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Conserved domains on  [gi|19112324|ref|NP_595532|]
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transcription factor TFIIH complex subunit Tfb4 [Schizosaccharomyces pombe]

Protein Classification

general transcription and DNA repair factor IIH subunit TFB4( domain architecture ID 10009145)

general transcription and DNA repair factor IIH subunit TFB4 is a component of the general transcription and DNA repair factor IIH (TFIIH) core complex, which is involved in general and transcription-coupled nucleotide excision repair (NER) of damaged DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II

Gene Ontology:  GO:0006289|GO:0006355|GO:0000439

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
TFB4 COG5242
RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit ...
1-297 1.63e-177

RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription / DNA replication, recombination, and repair];


:

Pssm-ID: 227567  Cd Length: 296  Bit Score: 491.48  E-value: 1.63e-177
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112324   1 MDEFQTLKQNASWDISEDAndtPSLLVVILDANPASWYSLSKKVPVSKVLADITVFLNAHLAFHHDNRVAVLASHSDKVE 80
Cdd:COG5242   1 MDAISTFKHARSKQVTEES---PSLLFVIIDLEPENWELTTEKGSRDKVLNDIVVFLNAHLAFSRNNRVAVVAGYSQGKT 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112324  81 YLYPSIAPEQKVAEVDPTKEANTYRKFREVDDLVLSGMKRLMSSTDKVSRKTMISGALSRALAYINQVQNKNTLRSRILI 160
Cdd:COG5242  78 YLYPSSESALKASESENTRNSDMYRRFRNVDETDITEIYRLIEHPHKNSQRYDVGGAMSLGLAYCNHRDEETSLKSRILI 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112324 161 FSLTG-DVALQYIPTMNCIFCAQKKNIPINVCNIEGGTLFLEQAADATGGIYLKVDNPKGLLQYLMMSLFPDQNLRKHLN 239
Cdd:COG5242 158 FTLSGrDRKDQYIPYMNCIFAAQKFGIPISVFSIFGNSKFLLQCCDATGGDYLTVEDTEGLLQYLLSLLFTDGELRPLGV 237
                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 19112324 240 TPNQANVDFRATCFCHKKVLDIGFVCSVCLSIFCEPRVHCSTCHTKF-TVEPMSKKLHT 297
Cdd:COG5242 238 KPNHGSVDFRATCYCHNRVVLLGFVCSVCLSVFCRPVPVCKKCKSKFsFRKPVVTKLES 296
 
Name Accession Description Interval E-value
TFB4 COG5242
RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit ...
1-297 1.63e-177

RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription / DNA replication, recombination, and repair];


Pssm-ID: 227567  Cd Length: 296  Bit Score: 491.48  E-value: 1.63e-177
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112324   1 MDEFQTLKQNASWDISEDAndtPSLLVVILDANPASWYSLSKKVPVSKVLADITVFLNAHLAFHHDNRVAVLASHSDKVE 80
Cdd:COG5242   1 MDAISTFKHARSKQVTEES---PSLLFVIIDLEPENWELTTEKGSRDKVLNDIVVFLNAHLAFSRNNRVAVVAGYSQGKT 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112324  81 YLYPSIAPEQKVAEVDPTKEANTYRKFREVDDLVLSGMKRLMSSTDKVSRKTMISGALSRALAYINQVQNKNTLRSRILI 160
Cdd:COG5242  78 YLYPSSESALKASESENTRNSDMYRRFRNVDETDITEIYRLIEHPHKNSQRYDVGGAMSLGLAYCNHRDEETSLKSRILI 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112324 161 FSLTG-DVALQYIPTMNCIFCAQKKNIPINVCNIEGGTLFLEQAADATGGIYLKVDNPKGLLQYLMMSLFPDQNLRKHLN 239
Cdd:COG5242 158 FTLSGrDRKDQYIPYMNCIFAAQKFGIPISVFSIFGNSKFLLQCCDATGGDYLTVEDTEGLLQYLLSLLFTDGELRPLGV 237
                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 19112324 240 TPNQANVDFRATCFCHKKVLDIGFVCSVCLSIFCEPRVHCSTCHTKF-TVEPMSKKLHT 297
Cdd:COG5242 238 KPNHGSVDFRATCYCHNRVVLLGFVCSVCLSVFCRPVPVCKKCKSKFsFRKPVVTKLES 296
tfb4 TIGR00627
transcription factor tfb4; All proteins in this family are part of the TFIIH complex which is ...
22-286 2.93e-148

transcription factor tfb4; All proteins in this family are part of the TFIIH complex which is involved in the initiation 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: 273181  Cd Length: 279  Bit Score: 416.93  E-value: 2.93e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112324    22 TPSLLVVILDANPASW--YSLSK-KVPVSKVLADITVFLNAHLAFHHDNRVAVLASHSDKVEYLYPS-IAPEQKVAEVDP 97
Cdd:TIGR00627   1 NPSLLVVIIEANPCSWgmLALAHgKRTISKVLRAIVVFLNAHLAFNANNKLAVIASHSQDNKYLYPStRCEDRNASELDP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112324    98 TKEAN-TYRKFREVDDLVLSGMKRLMSSTDKVSR---KTMISGALSRALAYIN----QVQNKNTLRSRILIFSLTGDVAL 169
Cdd:TIGR00627  81 KRLRElLYRDFRTVDETIVEEIKPLMAHADKHMKkdsRTVLAGALSDALGYINrseqSETASEKLKSRILVISITPDMAL 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112324   170 QYIPTMNCIFCAQKKNIPINVCNIEGG--TLFLEQAADATGGIYLKVDNPKGLLQYLMMSLFPDQNLRKHLNTPNQANVD 247
Cdd:TIGR00627 161 QYIPLMNCIFSAQKQNIPIDVVSIGGDftSGFLQQAADITGGSYLHVKKPQGLLQYLMTNMLPDPTLRAVLSKPNHNSVD 240
                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 19112324   248 FRATCFCHKKVLDIGFVCSVCLSIFCEPRVHCSTCHTKF 286
Cdd:TIGR00627 241 YRASCFCHHQLVSIGFVCSVCLSVLCQYTPICKTCKTAF 279
Tfb4 pfam03850
Transcription factor Tfb4; This family appears to be distantly related to the VWA domain.
23-283 1.46e-140

Transcription factor Tfb4; This family appears to be distantly related to the VWA domain.


Pssm-ID: 461076  Cd Length: 270  Bit Score: 397.04  E-value: 1.46e-140
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112324    23 PSLLVVILDANPASWYSLSKKVPVSKVLADITVFLNAHLAFHHDNRVAVLASHSDKVEYLYPSIAPEQKVAEVDPTKEA- 101
Cdd:pfam03850   1 PSLLVVVLDTNPLSWATLANRLTLSKVLASILVFLNAHLALNNSNQVAVIASHSQGAKYLYPSPRSASADGDVDPSGVGd 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112324   102 NTYRKFREVDDLVLSGMKRLMSSTDKVSRK---TMISGALSRALAYINQVQN----KNTLRSRILIFSLTGDVALQYIPT 174
Cdd:pfam03850  81 GKYRQFRNVDELVVEELRKLLSSTSVSDDAtetSLLAGALSLALCYINRVSRlvesGESLKSRILVVSGSPDSASQYIPI 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112324   175 MNCIFCAQKKNIPINVCNIEGGTL-FLEQAADATGGIYLKVDNPKGLLQYLMMSLFPDQNLRKHLNTPNQANVDFRATCF 253
Cdd:pfam03850 161 MNCIFAAQKLKIPIDVCKLGGDDSgFLQQASDITGGVYLKVPQPDGLLQYLLTAFLPDPSSRSHLVLPTPVNVDFRASCF 240
                         250       260       270
                  ....*....|....*....|....*....|
gi 19112324   254 CHKKVLDIGFVCSVCLSIFCEPRVHCSTCH 283
Cdd:pfam03850 241 CHRKVVDIGFVCSVCLSIFCEISPICPTCG 270
 
Name Accession Description Interval E-value
TFB4 COG5242
RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit ...
1-297 1.63e-177

RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription / DNA replication, recombination, and repair];


Pssm-ID: 227567  Cd Length: 296  Bit Score: 491.48  E-value: 1.63e-177
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112324   1 MDEFQTLKQNASWDISEDAndtPSLLVVILDANPASWYSLSKKVPVSKVLADITVFLNAHLAFHHDNRVAVLASHSDKVE 80
Cdd:COG5242   1 MDAISTFKHARSKQVTEES---PSLLFVIIDLEPENWELTTEKGSRDKVLNDIVVFLNAHLAFSRNNRVAVVAGYSQGKT 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112324  81 YLYPSIAPEQKVAEVDPTKEANTYRKFREVDDLVLSGMKRLMSSTDKVSRKTMISGALSRALAYINQVQNKNTLRSRILI 160
Cdd:COG5242  78 YLYPSSESALKASESENTRNSDMYRRFRNVDETDITEIYRLIEHPHKNSQRYDVGGAMSLGLAYCNHRDEETSLKSRILI 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112324 161 FSLTG-DVALQYIPTMNCIFCAQKKNIPINVCNIEGGTLFLEQAADATGGIYLKVDNPKGLLQYLMMSLFPDQNLRKHLN 239
Cdd:COG5242 158 FTLSGrDRKDQYIPYMNCIFAAQKFGIPISVFSIFGNSKFLLQCCDATGGDYLTVEDTEGLLQYLLSLLFTDGELRPLGV 237
                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 19112324 240 TPNQANVDFRATCFCHKKVLDIGFVCSVCLSIFCEPRVHCSTCHTKF-TVEPMSKKLHT 297
Cdd:COG5242 238 KPNHGSVDFRATCYCHNRVVLLGFVCSVCLSVFCRPVPVCKKCKSKFsFRKPVVTKLES 296
tfb4 TIGR00627
transcription factor tfb4; All proteins in this family are part of the TFIIH complex which is ...
22-286 2.93e-148

transcription factor tfb4; All proteins in this family are part of the TFIIH complex which is involved in the initiation 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: 273181  Cd Length: 279  Bit Score: 416.93  E-value: 2.93e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112324    22 TPSLLVVILDANPASW--YSLSK-KVPVSKVLADITVFLNAHLAFHHDNRVAVLASHSDKVEYLYPS-IAPEQKVAEVDP 97
Cdd:TIGR00627   1 NPSLLVVIIEANPCSWgmLALAHgKRTISKVLRAIVVFLNAHLAFNANNKLAVIASHSQDNKYLYPStRCEDRNASELDP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112324    98 TKEAN-TYRKFREVDDLVLSGMKRLMSSTDKVSR---KTMISGALSRALAYIN----QVQNKNTLRSRILIFSLTGDVAL 169
Cdd:TIGR00627  81 KRLRElLYRDFRTVDETIVEEIKPLMAHADKHMKkdsRTVLAGALSDALGYINrseqSETASEKLKSRILVISITPDMAL 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112324   170 QYIPTMNCIFCAQKKNIPINVCNIEGG--TLFLEQAADATGGIYLKVDNPKGLLQYLMMSLFPDQNLRKHLNTPNQANVD 247
Cdd:TIGR00627 161 QYIPLMNCIFSAQKQNIPIDVVSIGGDftSGFLQQAADITGGSYLHVKKPQGLLQYLMTNMLPDPTLRAVLSKPNHNSVD 240
                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 19112324   248 FRATCFCHKKVLDIGFVCSVCLSIFCEPRVHCSTCHTKF 286
Cdd:TIGR00627 241 YRASCFCHHQLVSIGFVCSVCLSVLCQYTPICKTCKTAF 279
Tfb4 pfam03850
Transcription factor Tfb4; This family appears to be distantly related to the VWA domain.
23-283 1.46e-140

Transcription factor Tfb4; This family appears to be distantly related to the VWA domain.


Pssm-ID: 461076  Cd Length: 270  Bit Score: 397.04  E-value: 1.46e-140
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112324    23 PSLLVVILDANPASWYSLSKKVPVSKVLADITVFLNAHLAFHHDNRVAVLASHSDKVEYLYPSIAPEQKVAEVDPTKEA- 101
Cdd:pfam03850   1 PSLLVVVLDTNPLSWATLANRLTLSKVLASILVFLNAHLALNNSNQVAVIASHSQGAKYLYPSPRSASADGDVDPSGVGd 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112324   102 NTYRKFREVDDLVLSGMKRLMSSTDKVSRK---TMISGALSRALAYINQVQN----KNTLRSRILIFSLTGDVALQYIPT 174
Cdd:pfam03850  81 GKYRQFRNVDELVVEELRKLLSSTSVSDDAtetSLLAGALSLALCYINRVSRlvesGESLKSRILVVSGSPDSASQYIPI 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112324   175 MNCIFCAQKKNIPINVCNIEGGTL-FLEQAADATGGIYLKVDNPKGLLQYLMMSLFPDQNLRKHLNTPNQANVDFRATCF 253
Cdd:pfam03850 161 MNCIFAAQKLKIPIDVCKLGGDDSgFLQQASDITGGVYLKVPQPDGLLQYLLTAFLPDPSSRSHLVLPTPVNVDFRASCF 240
                         250       260       270
                  ....*....|....*....|....*....|
gi 19112324   254 CHKKVLDIGFVCSVCLSIFCEPRVHCSTCH 283
Cdd:pfam03850 241 CHRKVVDIGFVCSVCLSIFCEISPICPTCG 270
 
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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