NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|56549649|ref|NP_002492|]
View 

nuclear factor 1 X-type isoform 2 [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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
CTF_NFI pfam00859
CTF/NF-I family transcription modulation region;
213-418 2.59e-98

CTF/NF-I family transcription modulation region;


:

Pssm-ID: 459967 [Multi-domain]  Cd Length: 288  Bit Score: 296.05  E-value: 2.59e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549649   213 QDCFVTSGVWNVTELVRVSQTPVATASGPNFSLADLESPSYYNINQVTLGRRSITSPPSTStTKRPK--SIDDSEMESPV 290
Cdd:pfam00859   1 QDSFVTSGVFSVTELVRVSRTPVATGTGPNFSLGELQGPLYYDLNPGVGLRRSLPSTSSSG-SKRHKsgSMEDDVDTSPG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549649   291 DDvFYpgtgRSPAAGSSQSSGWPNDVDAG---PASLKKSGKLDFCSALSSQGSSPRMAFTHHPLPVL---AGVRpGSPRa 364
Cdd:pfam00859  80 GD-YY----RSPSSPASSSRNWPHDVEGGmssPVKKKKPDKSDFSSPSPQDSSPRLMAFTQHHRPVIavhSGIS-RSPH- 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 56549649   365 TASALHFPSTSIIQQSSPYFTHPTIRYHHHHGQDSLKEFVQFVCSDGSGQATGQ 418
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 ...
 9-46 3.24e-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: 83.42  E-value: 3.24e-20
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 56549649     9 QDEFHPFIEALLPHVRAFSYTWFNLQARKRKYFKKHEK 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 ...
 68-170 4.20e-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: 4.20e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549649    68 KQKWASRLLAKLRKDIrpEFREDFVLTITGK---KPPCCVLSN--------PDQKGKIRRIDClrqadKVWRL-DLVMVI 135
Cdd:pfam03165   1 LKKAVESLLKKLKKKI--QQLEELELAVESRgdpPTGCVTIPRsldgrlqvAGRKGLPHVIYC-----RLWRWpDLQSQH 73

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 56549649   136 LFKGIPLESTDGeRLYKSPqcsnpgLCVQPHHIGV 170
Cdd:pfam03165  74 ELKAIPTCETAF-ESKKDE------VCINPYHYSR 101
 
Name Accession Description Interval E-value
CTF_NFI pfam00859
CTF/NF-I family transcription modulation region;
213-418 2.59e-98

CTF/NF-I family transcription modulation region;


Pssm-ID: 459967 [Multi-domain]  Cd Length: 288  Bit Score: 296.05  E-value: 2.59e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549649   213 QDCFVTSGVWNVTELVRVSQTPVATASGPNFSLADLESPSYYNINQVTLGRRSITSPPSTStTKRPK--SIDDSEMESPV 290
Cdd:pfam00859   1 QDSFVTSGVFSVTELVRVSRTPVATGTGPNFSLGELQGPLYYDLNPGVGLRRSLPSTSSSG-SKRHKsgSMEDDVDTSPG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549649   291 DDvFYpgtgRSPAAGSSQSSGWPNDVDAG---PASLKKSGKLDFCSALSSQGSSPRMAFTHHPLPVL---AGVRpGSPRa 364
Cdd:pfam00859  80 GD-YY----RSPSSPASSSRNWPHDVEGGmssPVKKKKPDKSDFSSPSPQDSSPRLMAFTQHHRPVIavhSGIS-RSPH- 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 56549649   365 TASALHFPSTSIIQQSSPYFTHPTIRYHHHHGQDSLKEFVQFVCSDGSGQATGQ 418
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 ...
 9-46 3.24e-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: 83.42  E-value: 3.24e-20
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 56549649     9 QDEFHPFIEALLPHVRAFSYTWFNLQARKRKYFKKHEK 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 ...
 68-170 4.20e-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: 4.20e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549649    68 KQKWASRLLAKLRKDIrpEFREDFVLTITGK---KPPCCVLSN--------PDQKGKIRRIDClrqadKVWRL-DLVMVI 135
Cdd:pfam03165   1 LKKAVESLLKKLKKKI--QQLEELELAVESRgdpPTGCVTIPRsldgrlqvAGRKGLPHVIYC-----RLWRWpDLQSQH 73

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 56549649   136 LFKGIPLESTDGeRLYKSPqcsnpgLCVQPHHIGV 170
Cdd:pfam03165  74 ELKAIPTCETAF-ESKKDE------VCINPYHYSR 101
DWA smart00523
Domain A in dwarfin family proteins;
67-168 4.05e-16

Domain A in dwarfin family proteins;


Pssm-ID: 214708  Cd Length: 109  Bit Score: 73.95  E-value: 4.05e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549649     67 IKQKWASRLLAKLRKDIRPEFREDFVLTIT--GKKPPCCVLSNPDQKGKirridcLRQADKVWRLDLVMVILFKGIPLES 144
Cdd:smart00523   1 VEEKWAKKATESLLKKLKKKQLEELLQAVEskGGPPTRCVLIPRSLDGR------LQVAHRKGLPHVLYCRLFRWPDLQS 74

                           90       100       110
                   ....*....|....*....|....*....|
gi 56549649    145 tdGERLYKSPQCSNPG------LCVQPHHI 168
Cdd:smart00523  75 --PHELKALPTCEHAFesksdeVCCNPYHY 102
ROM1 COG5422
RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction ...
 232-440 8.62e-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: 8.62e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549649  232 QTPVATASGPNFSLADLESPSYYNinqvtlgrrsitSPPSTSTTKRPKSIDDSEMeSPVDDVFypgtgrSPAAGSSQSSG 311
Cdd:COG5422   71 QIFSSFSSSPKLFQRRNSAGPITH------------SPSATSSTSSLNSNDGDQF-SPASDSL------SFNPSSTQSRK 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549649  312 WPNDVDAGPASLKKSgklDFCSALSSQGSSPRMAFTH----HPLPVLAGVRPGSPRATASA--LHFPSTSIIQQSSPY-- 383
Cdd:COG5422  132 DSGPGDGSPVQKRKN---PLLPSSSTHGTHPPIVFTDnngsHAGAPNARSRKEIPSLGSQSmqLPSPHFRQKFSSSDTsn 208

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 56549649  384 -FTHPTIRYHHHHGQDSLKEFVQFVCSDGSGQATGQHSQRQAPPLPTGLSASDPGTAT 440
Cdd:COG5422  209 gFSYPSIRKNSRHSSNSMPSFPHSSTAVLLKRHSGSSGASLISSNITPSSSNSEAMST 266
 
Name Accession Description Interval E-value
CTF_NFI pfam00859
CTF/NF-I family transcription modulation region;
213-418 2.59e-98

CTF/NF-I family transcription modulation region;


Pssm-ID: 459967 [Multi-domain]  Cd Length: 288  Bit Score: 296.05  E-value: 2.59e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549649   213 QDCFVTSGVWNVTELVRVSQTPVATASGPNFSLADLESPSYYNINQVTLGRRSITSPPSTStTKRPK--SIDDSEMESPV 290
Cdd:pfam00859   1 QDSFVTSGVFSVTELVRVSRTPVATGTGPNFSLGELQGPLYYDLNPGVGLRRSLPSTSSSG-SKRHKsgSMEDDVDTSPG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549649   291 DDvFYpgtgRSPAAGSSQSSGWPNDVDAG---PASLKKSGKLDFCSALSSQGSSPRMAFTHHPLPVL---AGVRpGSPRa 364
Cdd:pfam00859  80 GD-YY----RSPSSPASSSRNWPHDVEGGmssPVKKKKPDKSDFSSPSPQDSSPRLMAFTQHHRPVIavhSGIS-RSPH- 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 56549649   365 TASALHFPSTSIIQQSSPYFTHPTIRYHHHHGQDSLKEFVQFVCSDGSGQATGQ 418
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 ...
 9-46 3.24e-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: 83.42  E-value: 3.24e-20
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 56549649     9 QDEFHPFIEALLPHVRAFSYTWFNLQARKRKYFKKHEK 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 ...
 68-170 4.20e-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: 4.20e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549649    68 KQKWASRLLAKLRKDIrpEFREDFVLTITGK---KPPCCVLSN--------PDQKGKIRRIDClrqadKVWRL-DLVMVI 135
Cdd:pfam03165   1 LKKAVESLLKKLKKKI--QQLEELELAVESRgdpPTGCVTIPRsldgrlqvAGRKGLPHVIYC-----RLWRWpDLQSQH 73

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 56549649   136 LFKGIPLESTDGeRLYKSPqcsnpgLCVQPHHIGV 170
Cdd:pfam03165  74 ELKAIPTCETAF-ESKKDE------VCINPYHYSR 101
DWA smart00523
Domain A in dwarfin family proteins;
67-168 4.05e-16

Domain A in dwarfin family proteins;


Pssm-ID: 214708  Cd Length: 109  Bit Score: 73.95  E-value: 4.05e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549649     67 IKQKWASRLLAKLRKDIRPEFREDFVLTIT--GKKPPCCVLSNPDQKGKirridcLRQADKVWRLDLVMVILFKGIPLES 144
Cdd:smart00523   1 VEEKWAKKATESLLKKLKKKQLEELLQAVEskGGPPTRCVLIPRSLDGR------LQVAHRKGLPHVLYCRLFRWPDLQS 74

                           90       100       110
                   ....*....|....*....|....*....|
gi 56549649    145 tdGERLYKSPQCSNPG------LCVQPHHI 168
Cdd:smart00523  75 --PHELKALPTCEHAFesksdeVCCNPYHY 102
ROM1 COG5422
RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction ...
 232-440 8.62e-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: 8.62e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549649  232 QTPVATASGPNFSLADLESPSYYNinqvtlgrrsitSPPSTSTTKRPKSIDDSEMeSPVDDVFypgtgrSPAAGSSQSSG 311
Cdd:COG5422   71 QIFSSFSSSPKLFQRRNSAGPITH------------SPSATSSTSSLNSNDGDQF-SPASDSL------SFNPSSTQSRK 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549649  312 WPNDVDAGPASLKKSgklDFCSALSSQGSSPRMAFTH----HPLPVLAGVRPGSPRATASA--LHFPSTSIIQQSSPY-- 383
Cdd:COG5422  132 DSGPGDGSPVQKRKN---PLLPSSSTHGTHPPIVFTDnngsHAGAPNARSRKEIPSLGSQSmqLPSPHFRQKFSSSDTsn 208

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 56549649  384 -FTHPTIRYHHHHGQDSLKEFVQFVCSDGSGQATGQHSQRQAPPLPTGLSASDPGTAT 440
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH