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Conserved domains on  [gi|1720360610|ref|XP_030100800|]
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nuclear factor 1 C-type isoform X2 [Mus musculus]

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;
208-414 2.23e-116

CTF/NF-I family transcription modulation region;


:

Pssm-ID: 459967 [Multi-domain]  Cd Length: 288  Bit Score: 341.51  E-value: 2.23e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720360610 208 QESFVTSGVFSVTELIQVSRTPVVTGTGPNFSLGELQGHLAYDLNPaSAGMRRTLPSTSSSGSKRHKSGSMEEDVDTSPG 287
Cdd:pfam00859   1 QDSFVTSGVFSVTELVRVSRTPVATGTGPNFSLGELQGPLYYDLNP-GVGLRRSLPSTSSSGSKRHKSGSMEDDVDTSPG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720360610 288 GDYYTSPNSPTSSSRNWTEDIEGGISSPVKKTEMDKSPFNSPSPQD-SPRLSSFTQHHRPVIAVHSGIARSPHPTSALHF 366
Cdd:pfam00859  80 GDYYRSPSSPASSSRNWPHDVEGGMSSPVKKKKPDKSDFSSPSPQDsSPRLMAFTQHHRPVIAVHSGISRSPHPSSALHF 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1720360610 367 PATPILPQtASTYFPHTAIRYPPHLnPQDPLKDLVSLAC-DPATQQPGP 414
Cdd:pfam00859 160 PSSSILQQ-PSSYFPHPAIRYPPHL-PQDPLKDLVSLACyDPSSQQPSQ 206
NfI_DNAbd_pre-N pfam10524
Nuclear factor I protein pre-N-terminus; The Nuclear factor I (NFI) family of site-specific ...
 2-38 1.46e-19

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: 81.50  E-value: 1.46e-19
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1720360610   2 DEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHEK 38
Cdd:pfam10524   5 EDFHPFIEALLPYVKAFAYTWFNLQAAKRRHYKKHDK 41
MH1 super family cl00055
N-terminal Mad Homology 1 (MH1) domain; The MH1 is a small DNA-binding domain present in SMAD ...
 59-160 6.62e-19

N-terminal Mad Homology 1 (MH1) domain; The MH1 is a small DNA-binding domain present in SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways. MH1 binds to the DNA major groove in an unusual manner via a beta hairpin structure. It negatively regulates the functions of the MH2 domain, the C-terminal domain of SMAD. Receptor-regulated SMAD proteins (R-SMADs, including SMAD1, SMAD2, SMAD3, SMAD5, and SMAD9) are activated by phosphorylation by transforming growth factor (TGF)-beta type I receptors. The active R-SMAD associates with a common mediator SMAD (Co-SMAD or SMAD4) and other cofactors, which together translocate to the nucleus to regulate gene expression. The inhibitory or antagonistic SMADs (I-SMADs, including SMAD6 and SMAD7) negatively regulate TGF-beta signaling by competing with R-SMADs for type I receptor or Co-SMADs. MH1 domains of R-SMAD and SMAD4 contain a nuclear localization signal as well as DNA-binding activity. The activated R-SMAD/SMAD4 complex then binds with very low affinity to a DNA sequence CAGAC called SMAD-binding element (SBE) via the MH1 domain.


The actual alignment was detected with superfamily member smart00523:

Pssm-ID: 469592  Cd Length: 109  Bit Score: 81.66  E-value: 6.62e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720360610   59 VKQKWASRLLAKLRKDIRPECREDFVLAVTGKKAP--GCVLSNPDQKGKMRRidclrqADKVWRLDLVMVILFKGIPLES 136
Cdd:smart00523   1 VEEKWAKKATESLLKKLKKKQLEELLQAVESKGGPptRCVLIPRSLDGRLQV------AHRKGLPHVLYCRLFRWPDLQS 74

                           90       100       110
                   ....*....|....*....|....*....|
gi 1720360610  137 tdGERLVKAAACAHP------VLCVQPHHI 160
Cdd:smart00523  75 --PHELKALPTCEHAfesksdEVCCNPYHY 102
 
Name Accession Description Interval E-value
CTF_NFI pfam00859
CTF/NF-I family transcription modulation region;
208-414 2.23e-116

CTF/NF-I family transcription modulation region;


Pssm-ID: 459967 [Multi-domain]  Cd Length: 288  Bit Score: 341.51  E-value: 2.23e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720360610 208 QESFVTSGVFSVTELIQVSRTPVVTGTGPNFSLGELQGHLAYDLNPaSAGMRRTLPSTSSSGSKRHKSGSMEEDVDTSPG 287
Cdd:pfam00859   1 QDSFVTSGVFSVTELVRVSRTPVATGTGPNFSLGELQGPLYYDLNP-GVGLRRSLPSTSSSGSKRHKSGSMEDDVDTSPG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720360610 288 GDYYTSPNSPTSSSRNWTEDIEGGISSPVKKTEMDKSPFNSPSPQD-SPRLSSFTQHHRPVIAVHSGIARSPHPTSALHF 366
Cdd:pfam00859  80 GDYYRSPSSPASSSRNWPHDVEGGMSSPVKKKKPDKSDFSSPSPQDsSPRLMAFTQHHRPVIAVHSGISRSPHPSSALHF 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1720360610 367 PATPILPQtASTYFPHTAIRYPPHLnPQDPLKDLVSLAC-DPATQQPGP 414
Cdd:pfam00859 160 PSSSILQQ-PSSYFPHPAIRYPPHL-PQDPLKDLVSLACyDPSSQQPSQ 206
NfI_DNAbd_pre-N pfam10524
Nuclear factor I protein pre-N-terminus; The Nuclear factor I (NFI) family of site-specific ...
 2-38 1.46e-19

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: 81.50  E-value: 1.46e-19
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1720360610   2 DEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHEK 38
Cdd:pfam10524   5 EDFHPFIEALLPYVKAFAYTWFNLQAAKRRHYKKHDK 41
DWA smart00523
Domain A in dwarfin family proteins;
59-160 6.62e-19

Domain A in dwarfin family proteins;


Pssm-ID: 214708  Cd Length: 109  Bit Score: 81.66  E-value: 6.62e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720360610   59 VKQKWASRLLAKLRKDIRPECREDFVLAVTGKKAP--GCVLSNPDQKGKMRRidclrqADKVWRLDLVMVILFKGIPLES 136
Cdd:smart00523   1 VEEKWAKKATESLLKKLKKKQLEELLQAVESKGGPptRCVLIPRSLDGRLQV------AHRKGLPHVLYCRLFRWPDLQS 74

                           90       100       110
                   ....*....|....*....|....*....|
gi 1720360610  137 tdGERLVKAAACAHP------VLCVQPHHI 160
Cdd:smart00523  75 --PHELKALPTCEHAfesksdEVCCNPYHY 102
MH1 pfam03165
MH1 domain; The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related ...
 60-164 1.37e-18

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: 80.49  E-value: 1.37e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720360610  60 KQKWASRLLAKLRKDIrpECREDFVLAVTGKKAP--GCV---------LSNPDQKGKMRRIDClrqadKVWRL-DLVMVI 127
Cdd:pfam03165   1 LKKAVESLLKKLKKKI--QQLEELELAVESRGDPptGCVtiprsldgrLQVAGRKGLPHVIYC-----RLWRWpDLQSQH 73

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1720360610 128 LFKGIPLESTDGerlvkaaaCAHP-VLCVQPHHIGVAV 164
Cdd:pfam03165  74 ELKAIPTCETAF--------ESKKdEVCINPYHYSRVE 103
 
Name Accession Description Interval E-value
CTF_NFI pfam00859
CTF/NF-I family transcription modulation region;
208-414 2.23e-116

CTF/NF-I family transcription modulation region;


Pssm-ID: 459967 [Multi-domain]  Cd Length: 288  Bit Score: 341.51  E-value: 2.23e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720360610 208 QESFVTSGVFSVTELIQVSRTPVVTGTGPNFSLGELQGHLAYDLNPaSAGMRRTLPSTSSSGSKRHKSGSMEEDVDTSPG 287
Cdd:pfam00859   1 QDSFVTSGVFSVTELVRVSRTPVATGTGPNFSLGELQGPLYYDLNP-GVGLRRSLPSTSSSGSKRHKSGSMEDDVDTSPG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720360610 288 GDYYTSPNSPTSSSRNWTEDIEGGISSPVKKTEMDKSPFNSPSPQD-SPRLSSFTQHHRPVIAVHSGIARSPHPTSALHF 366
Cdd:pfam00859  80 GDYYRSPSSPASSSRNWPHDVEGGMSSPVKKKKPDKSDFSSPSPQDsSPRLMAFTQHHRPVIAVHSGISRSPHPSSALHF 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1720360610 367 PATPILPQtASTYFPHTAIRYPPHLnPQDPLKDLVSLAC-DPATQQPGP 414
Cdd:pfam00859 160 PSSSILQQ-PSSYFPHPAIRYPPHL-PQDPLKDLVSLACyDPSSQQPSQ 206
NfI_DNAbd_pre-N pfam10524
Nuclear factor I protein pre-N-terminus; The Nuclear factor I (NFI) family of site-specific ...
 2-38 1.46e-19

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: 81.50  E-value: 1.46e-19
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1720360610   2 DEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHEK 38
Cdd:pfam10524   5 EDFHPFIEALLPYVKAFAYTWFNLQAAKRRHYKKHDK 41
DWA smart00523
Domain A in dwarfin family proteins;
59-160 6.62e-19

Domain A in dwarfin family proteins;


Pssm-ID: 214708  Cd Length: 109  Bit Score: 81.66  E-value: 6.62e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720360610   59 VKQKWASRLLAKLRKDIRPECREDFVLAVTGKKAP--GCVLSNPDQKGKMRRidclrqADKVWRLDLVMVILFKGIPLES 136
Cdd:smart00523   1 VEEKWAKKATESLLKKLKKKQLEELLQAVESKGGPptRCVLIPRSLDGRLQV------AHRKGLPHVLYCRLFRWPDLQS 74

                           90       100       110
                   ....*....|....*....|....*....|
gi 1720360610  137 tdGERLVKAAACAHP------VLCVQPHHI 160
Cdd:smart00523  75 --PHELKALPTCEHAfesksdEVCCNPYHY 102
MH1 pfam03165
MH1 domain; The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related ...
 60-164 1.37e-18

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: 80.49  E-value: 1.37e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720360610  60 KQKWASRLLAKLRKDIrpECREDFVLAVTGKKAP--GCV---------LSNPDQKGKMRRIDClrqadKVWRL-DLVMVI 127
Cdd:pfam03165   1 LKKAVESLLKKLKKKI--QQLEELELAVESRGDPptGCVtiprsldgrLQVAGRKGLPHVIYC-----RLWRWpDLQSQH 73

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1720360610 128 LFKGIPLESTDGerlvkaaaCAHP-VLCVQPHHIGVAV 164
Cdd:pfam03165  74 ELKAIPTCETAF--------ESKKdEVCINPYHYSRVE 103
 
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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