NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|6980711|pdb|1C9B|I]
View 

Chain I, GENERAL TRANSCRIPTION FACTOR IIB

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
CYCLIN_TFIIB_rpt2 cd20552
second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 101-197 2.51e-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: 196.35  E-value: 2.51e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I      101 TTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSY 180
Cdd:cd20552   1 STEDFMSRFCSNLGLPNQVQKAATHIAKKAVELDLVAGRSPISVAAAAIYMASQLSEEKKTQKEIGDVAGVAEVTIRQSY 80

                        90
                ....*....|....*..
1C9B_I      181 RLIYPRAPDLFPTDFKF 197
Cdd:cd20552  81 KLLYPRAEKLFPPDFKF 97
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 2-183 1.67e-61

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


:

Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 193.89  E-value: 1.67e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I        2 DRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKE 81
Cdd:COG1405 119 ERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEKGLLRGRSIEGVAAAALYAACRQAGVPRTLDEIAEVSRVDRKE 198

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I       82 IGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRT 161
Cdd:COG1405 199 IARAYRLLNRELGLKVPPIDPIEYIPRIASELGLSEEVERRAREILEKAKEKGLTSGKNPAGLAAAALYLAALLLGEKVT 278

                       170       180
                ....*....|....*....|..
1C9B_I      162 QKEIGDIAGVADVTIRQSYRLI 183
Cdd:COG1405 279 QKEVAEVAGVTEVTIRNRYKEL 300
 
Name Accession Description Interval E-value
CYCLIN_TFIIB_rpt2 cd20552
second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 101-197 2.51e-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: 196.35  E-value: 2.51e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I      101 TTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSY 180
Cdd:cd20552   1 STEDFMSRFCSNLGLPNQVQKAATHIAKKAVELDLVAGRSPISVAAAAIYMASQLSEEKKTQKEIGDVAGVAEVTIRQSY 80

                        90
                ....*....|....*..
1C9B_I      181 RLIYPRAPDLFPTDFKF 197
Cdd:cd20552  81 KLLYPRAEKLFPPDFKF 97
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 2-183 1.67e-61

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 193.89  E-value: 1.67e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I        2 DRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKE 81
Cdd:COG1405 119 ERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEKGLLRGRSIEGVAAAALYAACRQAGVPRTLDEIAEVSRVDRKE 198

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I       82 IGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRT 161
Cdd:COG1405 199 IARAYRLLNRELGLKVPPIDPIEYIPRIASELGLSEEVERRAREILEKAKEKGLTSGKNPAGLAAAALYLAALLLGEKVT 278

                       170       180
                ....*....|....*....|..
1C9B_I      162 QKEIGDIAGVADVTIRQSYRLI 183
Cdd:COG1405 279 QKEVAEVAGVTEVTIRNRYKEL 300
tfb PRK00423
transcription initiation factor IIB; Reviewed
 1-181 1.14e-57

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 184.06  E-value: 1.14e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I         1 SDRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKK 80
Cdd:PRK00423 118 AERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRK 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I        81 EIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKR 160
Cdd:PRK00423 198 EIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERR 277

                        170       180
                 ....*....|....*....|.
1C9B_I       161 TQKEIGDIAGVADVTIRQSYR 181
Cdd:PRK00423 278 TQREVAEVAGVTEVTVRNRYK 298
CYCLIN_TFIIB_rpt1 cd20551
first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 7-94 8.94e-57

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: 174.31  E-value: 8.94e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I        7 NAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKEIGRCF 86
Cdd:cd20551   1 AAFKEIGEMADRMNLPRTIKDRAKELFKQVHDQKSLKGRSNDAIAAACLYIACRQEGVPRTFKEICAVSNVSKKEIGRCF 80


                ....*...
1C9B_I       87 KLILKALE 94
Cdd:cd20551  81 KLILKALE 88
TFIIB pfam00382
Transcription factor TFIIB repeat;
95-185 3.72e-30

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 106.57  E-value: 3.72e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I         95 TSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADV 174
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEY 80

                          90
                  ....*....|.
1C9B_I        175 TIRQSYRLIYP 185
Cdd:pfam00382  81 TIGKTFKELKK 91
TFIIB pfam00382
Transcription factor TFIIB repeat;
1-92 1.77e-29

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 105.03  E-value: 1.77e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I          1 SDRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKK 80
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEY 80

                          90
                  ....*....|..
1C9B_I         81 EIGRCFKLILKA 92
Cdd:pfam00382  81 TIGKTFKELKKA 92
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 12-91 1.23e-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: 63.77  E-value: 1.23e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I          12 ITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRI-SKKEIGRCFKLIL 90
Cdd:smart00385   3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYfTEEEILRMERLLL 82


                   .
1C9B_I          91 K 91
Cdd:smart00385  83 E 83
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 104-184 2.79e-12

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: 59.91  E-value: 2.79e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I         104 DFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADV-TIRQSYRL 182
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYFTEeEILRMERL 80


                   ..
1C9B_I         183 IY 184
Cdd:smart00385  81 LL 82
tfb PRK00423
transcription initiation factor IIB; Reviewed
 108-183 2.68e-11

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 61.18  E-value: 2.68e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
1C9B_I       108 RFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRLI 183
Cdd:PRK00423 131 RIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFL 206
 
Name Accession Description Interval E-value
CYCLIN_TFIIB_rpt2 cd20552
second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 101-197 2.51e-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: 196.35  E-value: 2.51e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I      101 TTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSY 180
Cdd:cd20552   1 STEDFMSRFCSNLGLPNQVQKAATHIAKKAVELDLVAGRSPISVAAAAIYMASQLSEEKKTQKEIGDVAGVAEVTIRQSY 80

                        90
                ....*....|....*..
1C9B_I      181 RLIYPRAPDLFPTDFKF 197
Cdd:cd20552  81 KLLYPRAEKLFPPDFKF 97
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 2-183 1.67e-61

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 193.89  E-value: 1.67e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I        2 DRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKE 81
Cdd:COG1405 119 ERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEKGLLRGRSIEGVAAAALYAACRQAGVPRTLDEIAEVSRVDRKE 198

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I       82 IGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRT 161
Cdd:COG1405 199 IARAYRLLNRELGLKVPPIDPIEYIPRIASELGLSEEVERRAREILEKAKEKGLTSGKNPAGLAAAALYLAALLLGEKVT 278

                       170       180
                ....*....|....*....|..
1C9B_I      162 QKEIGDIAGVADVTIRQSYRLI 183
Cdd:COG1405 279 QKEVAEVAGVTEVTIRNRYKEL 300
tfb PRK00423
transcription initiation factor IIB; Reviewed
 1-181 1.14e-57

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 184.06  E-value: 1.14e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I         1 SDRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKK 80
Cdd:PRK00423 118 AERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRK 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I        81 EIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKR 160
Cdd:PRK00423 198 EIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERR 277

                        170       180
                 ....*....|....*....|.
1C9B_I       161 TQKEIGDIAGVADVTIRQSYR 181
Cdd:PRK00423 278 TQREVAEVAGVTEVTVRNRYK 298
CYCLIN_TFIIB_rpt1 cd20551
first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 7-94 8.94e-57

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: 174.31  E-value: 8.94e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I        7 NAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKEIGRCF 86
Cdd:cd20551   1 AAFKEIGEMADRMNLPRTIKDRAKELFKQVHDQKSLKGRSNDAIAAACLYIACRQEGVPRTFKEICAVSNVSKKEIGRCF 80


                ....*...
1C9B_I       87 KLILKALE 94
Cdd:cd20551  81 KLILKALE 88
TFIIB pfam00382
Transcription factor TFIIB repeat;
95-185 3.72e-30

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 106.57  E-value: 3.72e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I         95 TSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADV 174
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEY 80

                          90
                  ....*....|.
1C9B_I        175 TIRQSYRLIYP 185
Cdd:pfam00382  81 TIGKTFKELKK 91
TFIIB pfam00382
Transcription factor TFIIB repeat;
1-92 1.77e-29

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 105.03  E-value: 1.77e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I          1 SDRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKK 80
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEY 80

                          90
                  ....*....|..
1C9B_I         81 EIGRCFKLILKA 92
Cdd:pfam00382  81 TIGKTFKELKKA 92
CYCLIN_TFIIB_archaea_like_rpt2 cd20550
second cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 104-181 2.27e-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: 99.20  E-value: 2.27e-27
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
1C9B_I      104 DFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYR 181
Cdd:cd20550   4 DYVPRFASKLGLSGEVQRKAIEILEKAKKKGLTSGKGPAGLAAAAIYIASLLTGERRTQKEIAEVAGVTEVTIRNRYK 81
CYCLIN_TFIIB_archaea_like_rpt1 cd20549
first cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 1-95 3.39e-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: 91.57  E-value: 3.39e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I        1 SDRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKK 80
Cdd:cd20549   5 AERNLAQALSELDRMASKLGLPRSVREEAAVIYRKAVEKGLVRGRSIESVVAAALYAACRICNVPRTLDEIAEATRVSRK 84

                        90
                ....*....|....*
1C9B_I       81 EIGRCFKLILKALET 95
Cdd:cd20549  85 EIARCYRLLARELNL 99
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 7-88 2.20e-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: 75.91  E-value: 2.20e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I        7 NAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKEIGRCF 86
Cdd:cd00043   1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEKELRKAE 80


                ..
1C9B_I       87 KL 88
Cdd:cd00043  81 KE 82
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 104-182 1.51e-15

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: 68.59  E-value: 1.51e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
1C9B_I      104 DFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRL 182
Cdd:cd00043   4 DFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEKELRKAEKE 82
CYCLIN_TFIIIB90_rpt1 cd20553
first cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 5-93 2.26e-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: 65.63  E-value: 2.26e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I        5 MMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKEIGR 84
Cdd:cd20553   3 LQNGRRKIQQLGSQLKLNQHHIDTAFRFYKLAVQRNFTRGRKTSHVAAACLYIVCRREKTPHMLIDFSDVLQVNVYVLGK 82


                ....*....
1C9B_I       85 CFKLILKAL 93
Cdd:cd20553  83 TFLKLCKLL 91
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 12-91 1.23e-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: 63.77  E-value: 1.23e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I          12 ITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRI-SKKEIGRCFKLIL 90
Cdd:smart00385   3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYfTEEEILRMERLLL 82


                   .
1C9B_I          91 K 91
Cdd:smart00385  83 E 83
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 104-184 2.79e-12

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: 59.91  E-value: 2.79e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I         104 DFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADV-TIRQSYRL 182
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYFTEeEILRMERL 80


                   ..
1C9B_I         183 IY 184
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 ...
 3-94 1.87e-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: 58.06  E-value: 1.87e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I        3 RAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKG--RAN-DAIASACLYIACRQEGVPRTFKEICAVSRISK 79
Cdd:cd20555   2 RGLKQGLKRVRDLCRVLRLSSVMEETAVELFEQAFKHPDFRHirLEKkEVLVGCCVYIVCRQNNWPVTMGDICSLLQCDV 81

                        90
                ....*....|....*
1C9B_I       80 KEIGRCFKLILKALE 94
Cdd:cd20555  82 SDFSSVYKELLKELN 96
tfb PRK00423
transcription initiation factor IIB; Reviewed
 108-183 2.68e-11

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 61.18  E-value: 2.68e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
1C9B_I       108 RFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRLI 183
Cdd:PRK00423 131 RIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFL 206
CYCLIN_TFIIB_archaea_like_rpt1 cd20549
first cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 108-183 1.16e-10

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: 56.13  E-value: 1.16e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
1C9B_I      108 RFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRLI 183
Cdd:cd20549  18 RMASKLGLPRSVREEAAVIYRKAVEKGLVRGRSIESVVAAALYAACRICNVPRTLDEIAEATRVSRKEIARCYRLL 93
CYCLIN_TFIIB_archaea_like_rpt2 cd20550
second cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 12-93 1.18e-06

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: 44.89  E-value: 1.18e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I       12 ITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKEIGRCFKLILK 91
Cdd:cd20550   6 VPRFASKLGLSGEVQRKAIEILEKAKKKGLTSGKGPAGLAAAAIYIASLLTGERRTQKEIAEVAGVTEVTIRNRYKELLE 85


                ..
1C9B_I       92 AL 93
Cdd:cd20550  86 AL 87
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 6-185 2.79e-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: 43.57  E-value: 2.79e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I        6 MNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKEI--- 82
Cdd:COG5333  46 IYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEpks 125

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I       83 --GRCFKLILKALET-SVDLITTGDF--MSRF---CSNLCLPKQVQMAAThIARKAVELDLVPGRSPISVAAAAIYMAsq 154
Cdd:COG5333 126 srERILEYEFELLEAlDFDLHVHHPYkyLEGFlkdLQEKDKYKLLQIAWK-IINDALRTDLCLLYPPHIIALAALLIA-- 202

                       170       180       190
                ....*....|....*....|....*....|.
1C9B_I      155 asAEKRTQKEIGDIAGVADVTIRQSYRLIYP 185
Cdd:COG5333 203 --CEVLGMPIIKLLDFVSYETKEEVIALNYK 231
CYCLIN_TFIIIB90_rpt2 cd20554
second cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 105-182 8.94e-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: 39.80  E-value: 8.94e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I      105 FMSRFCSNLCLPKqvqmaATH-IARKAVEL------D-LVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTI 176
Cdd:cd20554   8 YIHRFASKLEFGD-----KTHeVANTALRLvqrmkrDwIHTGRRPSGICGAALLIAARMHGFKRTVEEIVRVVRVCESTL 82


                ....*.
1C9B_I      177 RQsyRL 182
Cdd:cd20554  83 RK--RL 86
CYCLIN_TFIIIB90_rpt2 cd20554
second cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 43-78 4.14e-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: 37.88  E-value: 4.14e-04
                        10        20        30
                ....*....|....*....|....*....|....*.
1C9B_I       43 KGRANDAIASACLYIACRQEGVPRTFKEICAVSRIS 78
Cdd:cd20554  43 TGRRPSGICGAALLIAARMHGFKRTVEEIVRVVRVC 78
tfb PRK00423
transcription initiation factor IIB; Reviewed
 12-99 9.61e-04

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 39.22  E-value: 9.61e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1C9B_I        12 ITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKEIGRCFKLILK 91
Cdd:PRK00423 223 VPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAE 302


                 ....*...
1C9B_I        92 ALETSVDL 99
Cdd:PRK00423 303 KLDIKIPL 310
CYCLIN_ScCTK2-like_rpt1 cd20547
first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar ...
 6-75 4.76e-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: 35.40  E-value: 4.76e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
1C9B_I        6 MNAFKEITTMADRINLPRnivdRTNNLFKQVYEQKSLKGRANDA----IASACLYIACRQEGVPRTFKEICAVS 75
Cdd:cd20547   3 LAAFQFISQLCKKLKFPR----RTLGTAMLLYQRFHLFNPFTDSsnyeVALACLFLASKIEDTQKKSKDILAAS 72
CYCLIN_AtRBR_like cd20601
cyclin box found in Arabidopsis thaliana retinoblastoma-related protein 1 (AtRBR1) and similar ...
 12-76 5.97e-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: 35.44  E-value: 5.97e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
1C9B_I       12 ITTMADRINLPRNIVDRTNNLFKQV-YEQKSL-KGRANDAIASACLYIACRQEGVPRTFKEICAVSR 76
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH