQYVEGGDASYTASAIRSSTYQYPETPIYTQTAGTSYYEASGTAAQVSTPATSQTV---ASSGSVP 449
Cdd:pfam04589   66 QLQQVPVQHVYPNQVQYVEGGDAVYTTSTIRSSAYPYTETPLYTQGSGASYYEAQGGGAQVSTPATSLAVavsSSSVGIP 145


                   ....*....
gi 1958746005  450 MYVSGSPIV 458
Cdd:pfam04589  146 MDVGGSQIV 154
 
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 ...
 523-600 2.00e-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: 2.00e-43
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958746005  523 PATVQWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRSVFMGLRTRRLGTRGNSKYHYYGLRIKA 600
Cdd:pfam02257    2 VFALQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGIKPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
RFX1_trans_act pfam04589
RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding ...
 214-458 2.91e-37

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: 137.75  E-value: 2.91e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958746005  214 AGTPAGTVQQLQVHSVQQSVPVTQERSVVQATPQ-TKAGPVQQLTVQGLQPVHVAQEssgsqfparkaeqqetrptpppe 292
Cdd:pfam04589    7 SAPPAAVLQQLAPTQVVQPVPASQQRSVVQATPSaPKGGHVQQLSVPRLQQVHVTQE----------------------- 63

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958746005  293 ppprppgpgpaccgealqlgseqqpphyepgveqwvelvgvlpphlllpqqrvvfepqpglsaraspdlrvrihrmpqVQ 372
Cdd:pfam04589   64 ------------------------------------------------------------------------------VQ 65

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958746005  373 QLPQVPVPHVYSSQVQYVEGGDASYTASAIRSSTYQYPETPIYTQTAGTSYYEASGTAAQVSTPATSQTV---ASSGSVP 449
Cdd:pfam04589   66 QLQQVPVQHVYPNQVQYVEGGDAVYTTSTIRSSAYPYTETPLYTQGSGASYYEAQGGGAQVSTPATSLAVavsSSSVGIP 145


                   ....*....
gi 1958746005  450 MYVSGSPIV 458
Cdd:pfam04589  146 MDVGGSQIV 154
COG3378 COG3378
DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];
527-602 9.65e-06

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


Pssm-ID: 442605 [Multi-domain]  Cd Length: 403  Bit Score: 49.17  E-value: 9.65e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958746005  527 QWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRSVFMGLRTRRlgTRGNSKYHYYGLRIKASS 602
Cdd:COG3378    328 AFLEECCELDPGARVPKKDLYEAYREWCEDNGEKPLSKRTFGKELKKLGFEYEKRR--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 ...
 523-600 2.00e-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: 2.00e-43
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958746005  523 PATVQWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRSVFMGLRTRRLGTRGNSKYHYYGLRIKA 600
Cdd:pfam02257    2 VFALQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGIKPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
RFX1_trans_act pfam04589
RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding ...
 214-458 2.91e-37

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: 137.75  E-value: 2.91e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958746005  214 AGTPAGTVQQLQVHSVQQSVPVTQERSVVQATPQ-TKAGPVQQLTVQGLQPVHVAQEssgsqfparkaeqqetrptpppe 292
Cdd:pfam04589    7 SAPPAAVLQQLAPTQVVQPVPASQQRSVVQATPSaPKGGHVQQLSVPRLQQVHVTQE----------------------- 63

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958746005  293 ppprppgpgpaccgealqlgseqqpphyepgveqwvelvgvlpphlllpqqrvvfepqpglsaraspdlrvrihrmpqVQ 372
Cdd:pfam04589   64 ------------------------------------------------------------------------------VQ 65

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958746005  373 QLPQVPVPHVYSSQVQYVEGGDASYTASAIRSSTYQYPETPIYTQTAGTSYYEASGTAAQVSTPATSQTV---ASSGSVP 449
Cdd:pfam04589   66 QLQQVPVQHVYPNQVQYVEGGDAVYTTSTIRSSAYPYTETPLYTQGSGASYYEAQGGGAQVSTPATSLAVavsSSSVGIP 145


                   ....*....
gi 1958746005  450 MYVSGSPIV 458
Cdd:pfam04589  146 MDVGGSQIV 154
COG3378 COG3378
DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];
527-602 9.65e-06

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


Pssm-ID: 442605 [Multi-domain]  Cd Length: 403  Bit Score: 49.17  E-value: 9.65e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958746005  527 QWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRSVFMGLRTRRlgTRGNSKYHYYGLRIKASS 602
Cdd:COG3378    328 AFLEECCELDPGARVPKKDLYEAYREWCEDNGEKPLSKRTFGKELKKLGFEYEKRR--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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