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Conserved domains on  [gi|6677731|ref|NP_033082|]
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DNA-binding protein RFX2 isoform 2 [Mus musculus]

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
RFX1_trans_act pfam04589
RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding ...
 4-149 1.94e-47

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: 164.72  E-value: 1.94e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6677731      4 SEGGADSPASVA-LRPAA-----QPMPASPQRVLVQAAGSTPKGTPMQTLTLPRVQPVPP----------QVQHVYPAQV 67
Cdd:pfam04589   1 SDSGSDSAPPAAvLQQLAptqvvQPVPASQQRSVVQATPSAPKGGHVQQLSVPRLQQVHVtqevqqlqqvPVQHVYPNQV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6677731     68 QYVEGGDAVYANGAIR-AAYAYnPDPQLYAPSSAASYFETP-GGTQVTVAASSPPAVPSHGMVGITMDVSGTPIVSGAGA 145
Cdd:pfam04589  81 QYVEGGDAVYTTSTIRsSAYPY-TETPLYTQGSGASYYEAQgGGAQVSTPATSLAVAVSSSSVGIPMDVGGSQIVASSSA 159


                  ....
gi 6677731    146 YLIH 149
Cdd:pfam04589 160 ASGG 163
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 167-244 5.01e-45

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: 155.02  E-value: 5.01e-45
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6677731    167 PATLQWLLDNYETAEGVSLPRSSLYNHYLRHCQEHKLEPVNAASFGKLIRSVFMGLRTRRLGTRGNSKYHYYGIRLKP 244
Cdd:pfam02257   2 VFALQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGIKPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
 
Name Accession Description Interval E-value
RFX1_trans_act pfam04589
RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding ...
 4-149 1.94e-47

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: 164.72  E-value: 1.94e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6677731      4 SEGGADSPASVA-LRPAA-----QPMPASPQRVLVQAAGSTPKGTPMQTLTLPRVQPVPP----------QVQHVYPAQV 67
Cdd:pfam04589   1 SDSGSDSAPPAAvLQQLAptqvvQPVPASQQRSVVQATPSAPKGGHVQQLSVPRLQQVHVtqevqqlqqvPVQHVYPNQV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6677731     68 QYVEGGDAVYANGAIR-AAYAYnPDPQLYAPSSAASYFETP-GGTQVTVAASSPPAVPSHGMVGITMDVSGTPIVSGAGA 145
Cdd:pfam04589  81 QYVEGGDAVYTTSTIRsSAYPY-TETPLYTQGSGASYYEAQgGGAQVSTPATSLAVAVSSSSVGIPMDVGGSQIVASSSA 159


                  ....
gi 6677731    146 YLIH 149
Cdd:pfam04589 160 ASGG 163
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 167-244 5.01e-45

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: 155.02  E-value: 5.01e-45
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6677731    167 PATLQWLLDNYETAEGVSLPRSSLYNHYLRHCQEHKLEPVNAASFGKLIRSVFMGLRTRRLGTRGNSKYHYYGIRLKP 244
Cdd:pfam02257   2 VFALQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGIKPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
COG3378 COG3378
DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];
171-246 4.18e-09

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


Pssm-ID: 442605 [Multi-domain]  Cd Length: 403  Bit Score: 59.18  E-value: 4.18e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6677731  171 QWLLDNYETAEGVSLPRSSLYNHYLRHCQEHKLEPVNAASFGKLIRSVFMGLRTRRlgTRGNSKYHYYGIRLKPDS 246
Cdd:COG3378 328 AFLEECCELDPGARVPKKDLYEAYREWCEDNGEKPLSKRTFGKELKKLGFEYEKRR--TNGGKRRGYRGIRLKDDS 401
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
6-124 4.32e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 40.24  E-value: 4.32e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6677731     6 GGADSPASVALRPAAQPMPASPQRVLVQAAGSTPKGTPMQTltlPRVQPVPPQVQHVYPAQVQYVEGGDAVYANGAIRAA 85
Cdd:PRK12323 369 GGGAGPATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAA---PAAAAAARAVAAAPARRSPAPEALAAARQASARGPG 445

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 6677731    86 YAYNPDPQLYAPSSAASYFETPGGTQVTVAASSPPAVPS 124
Cdd:PRK12323 446 GAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAA 484
 
Name Accession Description Interval E-value
RFX1_trans_act pfam04589
RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding ...
 4-149 1.94e-47

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: 164.72  E-value: 1.94e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6677731      4 SEGGADSPASVA-LRPAA-----QPMPASPQRVLVQAAGSTPKGTPMQTLTLPRVQPVPP----------QVQHVYPAQV 67
Cdd:pfam04589   1 SDSGSDSAPPAAvLQQLAptqvvQPVPASQQRSVVQATPSAPKGGHVQQLSVPRLQQVHVtqevqqlqqvPVQHVYPNQV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6677731     68 QYVEGGDAVYANGAIR-AAYAYnPDPQLYAPSSAASYFETP-GGTQVTVAASSPPAVPSHGMVGITMDVSGTPIVSGAGA 145
Cdd:pfam04589  81 QYVEGGDAVYTTSTIRsSAYPY-TETPLYTQGSGASYYEAQgGGAQVSTPATSLAVAVSSSSVGIPMDVGGSQIVASSSA 159


                  ....
gi 6677731    146 YLIH 149
Cdd:pfam04589 160 ASGG 163
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 167-244 5.01e-45

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: 155.02  E-value: 5.01e-45
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6677731    167 PATLQWLLDNYETAEGVSLPRSSLYNHYLRHCQEHKLEPVNAASFGKLIRSVFMGLRTRRLGTRGNSKYHYYGIRLKP 244
Cdd:pfam02257   2 VFALQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGIKPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
COG3378 COG3378
DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];
171-246 4.18e-09

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


Pssm-ID: 442605 [Multi-domain]  Cd Length: 403  Bit Score: 59.18  E-value: 4.18e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6677731  171 QWLLDNYETAEGVSLPRSSLYNHYLRHCQEHKLEPVNAASFGKLIRSVFMGLRTRRlgTRGNSKYHYYGIRLKPDS 246
Cdd:COG3378 328 AFLEECCELDPGARVPKKDLYEAYREWCEDNGEKPLSKRTFGKELKKLGFEYEKRR--TNGGKRRGYRGIRLKDDS 401
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
6-124 4.32e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 40.24  E-value: 4.32e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6677731     6 GGADSPASVALRPAAQPMPASPQRVLVQAAGSTPKGTPMQTltlPRVQPVPPQVQHVYPAQVQYVEGGDAVYANGAIRAA 85
Cdd:PRK12323 369 GGGAGPATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAA---PAAAAAARAVAAAPARRSPAPEALAAARQASARGPG 445

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 6677731    86 YAYNPDPQLYAPSSAASYFETPGGTQVTVAASSPPAVPS 124
Cdd:PRK12323 446 GAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAA 484
 
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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