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Conserved domains on  [gi|1609559108|ref|NP_001356391|]
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nuclear factor 1 B-type isoform 9 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CTF_NFI pfam00859
CTF/NF-I family transcription modulation region;
231-438 1.58e-88

CTF/NF-I family transcription modulation region;


:

Pssm-ID: 459967 [Multi-domain]  Cd Length: 288  Bit Score: 273.33  E-value: 1.58e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559108 231 EDSFVKSGVFNVSELVRVSRTPITQGTGVNFPIGEIPSqPYYHDMNSGVNLQRSLSSPPS--SKRPKTISIDENMEPSPT 308
Cdd:pfam00859   1 QDSFVTSGVFSVTELVRVSRTPVATGTGPNFSLGELQG-PLYYDLNPGVGLRRSLPSTSSsgSKRHKSGSMEDDVDTSPG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559108 309 GDFYPSPSSPAAGSRTW-HERDQDMSSPTTMKKPEKPLFSSASPQDSSPRLSTFPQHHHPGIpgVAHSVIStRTPPPPSP 387
Cdd:pfam00859  80 GDYYRSPSSPASSSRNWpHDVEGGMSSPVKKKKPDKSDFSSPSPQDSSPRLMAFTQHHRPVI--AVHSGIS-RSPHPSSA 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1609559108 388 LPFPTQAILpPAPSSYFSHPTIRYPPHLnPQDTLKNYVP--SYDPSSPQTSQL 438
Cdd:pfam00859 157 LHFPSSSIL-QQPSSYFPHPAIRYPPHL-PQDPLKDLVSlaCYDPSSQQPSQP 207
NfI_DNAbd_pre-N pfam10524
Nuclear factor I protein pre-N-terminus; The Nuclear factor I (NFI) family of site-specific ...
 33-69 3.97e-18

Nuclear factor I protein pre-N-terminus; The Nuclear factor I (NFI) family of site-specific DNA-binding proteins (also known as CTF or CAAT box transcription factor) functions both in viral DNA replication and in the regulation of gene expression in higher organizms. The N-terminal 200 residues contains the DNA-binding and dimerization domain, but also has an 8-47 residue highly conserved region 5' of this, whose function is not known. Deletion of the N-terminal 200 amino acids removes the DNA-binding activity, dimerization-ability and the stimulation of adenovirus DNA replication.


:

Pssm-ID: 463134  Cd Length: 41  Bit Score: 77.65  E-value: 3.97e-18
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1609559108  33 DEFHPFIEALLPHVRAIAYTWFNLQARKRKYFKKHEK 69
Cdd:pfam10524   5 EDFHPFIEALLPYVKAFAYTWFNLQAAKRRHYKKHDK 41
MH1 super family cl45991
MH1 domain; The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related ...
 91-195 1.60e-17

MH1 domain; The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related proteins such as Smads. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain shows that a highly conserved 11 residue beta hairpin is used to bind the DNA consensus sequence GNCN in the major groove, shown to be vital for the transcriptional activation of target genes. Not all examples of MH1 can bind to DNA however. Smad2 cannot bind DNA and has a large insertion within the hairpin that presumably abolishes DNA binding. A basic helix (H2) in MH1 with the nuclear localization signal KKLKK has been shown to be essential for Smad3 nuclear import. Smads also use the MH1 domain to interact with transcription factors such as Jun, TFE3, Sp1, and Runx.


The actual alignment was detected with superfamily member pfam03165:

Pssm-ID: 460833  Cd Length: 103  Bit Score: 77.80  E-value: 1.60e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559108  91 KQKWASRLLAKLRKDIrqEYREDFVLTVTGK---KHPCCVLSN--------PDQKGKIRRIDClrqadKVWRL-DLVMVI 158
Cdd:pfam03165   1 LKKAVESLLKKLKKKI--QQLEELELAVESRgdpPTGCVTIPRsldgrlqvAGRKGLPHVIYC-----RLWRWpDLQSQH 73

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1609559108 159 LFKGIPLESTDGErlMKSPHCtnpalCVQPHHITVSV 195
Cdd:pfam03165  74 ELKAIPTCETAFE--SKKDEV-----CINPYHYSRVE 103
PRK15127 super family cl39118
multidrug efflux RND transporter permease subunit AcrB;
407-497 3.29e-04

multidrug efflux RND transporter permease subunit AcrB;


The actual alignment was detected with superfamily member PRK15127:

Pssm-ID: 185081 [Multi-domain]  Cd Length: 1049  Bit Score: 43.35  E-value: 3.29e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559108  407 PTIRYPPHLNPQDTLKNYVPSYDPSSPQTSQLRICDWTMNQNGRHLYPSTSEDTLG-----ITWQSpGTWASLVPFQVSN 481
Cdd:PRK15127    31 PVAQYPTIAPPAVTISASYPGADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGtvqitLTFES-GTDADIAQVQVQN 109

                           90       100
                   ....*....|....*....|
gi 1609559108  482 R----TPILPANVQNYGLNI 497
Cdd:PRK15127   110 KlqlaMPLLPQEVQQQGVSV 129
 
Name Accession Description Interval E-value
CTF_NFI pfam00859
CTF/NF-I family transcription modulation region;
231-438 1.58e-88

CTF/NF-I family transcription modulation region;


Pssm-ID: 459967 [Multi-domain]  Cd Length: 288  Bit Score: 273.33  E-value: 1.58e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559108 231 EDSFVKSGVFNVSELVRVSRTPITQGTGVNFPIGEIPSqPYYHDMNSGVNLQRSLSSPPS--SKRPKTISIDENMEPSPT 308
Cdd:pfam00859   1 QDSFVTSGVFSVTELVRVSRTPVATGTGPNFSLGELQG-PLYYDLNPGVGLRRSLPSTSSsgSKRHKSGSMEDDVDTSPG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559108 309 GDFYPSPSSPAAGSRTW-HERDQDMSSPTTMKKPEKPLFSSASPQDSSPRLSTFPQHHHPGIpgVAHSVIStRTPPPPSP 387
Cdd:pfam00859  80 GDYYRSPSSPASSSRNWpHDVEGGMSSPVKKKKPDKSDFSSPSPQDSSPRLMAFTQHHRPVI--AVHSGIS-RSPHPSSA 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1609559108 388 LPFPTQAILpPAPSSYFSHPTIRYPPHLnPQDTLKNYVP--SYDPSSPQTSQL 438
Cdd:pfam00859 157 LHFPSSSIL-QQPSSYFPHPAIRYPPHL-PQDPLKDLVSlaCYDPSSQQPSQP 207
NfI_DNAbd_pre-N pfam10524
Nuclear factor I protein pre-N-terminus; The Nuclear factor I (NFI) family of site-specific ...
 33-69 3.97e-18

Nuclear factor I protein pre-N-terminus; The Nuclear factor I (NFI) family of site-specific DNA-binding proteins (also known as CTF or CAAT box transcription factor) functions both in viral DNA replication and in the regulation of gene expression in higher organizms. The N-terminal 200 residues contains the DNA-binding and dimerization domain, but also has an 8-47 residue highly conserved region 5' of this, whose function is not known. Deletion of the N-terminal 200 amino acids removes the DNA-binding activity, dimerization-ability and the stimulation of adenovirus DNA replication.


Pssm-ID: 463134  Cd Length: 41  Bit Score: 77.65  E-value: 3.97e-18
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1609559108  33 DEFHPFIEALLPHVRAIAYTWFNLQARKRKYFKKHEK 69
Cdd:pfam10524   5 EDFHPFIEALLPYVKAFAYTWFNLQAAKRRHYKKHDK 41
MH1 pfam03165
MH1 domain; The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related ...
 91-195 1.60e-17

MH1 domain; The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related proteins such as Smads. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain shows that a highly conserved 11 residue beta hairpin is used to bind the DNA consensus sequence GNCN in the major groove, shown to be vital for the transcriptional activation of target genes. Not all examples of MH1 can bind to DNA however. Smad2 cannot bind DNA and has a large insertion within the hairpin that presumably abolishes DNA binding. A basic helix (H2) in MH1 with the nuclear localization signal KKLKK has been shown to be essential for Smad3 nuclear import. Smads also use the MH1 domain to interact with transcription factors such as Jun, TFE3, Sp1, and Runx.


Pssm-ID: 460833  Cd Length: 103  Bit Score: 77.80  E-value: 1.60e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559108  91 KQKWASRLLAKLRKDIrqEYREDFVLTVTGK---KHPCCVLSN--------PDQKGKIRRIDClrqadKVWRL-DLVMVI 158
Cdd:pfam03165   1 LKKAVESLLKKLKKKI--QQLEELELAVESRgdpPTGCVTIPRsldgrlqvAGRKGLPHVIYC-----RLWRWpDLQSQH 73

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1609559108 159 LFKGIPLESTDGErlMKSPHCtnpalCVQPHHITVSV 195
Cdd:pfam03165  74 ELKAIPTCETAFE--SKKDEV-----CINPYHYSRVE 103
DWA smart00523
Domain A in dwarfin family proteins;
90-198 6.97e-17

Domain A in dwarfin family proteins;


Pssm-ID: 214708  Cd Length: 109  Bit Score: 76.26  E-value: 6.97e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559108   90 IKQKWASRLLAKLRKDIRQEYREDFVLTVTGKKHPC--CVLSNPDQKGKirridcLRQADKVWRLDLVMVILFKGIPLES 167
Cdd:smart00523   1 VEEKWAKKATESLLKKLKKKQLEELLQAVESKGGPPtrCVLIPRSLDGR------LQVAHRKGLPHVLYCRLFRWPDLQS 74

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1609559108  168 tdGERLMKSPHC------TNPALCVQPHHITVSVKEL 198
Cdd:smart00523  75 --PHELKALPTCehafesKSDEVCCNPYHYSRVERPE 109
PRK15127 PRK15127
multidrug efflux RND transporter permease subunit AcrB;
407-497 3.29e-04

multidrug efflux RND transporter permease subunit AcrB;


Pssm-ID: 185081 [Multi-domain]  Cd Length: 1049  Bit Score: 43.35  E-value: 3.29e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559108  407 PTIRYPPHLNPQDTLKNYVPSYDPSSPQTSQLRICDWTMNQNGRHLYPSTSEDTLG-----ITWQSpGTWASLVPFQVSN 481
Cdd:PRK15127    31 PVAQYPTIAPPAVTISASYPGADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGtvqitLTFES-GTDADIAQVQVQN 109

                           90       100
                   ....*....|....*....|
gi 1609559108  482 R----TPILPANVQNYGLNI 497
Cdd:PRK15127   110 KlqlaMPLLPQEVQQQGVSV 129
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 287-436 3.61e-04

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 43.52  E-value: 3.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559108 287 SPPSSKRPKTISIDEnmepSPTGDFYP-SPSSPAAGSR-TWHERDQDMSSPTTMKKPEKPlfssASPQDSSPRLSTFPQH 364
Cdd:PTZ00449  608 RPKSPKLPELLDIPK----SPKRPESPkSPKRPPPPQRpSSPERPEGPKIIKSPKPPKSP----KPPFDPKFKEKFYDDY 679

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1609559108 365 hhpgIPGVAHSVISTRTPPPPSPLPFPTQAILPPAPSSYFSHPtiRYPPHLNPQDTLKNYVPSYDPSSPQTS 436
Cdd:PTZ00449  680 ----LDAAAKSKETKTTVVLDESFESILKETLPETPGTPFTTP--RPLPPKLPRDEEFPFEPIGDPDAEQPD 745
 
Name Accession Description Interval E-value
CTF_NFI pfam00859
CTF/NF-I family transcription modulation region;
231-438 1.58e-88

CTF/NF-I family transcription modulation region;


Pssm-ID: 459967 [Multi-domain]  Cd Length: 288  Bit Score: 273.33  E-value: 1.58e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559108 231 EDSFVKSGVFNVSELVRVSRTPITQGTGVNFPIGEIPSqPYYHDMNSGVNLQRSLSSPPS--SKRPKTISIDENMEPSPT 308
Cdd:pfam00859   1 QDSFVTSGVFSVTELVRVSRTPVATGTGPNFSLGELQG-PLYYDLNPGVGLRRSLPSTSSsgSKRHKSGSMEDDVDTSPG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559108 309 GDFYPSPSSPAAGSRTW-HERDQDMSSPTTMKKPEKPLFSSASPQDSSPRLSTFPQHHHPGIpgVAHSVIStRTPPPPSP 387
Cdd:pfam00859  80 GDYYRSPSSPASSSRNWpHDVEGGMSSPVKKKKPDKSDFSSPSPQDSSPRLMAFTQHHRPVI--AVHSGIS-RSPHPSSA 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1609559108 388 LPFPTQAILpPAPSSYFSHPTIRYPPHLnPQDTLKNYVP--SYDPSSPQTSQL 438
Cdd:pfam00859 157 LHFPSSSIL-QQPSSYFPHPAIRYPPHL-PQDPLKDLVSlaCYDPSSQQPSQP 207
NfI_DNAbd_pre-N pfam10524
Nuclear factor I protein pre-N-terminus; The Nuclear factor I (NFI) family of site-specific ...
 33-69 3.97e-18

Nuclear factor I protein pre-N-terminus; The Nuclear factor I (NFI) family of site-specific DNA-binding proteins (also known as CTF or CAAT box transcription factor) functions both in viral DNA replication and in the regulation of gene expression in higher organizms. The N-terminal 200 residues contains the DNA-binding and dimerization domain, but also has an 8-47 residue highly conserved region 5' of this, whose function is not known. Deletion of the N-terminal 200 amino acids removes the DNA-binding activity, dimerization-ability and the stimulation of adenovirus DNA replication.


Pssm-ID: 463134  Cd Length: 41  Bit Score: 77.65  E-value: 3.97e-18
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1609559108  33 DEFHPFIEALLPHVRAIAYTWFNLQARKRKYFKKHEK 69
Cdd:pfam10524   5 EDFHPFIEALLPYVKAFAYTWFNLQAAKRRHYKKHDK 41
MH1 pfam03165
MH1 domain; The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related ...
 91-195 1.60e-17

MH1 domain; The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related proteins such as Smads. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain shows that a highly conserved 11 residue beta hairpin is used to bind the DNA consensus sequence GNCN in the major groove, shown to be vital for the transcriptional activation of target genes. Not all examples of MH1 can bind to DNA however. Smad2 cannot bind DNA and has a large insertion within the hairpin that presumably abolishes DNA binding. A basic helix (H2) in MH1 with the nuclear localization signal KKLKK has been shown to be essential for Smad3 nuclear import. Smads also use the MH1 domain to interact with transcription factors such as Jun, TFE3, Sp1, and Runx.


Pssm-ID: 460833  Cd Length: 103  Bit Score: 77.80  E-value: 1.60e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559108  91 KQKWASRLLAKLRKDIrqEYREDFVLTVTGK---KHPCCVLSN--------PDQKGKIRRIDClrqadKVWRL-DLVMVI 158
Cdd:pfam03165   1 LKKAVESLLKKLKKKI--QQLEELELAVESRgdpPTGCVTIPRsldgrlqvAGRKGLPHVIYC-----RLWRWpDLQSQH 73

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1609559108 159 LFKGIPLESTDGErlMKSPHCtnpalCVQPHHITVSV 195
Cdd:pfam03165  74 ELKAIPTCETAFE--SKKDEV-----CINPYHYSRVE 103
DWA smart00523
Domain A in dwarfin family proteins;
90-198 6.97e-17

Domain A in dwarfin family proteins;


Pssm-ID: 214708  Cd Length: 109  Bit Score: 76.26  E-value: 6.97e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559108   90 IKQKWASRLLAKLRKDIRQEYREDFVLTVTGKKHPC--CVLSNPDQKGKirridcLRQADKVWRLDLVMVILFKGIPLES 167
Cdd:smart00523   1 VEEKWAKKATESLLKKLKKKQLEELLQAVESKGGPPtrCVLIPRSLDGR------LQVAHRKGLPHVLYCRLFRWPDLQS 74

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1609559108  168 tdGERLMKSPHC------TNPALCVQPHHITVSVKEL 198
Cdd:smart00523  75 --PHELKALPTCehafesKSDEVCCNPYHYSRVERPE 109
PRK15127 PRK15127
multidrug efflux RND transporter permease subunit AcrB;
407-497 3.29e-04

multidrug efflux RND transporter permease subunit AcrB;


Pssm-ID: 185081 [Multi-domain]  Cd Length: 1049  Bit Score: 43.35  E-value: 3.29e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559108  407 PTIRYPPHLNPQDTLKNYVPSYDPSSPQTSQLRICDWTMNQNGRHLYPSTSEDTLG-----ITWQSpGTWASLVPFQVSN 481
Cdd:PRK15127    31 PVAQYPTIAPPAVTISASYPGADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGtvqitLTFES-GTDADIAQVQVQN 109

                           90       100
                   ....*....|....*....|
gi 1609559108  482 R----TPILPANVQNYGLNI 497
Cdd:PRK15127   110 KlqlaMPLLPQEVQQQGVSV 129
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 287-436 3.61e-04

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 43.52  E-value: 3.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609559108 287 SPPSSKRPKTISIDEnmepSPTGDFYP-SPSSPAAGSR-TWHERDQDMSSPTTMKKPEKPlfssASPQDSSPRLSTFPQH 364
Cdd:PTZ00449  608 RPKSPKLPELLDIPK----SPKRPESPkSPKRPPPPQRpSSPERPEGPKIIKSPKPPKSP----KPPFDPKFKEKFYDDY 679

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1609559108 365 hhpgIPGVAHSVISTRTPPPPSPLPFPTQAILPPAPSSYFSHPtiRYPPHLNPQDTLKNYVPSYDPSSPQTS 436
Cdd:PTZ00449  680 ----LDAAAKSKETKTTVVLDESFESILKETLPETPGTPFTTP--RPLPPKLPRDEEFPFEPIGDPDAEQPD 745
Enamelin pfam15362
Enamelin; ENAMELIN is involved in the mineralization and structural organization of enamel. It ...
 311-351 5.08e-04

Enamelin; ENAMELIN is involved in the mineralization and structural organization of enamel. It is necessary for the extension of enamel during the secretory stage of dental enamel formation. The proteins are expressed in teeth, particularly in odontoblasts, ameloblasts and cementoblasts.


Pssm-ID: 464672 [Multi-domain]  Cd Length: 907  Bit Score: 42.90  E-value: 5.08e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1609559108 311 FYPSPSSPAAGSRTWHERDQdmsSPTTMKKPEKPLFSSASP 351
Cdd:pfam15362 393 YDPRENSPYLRSNTWDERDD---SPNTMGQPENPLYPMNTP 430
 
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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