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Conserved domains on  [gi|1028909945|pdb|5IYD|M]
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Chain M, Transcription initiation factor IIB

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 ...
 3-292 6.40e-88

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


:

Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 265.54  E-value: 6.40e-88
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M        3 STSRLDALPRVTCPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATkDPSRVGDSQNPLLSDGDLST 82
Cdd:COG1405   2 STTESEEEETSVCPECGGENLVTDTERGETVCEDCGLVVEEDVIDRGPEWRAFDSEERD-ERSRTGAPLTLARHDKGLST 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M       83 MIGKGTGAASfdefGNS-------------KYQNR-RTMSSSDRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQ 148
Cdd:COG1405  81 EIGWQDKDAY----GKSlsgrkrrqlarlrKWQNRsRVSSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEK 156

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M      149 KSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQV 228
Cdd:COG1405 157 GLLRGRSIEGVAAAALYAACRQAGVPRTLDEIAEVSRVDRKEIARAYRLLNRELGLKVPPIDPIEYIPRIASELGLSEEV 236

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|....
5IYD_M      229 QMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRLI 292
Cdd:COG1405 237 ERRAREILEKAKEKGLTSGKNPAGLAAAALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRYKEL 300
 
Name Accession Description Interval E-value
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 3-292 6.40e-88

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 265.54  E-value: 6.40e-88
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M        3 STSRLDALPRVTCPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATkDPSRVGDSQNPLLSDGDLST 82
Cdd:COG1405   2 STTESEEEETSVCPECGGENLVTDTERGETVCEDCGLVVEEDVIDRGPEWRAFDSEERD-ERSRTGAPLTLARHDKGLST 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M       83 MIGKGTGAASfdefGNS-------------KYQNR-RTMSSSDRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQ 148
Cdd:COG1405  81 EIGWQDKDAY----GKSlsgrkrrqlarlrKWQNRsRVSSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEK 156

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M      149 KSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQV 228
Cdd:COG1405 157 GLLRGRSIEGVAAAALYAACRQAGVPRTLDEIAEVSRVDRKEIARAYRLLNRELGLKVPPIDPIEYIPRIASELGLSEEV 236

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|....
5IYD_M      229 QMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRLI 292
Cdd:COG1405 237 ERRAREILEKAKEKGLTSGKNPAGLAAAALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRYKEL 300
tfb PRK00423
transcription initiation factor IIB; Reviewed
 15-290 6.47e-81

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 247.61  E-value: 6.47e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M        15 CPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDpSRVGDSQNPLLSDGDLSTMIGKGTGaasfD 94
Cdd:PRK00423  14 CPECGSDKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQREKR-SRVGAPMTYTIHDKGLSTDIDWRNK----D 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M        95 EFGNS-------------KYQNR-RTMSSSDRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIA 160
Cdd:PRK00423  89 SYGKSisgknraqlyrlrKWQRRiRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVV 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M       161 SACLYIACRQEGVPRTFKEICAVSRISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAV 240
Cdd:PRK00423 169 AAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSGEVQKKAIEILQKAK 248

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
5IYD_M       241 ELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYR 290
Cdd:PRK00423 249 EKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYK 298
CYCLIN_TFIIB_rpt2 cd20552
second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 210-306 1.60e-65

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: 200.97  E-value: 1.60e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M      210 TTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSY 289
Cdd:cd20552   1 STEDFMSRFCSNLGLPNQVQKAATHIAKKAVELDLVAGRSPISVAAAAIYMASQLSEEKKTQKEIGDVAGVAEVTIRQSY 80

                        90
                ....*....|....*..
5IYD_M      290 RLIYPRAPDLFPTDFKF 306
Cdd:cd20552  81 KLLYPRAEKLFPPDFKF 97
TFIIB pfam00382
Transcription factor TFIIB repeat;
204-294 1.36e-30

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 110.81  E-value: 1.36e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M        204 TSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADV 283
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEY 80

                          90
                  ....*....|.
5IYD_M        284 TIRQSYRLIYP 294
Cdd:pfam00382  81 TIGKTFKELKK 91
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 121-200 4.22e-14

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: 66.46  E-value: 4.22e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M         121 ITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRI-SKKEIGRCFKLIL 199
Cdd:smart00385   3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYfTEEEILRMERLLL 82


                   .
5IYD_M         200 K 200
Cdd:smart00385  83 E 83
 
Name Accession Description Interval E-value
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 3-292 6.40e-88

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 265.54  E-value: 6.40e-88
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M        3 STSRLDALPRVTCPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATkDPSRVGDSQNPLLSDGDLST 82
Cdd:COG1405   2 STTESEEEETSVCPECGGENLVTDTERGETVCEDCGLVVEEDVIDRGPEWRAFDSEERD-ERSRTGAPLTLARHDKGLST 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M       83 MIGKGTGAASfdefGNS-------------KYQNR-RTMSSSDRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQ 148
Cdd:COG1405  81 EIGWQDKDAY----GKSlsgrkrrqlarlrKWQNRsRVSSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEK 156

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M      149 KSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQV 228
Cdd:COG1405 157 GLLRGRSIEGVAAAALYAACRQAGVPRTLDEIAEVSRVDRKEIARAYRLLNRELGLKVPPIDPIEYIPRIASELGLSEEV 236

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|....
5IYD_M      229 QMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRLI 292
Cdd:COG1405 237 ERRAREILEKAKEKGLTSGKNPAGLAAAALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRYKEL 300
tfb PRK00423
transcription initiation factor IIB; Reviewed
 15-290 6.47e-81

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 247.61  E-value: 6.47e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M        15 CPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDpSRVGDSQNPLLSDGDLSTMIGKGTGaasfD 94
Cdd:PRK00423  14 CPECGSDKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQREKR-SRVGAPMTYTIHDKGLSTDIDWRNK----D 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M        95 EFGNS-------------KYQNR-RTMSSSDRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIA 160
Cdd:PRK00423  89 SYGKSisgknraqlyrlrKWQRRiRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVV 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M       161 SACLYIACRQEGVPRTFKEICAVSRISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAV 240
Cdd:PRK00423 169 AAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSGEVQKKAIEILQKAK 248

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
5IYD_M       241 ELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYR 290
Cdd:PRK00423 249 EKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYK 298
CYCLIN_TFIIB_rpt2 cd20552
second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 210-306 1.60e-65

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: 200.97  E-value: 1.60e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M      210 TTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSY 289
Cdd:cd20552   1 STEDFMSRFCSNLGLPNQVQKAATHIAKKAVELDLVAGRSPISVAAAAIYMASQLSEEKKTQKEIGDVAGVAEVTIRQSY 80

                        90
                ....*....|....*..
5IYD_M      290 RLIYPRAPDLFPTDFKF 306
Cdd:cd20552  81 KLLYPRAEKLFPPDFKF 97
CYCLIN_TFIIB_rpt1 cd20551
first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 116-203 8.76e-58

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: 180.86  E-value: 8.76e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M      116 NAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKEIGRCF 195
Cdd:cd20551   1 AAFKEIGEMADRMNLPRTIKDRAKELFKQVHDQKSLKGRSNDAIAAACLYIACRQEGVPRTFKEICAVSNVSKKEIGRCF 80


                ....*...
5IYD_M      196 KLILKALE 203
Cdd:cd20551  81 KLILKALE 88
TFIIB pfam00382
Transcription factor TFIIB repeat;
204-294 1.36e-30

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 110.81  E-value: 1.36e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M        204 TSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADV 283
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEY 80

                          90
                  ....*....|.
5IYD_M        284 TIRQSYRLIYP 294
Cdd:pfam00382  81 TIGKTFKELKK 91
TFIIB pfam00382
Transcription factor TFIIB repeat;
110-201 5.88e-30

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 109.27  E-value: 5.88e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M        110 SDRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKK 189
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEY 80

                          90
                  ....*....|..
5IYD_M        190 EIGRCFKLILKA 201
Cdd:pfam00382  81 TIGKTFKELKKA 92
CYCLIN_TFIIB_archaea_like_rpt2 cd20550
second cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 213-290 1.65e-27

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: 102.67  E-value: 1.65e-27
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
5IYD_M      213 DFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYR 290
Cdd:cd20550   4 DYVPRFASKLGLSGEVQRKAIEILEKAKKKGLTSGKGPAGLAAAAIYIASLLTGERRTQKEIAEVAGVTEVTIRNRYK 81
CYCLIN_TFIIB_archaea_like_rpt1 cd20549
first cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 108-204 5.21e-25

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: 96.58  E-value: 5.21e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M      108 SSSDRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRIS 187
Cdd:cd20549   3 TAAERNLAQALSELDRMASKLGLPRSVREEAAVIYRKAVEKGLVRGRSIESVVAAALYAACRICNVPRTLDEIAEATRVS 82

                        90
                ....*....|....*..
5IYD_M      188 KKEIGRCFKLILKALET 204
Cdd:cd20549  83 RKEIARCYRLLARELNL 99
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 116-197 2.63e-19

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: 80.53  E-value: 2.63e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M      116 NAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKEIGRCF 195
Cdd:cd00043   1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEKELRKAE 80


                ..
5IYD_M      196 KL 197
Cdd:cd00043  81 KE 82
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 213-291 2.03e-16

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: 72.83  E-value: 2.03e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
5IYD_M      213 DFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRL 291
Cdd:cd00043   4 DFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEKELRKAEKE 82
CYCLIN_TFIIIB90_rpt1 cd20553
first cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 114-202 2.54e-14

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: 67.56  E-value: 2.54e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M      114 MMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKEIGR 193
Cdd:cd20553   3 LQNGRRKIQQLGSQLKLNQHHIDTAFRFYKLAVQRNFTRGRKTSHVAAACLYIVCRREKTPHMLIDFSDVLQVNVYVLGK 82


                ....*....
5IYD_M      194 CFKLILKAL 202
Cdd:cd20553  83 TFLKLCKLL 91
TF_Zn_Ribbon pfam08271
TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the ...
 14-55 3.14e-14

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: 65.79  E-value: 3.14e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
5IYD_M         14 TCPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTF 55
Cdd:pfam08271   2 KCPNCGSTNLVEDYERGELVCTDCGLVLEDNSIDEGPEWREF 43
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 121-200 4.22e-14

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: 66.46  E-value: 4.22e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M         121 ITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRI-SKKEIGRCFKLIL 199
Cdd:smart00385   3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYfTEEEILRMERLLL 82


                   .
5IYD_M         200 K 200
Cdd:smart00385  83 E 83
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 213-293 9.59e-13

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: 62.61  E-value: 9.59e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M         213 DFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADV-TIRQSYRL 291
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYFTEeEILRMERL 80


                   ..
5IYD_M         292 IY 293
Cdd:smart00385  81 LL 82
CYCLIN_BRF2 cd20555
cyclin box found in B-related factor 2 (BRF-2) and similar proteins; BRF-2, also called ...
 112-203 1.79e-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: 59.60  E-value: 1.79e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M      112 RAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKG--RAN-DAIASACLYIACRQEGVPRTFKEICAVSRISK 188
Cdd:cd20555   2 RGLKQGLKRVRDLCRVLRLSSVMEETAVELFEQAFKHPDFRHirLEKkEVLVGCCVYIVCRQNNWPVTMGDICSLLQCDV 81

                        90
                ....*....|....*
5IYD_M      189 KEIGRCFKLILKALE 203
Cdd:cd20555  82 SDFSSVYKELLKELN 96
CYCLIN_TFIIB_archaea_like_rpt1 cd20549
first cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 217-292 8.86e-11

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: 57.67  E-value: 8.86e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
5IYD_M      217 RFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRLI 292
Cdd:cd20549  18 RMASKLGLPRSVREEAAVIYRKAVEKGLVRGRSIESVVAAALYAACRICNVPRTLDEIAEATRVSRKEIARCYRLL 93
CYCLIN_TFIIB_archaea_like_rpt2 cd20550
second cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 121-202 7.50e-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: 46.43  E-value: 7.50e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M      121 ITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKEIGRCFKLILK 200
Cdd:cd20550   6 VPRFASKLGLSGEVQRKAIEILEKAKKKGLTSGKGPAGLAAAAIYIASLLTGERRTQKEIAEVAGVTEVTIRNRYKELLE 85


                ..
5IYD_M      201 AL 202
Cdd:cd20550  86 AL 87
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 91-294 1.30e-06

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: 48.96  E-value: 1.30e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M       91 ASFDEFGN------SKYQNRRTMSSSDRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACL 164
Cdd:COG5333  16 LSFDSSQNaieldlLVLEPELTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCV 95

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M      165 YIACRQEGVPRTFKEICAVSRISKKEI-----GRCFKLILKALET-SVDLITTGDF--MSRF---CSNLCLPKQVQMAAT 233
Cdd:COG5333  96 YLACKVEDTPRDISIESFEARDLWSEEpkssrERILEYEFELLEAlDFDLHVHHPYkyLEGFlkdLQEKDKYKLLQIAWK 175

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|.
5IYD_M      234 hIARKAVELDLVPGRSPISVAAAAIYMAsqasAEKRTQKEIGDIAGVADVTIRQSYRLIYP 294
Cdd:COG5333 176 -IINDALRTDLCLLYPPHIIALAALLIA----CEVLGMPIIKLLDFVSYETKEEVIALNYK 231
CYCLIN_TFIIIB90_rpt2 cd20554
second cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 214-291 6.95e-05

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: 40.96  E-value: 6.95e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_M      214 FMSRFCSNLCLPKqvqmaATH-IARKAVEL------D-LVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTI 285
Cdd:cd20554   8 YIHRFASKLEFGD-----KTHeVANTALRLvqrmkrDwIHTGRRPSGICGAALLIAARMHGFKRTVEEIVRVVRVCESTL 82


                ....*.
5IYD_M      286 RQsyRL 291
Cdd:cd20554  83 RK--RL 86
CYCLIN_TFIIIB90_rpt2 cd20554
second cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 152-187 4.40e-04

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: 38.65  E-value: 4.40e-04
                        10        20        30
                ....*....|....*....|....*....|....*.
5IYD_M      152 KGRANDAIASACLYIACRQEGVPRTFKEICAVSRIS 187
Cdd:cd20554  43 TGRRPSGICGAALLIAARMHGFKRTVEEIVRVVRVC 78
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
 115-184 2.24e-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: 37.33  E-value: 2.24e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
5IYD_M      115 MNAFKEITTMADRINLPRnivdRTNNLFKQVYEQKSLKGRANDA----IASACLYIACRQEGVPRTFKEICAVS 184
Cdd:cd20547   3 LAAFQFISQLCKKLKFPR----RTLGTAMLLYQRFHLFNPFTDSsnyeVALACLFLASKIEDTQKKSKDILAAS 72
CYCLIN_AtRBR_like cd20601
cyclin box found in Arabidopsis thaliana retinoblastoma-related protein 1 (AtRBR1) and similar ...
 121-185 3.36e-03

cyclin box found in Arabidopsis thaliana retinoblastoma-related protein 1 (AtRBR1) and similar proteins; AtRBR1 is a key regulator of entry into cell division. It acts as a transcription repressor of E2F target genes, whose activity is required for progress from the G1 to the S phase of the cell cycle. AtRBR1 plays a central role in the mechanism controlling meristem cell differentiation, cell fate establishment and cell fate maintenance during organogenesis and gametogenesis. AtRBR1 contains one cyclin box. The cyclin box is a protein binding domain.


Pssm-ID: 410304  Cd Length: 129  Bit Score: 36.98  E-value: 3.36e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
5IYD_M      121 ITTMADRINLPRNIVDRTNNLFKQV-YEQKSL-KGRANDAIASACLYIACRQEGVPRTFKEICAVSR 185
Cdd:cd20601  16 IADLCERLQQPQLVVEQVYRLIEHVlYEQTGLfFNRHIDQIILCCLYGVCKVHKLNVTFREIIYQYR 82
 
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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