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Conserved domains on  [gi|1552040518|ref|NP_001355002|]
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DNA-binding protein RFX7 isoform 2 [Homo sapiens]

Protein Classification

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 ...
8-86 7.07e-37

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: 133.44  E-value: 7.07e-37
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1552040518    8 QMHAFSWIRNTLEEHPETSLPKQEVYDEYKSYCDNLGYHPLSAADFGKIMKNVFPNMKARRLGTRGKSKYCYSGLRKKA 86
Cdd:pfam02257    1 QVFALQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGIKPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
Herpes_BLLF1 super family cl37540
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
161-471 3.60e-03

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


The actual alignment was detected with superfamily member pfam05109:

Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 41.83  E-value: 3.60e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1552040518  161 SMAALTVMAAAPAGMKGITQPSAFIPTAESNSFQPQVKTLPSPIDAKQQLQRKIQKKQQEQKLQSPLPGESAAKKSeSAT 240
Cdd:pfam05109  467 TVSTADVTSPTPAGTTSGASPVTPSPSPRDNGTESKAPDMTSPTSAVTTPTPNATSPTPAVTTPTPNATSPTLGKT-SPT 545
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1552040518  241 SNGVTNLPNG---NPSILSPQPIGIV--------VAAVPSPIPvQRTRQLVTSPSPMSSSDGKVL--PLNVQVVTQHMQS 307
Cdd:pfam05109  546 SAVTTPTPNAtspTPAVTTPTPNATIptlgktspTSAVTTPTP-NATSPTVGETSPQANTTNHTLggTSSTPVVTSPPKN 624
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1552040518  308 VKQAPKTPQ-NVPASPGGDRSARHRYPQILPKPANTSALTIRSP--TTVLFTSSPIKTAVVPAS----HMSSLNVVK--- 377
Cdd:pfam05109  625 ATSAVTTGQhNITSSSTSSMSLRPSSISETLSPSTSDNSTSHMPllTSAHPTGGENITQVTPAStsthHVSTSSPAPrpg 704
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1552040518  378 MTTISLTPSNSNTPLKhSASVSSATGTTEESRSVPQIKNG---SVVSLQSPGSRSSSAGGTS-----AVEVKVEPETS-- 447
Cdd:pfam05109  705 TTSQASGPGNSSTSTK-PGEVNVTKGTPPKNATSPQAPSGqktAVPTVTSTGGKANSTTGGKhttghGARTSTEPTTDyg 783
                          330       340
                   ....*....|....*....|....
gi 1552040518  448 SDEHPVQCQENSDEAKAPQTPSAL 471
Cdd:pfam05109  784 GDSTTPRTRYNATTYLPPSTSSKL 807
MSCRAMM_ClfA super family cl41352
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
371-648 5.77e-03

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


The actual alignment was detected with superfamily member NF033609:

Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 41.05  E-value: 5.77e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1552040518  371 SSLNVVKMTTISLTPSNSNTPLKHSASVSSATGTTEESRSVPQIKNGSVVSLQSPGSRSSSAGGTSavevkvepETSSDE 450
Cdd:NF033609    39 ASENSVTQSDSASNESKSNDSSSVSAAPKTDDTNVSDTKTSSNTNNGETSVAQNPAQQETTQSAST--------NATTEE 110
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1552040518  451 HPVQCQENSDEAKAPQTPSALLGQKSNTDGALQKPSNEgvieikatkVCDQRTKCKSRCNEmlPGTSTGNNQSTITLSVA 530
Cdd:NF033609   111 TPVTGEATTTATNQANTPATTQSSNTNAEELVNQTSNE---------TTSNDTNTVSSVNS--PQNSTNAENVSTTQDTS 179
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1552040518  531 SQNLTFTSSSSPPNGDSINKD---PKLCTKSPRKR-LSSTLQETQVPPVKKPIVEQL--------SAATIEGQKQGSVKK 598
Cdd:NF033609   180 TEATPSNNESAPQSTDASNKDvvnQAVNTSAPRMRaFSLAAVAADAPAAGTDITNQLtnvtvgidSGTTVYPHQAGYVKL 259
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1552040518  599 DQ--KVPHSGkTEGSTAGAQIPSKVSVNVSSHIGANQPLNSSALVISDSALE 648
Cdd:NF033609   260 NYgfSVPNSA-VKGDTFKITVPKELNLNGVTSTAKVPPIMAGDQVLANGVID 310
 
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 ...
8-86 7.07e-37

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: 133.44  E-value: 7.07e-37
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1552040518    8 QMHAFSWIRNTLEEHPETSLPKQEVYDEYKSYCDNLGYHPLSAADFGKIMKNVFPNMKARRLGTRGKSKYCYSGLRKKA 86
Cdd:pfam02257    1 QVFALQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGIKPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
COG3378 COG3378
DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];
14-85 4.65e-09

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


Pssm-ID: 442605 [Multi-domain]  Cd Length: 403  Bit Score: 60.34  E-value: 4.65e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1552040518   14 WIRNTLEEHPETSLPKQEVYDEYKSYCDNLGYHPLSAADFGKIMKNVFPNMKARRlgTRGKSKYCYSGLRKK 85
Cdd:COG3378    329 FLEECCELDPGARVPKKDLYEAYREWCEDNGEKPLSKRTFGKELKKLGFEYEKRR--TNGGKRRGYRGIRLK 398
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
161-471 3.60e-03

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 41.83  E-value: 3.60e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1552040518  161 SMAALTVMAAAPAGMKGITQPSAFIPTAESNSFQPQVKTLPSPIDAKQQLQRKIQKKQQEQKLQSPLPGESAAKKSeSAT 240
Cdd:pfam05109  467 TVSTADVTSPTPAGTTSGASPVTPSPSPRDNGTESKAPDMTSPTSAVTTPTPNATSPTPAVTTPTPNATSPTLGKT-SPT 545
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1552040518  241 SNGVTNLPNG---NPSILSPQPIGIV--------VAAVPSPIPvQRTRQLVTSPSPMSSSDGKVL--PLNVQVVTQHMQS 307
Cdd:pfam05109  546 SAVTTPTPNAtspTPAVTTPTPNATIptlgktspTSAVTTPTP-NATSPTVGETSPQANTTNHTLggTSSTPVVTSPPKN 624
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1552040518  308 VKQAPKTPQ-NVPASPGGDRSARHRYPQILPKPANTSALTIRSP--TTVLFTSSPIKTAVVPAS----HMSSLNVVK--- 377
Cdd:pfam05109  625 ATSAVTTGQhNITSSSTSSMSLRPSSISETLSPSTSDNSTSHMPllTSAHPTGGENITQVTPAStsthHVSTSSPAPrpg 704
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1552040518  378 MTTISLTPSNSNTPLKhSASVSSATGTTEESRSVPQIKNG---SVVSLQSPGSRSSSAGGTS-----AVEVKVEPETS-- 447
Cdd:pfam05109  705 TTSQASGPGNSSTSTK-PGEVNVTKGTPPKNATSPQAPSGqktAVPTVTSTGGKANSTTGGKhttghGARTSTEPTTDyg 783
                          330       340
                   ....*....|....*....|....
gi 1552040518  448 SDEHPVQCQENSDEAKAPQTPSAL 471
Cdd:pfam05109  784 GDSTTPRTRYNATTYLPPSTSSKL 807
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
371-648 5.77e-03

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 41.05  E-value: 5.77e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1552040518  371 SSLNVVKMTTISLTPSNSNTPLKHSASVSSATGTTEESRSVPQIKNGSVVSLQSPGSRSSSAGGTSavevkvepETSSDE 450
Cdd:NF033609    39 ASENSVTQSDSASNESKSNDSSSVSAAPKTDDTNVSDTKTSSNTNNGETSVAQNPAQQETTQSAST--------NATTEE 110
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1552040518  451 HPVQCQENSDEAKAPQTPSALLGQKSNTDGALQKPSNEgvieikatkVCDQRTKCKSRCNEmlPGTSTGNNQSTITLSVA 530
Cdd:NF033609   111 TPVTGEATTTATNQANTPATTQSSNTNAEELVNQTSNE---------TTSNDTNTVSSVNS--PQNSTNAENVSTTQDTS 179
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1552040518  531 SQNLTFTSSSSPPNGDSINKD---PKLCTKSPRKR-LSSTLQETQVPPVKKPIVEQL--------SAATIEGQKQGSVKK 598
Cdd:NF033609   180 TEATPSNNESAPQSTDASNKDvvnQAVNTSAPRMRaFSLAAVAADAPAAGTDITNQLtnvtvgidSGTTVYPHQAGYVKL 259
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1552040518  599 DQ--KVPHSGkTEGSTAGAQIPSKVSVNVSSHIGANQPLNSSALVISDSALE 648
Cdd:NF033609   260 NYgfSVPNSA-VKGDTFKITVPKELNLNGVTSTAKVPPIMAGDQVLANGVID 310
 
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 ...
8-86 7.07e-37

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: 133.44  E-value: 7.07e-37
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1552040518    8 QMHAFSWIRNTLEEHPETSLPKQEVYDEYKSYCDNLGYHPLSAADFGKIMKNVFPNMKARRLGTRGKSKYCYSGLRKKA 86
Cdd:pfam02257    1 QVFALQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGIKPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
COG3378 COG3378
DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];
14-85 4.65e-09

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


Pssm-ID: 442605 [Multi-domain]  Cd Length: 403  Bit Score: 60.34  E-value: 4.65e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1552040518   14 WIRNTLEEHPETSLPKQEVYDEYKSYCDNLGYHPLSAADFGKIMKNVFPNMKARRlgTRGKSKYCYSGLRKK 85
Cdd:COG3378    329 FLEECCELDPGARVPKKDLYEAYREWCEDNGEKPLSKRTFGKELKKLGFEYEKRR--TNGGKRRGYRGIRLK 398
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
161-471 3.60e-03

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 41.83  E-value: 3.60e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1552040518  161 SMAALTVMAAAPAGMKGITQPSAFIPTAESNSFQPQVKTLPSPIDAKQQLQRKIQKKQQEQKLQSPLPGESAAKKSeSAT 240
Cdd:pfam05109  467 TVSTADVTSPTPAGTTSGASPVTPSPSPRDNGTESKAPDMTSPTSAVTTPTPNATSPTPAVTTPTPNATSPTLGKT-SPT 545
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1552040518  241 SNGVTNLPNG---NPSILSPQPIGIV--------VAAVPSPIPvQRTRQLVTSPSPMSSSDGKVL--PLNVQVVTQHMQS 307
Cdd:pfam05109  546 SAVTTPTPNAtspTPAVTTPTPNATIptlgktspTSAVTTPTP-NATSPTVGETSPQANTTNHTLggTSSTPVVTSPPKN 624
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1552040518  308 VKQAPKTPQ-NVPASPGGDRSARHRYPQILPKPANTSALTIRSP--TTVLFTSSPIKTAVVPAS----HMSSLNVVK--- 377
Cdd:pfam05109  625 ATSAVTTGQhNITSSSTSSMSLRPSSISETLSPSTSDNSTSHMPllTSAHPTGGENITQVTPAStsthHVSTSSPAPrpg 704
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1552040518  378 MTTISLTPSNSNTPLKhSASVSSATGTTEESRSVPQIKNG---SVVSLQSPGSRSSSAGGTS-----AVEVKVEPETS-- 447
Cdd:pfam05109  705 TTSQASGPGNSSTSTK-PGEVNVTKGTPPKNATSPQAPSGqktAVPTVTSTGGKANSTTGGKhttghGARTSTEPTTDyg 783
                          330       340
                   ....*....|....*....|....
gi 1552040518  448 SDEHPVQCQENSDEAKAPQTPSAL 471
Cdd:pfam05109  784 GDSTTPRTRYNATTYLPPSTSSKL 807
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
371-648 5.77e-03

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 41.05  E-value: 5.77e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1552040518  371 SSLNVVKMTTISLTPSNSNTPLKHSASVSSATGTTEESRSVPQIKNGSVVSLQSPGSRSSSAGGTSavevkvepETSSDE 450
Cdd:NF033609    39 ASENSVTQSDSASNESKSNDSSSVSAAPKTDDTNVSDTKTSSNTNNGETSVAQNPAQQETTQSAST--------NATTEE 110
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1552040518  451 HPVQCQENSDEAKAPQTPSALLGQKSNTDGALQKPSNEgvieikatkVCDQRTKCKSRCNEmlPGTSTGNNQSTITLSVA 530
Cdd:NF033609   111 TPVTGEATTTATNQANTPATTQSSNTNAEELVNQTSNE---------TTSNDTNTVSSVNS--PQNSTNAENVSTTQDTS 179
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1552040518  531 SQNLTFTSSSSPPNGDSINKD---PKLCTKSPRKR-LSSTLQETQVPPVKKPIVEQL--------SAATIEGQKQGSVKK 598
Cdd:NF033609   180 TEATPSNNESAPQSTDASNKDvvnQAVNTSAPRMRaFSLAAVAADAPAAGTDITNQLtnvtvgidSGTTVYPHQAGYVKL 259
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1552040518  599 DQ--KVPHSGkTEGSTAGAQIPSKVSVNVSSHIGANQPLNSSALVISDSALE 648
Cdd:NF033609   260 NYgfSVPNSA-VKGDTFKITVPKELNLNGVTSTAKVPPIMAGDQVLANGVID 310
 
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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