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Conserved domains on  [gi|2462492152|ref|XP_054185928|]
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general transcription factor IIH subunit 2 isoform X3 [Homo sapiens]

Protein Classification

vWA_transcription_factor_IIH_type and C1_4 domain-containing protein( domain architecture ID 10106913)

vWA_transcription_factor_IIH_type and C1_4 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
vWA_transcription_factor_IIH_type cd01453
Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five ...
 1-179 1.07e-104

Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins contain a VWA domain. The p44 subunit of TFIIH functions as a DNA helicase in RNA polymerase II transcription initiation and DNA repair, and its transcriptional activity is dependent on its C-terminal Zn-binding domains. The function of the vWA domain is unclear, but may be involved in complex assembly. The MIDAS motif is not conserved in this sub-group.


:

Pssm-ID: 238730  Cd Length: 183  Bit Score: 304.64  E-value: 1.07e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152   1 MRHLYVVVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKKAvdM 80
Cdd:cd01453     3 MRHLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEKLTDLTGNPRKHIQALKTA--R 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152  81 TCHGEPSLYNSLSIAMQTLKHMPGHTSREVLIIFSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETGG 160
Cdd:cd01453    81 ECSGEPSLQNGLEMALESLKHMPSHGSREVLIIFSSLSTCDPGNIYETIDKLKKENIRVSVIGLSAEMHICKEICKATNG 160

                         170
                  ....*....|....*....
gi 2462492152 161 TYHVILDESHYKELLTHHV 179
Cdd:cd01453   161 TYKVILDETHLKELLLEHV 179
C1_4 super family cl06838
TFIIH C1-like domain; The carboxyl-terminal region of TFIIH is essential for transcription ...
 231-331 1.31e-55

TFIIH C1-like domain; The carboxyl-terminal region of TFIIH is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterized by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C (pfam00130).


The actual alignment was detected with superfamily member TIGR00622:

Pssm-ID: 352591  Cd Length: 112  Bit Score: 177.05  E-value: 1.31e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152 231 GYFCPQCRAKYCELPVECKICGLTLVSAPHLARSYHHLFPLDAFQEIPLEEYNGERFCYGCQ-----------GELKDQH 299
Cdd:TIGR00622   1 GYFCPQCRAKVCELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQgpfpkppvspfDELKDSH 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2462492152 300 VYVCAVCQNVFCVDCDVFVHDSLHCCPGCIHK 331
Cdd:TIGR00622  81 RYVCAVCKNVFCVDCDVFVHESLHCCPGCIHK 112
 
Name Accession Description Interval E-value
vWA_transcription_factor_IIH_type cd01453
Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five ...
 1-179 1.07e-104

Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins contain a VWA domain. The p44 subunit of TFIIH functions as a DNA helicase in RNA polymerase II transcription initiation and DNA repair, and its transcriptional activity is dependent on its C-terminal Zn-binding domains. The function of the vWA domain is unclear, but may be involved in complex assembly. The MIDAS motif is not conserved in this sub-group.


Pssm-ID: 238730  Cd Length: 183  Bit Score: 304.64  E-value: 1.07e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152   1 MRHLYVVVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKKAvdM 80
Cdd:cd01453     3 MRHLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEKLTDLTGNPRKHIQALKTA--R 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152  81 TCHGEPSLYNSLSIAMQTLKHMPGHTSREVLIIFSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETGG 160
Cdd:cd01453    81 ECSGEPSLQNGLEMALESLKHMPSHGSREVLIIFSSLSTCDPGNIYETIDKLKKENIRVSVIGLSAEMHICKEICKATNG 160

                         170
                  ....*....|....*....
gi 2462492152 161 TYHVILDESHYKELLTHHV 179
Cdd:cd01453   161 TYKVILDETHLKELLLEHV 179
Ssl1 pfam04056
Ssl1-like; Ssl1-like proteins are 40kDa subunits of the Transcription factor II H complex.
 7-179 1.84e-104

Ssl1-like; Ssl1-like proteins are 40kDa subunits of the Transcription factor II H complex.


Pssm-ID: 461149  Cd Length: 178  Bit Score: 303.58  E-value: 1.84e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152   7 VVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKKAVDMTCHGEP 86
Cdd:pfam04056   1 VLDCSRSMEEKDLRPSRFACTIKYLETFVEEFFDQNPISQIGLITCKDGRAHRLTDLTGNPRVHIKALKSLREAECGGDP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152  87 SLYNSLSIAMQTLKHMPGHTSREVLIIFSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETGGTYHVIL 166
Cdd:pfam04056  81 SLQNALELARASLKHVPSHGSREVLIIFGSLSTCDPGDIYSTIDTLKKEKIRCSVIGLSAEVFICKELCKATNGTYSVAL 160

                         170
                  ....*....|...
gi 2462492152 167 DESHYKELLTHHV 179
Cdd:pfam04056 161 DETHLKELLLEHV 173
SSL1 COG5151
RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit ...
 1-328 7.75e-91

RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair];


Pssm-ID: 227480 [Multi-domain]  Cd Length: 421  Bit Score: 277.65  E-value: 7.75e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152   1 MRHLYVVVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKKAVDm 80
Cdd:COG5151    87 IRHLHLILDVSEAMDESDFLPTRRANVIKYAEGFVPEFFSQNPISQLSIISIRDGCAKYTSSMDGNPQAHIGQLKSKRD- 165

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152  81 tCHGEPSLYNSLSIAMQTLKHMPGHTSREVLIIFSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETG- 159
Cdd:COG5151   166 -CSGNFSLQNALEMARIELMKNTMHGTREVLIIFGSTSTRDPGDIAETIDKLVAYNIRVHFIGLCAEVAICKEICKATNs 244

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152 160 ---GTYHVILDESHYKELLTHHVS-PPPASSSSECSLIRMGFPQHTIASLsdqdakPSFSMAHLDgntepgLTLGGYFCP 235
Cdd:COG5151   245 steGRYYVPVDEGHLSELMRELSHpTDFNGTKTDLSLVKMGFPSPMMEQL------PSVCACHSE------VKGGGYECP 312

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152 236 QCRAKYCELPVECKICGLTLVSAPHLARSYHHLFPLDAFQEIPLEEYNGERFCYGCQG-----------ELKDQHVYVCA 304
Cdd:COG5151   313 VCKTKVCSLPISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFVCQGpfpkppvspfdESTSSGRYQCE 392

                         330       340
                  ....*....|....*....|....
gi 2462492152 305 VCQNVFCVDCDVFVHDSLHCCPGC 328
Cdd:COG5151   393 LCKSTFCSDCDVFIHETLHFCIGC 416
ssl1 TIGR00622
transcription factor ssl1; All proteins in this family for which functions are known are ...
 231-331 1.31e-55

transcription factor ssl1; All proteins in this family for which functions are known are components of the TFIIH complex which is involved in the initiaiton of transcription and nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129709  Cd Length: 112  Bit Score: 177.05  E-value: 1.31e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152 231 GYFCPQCRAKYCELPVECKICGLTLVSAPHLARSYHHLFPLDAFQEIPLEEYNGERFCYGCQ-----------GELKDQH 299
Cdd:TIGR00622   1 GYFCPQCRAKVCELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQgpfpkppvspfDELKDSH 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2462492152 300 VYVCAVCQNVFCVDCDVFVHDSLHCCPGCIHK 331
Cdd:TIGR00622  81 RYVCAVCKNVFCVDCDVFVHESLHCCPGCIHK 112
C1_4 smart01047
TFIIH C1-like domain; The carboxyl-terminal region of TFIIH is essential for transcription ...
 288-329 1.49e-15

TFIIH C1-like domain; The carboxyl-terminal region of TFIIH is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C.


Pssm-ID: 214993  Cd Length: 49  Bit Score: 69.70  E-value: 1.49e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2462492152  288 CYGCQGEL---KDQHV----YVCAVCQNVFCVDCDVFVHDSLHCCPGCI 329
Cdd:smart01047   1 CFGCQSPFpnsKDKSVtssrYRCTKCKQVFCIDCDVFIHETLHNCPGCE 49
VWA smart00327
von Willebrand factor (vWF) type A domain; VWA domains in extracellular eukaryotic proteins ...
 3-170 3.20e-15

von Willebrand factor (vWF) type A domain; VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods.


Pssm-ID: 214621 [Multi-domain]  Cd Length: 175  Bit Score: 72.49  E-value: 3.20e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152    3 HLYVVVDGSRTMEdqdlkPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTkSKRAEKLTELsgNPRKHITSLKKAVDM-- 80
Cdd:smart00327   1 DVVFLLDGSGSMG-----GNRFELAKEFVLKLVEQLDIGPDGDRVGLVTF-SDDARVLFPL--NDSRSKDALLEALASls 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152   81 -TCHGEPSLYNSLSIAMQTLKHMPGHTSRE---VLIIFSSLT-TCDPSNIYDLIKTLKAAKIRVSVIGLSAEV--RVCTV 153
Cdd:smart00327  73 yKLGGGTNLGAALQYALENLFSKSAGSRRGapkVVILITDGEsNDGPKDLLKAAKELKRSGVKVFVVGVGNDVdeEELKK 152

                          170
                   ....*....|....*..
gi 2462492152  154 LARETGGTYHVILDESH 170
Cdd:smart00327 153 LASAPGGVYVFLPELLD 169
C1_4 pfam07975
TFIIH C1-like domain; The carboxyl-terminal region of TFIIH is essential for transcription ...
 287-328 7.50e-12

TFIIH C1-like domain; The carboxyl-terminal region of TFIIH is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterized by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C (pfam00130).


Pssm-ID: 336887  Cd Length: 55  Bit Score: 59.80  E-value: 7.50e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2462492152 287 FCYGCQ-----------GELKDQHVYVCAVCQNVFCVDCDVFVHDSLHCCPGC 328
Cdd:pfam07975   1 NCYGCQkkfpkginkktDELLTSSRYRCPKCKQDFCIDCDVFIHESLHNCPGC 53
PLN03144 PLN03144
Carbon catabolite repressor protein 4 homolog; Provisional
 244-328 2.83e-03

Carbon catabolite repressor protein 4 homolog; Provisional


Pssm-ID: 178689 [Multi-domain]  Cd Length: 606  Bit Score: 39.33  E-value: 2.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152 244 LPVECKICGLTLVSAPHLARSYHHLFPLDAFQEIPLEEYNGERFCYGCQgelKDQHVYVC-------AVCQNVFCVDCDV 316
Cdd:PLN03144    9 LPSDIPIVGCELTPYVLLRRPDGTLTTDDVPESAPLDGYFLRYRWYRIQ---SDRKVAVCsvhpsepATLQCVGCVKAKL 85

                          90
                  ....*....|..
gi 2462492152 317 FVHDSLHCCPGC 328
Cdd:PLN03144   86 PVSKSYHCSPKC 97
 
Name Accession Description Interval E-value
vWA_transcription_factor_IIH_type cd01453
Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five ...
 1-179 1.07e-104

Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins contain a VWA domain. The p44 subunit of TFIIH functions as a DNA helicase in RNA polymerase II transcription initiation and DNA repair, and its transcriptional activity is dependent on its C-terminal Zn-binding domains. The function of the vWA domain is unclear, but may be involved in complex assembly. The MIDAS motif is not conserved in this sub-group.


Pssm-ID: 238730  Cd Length: 183  Bit Score: 304.64  E-value: 1.07e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152   1 MRHLYVVVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKKAvdM 80
Cdd:cd01453     3 MRHLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEKLTDLTGNPRKHIQALKTA--R 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152  81 TCHGEPSLYNSLSIAMQTLKHMPGHTSREVLIIFSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETGG 160
Cdd:cd01453    81 ECSGEPSLQNGLEMALESLKHMPSHGSREVLIIFSSLSTCDPGNIYETIDKLKKENIRVSVIGLSAEMHICKEICKATNG 160

                         170
                  ....*....|....*....
gi 2462492152 161 TYHVILDESHYKELLTHHV 179
Cdd:cd01453   161 TYKVILDETHLKELLLEHV 179
Ssl1 pfam04056
Ssl1-like; Ssl1-like proteins are 40kDa subunits of the Transcription factor II H complex.
 7-179 1.84e-104

Ssl1-like; Ssl1-like proteins are 40kDa subunits of the Transcription factor II H complex.


Pssm-ID: 461149  Cd Length: 178  Bit Score: 303.58  E-value: 1.84e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152   7 VVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKKAVDMTCHGEP 86
Cdd:pfam04056   1 VLDCSRSMEEKDLRPSRFACTIKYLETFVEEFFDQNPISQIGLITCKDGRAHRLTDLTGNPRVHIKALKSLREAECGGDP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152  87 SLYNSLSIAMQTLKHMPGHTSREVLIIFSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETGGTYHVIL 166
Cdd:pfam04056  81 SLQNALELARASLKHVPSHGSREVLIIFGSLSTCDPGDIYSTIDTLKKEKIRCSVIGLSAEVFICKELCKATNGTYSVAL 160

                         170
                  ....*....|...
gi 2462492152 167 DESHYKELLTHHV 179
Cdd:pfam04056 161 DETHLKELLLEHV 173
SSL1 COG5151
RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit ...
 1-328 7.75e-91

RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair];


Pssm-ID: 227480 [Multi-domain]  Cd Length: 421  Bit Score: 277.65  E-value: 7.75e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152   1 MRHLYVVVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKKAVDm 80
Cdd:COG5151    87 IRHLHLILDVSEAMDESDFLPTRRANVIKYAEGFVPEFFSQNPISQLSIISIRDGCAKYTSSMDGNPQAHIGQLKSKRD- 165

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152  81 tCHGEPSLYNSLSIAMQTLKHMPGHTSREVLIIFSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETG- 159
Cdd:COG5151   166 -CSGNFSLQNALEMARIELMKNTMHGTREVLIIFGSTSTRDPGDIAETIDKLVAYNIRVHFIGLCAEVAICKEICKATNs 244

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152 160 ---GTYHVILDESHYKELLTHHVS-PPPASSSSECSLIRMGFPQHTIASLsdqdakPSFSMAHLDgntepgLTLGGYFCP 235
Cdd:COG5151   245 steGRYYVPVDEGHLSELMRELSHpTDFNGTKTDLSLVKMGFPSPMMEQL------PSVCACHSE------VKGGGYECP 312

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152 236 QCRAKYCELPVECKICGLTLVSAPHLARSYHHLFPLDAFQEIPLEEYNGERFCYGCQG-----------ELKDQHVYVCA 304
Cdd:COG5151   313 VCKTKVCSLPISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFVCQGpfpkppvspfdESTSSGRYQCE 392

                         330       340
                  ....*....|....*....|....
gi 2462492152 305 VCQNVFCVDCDVFVHDSLHCCPGC 328
Cdd:COG5151   393 LCKSTFCSDCDVFIHETLHFCIGC 416
ssl1 TIGR00622
transcription factor ssl1; All proteins in this family for which functions are known are ...
 231-331 1.31e-55

transcription factor ssl1; All proteins in this family for which functions are known are components of the TFIIH complex which is involved in the initiaiton of transcription and nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129709  Cd Length: 112  Bit Score: 177.05  E-value: 1.31e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152 231 GYFCPQCRAKYCELPVECKICGLTLVSAPHLARSYHHLFPLDAFQEIPLEEYNGERFCYGCQ-----------GELKDQH 299
Cdd:TIGR00622   1 GYFCPQCRAKVCELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQgpfpkppvspfDELKDSH 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2462492152 300 VYVCAVCQNVFCVDCDVFVHDSLHCCPGCIHK 331
Cdd:TIGR00622  81 RYVCAVCKNVFCVDCDVFVHESLHCCPGCIHK 112
C1_4 smart01047
TFIIH C1-like domain; The carboxyl-terminal region of TFIIH is essential for transcription ...
 288-329 1.49e-15

TFIIH C1-like domain; The carboxyl-terminal region of TFIIH is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C.


Pssm-ID: 214993  Cd Length: 49  Bit Score: 69.70  E-value: 1.49e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2462492152  288 CYGCQGEL---KDQHV----YVCAVCQNVFCVDCDVFVHDSLHCCPGCI 329
Cdd:smart01047   1 CFGCQSPFpnsKDKSVtssrYRCTKCKQVFCIDCDVFIHETLHNCPGCE 49
VWA smart00327
von Willebrand factor (vWF) type A domain; VWA domains in extracellular eukaryotic proteins ...
 3-170 3.20e-15

von Willebrand factor (vWF) type A domain; VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods.


Pssm-ID: 214621 [Multi-domain]  Cd Length: 175  Bit Score: 72.49  E-value: 3.20e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152    3 HLYVVVDGSRTMEdqdlkPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTkSKRAEKLTELsgNPRKHITSLKKAVDM-- 80
Cdd:smart00327   1 DVVFLLDGSGSMG-----GNRFELAKEFVLKLVEQLDIGPDGDRVGLVTF-SDDARVLFPL--NDSRSKDALLEALASls 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152   81 -TCHGEPSLYNSLSIAMQTLKHMPGHTSRE---VLIIFSSLT-TCDPSNIYDLIKTLKAAKIRVSVIGLSAEV--RVCTV 153
Cdd:smart00327  73 yKLGGGTNLGAALQYALENLFSKSAGSRRGapkVVILITDGEsNDGPKDLLKAAKELKRSGVKVFVVGVGNDVdeEELKK 152

                          170
                   ....*....|....*..
gi 2462492152  154 LARETGGTYHVILDESH 170
Cdd:smart00327 153 LASAPGGVYVFLPELLD 169
VWA_2 pfam13519
von Willebrand factor type A domain;
4-113 3.12e-12

von Willebrand factor type A domain;


Pssm-ID: 463909 [Multi-domain]  Cd Length: 103  Bit Score: 62.31  E-value: 3.12e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152   4 LYVVVDGSRTMEDQDLKPNRLTctlkLLEYFVEEYFDQNPISQIGIIVTkSKRAEKLTELSGNPRKHITSLKKAVDMTch 83
Cdd:pfam13519   1 LVFVLDTSGSMRNGDYGPTRLE----AAKDAVLALLKSLPGDRVGLVTF-GDGPEVLIPLTKDRAKILRALRRLEPKG-- 73

                          90       100       110
                  ....*....|....*....|....*....|
gi 2462492152  84 GEPSLYNSLSIAMQTLKHMPGHTSREVLII 113
Cdd:pfam13519  74 GGTNLAAALQLARAALKHRRKNQPRRIVLI 103
C1_4 pfam07975
TFIIH C1-like domain; The carboxyl-terminal region of TFIIH is essential for transcription ...
 287-328 7.50e-12

TFIIH C1-like domain; The carboxyl-terminal region of TFIIH is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterized by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C (pfam00130).


Pssm-ID: 336887  Cd Length: 55  Bit Score: 59.80  E-value: 7.50e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2462492152 287 FCYGCQ-----------GELKDQHVYVCAVCQNVFCVDCDVFVHDSLHCCPGC 328
Cdd:pfam07975   1 NCYGCQkkfpkginkktDELLTSSRYRCPKCKQDFCIDCDVFIHESLHNCPGC 53
vWFA cd00198
Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation ...
 2-148 2.35e-09

Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains.


Pssm-ID: 238119 [Multi-domain]  Cd Length: 161  Bit Score: 55.65  E-value: 2.35e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152   2 RHLYVVVDGSRTMEDQDLKPnrltcTLKLLEYFVEEYFDQNPISQIGIiVTKSKRAEklTELSGNPRKHITSLKKAVD-- 79
Cdd:cd00198     1 ADIVFLLDVSGSMGGEKLDK-----AKEALKALVSSLSASPPGDRVGL-VTFGSNAR--VVLPLTTDTDKADLLEAIDal 72

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462492152  80 -MTCHGEPSLYNSLSIAMQTLKHMPGHTSREVLIIFSS-LTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEV 148
Cdd:cd00198    73 kKGLGGGTNIGAALRLALELLKSAKRPNARRVIILLTDgEPNDGPELLAEAARELRKLGITVYTIGIGDDA 143
ChlD COG1240
vWFA (von Willebrand factor type A) domain of Mg and Co chelatases [Coenzyme transport and ...
 2-169 2.73e-09

vWFA (von Willebrand factor type A) domain of Mg and Co chelatases [Coenzyme transport and metabolism];


Pssm-ID: 440853 [Multi-domain]  Cd Length: 262  Bit Score: 57.26  E-value: 2.73e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152   2 RHLYVVVDGSRTMEDQdlkpNRLTCTLKLLEYFVEEYFDQNpisQIGIIVTkSKRAEKLTELSGNprkhITSLKKAVD-M 80
Cdd:COG1240    93 RDVVLVVDASGSMAAE----NRLEAAKGALLDFLDDYRPRD---RVGLVAF-GGEAEVLLPLTRD----REALKRALDeL 160

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152  81 TCHGEPSLYNSLSIAMQTLKHMPGHTSReVLIIFS-SLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEV---RVCTVLAR 156
Cdd:COG1240   161 PPGGGTPLGDALALALELLKRADPARRK-VIVLLTdGRDNAGRIDPLEAAELAAAAGIRIYTIGVGTEAvdeGLLREIAE 239

                         170
                  ....*....|...
gi 2462492152 157 ETGGTYHVILDES 169
Cdd:COG1240   240 ATGGRYFRADDLS 252
PLN03144 PLN03144
Carbon catabolite repressor protein 4 homolog; Provisional
 244-328 2.83e-03

Carbon catabolite repressor protein 4 homolog; Provisional


Pssm-ID: 178689 [Multi-domain]  Cd Length: 606  Bit Score: 39.33  E-value: 2.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152 244 LPVECKICGLTLVSAPHLARSYHHLFPLDAFQEIPLEEYNGERFCYGCQgelKDQHVYVC-------AVCQNVFCVDCDV 316
Cdd:PLN03144    9 LPSDIPIVGCELTPYVLLRRPDGTLTTDDVPESAPLDGYFLRYRWYRIQ---SDRKVAVCsvhpsepATLQCVGCVKAKL 85

                          90
                  ....*....|..
gi 2462492152 317 FVHDSLHCCPGC 328
Cdd:PLN03144   86 PVSKSYHCSPKC 97
VWA_26S_proteasome_subunit cd01452
26S proteasome plays a major role in eukaryotic protein breakdown, especially for ...
 6-142 3.16e-03

26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins. It is an ATP-dependent protease responsible for the bulk of non-lysosomal proteolysis in eukaryotes, often using covalent modification of proteins by ubiquitylation. It consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The CP is an ATP independent peptidase consisting of hydrolyzing activities. One or both ends of CP carry the RP that confers both ubiquitin and ATP dependence to the 26S proteosome. The RP's proposed functions include recognition of substrates and translocation of these to CP for proteolysis. The RP can dissociate into a stable lid and base subcomplexes. The base is composed of three non-ATPase subunits (Rpn 1, 2 and 10). A single residue in the vWA domain of Rpn10 has been implicated to be responsible for stabilizing the lid-base association.


Pssm-ID: 238729  Cd Length: 187  Bit Score: 38.11  E-value: 3.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462492152   6 VVVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSL-KKAVDMTCHg 84
Cdd:cd01452     8 ICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNPENNVGLMTMAGNSPEVLVTLTNDQGKILSKLhDVQPKGKAN- 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462492152  85 epsLYNSLSIAMQTLKHMPGHTSREVLIIF-SSLTTCDPSNIYDLIKTLKAAKIRVSVI 142
Cdd:cd01452    87 ---FITGIQIAQLALKHRQNKNQKQRIVAFvGSPIEEDEKDLVKLAKRLKKNNVSVDII 142
 
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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