NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|768003384|ref|XP_011526472|]
View 

MHC class II regulatory factor RFX1 isoform X3 [Homo sapiens]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 107-373 7.46e-44

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: 156.24  E-value: 7.46e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768003384  107 SSSKTAGAPTGTVPQQLQVHGVQQSVPVTQERSVVQATPQAPKPGPVQPLTVQGLQPVHVAQEssgsqfparkaeqrdpr 186
Cdd:pfam04589   1 SDSGSDSAPPAAVLQQLAPTQVVQPVPASQQRSVVQATPSAPKGGHVQQLSVPRLQQVHVTQE----------------- 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768003384  187 ptpppeppprppacsgeapqlgspepppphyepgaeqwvelvgvlpphlllpqqkvvfeplsrlparaspdqrvriqrip 266
Cdd:pfam04589     --------------------------------------------------------------------------------

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768003384  267 qvlvfgtaatalkVQQLQQVPVPHVYSSQVQYVEGGDASYTASAIRSSTYSYPETPLYTQTASTSYYEAAGTATQVSTPA 346
Cdd:pfam04589  64 -------------VQQLQQVPVQHVYPNQVQYVEGGDAVYTTSTIRSSAYPYTETPLYTQGSGASYYEAQGGGAQVSTPA 130

                         250       260       270
                  ....*....|....*....|....*....|
gi 768003384  347 TSQAV---ASSGSMPMYVSGSQVVASSTST 373
Cdd:pfam04589 131 TSLAVavsSSSVGIPMDVGGSQIVASSSAA 160
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 437-514 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: 151.93  E-value: 1.83e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 768003384  437 PATVQWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRSVFMGLRTRRLGTRGNSKYHYYGLRIKA 514
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 ...
 107-373 7.46e-44

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: 156.24  E-value: 7.46e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768003384  107 SSSKTAGAPTGTVPQQLQVHGVQQSVPVTQERSVVQATPQAPKPGPVQPLTVQGLQPVHVAQEssgsqfparkaeqrdpr 186
Cdd:pfam04589   1 SDSGSDSAPPAAVLQQLAPTQVVQPVPASQQRSVVQATPSAPKGGHVQQLSVPRLQQVHVTQE----------------- 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768003384  187 ptpppeppprppacsgeapqlgspepppphyepgaeqwvelvgvlpphlllpqqkvvfeplsrlparaspdqrvriqrip 266
Cdd:pfam04589     --------------------------------------------------------------------------------

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768003384  267 qvlvfgtaatalkVQQLQQVPVPHVYSSQVQYVEGGDASYTASAIRSSTYSYPETPLYTQTASTSYYEAAGTATQVSTPA 346
Cdd:pfam04589  64 -------------VQQLQQVPVQHVYPNQVQYVEGGDAVYTTSTIRSSAYPYTETPLYTQGSGASYYEAQGGGAQVSTPA 130

                         250       260       270
                  ....*....|....*....|....*....|
gi 768003384  347 TSQAV---ASSGSMPMYVSGSQVVASSTST 373
Cdd:pfam04589 131 TSLAVavsSSSVGIPMDVGGSQIVASSSAA 160
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 437-514 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: 151.93  E-value: 1.83e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 768003384  437 PATVQWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRSVFMGLRTRRLGTRGNSKYHYYGLRIKA 514
Cdd:pfam02257   2 VFALQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGIKPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
COG3378 COG3378
DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];
441-516 8.73e-06

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


Pssm-ID: 442605 [Multi-domain]  Cd Length: 403  Bit Score: 49.17  E-value: 8.73e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 768003384 441 QWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRSVFMGLRTRRlgTRGNSKYHYYGLRIKASS 516
Cdd:COG3378  328 AFLEECCELDPGARVPKKDLYEAYREWCEDNGEKPLSKRTFGKELKKLGFEYEKRR--TNGGKRRGYRGIRLKDDS 401
 
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 ...
 107-373 7.46e-44

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: 156.24  E-value: 7.46e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768003384  107 SSSKTAGAPTGTVPQQLQVHGVQQSVPVTQERSVVQATPQAPKPGPVQPLTVQGLQPVHVAQEssgsqfparkaeqrdpr 186
Cdd:pfam04589   1 SDSGSDSAPPAAVLQQLAPTQVVQPVPASQQRSVVQATPSAPKGGHVQQLSVPRLQQVHVTQE----------------- 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768003384  187 ptpppeppprppacsgeapqlgspepppphyepgaeqwvelvgvlpphlllpqqkvvfeplsrlparaspdqrvriqrip 266
Cdd:pfam04589     --------------------------------------------------------------------------------

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768003384  267 qvlvfgtaatalkVQQLQQVPVPHVYSSQVQYVEGGDASYTASAIRSSTYSYPETPLYTQTASTSYYEAAGTATQVSTPA 346
Cdd:pfam04589  64 -------------VQQLQQVPVQHVYPNQVQYVEGGDAVYTTSTIRSSAYPYTETPLYTQGSGASYYEAQGGGAQVSTPA 130

                         250       260       270
                  ....*....|....*....|....*....|
gi 768003384  347 TSQAV---ASSGSMPMYVSGSQVVASSTST 373
Cdd:pfam04589 131 TSLAVavsSSSVGIPMDVGGSQIVASSSAA 160
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 437-514 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: 151.93  E-value: 1.83e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 768003384  437 PATVQWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRSVFMGLRTRRLGTRGNSKYHYYGLRIKA 514
Cdd:pfam02257   2 VFALQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGIKPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
COG3378 COG3378
DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];
441-516 8.73e-06

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


Pssm-ID: 442605 [Multi-domain]  Cd Length: 403  Bit Score: 49.17  E-value: 8.73e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 768003384 441 QWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRSVFMGLRTRRlgTRGNSKYHYYGLRIKASS 516
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH