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Conserved domains on  [gi|6981266|ref|NP_037120|]
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nuclear factor 1 A-type [Rattus norvegicus]

Protein Classification

nuclear factor I( domain architecture ID 12106891)

nuclear factor I (NFI) is a CCAAT-box-binding protein active in transcription and DNA replication

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;
214-501 7.05e-101

CTF/NF-I family transcription modulation region;


:

Pssm-ID: 459967 [Multi-domain]  Cd Length: 288  Bit Score: 304.91  E-value: 7.05e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6981266    214 QDSFVTSGVFSVTELVRVSQTPIAAGTGPNFSLSDLESSSYYSMSPGA-MRRSLPsTSSTSSTKRLKSV---EDEMDSPG 289
Cdd:pfam00859   1 QDSFVTSGVFSVTELVRVSRTPVATGTGPNFSLGELQGPLYYDLNPGVgLRRSLP-STSSSGSKRHKSGsmeDDVDTSPG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6981266    290 EEpFYTgqgRSPGSGSQSSGW-HEVEPGMPSPTTLKKSEKSGFSSPSPSQTSSLGTAFTQHHRPVI---TGPRASPHaTP 365
Cdd:pfam00859  80 GD-YYR---SPSSPASSSRNWpHDVEGGMSSPVKKKKPDKSDFSSPSPQDSSPRLMAFTQHHRPVIavhSGISRSPH-PS 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6981266    366 STLHFPTSPIIQQPGPYFSHPAIRYHP---QETLKEFVQLVCPD-AGQQAGQvgflnPNGSSQGKVHNPFLPTPMLPPPP 441
Cdd:pfam00859 155 SALHFPSSSILQQPSSYFPHPAIRYPPhlpQDPLKDLVSLACYDpSSQQPSQ-----PNGSGQGKVPGHFISTQMLAPPP 229

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 6981266    442 PPPMARPVPLPMpDTKPPTTSTEGGAASPTSPTYSTPSTSPANRFVSVGPRDPSFVNIPQ 501
Cdd:pfam00859 230 HPPVARPVPLPM-DTKPITTSTEGGASSPTSPTYSAPGTPPANRFVGLGPRDPGFLYQAQ 288
NfI_DNAbd_pre-N pfam10524
Nuclear factor I protein pre-N-terminus; The Nuclear factor I (NFI) family of site-specific ...
 9-46 6.84e-20

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: 82.65  E-value: 6.84e-20
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 6981266      9 QDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHEK 46
Cdd:pfam10524   4 QEDFHPFIEALLPYVKAFAYTWFNLQAAKRRHYKKHDK 41
MH1 super family cl45991
MH1 domain; The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related ...
 68-172 2.77e-19

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: 82.80  E-value: 2.77e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6981266     68 KQKWASRLLAKLRKDIrpEYREDFVLTVTGK---KPPCCVLSN--------PDQKGKMRRIDClrqadKVWRL-DLVMVI 135
Cdd:pfam03165   1 LKKAVESLLKKLKKKI--QQLEELELAVESRgdpPTGCVTIPRsldgrlqvAGRKGLPHVIYC-----RLWRWpDLQSQH 73

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 6981266    136 LFKGIPLESTDGeRLVKSPqcsnpgLCVQPHHIGVSV 172
Cdd:pfam03165  74 ELKAIPTCETAF-ESKKDE------VCINPYHYSRVE 103
 
Name Accession Description Interval E-value
CTF_NFI pfam00859
CTF/NF-I family transcription modulation region;
214-501 7.05e-101

CTF/NF-I family transcription modulation region;


Pssm-ID: 459967 [Multi-domain]  Cd Length: 288  Bit Score: 304.91  E-value: 7.05e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6981266    214 QDSFVTSGVFSVTELVRVSQTPIAAGTGPNFSLSDLESSSYYSMSPGA-MRRSLPsTSSTSSTKRLKSV---EDEMDSPG 289
Cdd:pfam00859   1 QDSFVTSGVFSVTELVRVSRTPVATGTGPNFSLGELQGPLYYDLNPGVgLRRSLP-STSSSGSKRHKSGsmeDDVDTSPG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6981266    290 EEpFYTgqgRSPGSGSQSSGW-HEVEPGMPSPTTLKKSEKSGFSSPSPSQTSSLGTAFTQHHRPVI---TGPRASPHaTP 365
Cdd:pfam00859  80 GD-YYR---SPSSPASSSRNWpHDVEGGMSSPVKKKKPDKSDFSSPSPQDSSPRLMAFTQHHRPVIavhSGISRSPH-PS 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6981266    366 STLHFPTSPIIQQPGPYFSHPAIRYHP---QETLKEFVQLVCPD-AGQQAGQvgflnPNGSSQGKVHNPFLPTPMLPPPP 441
Cdd:pfam00859 155 SALHFPSSSILQQPSSYFPHPAIRYPPhlpQDPLKDLVSLACYDpSSQQPSQ-----PNGSGQGKVPGHFISTQMLAPPP 229

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 6981266    442 PPPMARPVPLPMpDTKPPTTSTEGGAASPTSPTYSTPSTSPANRFVSVGPRDPSFVNIPQ 501
Cdd:pfam00859 230 HPPVARPVPLPM-DTKPITTSTEGGASSPTSPTYSAPGTPPANRFVGLGPRDPGFLYQAQ 288
NfI_DNAbd_pre-N pfam10524
Nuclear factor I protein pre-N-terminus; The Nuclear factor I (NFI) family of site-specific ...
 9-46 6.84e-20

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: 82.65  E-value: 6.84e-20
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 6981266      9 QDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHEK 46
Cdd:pfam10524   4 QEDFHPFIEALLPYVKAFAYTWFNLQAAKRRHYKKHDK 41
MH1 pfam03165
MH1 domain; The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related ...
 68-172 2.77e-19

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: 82.80  E-value: 2.77e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6981266     68 KQKWASRLLAKLRKDIrpEYREDFVLTVTGK---KPPCCVLSN--------PDQKGKMRRIDClrqadKVWRL-DLVMVI 135
Cdd:pfam03165   1 LKKAVESLLKKLKKKI--QQLEELELAVESRgdpPTGCVTIPRsldgrlqvAGRKGLPHVIYC-----RLWRWpDLQSQH 73

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 6981266    136 LFKGIPLESTDGeRLVKSPqcsnpgLCVQPHHIGVSV 172
Cdd:pfam03165  74 ELKAIPTCETAF-ESKKDE------VCINPYHYSRVE 103
DWA smart00523
Domain A in dwarfin family proteins;
67-175 6.32e-17

Domain A in dwarfin family proteins;


Pssm-ID: 214708  Cd Length: 109  Bit Score: 76.26  E-value: 6.32e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6981266      67 VKQKWASRLLAKLRKDIRPEYREDFVLTVT--GKKPPCCVLSNPDQKGKMRRidclrqADKVWRLDLVMVILFKGIPLES 144
Cdd:smart00523   1 VEEKWAKKATESLLKKLKKKQLEELLQAVEskGGPPTRCVLIPRSLDGRLQV------AHRKGLPHVLYCRLFRWPDLQS 74

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 6981266     145 tdGERLVKSPQCSNPG------LCVQPHHIGVSVKEL 175
Cdd:smart00523  75 --PHELKALPTCEHAFesksdeVCCNPYHYSRVERPE 109
 
Name Accession Description Interval E-value
CTF_NFI pfam00859
CTF/NF-I family transcription modulation region;
214-501 7.05e-101

CTF/NF-I family transcription modulation region;


Pssm-ID: 459967 [Multi-domain]  Cd Length: 288  Bit Score: 304.91  E-value: 7.05e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6981266    214 QDSFVTSGVFSVTELVRVSQTPIAAGTGPNFSLSDLESSSYYSMSPGA-MRRSLPsTSSTSSTKRLKSV---EDEMDSPG 289
Cdd:pfam00859   1 QDSFVTSGVFSVTELVRVSRTPVATGTGPNFSLGELQGPLYYDLNPGVgLRRSLP-STSSSGSKRHKSGsmeDDVDTSPG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6981266    290 EEpFYTgqgRSPGSGSQSSGW-HEVEPGMPSPTTLKKSEKSGFSSPSPSQTSSLGTAFTQHHRPVI---TGPRASPHaTP 365
Cdd:pfam00859  80 GD-YYR---SPSSPASSSRNWpHDVEGGMSSPVKKKKPDKSDFSSPSPQDSSPRLMAFTQHHRPVIavhSGISRSPH-PS 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6981266    366 STLHFPTSPIIQQPGPYFSHPAIRYHP---QETLKEFVQLVCPD-AGQQAGQvgflnPNGSSQGKVHNPFLPTPMLPPPP 441
Cdd:pfam00859 155 SALHFPSSSILQQPSSYFPHPAIRYPPhlpQDPLKDLVSLACYDpSSQQPSQ-----PNGSGQGKVPGHFISTQMLAPPP 229

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 6981266    442 PPPMARPVPLPMpDTKPPTTSTEGGAASPTSPTYSTPSTSPANRFVSVGPRDPSFVNIPQ 501
Cdd:pfam00859 230 HPPVARPVPLPM-DTKPITTSTEGGASSPTSPTYSAPGTPPANRFVGLGPRDPGFLYQAQ 288
NfI_DNAbd_pre-N pfam10524
Nuclear factor I protein pre-N-terminus; The Nuclear factor I (NFI) family of site-specific ...
 9-46 6.84e-20

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: 82.65  E-value: 6.84e-20
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 6981266      9 QDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHEK 46
Cdd:pfam10524   4 QEDFHPFIEALLPYVKAFAYTWFNLQAAKRRHYKKHDK 41
MH1 pfam03165
MH1 domain; The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related ...
 68-172 2.77e-19

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: 82.80  E-value: 2.77e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6981266     68 KQKWASRLLAKLRKDIrpEYREDFVLTVTGK---KPPCCVLSN--------PDQKGKMRRIDClrqadKVWRL-DLVMVI 135
Cdd:pfam03165   1 LKKAVESLLKKLKKKI--QQLEELELAVESRgdpPTGCVTIPRsldgrlqvAGRKGLPHVIYC-----RLWRWpDLQSQH 73

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 6981266    136 LFKGIPLESTDGeRLVKSPqcsnpgLCVQPHHIGVSV 172
Cdd:pfam03165  74 ELKAIPTCETAF-ESKKDE------VCINPYHYSRVE 103
DWA smart00523
Domain A in dwarfin family proteins;
67-175 6.32e-17

Domain A in dwarfin family proteins;


Pssm-ID: 214708  Cd Length: 109  Bit Score: 76.26  E-value: 6.32e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6981266      67 VKQKWASRLLAKLRKDIRPEYREDFVLTVT--GKKPPCCVLSNPDQKGKMRRidclrqADKVWRLDLVMVILFKGIPLES 144
Cdd:smart00523   1 VEEKWAKKATESLLKKLKKKQLEELLQAVEskGGPPTRCVLIPRSLDGRLQV------AHRKGLPHVLYCRLFRWPDLQS 74

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 6981266     145 tdGERLVKSPQCSNPG------LCVQPHHIGVSVKEL 175
Cdd:smart00523  75 --PHELKALPTCEHAFesksdeVCCNPYHYSRVERPE 109
 
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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