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Conserved domains on  [gi|402534522|ref|NP_001257973|]
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nuclear factor 1 X-type isoform 3 [Homo sapiens]

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;
205-410 1.36e-98

CTF/NF-I family transcription modulation region;


:

Pssm-ID: 459967 [Multi-domain]  Cd Length: 288  Bit Score: 296.44  E-value: 1.36e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402534522  205 QDCFVTSGVWNVTELVRVSQTPVATASGPNFSLADLESPSYYNINQVTLGRRSITSPPSTStTKRPK--SIDDSEMESPV 282
Cdd:pfam00859   1 QDSFVTSGVFSVTELVRVSRTPVATGTGPNFSLGELQGPLYYDLNPGVGLRRSLPSTSSSG-SKRHKsgSMEDDVDTSPG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402534522  283 DDvFYpgtgRSPAAGSSQSSGWPNDVDAG---PASLKKSGKLDFCSALSSQGSSPRMAFTHHPLPVL---AGVRpGSPRa 356
Cdd:pfam00859  80 GD-YY----RSPSSPASSSRNWPHDVEGGmssPVKKKKPDKSDFSSPSPQDSSPRLMAFTQHHRPVIavhSGIS-RSPH- 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 402534522  357 TASALHFPSTSIIQQSSPYFTHPTIRYHHHHGQDSLKEFVQFVCSDGSGQATGQ 410
Cdd:pfam00859 153 PSSALHFPSSSILQQPSSYFPHPAIRYPPHLPQDPLKDLVSLACYDPSSQQPSQ 206
NfI_DNAbd_pre-N pfam10524
Nuclear factor I protein pre-N-terminus; The Nuclear factor I (NFI) family of site-specific ...
 2-38 2.16e-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: 81.11  E-value: 2.16e-19
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 402534522    2 DEFHPFIEALLPHVRAFSYTWFNLQARKRKYFKKHEK 38
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 ...
 60-162 3.30e-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: 76.64  E-value: 3.30e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402534522   60 KQKWASRLLAKLRKDIrpEFREDFVLTITGK---KPPCCVLSN--------PDQKGKIRRIDClrqadKVWRL-DLVMVI 127
Cdd:pfam03165   1 LKKAVESLLKKLKKKI--QQLEELELAVESRgdpPTGCVTIPRsldgrlqvAGRKGLPHVIYC-----RLWRWpDLQSQH 73

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 402534522  128 LFKGIPLESTDGeRLYKSPqcsnpgLCVQPHHIGV 162
Cdd:pfam03165  74 ELKAIPTCETAF-ESKKDE------VCINPYHYSR 101
 
Name Accession Description Interval E-value
CTF_NFI pfam00859
CTF/NF-I family transcription modulation region;
205-410 1.36e-98

CTF/NF-I family transcription modulation region;


Pssm-ID: 459967 [Multi-domain]  Cd Length: 288  Bit Score: 296.44  E-value: 1.36e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402534522  205 QDCFVTSGVWNVTELVRVSQTPVATASGPNFSLADLESPSYYNINQVTLGRRSITSPPSTStTKRPK--SIDDSEMESPV 282
Cdd:pfam00859   1 QDSFVTSGVFSVTELVRVSRTPVATGTGPNFSLGELQGPLYYDLNPGVGLRRSLPSTSSSG-SKRHKsgSMEDDVDTSPG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402534522  283 DDvFYpgtgRSPAAGSSQSSGWPNDVDAG---PASLKKSGKLDFCSALSSQGSSPRMAFTHHPLPVL---AGVRpGSPRa 356
Cdd:pfam00859  80 GD-YY----RSPSSPASSSRNWPHDVEGGmssPVKKKKPDKSDFSSPSPQDSSPRLMAFTQHHRPVIavhSGIS-RSPH- 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 402534522  357 TASALHFPSTSIIQQSSPYFTHPTIRYHHHHGQDSLKEFVQFVCSDGSGQATGQ 410
Cdd:pfam00859 153 PSSALHFPSSSILQQPSSYFPHPAIRYPPHLPQDPLKDLVSLACYDPSSQQPSQ 206
NfI_DNAbd_pre-N pfam10524
Nuclear factor I protein pre-N-terminus; The Nuclear factor I (NFI) family of site-specific ...
 2-38 2.16e-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: 81.11  E-value: 2.16e-19
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 402534522    2 DEFHPFIEALLPHVRAFSYTWFNLQARKRKYFKKHEK 38
Cdd:pfam10524   5 EDFHPFIEALLPYVKAFAYTWFNLQAAKRRHYKKHDK 41
MH1 pfam03165
MH1 domain; The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related ...
 60-162 3.30e-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: 76.64  E-value: 3.30e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402534522   60 KQKWASRLLAKLRKDIrpEFREDFVLTITGK---KPPCCVLSN--------PDQKGKIRRIDClrqadKVWRL-DLVMVI 127
Cdd:pfam03165   1 LKKAVESLLKKLKKKI--QQLEELELAVESRgdpPTGCVTIPRsldgrlqvAGRKGLPHVIYC-----RLWRWpDLQSQH 73

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 402534522  128 LFKGIPLESTDGeRLYKSPqcsnpgLCVQPHHIGV 162
Cdd:pfam03165  74 ELKAIPTCETAF-ESKKDE------VCINPYHYSR 101
DWA smart00523
Domain A in dwarfin family proteins;
59-160 3.19e-16

Domain A in dwarfin family proteins;


Pssm-ID: 214708  Cd Length: 109  Bit Score: 74.34  E-value: 3.19e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402534522    59 IKQKWASRLLAKLRKDIRPEFREDFVLTIT--GKKPPCCVLSNPDQKGKirridcLRQADKVWRLDLVMVILFKGIPLES 136
Cdd:smart00523   1 VEEKWAKKATESLLKKLKKKQLEELLQAVEskGGPPTRCVLIPRSLDGR------LQVAHRKGLPHVLYCRLFRWPDLQS 74

                           90       100       110
                   ....*....|....*....|....*....|
gi 402534522   137 tdGERLYKSPQCSNPG------LCVQPHHI 160
Cdd:smart00523  75 --PHELKALPTCEHAFesksdeVCCNPYHY 102
ROM1 COG5422
RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction ...
 224-432 8.39e-03

RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms];


Pssm-ID: 227709 [Multi-domain]  Cd Length: 1175  Bit Score: 38.72  E-value: 8.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402534522  224 QTPVATASGPNFSLADLESPSYYNinqvtlgrrsitSPPSTSTTKRPKSIDDSEMeSPVDDVFypgtgrSPAAGSSQSSG 303
Cdd:COG5422    71 QIFSSFSSSPKLFQRRNSAGPITH------------SPSATSSTSSLNSNDGDQF-SPASDSL------SFNPSSTQSRK 131

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402534522  304 WPNDVDAGPASLKKSgklDFCSALSSQGSSPRMAFTH----HPLPVLAGVRPGSPRATASA--LHFPSTSIIQQSSPY-- 375
Cdd:COG5422   132 DSGPGDGSPVQKRKN---PLLPSSSTHGTHPPIVFTDnngsHAGAPNARSRKEIPSLGSQSmqLPSPHFRQKFSSSDTsn 208

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 402534522  376 -FTHPTIRYHHHHGQDSLKEFVQFVCSDGSGQATGQHSQRQAPPLPTGLSASDPGTAT 432
Cdd:COG5422   209 gFSYPSIRKNSRHSSNSMPSFPHSSTAVLLKRHSGSSGASLISSNITPSSSNSEAMST 266
 
Name Accession Description Interval E-value
CTF_NFI pfam00859
CTF/NF-I family transcription modulation region;
205-410 1.36e-98

CTF/NF-I family transcription modulation region;


Pssm-ID: 459967 [Multi-domain]  Cd Length: 288  Bit Score: 296.44  E-value: 1.36e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402534522  205 QDCFVTSGVWNVTELVRVSQTPVATASGPNFSLADLESPSYYNINQVTLGRRSITSPPSTStTKRPK--SIDDSEMESPV 282
Cdd:pfam00859   1 QDSFVTSGVFSVTELVRVSRTPVATGTGPNFSLGELQGPLYYDLNPGVGLRRSLPSTSSSG-SKRHKsgSMEDDVDTSPG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402534522  283 DDvFYpgtgRSPAAGSSQSSGWPNDVDAG---PASLKKSGKLDFCSALSSQGSSPRMAFTHHPLPVL---AGVRpGSPRa 356
Cdd:pfam00859  80 GD-YY----RSPSSPASSSRNWPHDVEGGmssPVKKKKPDKSDFSSPSPQDSSPRLMAFTQHHRPVIavhSGIS-RSPH- 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 402534522  357 TASALHFPSTSIIQQSSPYFTHPTIRYHHHHGQDSLKEFVQFVCSDGSGQATGQ 410
Cdd:pfam00859 153 PSSALHFPSSSILQQPSSYFPHPAIRYPPHLPQDPLKDLVSLACYDPSSQQPSQ 206
NfI_DNAbd_pre-N pfam10524
Nuclear factor I protein pre-N-terminus; The Nuclear factor I (NFI) family of site-specific ...
 2-38 2.16e-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: 81.11  E-value: 2.16e-19
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 402534522    2 DEFHPFIEALLPHVRAFSYTWFNLQARKRKYFKKHEK 38
Cdd:pfam10524   5 EDFHPFIEALLPYVKAFAYTWFNLQAAKRRHYKKHDK 41
MH1 pfam03165
MH1 domain; The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related ...
 60-162 3.30e-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: 76.64  E-value: 3.30e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402534522   60 KQKWASRLLAKLRKDIrpEFREDFVLTITGK---KPPCCVLSN--------PDQKGKIRRIDClrqadKVWRL-DLVMVI 127
Cdd:pfam03165   1 LKKAVESLLKKLKKKI--QQLEELELAVESRgdpPTGCVTIPRsldgrlqvAGRKGLPHVIYC-----RLWRWpDLQSQH 73

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 402534522  128 LFKGIPLESTDGeRLYKSPqcsnpgLCVQPHHIGV 162
Cdd:pfam03165  74 ELKAIPTCETAF-ESKKDE------VCINPYHYSR 101
DWA smart00523
Domain A in dwarfin family proteins;
59-160 3.19e-16

Domain A in dwarfin family proteins;


Pssm-ID: 214708  Cd Length: 109  Bit Score: 74.34  E-value: 3.19e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402534522    59 IKQKWASRLLAKLRKDIRPEFREDFVLTIT--GKKPPCCVLSNPDQKGKirridcLRQADKVWRLDLVMVILFKGIPLES 136
Cdd:smart00523   1 VEEKWAKKATESLLKKLKKKQLEELLQAVEskGGPPTRCVLIPRSLDGR------LQVAHRKGLPHVLYCRLFRWPDLQS 74

                           90       100       110
                   ....*....|....*....|....*....|
gi 402534522   137 tdGERLYKSPQCSNPG------LCVQPHHI 160
Cdd:smart00523  75 --PHELKALPTCEHAFesksdeVCCNPYHY 102
ROM1 COG5422
RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction ...
 224-432 8.39e-03

RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms];


Pssm-ID: 227709 [Multi-domain]  Cd Length: 1175  Bit Score: 38.72  E-value: 8.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402534522  224 QTPVATASGPNFSLADLESPSYYNinqvtlgrrsitSPPSTSTTKRPKSIDDSEMeSPVDDVFypgtgrSPAAGSSQSSG 303
Cdd:COG5422    71 QIFSSFSSSPKLFQRRNSAGPITH------------SPSATSSTSSLNSNDGDQF-SPASDSL------SFNPSSTQSRK 131

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402534522  304 WPNDVDAGPASLKKSgklDFCSALSSQGSSPRMAFTH----HPLPVLAGVRPGSPRATASA--LHFPSTSIIQQSSPY-- 375
Cdd:COG5422   132 DSGPGDGSPVQKRKN---PLLPSSSTHGTHPPIVFTDnngsHAGAPNARSRKEIPSLGSQSmqLPSPHFRQKFSSSDTsn 208

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 402534522  376 -FTHPTIRYHHHHGQDSLKEFVQFVCSDGSGQATGQHSQRQAPPLPTGLSASDPGTAT 432
Cdd:COG5422   209 gFSYPSIRKNSRHSSNSMPSFPHSSTAVLLKRHSGSSGASLISSNITPSSSNSEAMST 266
 
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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