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Conserved domains on  [gi|1237938364|ref|NP_001341366|]
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general transcription factor IIH subunit 2-like protein isoform 1 [Homo sapiens]

Protein Classification

vWA domain-containing protein( domain architecture ID 13419840)

vWA (von Willebrand factor type A) domain-containing protein, similar to general transcription factor IIH subunit 2

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 ...
56-235 8.23e-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: 311.96  E-value: 8.23e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364  56 GMMRHLYVVVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKEAv 135
Cdd:cd01453     1 GIMRHLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEKLTDLTGNPRKHIQALKTA- 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364 136 dMTCHGEPSLYNSLSMAMQTLKHMPGHTSREVLIIFSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARET 215
Cdd:cd01453    80 -RECSGEPSLQNGLEMALESLKHMPSHGSREVLIIFSSLSTCDPGNIYETIDKLKKENIRVSVIGLSAEMHICKEICKAT 158
                         170       180
                  ....*....|....*....|
gi 1237938364 216 GGTYHVILDESHYKELLTHH 235
Cdd:cd01453   159 NGTYKVILDETHLKELLLEH 178
SSL1 super family cl34921
RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit ...
11-385 1.09e-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: 315.40  E-value: 1.09e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364  11 WEGGYERTWEILKEDESGSLKATIEDILFKAKRKRVFEHHGQVRLGMMRHLYVVVDGSRTMEDQDLKPNRLTCTLKLLEY 90
Cdd:COG5151    40 WEQEYKRSWDDVNDDKEGSLVGVVAEFNLETKAPYSNNRTTPLQRGIIRHLHLILDVSEAMDESDFLPTRRANVIKYAEG 119
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364  91 FVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKEAVDmtCHGEPSLYNSLSMAMQTLKHMPGHTSREVLII 170
Cdd:COG5151   120 FVPEFFSQNPISQLSIISIRDGCAKYTSSMDGNPQAHIGQLKSKRD--CSGNFSLQNALEMARIELMKNTMHGTREVLII 197
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364 171 FSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETG----GTYHVILDESHYKELL---THHLSPPPASS 243
Cdd:COG5151   198 FGSTSTRDPGDIAETIDKLVAYNIRVHFIGLCAEVAICKEICKATNssteGRYYVPVDEGHLSELMrelSHPTDFNGTKT 277
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364 244 SSecSLIRMGFPQHTIASLsdqdakPSFSMAHLDgntepgLTLGGYFCPQCRAKYCELPVECKICGLTLVSAPHLARSYH 323
Cdd:COG5151   278 DL--SLVKMGFPSPMMEQL------PSVCACHSE------VKGGGYECPVCKTKVCSLPISCPICSLQLILSTHLARSYH 343
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1237938364 324 HLFPLDAFQEIPLEEYNGERFCYGCQG-----------ELKDQHVYVCAVCQNVFCVDCDVFVHDSLHCCPGC 385
Cdd:COG5151   344 HLYPLKPFVEKPEGTNPKSTHCFVCQGpfpkppvspfdESTSSGRYQCELCKSTFCSDCDVFIHETLHFCIGC 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 ...
56-235 8.23e-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: 311.96  E-value: 8.23e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364  56 GMMRHLYVVVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKEAv 135
Cdd:cd01453     1 GIMRHLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEKLTDLTGNPRKHIQALKTA- 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364 136 dMTCHGEPSLYNSLSMAMQTLKHMPGHTSREVLIIFSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARET 215
Cdd:cd01453    80 -RECSGEPSLQNGLEMALESLKHMPSHGSREVLIIFSSLSTCDPGNIYETIDKLKKENIRVSVIGLSAEMHICKEICKAT 158
                         170       180
                  ....*....|....*....|
gi 1237938364 216 GGTYHVILDESHYKELLTHH 235
Cdd:cd01453   159 NGTYKVILDETHLKELLLEH 178
SSL1 COG5151
RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit ...
11-385 1.09e-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: 315.40  E-value: 1.09e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364  11 WEGGYERTWEILKEDESGSLKATIEDILFKAKRKRVFEHHGQVRLGMMRHLYVVVDGSRTMEDQDLKPNRLTCTLKLLEY 90
Cdd:COG5151    40 WEQEYKRSWDDVNDDKEGSLVGVVAEFNLETKAPYSNNRTTPLQRGIIRHLHLILDVSEAMDESDFLPTRRANVIKYAEG 119
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364  91 FVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKEAVDmtCHGEPSLYNSLSMAMQTLKHMPGHTSREVLII 170
Cdd:COG5151   120 FVPEFFSQNPISQLSIISIRDGCAKYTSSMDGNPQAHIGQLKSKRD--CSGNFSLQNALEMARIELMKNTMHGTREVLII 197
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364 171 FSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETG----GTYHVILDESHYKELL---THHLSPPPASS 243
Cdd:COG5151   198 FGSTSTRDPGDIAETIDKLVAYNIRVHFIGLCAEVAICKEICKATNssteGRYYVPVDEGHLSELMrelSHPTDFNGTKT 277
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364 244 SSecSLIRMGFPQHTIASLsdqdakPSFSMAHLDgntepgLTLGGYFCPQCRAKYCELPVECKICGLTLVSAPHLARSYH 323
Cdd:COG5151   278 DL--SLVKMGFPSPMMEQL------PSVCACHSE------VKGGGYECPVCKTKVCSLPISCPICSLQLILSTHLARSYH 343
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1237938364 324 HLFPLDAFQEIPLEEYNGERFCYGCQG-----------ELKDQHVYVCAVCQNVFCVDCDVFVHDSLHCCPGC 385
Cdd:COG5151   344 HLYPLKPFVEKPEGTNPKSTHCFVCQGpfpkppvspfdESTSSGRYQCELCKSTFCSDCDVFIHETLHFCIGC 416
Ssl1 pfam04056
Ssl1-like; Ssl1-like proteins are 40kDa subunits of the Transcription factor II H complex.
64-235 1.70e-104

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


Pssm-ID: 461149  Cd Length: 178  Bit Score: 305.89  E-value: 1.70e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364  64 VVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKEAVDMTCHGEP 143
Cdd:pfam04056   1 VLDCSRSMEEKDLRPSRFACTIKYLETFVEEFFDQNPISQIGLITCKDGRAHRLTDLTGNPRVHIKALKSLREAECGGDP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364 144 SLYNSLSMAMQTLKHMPGHTSREVLIIFSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETGGTYHVIL 223
Cdd:pfam04056  81 SLQNALELARASLKHVPSHGSREVLIIFGSLSTCDPGDIYSTIDTLKKEKIRCSVIGLSAEVFICKELCKATNGTYSVAL 160
                         170
                  ....*....|..
gi 1237938364 224 DESHYKELLTHH 235
Cdd:pfam04056 161 DETHLKELLLEH 172
ssl1 TIGR00622
transcription factor ssl1; All proteins in this family for which functions are known are ...
288-388 2.03e-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: 2.03e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364 288 GYFCPQCRAKYCELPVECKICGLTLVSAPHLARSYHHLFPLDAFQEIPLEEYNGERFCYGCQ-----------GELKDQH 356
Cdd:TIGR00622   1 GYFCPQCRAKVCELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQgpfpkppvspfDELKDSH 80
                          90       100       110
                  ....*....|....*....|....*....|..
gi 1237938364 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 1.50e-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: 1.50e-16
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1237938364  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 1.19e-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: 74.41  E-value: 1.19e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364   60 HLYVVVDGSRTMEdqdlkPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTkSKRAEKLTELsgNPRKHITSLKEAVDM-- 137
Cdd:smart00327   1 DVVFLLDGSGSMG-----GNRFELAKEFVLKLVEQLDIGPDGDRVGLVTF-SDDARVLFPL--NDSRSKDALLEALASls 72
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364  138 -TCHGEPSLYNSLSMAMQTLKHMPGHTSRE---VLIIFSSLT-TCDPSNIYDLIKTLKAAKIRVSVIGLSAEV--RVCTV 210
Cdd:smart00327  73 yKLGGGTNLGAALQYALENLFSKSAGSRRGapkVVILITDGEsNDGPKDLLKAAKELKRSGVKVFVVGVGNDVdeEELKK 152
                          170
                   ....*....|....*..
gi 1237938364  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 1.20e-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: 1.20e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1237938364 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 1.06e-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: 58.80  E-value: 1.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364  59 RHLYVVVDGSRTMEDQdlkpNRLTCTLKLLEYFVEEYFDQNpisQIGIIVTkSKRAEKLTELSGNprkhITSLKEAVD-M 137
Cdd:COG1240    93 RDVVLVVDASGSMAAE----NRLEAAKGALLDFLDDYRPRD---RVGLVAF-GGEAEVLLPLTRD----REALKRALDeL 160
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364 138 TCHGEPSLYNSLSMAMQTLKHMPGHTSReVLIIFS-SLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEV---RVCTVLAR 213
Cdd:COG1240   161 PPGGGTPLGDALALALELLKRADPARRK-VIVLLTdGRDNAGRIDPLEAAELAAAAGIRIYTIGVGTEAvdeGLLREIAE 239
                         170
                  ....*....|...
gi 1237938364 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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364 301 LPVECKICGLTLVSAPHLARSYHHLFPLDAFQEIPLEEYNGERFCYGCQgelKDQHVYVC-------AVCQNVFCVDCDV 373
Cdd:PLN03144    9 LPSDIPIVGCELTPYVLLRRPDGTLTTDDVPESAPLDGYFLRYRWYRIQ---SDRKVAVCsvhpsepATLQCVGCVKAKL 85
                          90
                  ....*....|..
gi 1237938364 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 ...
56-235 8.23e-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: 311.96  E-value: 8.23e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364  56 GMMRHLYVVVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKEAv 135
Cdd:cd01453     1 GIMRHLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEKLTDLTGNPRKHIQALKTA- 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364 136 dMTCHGEPSLYNSLSMAMQTLKHMPGHTSREVLIIFSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARET 215
Cdd:cd01453    80 -RECSGEPSLQNGLEMALESLKHMPSHGSREVLIIFSSLSTCDPGNIYETIDKLKKENIRVSVIGLSAEMHICKEICKAT 158
                         170       180
                  ....*....|....*....|
gi 1237938364 216 GGTYHVILDESHYKELLTHH 235
Cdd:cd01453   159 NGTYKVILDETHLKELLLEH 178
SSL1 COG5151
RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit ...
11-385 1.09e-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: 315.40  E-value: 1.09e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364  11 WEGGYERTWEILKEDESGSLKATIEDILFKAKRKRVFEHHGQVRLGMMRHLYVVVDGSRTMEDQDLKPNRLTCTLKLLEY 90
Cdd:COG5151    40 WEQEYKRSWDDVNDDKEGSLVGVVAEFNLETKAPYSNNRTTPLQRGIIRHLHLILDVSEAMDESDFLPTRRANVIKYAEG 119
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364  91 FVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKEAVDmtCHGEPSLYNSLSMAMQTLKHMPGHTSREVLII 170
Cdd:COG5151   120 FVPEFFSQNPISQLSIISIRDGCAKYTSSMDGNPQAHIGQLKSKRD--CSGNFSLQNALEMARIELMKNTMHGTREVLII 197
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364 171 FSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETG----GTYHVILDESHYKELL---THHLSPPPASS 243
Cdd:COG5151   198 FGSTSTRDPGDIAETIDKLVAYNIRVHFIGLCAEVAICKEICKATNssteGRYYVPVDEGHLSELMrelSHPTDFNGTKT 277
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364 244 SSecSLIRMGFPQHTIASLsdqdakPSFSMAHLDgntepgLTLGGYFCPQCRAKYCELPVECKICGLTLVSAPHLARSYH 323
Cdd:COG5151   278 DL--SLVKMGFPSPMMEQL------PSVCACHSE------VKGGGYECPVCKTKVCSLPISCPICSLQLILSTHLARSYH 343
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1237938364 324 HLFPLDAFQEIPLEEYNGERFCYGCQG-----------ELKDQHVYVCAVCQNVFCVDCDVFVHDSLHCCPGC 385
Cdd:COG5151   344 HLYPLKPFVEKPEGTNPKSTHCFVCQGpfpkppvspfdESTSSGRYQCELCKSTFCSDCDVFIHETLHFCIGC 416
Ssl1 pfam04056
Ssl1-like; Ssl1-like proteins are 40kDa subunits of the Transcription factor II H complex.
64-235 1.70e-104

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


Pssm-ID: 461149  Cd Length: 178  Bit Score: 305.89  E-value: 1.70e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364  64 VVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKEAVDMTCHGEP 143
Cdd:pfam04056   1 VLDCSRSMEEKDLRPSRFACTIKYLETFVEEFFDQNPISQIGLITCKDGRAHRLTDLTGNPRVHIKALKSLREAECGGDP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364 144 SLYNSLSMAMQTLKHMPGHTSREVLIIFSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETGGTYHVIL 223
Cdd:pfam04056  81 SLQNALELARASLKHVPSHGSREVLIIFGSLSTCDPGDIYSTIDTLKKEKIRCSVIGLSAEVFICKELCKATNGTYSVAL 160
                         170
                  ....*....|..
gi 1237938364 224 DESHYKELLTHH 235
Cdd:pfam04056 161 DETHLKELLLEH 172
ssl1 TIGR00622
transcription factor ssl1; All proteins in this family for which functions are known are ...
288-388 2.03e-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: 2.03e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364 288 GYFCPQCRAKYCELPVECKICGLTLVSAPHLARSYHHLFPLDAFQEIPLEEYNGERFCYGCQ-----------GELKDQH 356
Cdd:TIGR00622   1 GYFCPQCRAKVCELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQgpfpkppvspfDELKDSH 80
                          90       100       110
                  ....*....|....*....|....*....|..
gi 1237938364 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 1.50e-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: 1.50e-16
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1237938364  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 1.19e-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: 74.41  E-value: 1.19e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364   60 HLYVVVDGSRTMEdqdlkPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTkSKRAEKLTELsgNPRKHITSLKEAVDM-- 137
Cdd:smart00327   1 DVVFLLDGSGSMG-----GNRFELAKEFVLKLVEQLDIGPDGDRVGLVTF-SDDARVLFPL--NDSRSKDALLEALASls 72
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364  138 -TCHGEPSLYNSLSMAMQTLKHMPGHTSRE---VLIIFSSLT-TCDPSNIYDLIKTLKAAKIRVSVIGLSAEV--RVCTV 210
Cdd:smart00327  73 yKLGGGTNLGAALQYALENLFSKSAGSRRGapkVVILITDGEsNDGPKDLLKAAKELKRSGVKVFVVGVGNDVdeEELKK 152
                          170
                   ....*....|....*..
gi 1237938364  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 1.20e-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: 1.20e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1237938364 344 FCYGCQ-----------GELKDQHVYVCAVCQNVFCVDCDVFVHDSLHCCPGC 385
Cdd:pfam07975   1 NCYGCQkkfpkginkktDELLTSSRYRCPKCKQDFCIDCDVFIHESLHNCPGC 53
VWA_2 pfam13519
von Willebrand factor type A domain;
61-170 1.35e-12

von Willebrand factor type A domain;


Pssm-ID: 463909 [Multi-domain]  Cd Length: 103  Bit Score: 63.47  E-value: 1.35e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364  61 LYVVVDGSRTMEDQDLKPNRLTctlkLLEYFVEEYFDQNPISQIGIIVTkSKRAEKLTELSGNPRKHITSLKEAVDMTch 140
Cdd:pfam13519   1 LVFVLDTSGSMRNGDYGPTRLE----AAKDAVLALLKSLPGDRVGLVTF-GDGPEVLIPLTKDRAKILRALRRLEPKG-- 73
                          90       100       110
                  ....*....|....*....|....*....|
gi 1237938364 141 GEPSLYNSLSMAMQTLKHMPGHTSREVLII 170
Cdd:pfam13519  74 GGTNLAAALQLARAALKHRRKNQPRRIVLI 103
ChlD COG1240
vWFA (von Willebrand factor type A) domain of Mg and Co chelatases [Coenzyme transport and ...
59-226 1.06e-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: 58.80  E-value: 1.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364  59 RHLYVVVDGSRTMEDQdlkpNRLTCTLKLLEYFVEEYFDQNpisQIGIIVTkSKRAEKLTELSGNprkhITSLKEAVD-M 137
Cdd:COG1240    93 RDVVLVVDASGSMAAE----NRLEAAKGALLDFLDDYRPRD---RVGLVAF-GGEAEVLLPLTRD----REALKRALDeL 160
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364 138 TCHGEPSLYNSLSMAMQTLKHMPGHTSReVLIIFS-SLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEV---RVCTVLAR 213
Cdd:COG1240   161 PPGGGTPLGDALALALELLKRADPARRK-VIVLLTdGRDNAGRIDPLEAAELAAAAGIRIYTIGVGTEAvdeGLLREIAE 239
                         170
                  ....*....|...
gi 1237938364 214 ETGGTYHVILDES 226
Cdd:COG1240   240 ATGGRYFRADDLS 252
vWFA cd00198
Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation ...
59-205 1.24e-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: 56.81  E-value: 1.24e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364  59 RHLYVVVDGSRTMEDQDLKPnrltcTLKLLEYFVEEYFDQNPISQIGIiVTKSKRAEklTELSGNPRKHITSLKEAVD-- 136
Cdd:cd00198     1 ADIVFLLDVSGSMGGEKLDK-----AKEALKALVSSLSASPPGDRVGL-VTFGSNAR--VVLPLTTDTDKADLLEAIDal 72
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1237938364 137 -MTCHGEPSLYNSLSMAMQTLKHMPGHTSREVLIIFSS-LTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEV 205
Cdd:cd00198    73 kKGLGGGTNIGAALRLALELLKSAKRPNARRVIILLTDgEPNDGPELLAEAARELRKLGITVYTIGIGDDA 143
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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1237938364 301 LPVECKICGLTLVSAPHLARSYHHLFPLDAFQEIPLEEYNGERFCYGCQgelKDQHVYVC-------AVCQNVFCVDCDV 373
Cdd:PLN03144    9 LPSDIPIVGCELTPYVLLRRPDGTLTTDDVPESAPLDGYFLRYRWYRIQ---SDRKVAVCsvhpsepATLQCVGCVKAKL 85
                          90
                  ....*....|..
gi 1237938364 374 FVHDSLHCCPGC 385
Cdd:PLN03144   86 PVSKSYHCSPKC 97
 
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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