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Conserved domains on  [gi|1028909829|pdb|5IY8|0]
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Chain 0, General transcription factor IIH subunit 2

Protein Classification

VWA domain-containing protein( domain architecture ID 13419840)

VWA (von Willebrand factor type A) 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 ...
 56-236 7.14e-107

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: 312.34  E-value: 7.14e-107
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0       56 GMMRHLYVVVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKKAv 135
Cdd:cd01453   1 GIMRHLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEKLTDLTGNPRKHIQALKTA- 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0      136 dMTCHGEPSLYNSLSIAMQTLKHMPGHTSREVLIIFSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARET 215
Cdd:cd01453  80 -RECSGEPSLQNGLEMALESLKHMPSHGSREVLIIFSSLSTCDPGNIYETIDKLKKENIRVSVIGLSAEMHICKEICKAT 158

                       170       180
                ....*....|....*....|.
5IY8_0      216 GGTYHVILDESHYKELLTHHV 236
Cdd:cd01453 159 NGTYKVILDETHLKELLLEHV 179
SSL1 super family cl34921
RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit ...
 11-385 3.44e-104

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


The actual alignment was detected with superfamily member COG5151:

Pssm-ID: 227480 [Multi-domain]  Cd Length: 421  Bit Score: 314.24  E-value: 3.44e-104
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0       11 WEGGYERTWEILKEDESGSLKATIEDILFKAKRKRVFEHHGQVRLGMMRHLYVVVDGSRTMEDQDLKPNRLTCTLKLLEY 90
Cdd:COG5151  40 WEQEYKRSWDDVNDDKEGSLVGVVAEFNLETKAPYSNNRTTPLQRGIIRHLHLILDVSEAMDESDFLPTRRANVIKYAEG 119

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0       91 FVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKKAVDmtCHGEPSLYNSLSIAMQTLKHMPGHTSREVLII 170
Cdd:COG5151 120 FVPEFFSQNPISQLSIISIRDGCAKYTSSMDGNPQAHIGQLKSKRD--CSGNFSLQNALEMARIELMKNTMHGTREVLII 197

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0      171 FSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETG----GTYHVILDESHYKELLTHHVS-PPPASSSS 245
Cdd:COG5151 198 FGSTSTRDPGDIAETIDKLVAYNIRVHFIGLCAEVAICKEICKATNssteGRYYVPVDEGHLSELMRELSHpTDFNGTKT 277

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0      246 ECSLIRMGFPQHTIASLsdqdakPSFSMAHLDgntepgLTLGGYFCPQCRAKYCELPVECKICGLTLVSAPHLARSYHHL 325
Cdd:COG5151 278 DLSLVKMGFPSPMMEQL------PSVCACHSE------VKGGGYECPVCKTKVCSLPISCPICSLQLILSTHLARSYHHL 345

                       330       340       350       360       370       380       390
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
5IY8_0      326 FPLDAFQEIPLEEYNGERFCYGCQG-----------ELKDQHVYVCAVCQNVFCVDCDVFVHDSLHCCPGC 385
Cdd:COG5151 346 YPLKPFVEKPEGTNPKSTHCFVCQGpfpkppvspfdESTSSGRYQCELCKSTFCSDCDVFIHETLHFCIGC 416
 
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 ...
 56-236 7.14e-107

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: 312.34  E-value: 7.14e-107
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0       56 GMMRHLYVVVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKKAv 135
Cdd:cd01453   1 GIMRHLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEKLTDLTGNPRKHIQALKTA- 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0      136 dMTCHGEPSLYNSLSIAMQTLKHMPGHTSREVLIIFSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARET 215
Cdd:cd01453  80 -RECSGEPSLQNGLEMALESLKHMPSHGSREVLIIFSSLSTCDPGNIYETIDKLKKENIRVSVIGLSAEMHICKEICKAT 158

                       170       180
                ....*....|....*....|.
5IY8_0      216 GGTYHVILDESHYKELLTHHV 236
Cdd:cd01453 159 NGTYKVILDETHLKELLLEHV 179
Ssl1 pfam04056
Ssl1-like; Ssl1-like proteins are 40kDa subunits of the Transcription factor II H complex.
 64-236 1.17e-104

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


Pssm-ID: 461149  Cd Length: 178  Bit Score: 306.28  E-value: 1.17e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0         64 VVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKKAVDMTCHGEP 143
Cdd:pfam04056   1 VLDCSRSMEEKDLRPSRFACTIKYLETFVEEFFDQNPISQIGLITCKDGRAHRLTDLTGNPRVHIKALKSLREAECGGDP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0        144 SLYNSLSIAMQTLKHMPGHTSREVLIIFSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETGGTYHVIL 223
Cdd:pfam04056  81 SLQNALELARASLKHVPSHGSREVLIIFGSLSTCDPGDIYSTIDTLKKEKIRCSVIGLSAEVFICKELCKATNGTYSVAL 160

                         170
                  ....*....|...
5IY8_0        224 DESHYKELLTHHV 236
Cdd:pfam04056 161 DETHLKELLLEHV 173
SSL1 COG5151
RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit ...
 11-385 3.44e-104

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: 314.24  E-value: 3.44e-104
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0       11 WEGGYERTWEILKEDESGSLKATIEDILFKAKRKRVFEHHGQVRLGMMRHLYVVVDGSRTMEDQDLKPNRLTCTLKLLEY 90
Cdd:COG5151  40 WEQEYKRSWDDVNDDKEGSLVGVVAEFNLETKAPYSNNRTTPLQRGIIRHLHLILDVSEAMDESDFLPTRRANVIKYAEG 119

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0       91 FVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKKAVDmtCHGEPSLYNSLSIAMQTLKHMPGHTSREVLII 170
Cdd:COG5151 120 FVPEFFSQNPISQLSIISIRDGCAKYTSSMDGNPQAHIGQLKSKRD--CSGNFSLQNALEMARIELMKNTMHGTREVLII 197

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0      171 FSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETG----GTYHVILDESHYKELLTHHVS-PPPASSSS 245
Cdd:COG5151 198 FGSTSTRDPGDIAETIDKLVAYNIRVHFIGLCAEVAICKEICKATNssteGRYYVPVDEGHLSELMRELSHpTDFNGTKT 277

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0      246 ECSLIRMGFPQHTIASLsdqdakPSFSMAHLDgntepgLTLGGYFCPQCRAKYCELPVECKICGLTLVSAPHLARSYHHL 325
Cdd:COG5151 278 DLSLVKMGFPSPMMEQL------PSVCACHSE------VKGGGYECPVCKTKVCSLPISCPICSLQLILSTHLARSYHHL 345

                       330       340       350       360       370       380       390
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
5IY8_0      326 FPLDAFQEIPLEEYNGERFCYGCQG-----------ELKDQHVYVCAVCQNVFCVDCDVFVHDSLHCCPGC 385
Cdd:COG5151 346 YPLKPFVEKPEGTNPKSTHCFVCQGpfpkppvspfdESTSSGRYQCELCKSTFCSDCDVFIHETLHFCIGC 416
ssl1 TIGR00622
transcription factor ssl1; All proteins in this family for which functions are known are ...
 288-388 1.99e-57

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: 183.21  E-value: 1.99e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0        288 GYFCPQCRAKYCELPVECKICGLTLVSAPHLARSYHHLFPLDAFQEIPLEEYNGERFCYGCQ-----------GELKDQH 356
Cdd:TIGR00622   1 GYFCPQCRAKVCELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQgpfpkppvspfDELKDSH 80

                          90       100       110
                  ....*....|....*....|....*....|..
5IY8_0        357 VYVCAVCQNVFCVDCDVFVHDSLHCCPGCIHK 388
Cdd:TIGR00622  81 RYVCAVCKNVFCVDCDVFVHESLHCCPGCIHK 112
C1_4 smart01047
TFIIH C1-like domain; The carboxyl-terminal region of TFIIH is essential for transcription ...
 345-386 1.57e-16

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: 72.78  E-value: 1.57e-16
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
5IY8_0         345 CYGCQGEL---KDQHV----YVCAVCQNVFCVDCDVFVHDSLHCCPGCI 386
Cdd:smart01047   1 CFGCQSPFpnsKDKSVtssrYRCTKCKQVFCIDCDVFIHETLHNCPGCE 49
VWA smart00327
von Willebrand factor (vWF) type A domain; VWA domains in extracellular eukaryotic proteins ...
 60-227 4.80e-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: 4.80e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0          60 HLYVVVDGSRTMEdqdlkPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTkSKRAEKLTELsgNPRKHITSLKKAVDM-- 137
Cdd:smart00327   1 DVVFLLDGSGSMG-----GNRFELAKEFVLKLVEQLDIGPDGDRVGLVTF-SDDARVLFPL--NDSRSKDALLEALASls 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0         138 -TCHGEPSLYNSLSIAMQTLKHMPGHTSRE---VLIIFSSLT-TCDPSNIYDLIKTLKAAKIRVSVIGLSAEV--RVCTV 210
Cdd:smart00327  73 yKLGGGTNLGAALQYALENLFSKSAGSRRGapkVVILITDGEsNDGPKDLLKAAKELKRSGVKVFVVGVGNDVdeEELKK 152

                          170
                   ....*....|....*..
5IY8_0         211 LARETGGTYHVILDESH 227
Cdd:smart00327 153 LASAPGGVYVFLPELLD 169
C1_4 pfam07975
TFIIH C1-like domain; The carboxyl-terminal region of TFIIH is essential for transcription ...
 344-385 1.23e-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: 62.11  E-value: 1.23e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
5IY8_0        344 FCYGCQ-----------GELKDQHVYVCAVCQNVFCVDCDVFVHDSLHCCPGC 385
Cdd:pfam07975   1 NCYGCQkkfpkginkktDELLTSSRYRCPKCKQDFCIDCDVFIHESLHNCPGC 53
ChlD COG1240
vWFA (von Willebrand factor type A) domain of Mg and Co chelatases [Coenzyme transport and ...
 59-226 3.65e-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: 3.65e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0       59 RHLYVVVDGSRTMEDQdlkpNRLTCTLKLLEYFVEEYFDQNpisQIGIIVTkSKRAEKLTELSGNprkhITSLKKAVD-M 137
Cdd:COG1240  93 RDVVLVVDASGSMAAE----NRLEAAKGALLDFLDDYRPRD---RVGLVAF-GGEAEVLLPLTRD----REALKRALDeL 160

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0      138 TCHGEPSLYNSLSIAMQTLKHMPGHTSReVLIIFS-SLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEV---RVCTVLAR 213
Cdd:COG1240 161 PPGGGTPLGDALALALELLKRADPARRK-VIVLLTdGRDNAGRIDPLEAAELAAAAGIRIYTIGVGTEAvdeGLLREIAE 239

                       170
                ....*....|...
5IY8_0      214 ETGGTYHVILDES 226
Cdd:COG1240 240 ATGGRYFRADDLS 252
PLN03144 PLN03144
Carbon catabolite repressor protein 4 homolog; Provisional
 301-385 3.02e-03

Carbon catabolite repressor protein 4 homolog; Provisional


Pssm-ID: 178689 [Multi-domain]  Cd Length: 606  Bit Score: 39.71  E-value: 3.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0       301 LPVECKICGLTLVSAPHLARSYHHLFPLDAFQEIPLEEYNGERFCYGCQgelKDQHVYVC-------AVCQNVFCVDCDV 373
Cdd:PLN03144   9 LPSDIPIVGCELTPYVLLRRPDGTLTTDDVPESAPLDGYFLRYRWYRIQ---SDRKVAVCsvhpsepATLQCVGCVKAKL 85

                         90
                 ....*....|..
5IY8_0       374 FVHDSLHCCPGC 385
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 ...
 56-236 7.14e-107

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: 312.34  E-value: 7.14e-107
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0       56 GMMRHLYVVVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKKAv 135
Cdd:cd01453   1 GIMRHLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEKLTDLTGNPRKHIQALKTA- 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0      136 dMTCHGEPSLYNSLSIAMQTLKHMPGHTSREVLIIFSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARET 215
Cdd:cd01453  80 -RECSGEPSLQNGLEMALESLKHMPSHGSREVLIIFSSLSTCDPGNIYETIDKLKKENIRVSVIGLSAEMHICKEICKAT 158

                       170       180
                ....*....|....*....|.
5IY8_0      216 GGTYHVILDESHYKELLTHHV 236
Cdd:cd01453 159 NGTYKVILDETHLKELLLEHV 179
Ssl1 pfam04056
Ssl1-like; Ssl1-like proteins are 40kDa subunits of the Transcription factor II H complex.
 64-236 1.17e-104

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


Pssm-ID: 461149  Cd Length: 178  Bit Score: 306.28  E-value: 1.17e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0         64 VVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKKAVDMTCHGEP 143
Cdd:pfam04056   1 VLDCSRSMEEKDLRPSRFACTIKYLETFVEEFFDQNPISQIGLITCKDGRAHRLTDLTGNPRVHIKALKSLREAECGGDP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0        144 SLYNSLSIAMQTLKHMPGHTSREVLIIFSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETGGTYHVIL 223
Cdd:pfam04056  81 SLQNALELARASLKHVPSHGSREVLIIFGSLSTCDPGDIYSTIDTLKKEKIRCSVIGLSAEVFICKELCKATNGTYSVAL 160

                         170
                  ....*....|...
5IY8_0        224 DESHYKELLTHHV 236
Cdd:pfam04056 161 DETHLKELLLEHV 173
SSL1 COG5151
RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit ...
 11-385 3.44e-104

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: 314.24  E-value: 3.44e-104
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0       11 WEGGYERTWEILKEDESGSLKATIEDILFKAKRKRVFEHHGQVRLGMMRHLYVVVDGSRTMEDQDLKPNRLTCTLKLLEY 90
Cdd:COG5151  40 WEQEYKRSWDDVNDDKEGSLVGVVAEFNLETKAPYSNNRTTPLQRGIIRHLHLILDVSEAMDESDFLPTRRANVIKYAEG 119

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0       91 FVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKKAVDmtCHGEPSLYNSLSIAMQTLKHMPGHTSREVLII 170
Cdd:COG5151 120 FVPEFFSQNPISQLSIISIRDGCAKYTSSMDGNPQAHIGQLKSKRD--CSGNFSLQNALEMARIELMKNTMHGTREVLII 197

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0      171 FSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETG----GTYHVILDESHYKELLTHHVS-PPPASSSS 245
Cdd:COG5151 198 FGSTSTRDPGDIAETIDKLVAYNIRVHFIGLCAEVAICKEICKATNssteGRYYVPVDEGHLSELMRELSHpTDFNGTKT 277

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0      246 ECSLIRMGFPQHTIASLsdqdakPSFSMAHLDgntepgLTLGGYFCPQCRAKYCELPVECKICGLTLVSAPHLARSYHHL 325
Cdd:COG5151 278 DLSLVKMGFPSPMMEQL------PSVCACHSE------VKGGGYECPVCKTKVCSLPISCPICSLQLILSTHLARSYHHL 345

                       330       340       350       360       370       380       390
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
5IY8_0      326 FPLDAFQEIPLEEYNGERFCYGCQG-----------ELKDQHVYVCAVCQNVFCVDCDVFVHDSLHCCPGC 385
Cdd:COG5151 346 YPLKPFVEKPEGTNPKSTHCFVCQGpfpkppvspfdESTSSGRYQCELCKSTFCSDCDVFIHETLHFCIGC 416
ssl1 TIGR00622
transcription factor ssl1; All proteins in this family for which functions are known are ...
 288-388 1.99e-57

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: 183.21  E-value: 1.99e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0        288 GYFCPQCRAKYCELPVECKICGLTLVSAPHLARSYHHLFPLDAFQEIPLEEYNGERFCYGCQ-----------GELKDQH 356
Cdd:TIGR00622   1 GYFCPQCRAKVCELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQgpfpkppvspfDELKDSH 80

                          90       100       110
                  ....*....|....*....|....*....|..
5IY8_0        357 VYVCAVCQNVFCVDCDVFVHDSLHCCPGCIHK 388
Cdd:TIGR00622  81 RYVCAVCKNVFCVDCDVFVHESLHCCPGCIHK 112
C1_4 smart01047
TFIIH C1-like domain; The carboxyl-terminal region of TFIIH is essential for transcription ...
 345-386 1.57e-16

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: 72.78  E-value: 1.57e-16
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
5IY8_0         345 CYGCQGEL---KDQHV----YVCAVCQNVFCVDCDVFVHDSLHCCPGCI 386
Cdd:smart01047   1 CFGCQSPFpnsKDKSVtssrYRCTKCKQVFCIDCDVFIHETLHNCPGCE 49
VWA smart00327
von Willebrand factor (vWF) type A domain; VWA domains in extracellular eukaryotic proteins ...
 60-227 4.80e-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: 4.80e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0          60 HLYVVVDGSRTMEdqdlkPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTkSKRAEKLTELsgNPRKHITSLKKAVDM-- 137
Cdd:smart00327   1 DVVFLLDGSGSMG-----GNRFELAKEFVLKLVEQLDIGPDGDRVGLVTF-SDDARVLFPL--NDSRSKDALLEALASls 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0         138 -TCHGEPSLYNSLSIAMQTLKHMPGHTSRE---VLIIFSSLT-TCDPSNIYDLIKTLKAAKIRVSVIGLSAEV--RVCTV 210
Cdd:smart00327  73 yKLGGGTNLGAALQYALENLFSKSAGSRRGapkVVILITDGEsNDGPKDLLKAAKELKRSGVKVFVVGVGNDVdeEELKK 152

                          170
                   ....*....|....*..
5IY8_0         211 LARETGGTYHVILDESH 227
Cdd:smart00327 153 LASAPGGVYVFLPELLD 169
C1_4 pfam07975
TFIIH C1-like domain; The carboxyl-terminal region of TFIIH is essential for transcription ...
 344-385 1.23e-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: 62.11  E-value: 1.23e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
5IY8_0        344 FCYGCQ-----------GELKDQHVYVCAVCQNVFCVDCDVFVHDSLHCCPGC 385
Cdd:pfam07975   1 NCYGCQkkfpkginkktDELLTSSRYRCPKCKQDFCIDCDVFIHESLHNCPGC 53
VWA_2 pfam13519
von Willebrand factor type A domain;
61-170 4.03e-12

von Willebrand factor type A domain;


Pssm-ID: 463909 [Multi-domain]  Cd Length: 103  Bit Score: 62.31  E-value: 4.03e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0         61 LYVVVDGSRTMEDQDLKPNRLTctlkLLEYFVEEYFDQNPISQIGIIVTkSKRAEKLTELSGNPRKHITSLKKAVDMTch 140
Cdd:pfam13519   1 LVFVLDTSGSMRNGDYGPTRLE----AAKDAVLALLKSLPGDRVGLVTF-GDGPEVLIPLTKDRAKILRALRRLEPKG-- 73

                          90       100       110
                  ....*....|....*....|....*....|
5IY8_0        141 GEPSLYNSLSIAMQTLKHMPGHTSREVLII 170
Cdd:pfam13519  74 GGTNLAAALQLARAALKHRRKNQPRRIVLI 103
vWFA cd00198
Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation ...
 59-205 2.97e-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: 2.97e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0       59 RHLYVVVDGSRTMEDQDLKPnrltcTLKLLEYFVEEYFDQNPISQIGIiVTKSKRAEklTELSGNPRKHITSLKKAVD-- 136
Cdd:cd00198   1 ADIVFLLDVSGSMGGEKLDK-----AKEALKALVSSLSASPPGDRVGL-VTFGSNAR--VVLPLTTDTDKADLLEAIDal 72

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
5IY8_0      137 -MTCHGEPSLYNSLSIAMQTLKHMPGHTSREVLIIFSS-LTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEV 205
Cdd:cd00198  73 kKGLGGGTNIGAALRLALELLKSAKRPNARRVIILLTDgEPNDGPELLAEAARELRKLGITVYTIGIGDDA 143
ChlD COG1240
vWFA (von Willebrand factor type A) domain of Mg and Co chelatases [Coenzyme transport and ...
 59-226 3.65e-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: 3.65e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0       59 RHLYVVVDGSRTMEDQdlkpNRLTCTLKLLEYFVEEYFDQNpisQIGIIVTkSKRAEKLTELSGNprkhITSLKKAVD-M 137
Cdd:COG1240  93 RDVVLVVDASGSMAAE----NRLEAAKGALLDFLDDYRPRD---RVGLVAF-GGEAEVLLPLTRD----REALKRALDeL 160

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0      138 TCHGEPSLYNSLSIAMQTLKHMPGHTSReVLIIFS-SLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEV---RVCTVLAR 213
Cdd:COG1240 161 PPGGGTPLGDALALALELLKRADPARRK-VIVLLTdGRDNAGRIDPLEAAELAAAAGIRIYTIGVGTEAvdeGLLREIAE 239

                       170
                ....*....|...
5IY8_0      214 ETGGTYHVILDES 226
Cdd:COG1240 240 ATGGRYFRADDLS 252
PLN03144 PLN03144
Carbon catabolite repressor protein 4 homolog; Provisional
 301-385 3.02e-03

Carbon catabolite repressor protein 4 homolog; Provisional


Pssm-ID: 178689 [Multi-domain]  Cd Length: 606  Bit Score: 39.71  E-value: 3.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0       301 LPVECKICGLTLVSAPHLARSYHHLFPLDAFQEIPLEEYNGERFCYGCQgelKDQHVYVC-------AVCQNVFCVDCDV 373
Cdd:PLN03144   9 LPSDIPIVGCELTPYVLLRRPDGTLTTDDVPESAPLDGYFLRYRWYRIQ---SDRKVAVCsvhpsepATLQCVGCVKAKL 85

                         90
                 ....*....|..
5IY8_0       374 FVHDSLHCCPGC 385
Cdd:PLN03144  86 PVSKSYHCSPKC 97
VWA_26S_proteasome_subunit cd01452
26S proteasome plays a major role in eukaryotic protein breakdown, especially for ...
 63-199 3.91e-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: 3.91e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IY8_0       63 VVVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSL-KKAVDMTCHg 141
Cdd:cd01452   8 ICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNPENNVGLMTMAGNSPEVLVTLTNDQGKILSKLhDVQPKGKAN- 86

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
5IY8_0      142 epsLYNSLSIAMQTLKHMPGHTSREVLIIF-SSLTTCDPSNIYDLIKTLKAAKIRVSVI 199
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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