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Conserved domains on  [gi|442627311|ref|NP_001260349|]
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transcription factor IIB, isoform B [Drosophila melanogaster]

Protein Classification

transcription initiation factor IIB( domain architecture ID 11443977)

transcription initiation factor IIB (TFIIB) stabilizes TBP binding to an archaeal box-A promoter; also responsible for recruiting RNA polymerase II to the pre-initiation complex (DNA-TBP-TFIIB)

EC:  2.3.1.48
Gene Ontology:  GO:0006352|GO:0070897|GO:0008270|GO:0003677|GO:0140297|GO:0004402
PubMed:  34797379|16858867

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 1-289 6.73e-89

Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription];


:

Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 267.85  E-value: 6.73e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311   1 MASTSRLDNNKVCCyahPE---SPLIEDYRAGDMICSECGLVVGDRVIDVGSEWRTFSNEkSGVDPSRVGGPENPLLSGG 77
Cdd:COG1405    1 MSTTESEEEETSVC---PEcggENLVTDTERGETVCEDCGLVVEEDVIDRGPEWRAFDSE-ERDERSRTGAPLTLARHDK 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311  78 DLSTIIGpgtgSASFDAFGAP-------------KYQNR-RTMSSSDRSLISAFKEISSMADRINLPKTIVDRANNLFKQ 143
Cdd:COG1405   77 GLSTEIG----WQDKDAYGKSlsgrkrrqlarlrKWQNRsRVSSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRK 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311 144 VHDGKNLKGRSNDAKASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLTLKALETSVDLITTADFMCRFCANLDL 223
Cdd:COG1405  153 AVEKGLLRGRSIEGVAAAALYAACRQAGVPRTLDEIAEVSRVDRKEIARAYRLLNRELGLKVPPIDPIEYIPRIASELGL 232

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 442627311 224 PNMVQRAATHIAKKAVEMDIVPGRSPISVAAAAIYMASQASEHKRSQKEIGDIAGVADVTIRQSYK 289
Cdd:COG1405  233 SEEVERRAREILEKAKEKGLTSGKNPAGLAAAALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRYK 298
 
Name Accession Description Interval E-value
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 1-289 6.73e-89

Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription];


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 267.85  E-value: 6.73e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311   1 MASTSRLDNNKVCCyahPE---SPLIEDYRAGDMICSECGLVVGDRVIDVGSEWRTFSNEkSGVDPSRVGGPENPLLSGG 77
Cdd:COG1405    1 MSTTESEEEETSVC---PEcggENLVTDTERGETVCEDCGLVVEEDVIDRGPEWRAFDSE-ERDERSRTGAPLTLARHDK 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311  78 DLSTIIGpgtgSASFDAFGAP-------------KYQNR-RTMSSSDRSLISAFKEISSMADRINLPKTIVDRANNLFKQ 143
Cdd:COG1405   77 GLSTEIG----WQDKDAYGKSlsgrkrrqlarlrKWQNRsRVSSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRK 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311 144 VHDGKNLKGRSNDAKASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLTLKALETSVDLITTADFMCRFCANLDL 223
Cdd:COG1405  153 AVEKGLLRGRSIEGVAAAALYAACRQAGVPRTLDEIAEVSRVDRKEIARAYRLLNRELGLKVPPIDPIEYIPRIASELGL 232

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 442627311 224 PNMVQRAATHIAKKAVEMDIVPGRSPISVAAAAIYMASQASEHKRSQKEIGDIAGVADVTIRQSYK 289
Cdd:COG1405  233 SEEVERRAREILEKAKEKGLTSGKNPAGLAAAALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRYK 298
tfb PRK00423
transcription initiation factor IIB; Reviewed
 1-289 7.67e-80

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 244.92  E-value: 7.67e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311   1 MASTSRLDNNKVCcyahPESP---LIEDYRAGDMICSECGLVVGDRVIDVGSEWRTFSNEKSGvDPSRVGGPENPLLSGG 77
Cdd:PRK00423   2 LKLVLEEEEKLVC----PECGsdkLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQRE-KRSRVGAPMTYTIHDK 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311  78 DLSTIIGPGTGsasfDAFGAP-------------KYQNR-RTMSSSDRSLISAFKEISSMADRINLPKTIVDRANNLFKQ 143
Cdd:PRK00423  77 GLSTDIDWRNK----DSYGKSisgknraqlyrlrKWQRRiRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRK 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311 144 VHDGKNLKGRSNDAKASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLTLKALETSVDLITTADFMCRFCANLDL 223
Cdd:PRK00423 153 AVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGL 232

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 442627311 224 PNMVQRAATHIAKKAVEMDIVPGRSPISVAAAAIYMASQASEHKRSQKEIGDIAGVADVTIRQSYK 289
Cdd:PRK00423 233 SGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYK 298
CYCLIN_TFIIB_rpt2 cd20552
second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 209-305 9.37e-67

second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; TFIIB, also called B-related factor 2 (BRF-2) or S300-II, is a general transcription factor that plays a role in transcription initiation by RNA polymerase II (Pol II). It is involved in the pre-initiation complex (PIC) formation and Pol II recruitment at promoter DNA. TFIIB contains two cyclin boxes. This model corresponds to the second one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIB.


Pssm-ID: 410255 [Multi-domain]  Cd Length: 97  Bit Score: 204.05  E-value: 9.37e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311 209 TTADFMCRFCANLDLPNMVQRAATHIAKKAVEMDIVPGRSPISVAAAAIYMASQASEHKRSQKEIGDIAGVADVTIRQSY 288
Cdd:cd20552    1 STEDFMSRFCSNLGLPNQVQKAATHIAKKAVELDLVAGRSPISVAAAAIYMASQLSEEKKTQKEIGDVAGVAEVTIRQSY 80

                         90
                 ....*....|....*..
gi 442627311 289 KLMYPHAAKLFPEDFKF 305
Cdd:cd20552   81 KLLYPRAEKLFPPDFKF 97
TFIIB pfam00382
Transcription factor TFIIB repeat;
203-294 1.33e-36

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 126.60  E-value: 1.33e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311  203 TSVDLITTADFMCRFCANLDLPNMVQRAATHIAKKAVEMDIVPGRSPISVAAAAIYMASQASEHKRSQKEIGDIAGVADV 282
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEY 80

                          90
                  ....*....|..
gi 442627311  283 TIRQSYKLMYPH 294
Cdd:pfam00382  81 TIGKTFKELKKA 92
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 212-292 2.25e-11

domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.


Pssm-ID: 214641 [Multi-domain]  Cd Length: 83  Bit Score: 59.14  E-value: 2.25e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311   212 DFMCRFCANLDLPNMVQRAATHIAKKAVEMDIVPGRSPISVAAAAIYMASQASEHKRSQKEIGDIAGVADV-TIRQSYKL 290
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYFTEeEILRMERL 80


                   ..
gi 442627311   291 MY 292
Cdd:smart00385  81 LL 82
 
Name Accession Description Interval E-value
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 1-289 6.73e-89

Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription];


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 267.85  E-value: 6.73e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311   1 MASTSRLDNNKVCCyahPE---SPLIEDYRAGDMICSECGLVVGDRVIDVGSEWRTFSNEkSGVDPSRVGGPENPLLSGG 77
Cdd:COG1405    1 MSTTESEEEETSVC---PEcggENLVTDTERGETVCEDCGLVVEEDVIDRGPEWRAFDSE-ERDERSRTGAPLTLARHDK 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311  78 DLSTIIGpgtgSASFDAFGAP-------------KYQNR-RTMSSSDRSLISAFKEISSMADRINLPKTIVDRANNLFKQ 143
Cdd:COG1405   77 GLSTEIG----WQDKDAYGKSlsgrkrrqlarlrKWQNRsRVSSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRK 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311 144 VHDGKNLKGRSNDAKASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLTLKALETSVDLITTADFMCRFCANLDL 223
Cdd:COG1405  153 AVEKGLLRGRSIEGVAAAALYAACRQAGVPRTLDEIAEVSRVDRKEIARAYRLLNRELGLKVPPIDPIEYIPRIASELGL 232

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 442627311 224 PNMVQRAATHIAKKAVEMDIVPGRSPISVAAAAIYMASQASEHKRSQKEIGDIAGVADVTIRQSYK 289
Cdd:COG1405  233 SEEVERRAREILEKAKEKGLTSGKNPAGLAAAALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRYK 298
tfb PRK00423
transcription initiation factor IIB; Reviewed
 1-289 7.67e-80

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 244.92  E-value: 7.67e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311   1 MASTSRLDNNKVCcyahPESP---LIEDYRAGDMICSECGLVVGDRVIDVGSEWRTFSNEKSGvDPSRVGGPENPLLSGG 77
Cdd:PRK00423   2 LKLVLEEEEKLVC----PECGsdkLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQRE-KRSRVGAPMTYTIHDK 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311  78 DLSTIIGPGTGsasfDAFGAP-------------KYQNR-RTMSSSDRSLISAFKEISSMADRINLPKTIVDRANNLFKQ 143
Cdd:PRK00423  77 GLSTDIDWRNK----DSYGKSisgknraqlyrlrKWQRRiRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRK 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311 144 VHDGKNLKGRSNDAKASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLTLKALETSVDLITTADFMCRFCANLDL 223
Cdd:PRK00423 153 AVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGL 232

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 442627311 224 PNMVQRAATHIAKKAVEMDIVPGRSPISVAAAAIYMASQASEHKRSQKEIGDIAGVADVTIRQSYK 289
Cdd:PRK00423 233 SGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYK 298
CYCLIN_TFIIB_rpt2 cd20552
second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 209-305 9.37e-67

second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; TFIIB, also called B-related factor 2 (BRF-2) or S300-II, is a general transcription factor that plays a role in transcription initiation by RNA polymerase II (Pol II). It is involved in the pre-initiation complex (PIC) formation and Pol II recruitment at promoter DNA. TFIIB contains two cyclin boxes. This model corresponds to the second one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIB.


Pssm-ID: 410255 [Multi-domain]  Cd Length: 97  Bit Score: 204.05  E-value: 9.37e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311 209 TTADFMCRFCANLDLPNMVQRAATHIAKKAVEMDIVPGRSPISVAAAAIYMASQASEHKRSQKEIGDIAGVADVTIRQSY 288
Cdd:cd20552    1 STEDFMSRFCSNLGLPNQVQKAATHIAKKAVELDLVAGRSPISVAAAAIYMASQLSEEKKTQKEIGDVAGVAEVTIRQSY 80

                         90
                 ....*....|....*..
gi 442627311 289 KLMYPHAAKLFPEDFKF 305
Cdd:cd20552   81 KLLYPRAEKLFPPDFKF 97
CYCLIN_TFIIB_rpt1 cd20551
first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 115-202 2.17e-55

first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; TFIIB, also called B-related factor 2 (BRF-2) or S300-II, is a general transcription factor that plays a role in transcription initiation by RNA polymerase II (Pol II). It is involved in the pre-initiation complex (PIC) formation and Pol II recruitment at promoter DNA. TFIIB contains two cyclin boxes. This model corresponds to the first one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIB.


Pssm-ID: 410254 [Multi-domain]  Cd Length: 88  Bit Score: 174.70  E-value: 2.17e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311 115 SAFKEISSMADRINLPKTIVDRANNLFKQVHDGKNLKGRSNDAKASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCF 194
Cdd:cd20551    1 AAFKEIGEMADRMNLPRTIKDRAKELFKQVHDQKSLKGRSNDAIAAACLYIACRQEGVPRTFKEICAVSNVSKKEIGRCF 80


                 ....*...
gi 442627311 195 KLTLKALE 202
Cdd:cd20551   81 KLILKALE 88
TFIIB pfam00382
Transcription factor TFIIB repeat;
203-294 1.33e-36

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 126.60  E-value: 1.33e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311  203 TSVDLITTADFMCRFCANLDLPNMVQRAATHIAKKAVEMDIVPGRSPISVAAAAIYMASQASEHKRSQKEIGDIAGVADV 282
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEY 80

                          90
                  ....*....|..
gi 442627311  283 TIRQSYKLMYPH 294
Cdd:pfam00382  81 TIGKTFKELKKA 92
TFIIB pfam00382
Transcription factor TFIIB repeat;
109-200 1.28e-35

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 123.91  E-value: 1.28e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311  109 SDRSLISAFKEISSMADRINLPKTIVDRANNLFKQVHDGKNLKGRSNDAKASACLYIACRQEGVPRTFKEICAVSKISKK 188
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEY 80

                          90
                  ....*....|..
gi 442627311  189 EIGRCFKLTLKA 200
Cdd:pfam00382  81 TIGKTFKELKKA 92
CYCLIN_TFIIB_archaea_like_rpt2 cd20550
second cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 211-289 1.46e-26

second cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar proteins; Archaeal TFIIB stabilizes TATA-binding protein (TBP) binding to an archaeal box-A promoter. It is also responsible for recruiting RNA polymerase II to the pre-initiation complex (DNA-TBP-TFIIB). TFIIB contains two cyclin boxes. This model corresponds to the second one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIB.


Pssm-ID: 410253 [Multi-domain]  Cd Length: 87  Bit Score: 99.97  E-value: 1.46e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 442627311 211 ADFMCRFCANLDLPNMVQRAATHIAKKAVEMDIVPGRSPISVAAAAIYMASQASEHKRSQKEIGDIAGVADVTIRQSYK 289
Cdd:cd20550    3 ADYVPRFASKLGLSGEVQRKAIEILEKAKKKGLTSGKGPAGLAAAAIYIASLLTGERRTQKEIAEVAGVTEVTIRNRYK 81
CYCLIN_TFIIB_archaea_like_rpt1 cd20549
first cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 107-203 3.63e-24

first cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar proteins; Archaeal TFIIB stabilizes TATA-binding protein (TBP) binding to an archaeal box-A promoter. It is also responsible for recruiting RNA polymerase II to the pre-initiation complex (DNA-TBP-TFIIB). TFIIB contains two cyclin boxes. This model corresponds to the first one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIB.


Pssm-ID: 410252 [Multi-domain]  Cd Length: 99  Bit Score: 94.27  E-value: 3.63e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311 107 SSSDRSLISAFKEISSMADRINLPKTIVDRANNLFKQVHDGKNLKGRSNDAKASACLYIACRQEGVPRTFKEICAVSKIS 186
Cdd:cd20549    3 TAAERNLAQALSELDRMASKLGLPRSVREEAAVIYRKAVEKGLVRGRSIESVVAAALYAACRICNVPRTLDEIAEATRVS 82

                         90
                 ....*....|....*..
gi 442627311 187 KKEIGRCFKLTLKALET 203
Cdd:cd20549   83 RKEIARCYRLLARELNL 99
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 115-196 2.10e-18

Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in cell-cycle and transcriptional control. It is about 100 amino acids in length, composed of five helices, and is present in cyclins, transcription initiation factor IIB (TFIIB), and retinoblastoma tumour suppressor protein (Rb). Cyclins consist of 8 classes of cell cycle regulators that function as regulatory subunits of cyclin-dependent kinases (CDKs), which are serine/threonine kinases. The catalytic activities of CDKs are modulated not only by their interactions with cyclins but also by CDK inhibitors (CKIs). CDKs, cyclins and CKIs play key roles in transcription, epigenetic regulation, metabolism, stem cell self-renewal, neuronal functions, and spermatogenesis. TFIIB is a transcription factor that binds the TATA box. Members in this superfamily contain one or two copies of the cyclin box.


Pssm-ID: 410207 [Multi-domain]  Cd Length: 82  Bit Score: 78.22  E-value: 2.10e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311 115 SAFKEISSMADRINLPKTIVDRANNLFKQVHDGKNLKGRSNDAKASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCF 194
Cdd:cd00043    1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEKELRKAE 80


                 ..
gi 442627311 195 KL 196
Cdd:cd00043   81 KE 82
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 209-290 2.81e-17

Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in cell-cycle and transcriptional control. It is about 100 amino acids in length, composed of five helices, and is present in cyclins, transcription initiation factor IIB (TFIIB), and retinoblastoma tumour suppressor protein (Rb). Cyclins consist of 8 classes of cell cycle regulators that function as regulatory subunits of cyclin-dependent kinases (CDKs), which are serine/threonine kinases. The catalytic activities of CDKs are modulated not only by their interactions with cyclins but also by CDK inhibitors (CKIs). CDKs, cyclins and CKIs play key roles in transcription, epigenetic regulation, metabolism, stem cell self-renewal, neuronal functions, and spermatogenesis. TFIIB is a transcription factor that binds the TATA box. Members in this superfamily contain one or two copies of the cyclin box.


Pssm-ID: 410207 [Multi-domain]  Cd Length: 82  Bit Score: 75.14  E-value: 2.81e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311 209 TTADFMCRFCANLDLPNMVQRAATHIAKKAVEMDIVPGRSPISVAAAAIYMASQASEHKRSQKEIGDIAGVADVTIRQSY 288
Cdd:cd00043    1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEKELRKAE 80


                 ..
gi 442627311 289 KL 290
Cdd:cd00043   81 KE 82
CYCLIN_BRF2 cd20555
cyclin box found in B-related factor 2 (BRF-2) and similar proteins; BRF-2, also called ...
 111-202 1.16e-11

cyclin box found in B-related factor 2 (BRF-2) and similar proteins; BRF-2, also called transcription factor IIIB 50 kDa subunit (TFIIIB50), or BRFU, is a general activator of RNA polymerase (Pol) III transcription and is required for Pol III transcription of genes with promoter elements upstream of the initiation sites. It recruits Pol III to type III gene-external promoters, including the U6 spliceosomal RNA and selenocysteine tRNA genes. BRF-2 contains one cyclin box. The cyclin box fold is generally a protein binding domain, but binds DNA in BRF-2.


Pssm-ID: 410258 [Multi-domain]  Cd Length: 97  Bit Score: 60.37  E-value: 1.16e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311 111 RSLISAFKEISSMADRINLPKTIVDRANNLFKQVHDGKNLKGRSNDAK---ASACLYIACRQEGVPRTFKEICAVSKISK 187
Cdd:cd20555    2 RGLKQGLKRVRDLCRVLRLSSVMEETAVELFEQAFKHPDFRHIRLEKKevlVGCCVYIVCRQNNWPVTMGDICSLLQCDV 81

                         90
                 ....*....|....*
gi 442627311 188 KEIGRCFKLTLKALE 202
Cdd:cd20555   82 SDFSSVYKELLKELN 96
CYCLIN_TFIIIB90_rpt1 cd20553
first cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 116-194 2.07e-11

first cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar proteins; TFIIIB90, also called B-related factor 1 (BRF-1), or TATA box-binding protein-associated factor, RNA polymerase III, subunit 2 (TAF3B2), is a general activator of RNA polymerase which utilizes different TFIIIB complexes at structurally distinct promoters. TFIIIB90 contains two cyclin boxes. This model corresponds to the first one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIIB90.


Pssm-ID: 410256 [Multi-domain]  Cd Length: 91  Bit Score: 59.47  E-value: 2.07e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311 116 AFKEISSMADRINLPKTIVDRANNLFKQVHDgKNL-KGRSNDAKASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCF 194
Cdd:cd20553    6 GRRKIQQLGSQLKLNQHHIDTAFRFYKLAVQ-RNFtRGRKTSHVAAACLYIVCRREKTPHMLIDFSDVLQVNVYVLGKTF 84
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 212-292 2.25e-11

domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.


Pssm-ID: 214641 [Multi-domain]  Cd Length: 83  Bit Score: 59.14  E-value: 2.25e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311   212 DFMCRFCANLDLPNMVQRAATHIAKKAVEMDIVPGRSPISVAAAAIYMASQASEHKRSQKEIGDIAGVADV-TIRQSYKL 290
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYFTEeEILRMERL 80


                   ..
gi 442627311   291 MY 292
Cdd:smart00385  81 LL 82
TF_Zn_Ribbon pfam08271
TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the ...
 22-54 1.27e-10

TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure.


Pssm-ID: 400527 [Multi-domain]  Cd Length: 43  Bit Score: 55.78  E-value: 1.27e-10
                          10        20        30
                  ....*....|....*....|....*....|...
gi 442627311   22 LIEDYRAGDMICSECGLVVGDRVIDVGSEWRTF 54
Cdd:pfam08271  11 LVEDYERGELVCTDCGLVLEDNSIDEGPEWREF 43
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 120-199 3.13e-10

domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.


Pssm-ID: 214641 [Multi-domain]  Cd Length: 83  Bit Score: 55.68  E-value: 3.13e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311   120 ISSMADRINLPKTIVDRANNLFKQVHDGKNLKGRSNDAKASACLYIACRQEGVPRTFKEICAVSKI-SKKEIGRCFKLTL 198
Cdd:smart00385   3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYfTEEEILRMERLLL 82


                   .
gi 442627311   199 K 199
Cdd:smart00385  83 E 83
CYCLIN_TFIIB_archaea_like_rpt1 cd20549
first cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 216-291 1.35e-07

first cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar proteins; Archaeal TFIIB stabilizes TATA-binding protein (TBP) binding to an archaeal box-A promoter. It is also responsible for recruiting RNA polymerase II to the pre-initiation complex (DNA-TBP-TFIIB). TFIIB contains two cyclin boxes. This model corresponds to the first one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIB.


Pssm-ID: 410252 [Multi-domain]  Cd Length: 99  Bit Score: 48.81  E-value: 1.35e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 442627311 216 RFCANLDLPNMVQRAATHIAKKAVEMDIVPGRSPISVAAAAIYMASQASEHKRSQKEIGDIAGVADVTIRQSYKLM 291
Cdd:cd20549   18 RMASKLGLPRSVREEAAVIYRKAVEKGLVRGRSIESVVAAALYAACRICNVPRTLDEIAEATRVSRKEIARCYRLL 93
CYCLIN_TFIIB_archaea_like_rpt2 cd20550
second cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 115-186 5.15e-07

second cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar proteins; Archaeal TFIIB stabilizes TATA-binding protein (TBP) binding to an archaeal box-A promoter. It is also responsible for recruiting RNA polymerase II to the pre-initiation complex (DNA-TBP-TFIIB). TFIIB contains two cyclin boxes. This model corresponds to the second one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIB.


Pssm-ID: 410253 [Multi-domain]  Cd Length: 87  Bit Score: 46.81  E-value: 5.15e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 442627311 115 SAFKEISSMADRINLPKTIVDRANNLFKQVHDGKNLKGRSNDAKASACLYIACRQEGVPRTFKEICAVSKIS 186
Cdd:cd20550    1 DPADYVPRFASKLGLSGEVQRKAIEILEKAKKKGLTSGKGPAGLAAAAIYIASLLTGERRTQKEIAEVAGVT 72
CYCLIN_TFIIIB90_rpt2 cd20554
second cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 213-286 8.71e-06

second cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar proteins; TFIIIB90, also called B-related factor 1 (BRF-1), or TATA box-binding protein-associated factor, RNA polymerase III, subunit 2 (TAF3B2), is a general activator of RNA polymerase which utilizes different TFIIIB complexes at structurally distinct promoters. TFIIIB90 contains two cyclin boxes. This model corresponds to the second one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIIB90.


Pssm-ID: 410257 [Multi-domain]  Cd Length: 92  Bit Score: 43.66  E-value: 8.71e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311 213 FMCRFCANLDLPNMVQRaathIAKKAVE----MD---IVPGRSPISVAAAAIYMASQASEHKRSQKEIGDIAGVADVTIR 285
Cdd:cd20554    8 YIHRFASKLEFGDKTHE----VANTALRlvqrMKrdwIHTGRRPSGICGAALLIAARMHGFKRTVEEIVRVVRVCESTLR 83


                 .
gi 442627311 286 Q 286
Cdd:cd20554   84 K 84
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 99-260 2.43e-05

Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair];


Pssm-ID: 227640 [Multi-domain]  Cd Length: 297  Bit Score: 45.11  E-value: 2.43e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311  99 KYQNRRTMSSSDRSLISAFKEISSMADRINLPKTIVDRANNLFKQVHDGKNLKGRSNDAKASACLYIACRQEGVPRTFKE 178
Cdd:COG5333   31 VLEPELTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISI 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627311 179 ICAV-----SKISKKEIGRCFKLTLKALET-SVDLITTADF--MCRF---CANLDLPNMVQRAAThIAKKAVEMDIVPGR 247
Cdd:COG5333  111 ESFEardlwSEEPKSSRERILEYEFELLEAlDFDLHVHHPYkyLEGFlkdLQEKDKYKLLQIAWK-IINDALRTDLCLLY 189

                        170
                 ....*....|...
gi 442627311 248 SPISVAAAAIYMA 260
Cdd:COG5333  190 PPHIIALAALLIA 202
CYCLIN_TFIIIB90_rpt2 cd20554
second cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 161-186 1.27e-03

second cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar proteins; TFIIIB90, also called B-related factor 1 (BRF-1), or TATA box-binding protein-associated factor, RNA polymerase III, subunit 2 (TAF3B2), is a general activator of RNA polymerase which utilizes different TFIIIB complexes at structurally distinct promoters. TFIIIB90 contains two cyclin boxes. This model corresponds to the second one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIIB90.


Pssm-ID: 410257 [Multi-domain]  Cd Length: 92  Bit Score: 37.49  E-value: 1.27e-03
                         10        20
                 ....*....|....*....|....*.
gi 442627311 161 ACLYIACRQEGVPRTFKEICAVSKIS 186
Cdd:cd20554   53 AALLIAARMHGFKRTVEEIVRVVRVC 78
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
 116-183 5.83e-03

first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar proteins; CTK2, also called CTD kinase subunit beta, CTDK-I subunit beta, or CTD kinase 38 kDa subunit, is the cyclin subunit of the CTDK-I complex, which hyperphosphorylates the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit. CTK2 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410250 [Multi-domain]  Cd Length: 110  Bit Score: 35.78  E-value: 5.83e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 442627311 116 AFKEISSMADRINLPKTIVDRANNLFKQVHdgknLKGRSNDAK----ASACLYIACRQEGVPRTFKEICAVS 183
Cdd:cd20547    5 AFQFISQLCKKLKFPRRTLGTAMLLYQRFH----LFNPFTDSSnyevALACLFLASKIEDTQKKSKDILAAS 72
 
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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