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Conserved domains on  [gi|15227397|ref|NP_181694|]
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transcription factor IIB [Arabidopsis thaliana]

Protein Classification

transcription initiation factor IIB family protein( domain architecture ID 11443977)

transcription initiation factor IIB family protein similar to transcription factor IIB (TFIIB), which is one of the basal general transcription factors of the preinitiation complex of eukaryotic RNA polymerase II, or the 50kDa subunit of transcription factor IIIB, a general activator of RNA polymerase III transcription

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 ...
 6-288 1.52e-69

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


:

Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 218.54  E-value: 1.52e-69
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397   6 CTDCKKETeLVVDHSAGDTLCSECGLVLESHSIDETSEWRTFANESsNSDPNRVGGPTNPLLADSALTTVIAKPN-GSSG 84
Cdd:COG1405  14 CPECGGEN-LVTDTERGETVCEDCGLVVEEDVIDRGPEWRAFDSEE-RDERSRTGAPLTLARHDKGLSTEIGWQDkDAYG 91

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397  85 DFLSSS-------LGRWQNR---NSNSDRGLIQAFKTIATMSERLGLVATIKDRANELYKRLEDQKSSRGRNQDALYAAC 154
Cdd:COG1405  92 KSLSGRkrrqlarLRKWQNRsrvSSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEKGLLRGRSIEGVAAAA 171

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397 155 LYIACRQEDKPRTIKEICVIANgATKKEIGRAKDYIVKTLGLEPGQsvdlgtIHAGDFMRRFCSNLAMSNHAVKAAQEAV 234
Cdd:COG1405 172 LYAACRQAGVPRTLDEIAEVSR-VDRKEIARAYRLLNRELGLKVPP------IDPIEYIPRIASELGLSEEVERRAREIL 244

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 15227397 235 QKSEEFDIR--RSPISIAAVVIYIITQLSDDKKTLKDISHATGVAEGTIRNSYKDL 288
Cdd:COG1405 245 EKAKEKGLTsgKNPAGLAAAALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRYKEL 300
 
Name Accession Description Interval E-value
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 6-288 1.52e-69

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 218.54  E-value: 1.52e-69
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397   6 CTDCKKETeLVVDHSAGDTLCSECGLVLESHSIDETSEWRTFANESsNSDPNRVGGPTNPLLADSALTTVIAKPN-GSSG 84
Cdd:COG1405  14 CPECGGEN-LVTDTERGETVCEDCGLVVEEDVIDRGPEWRAFDSEE-RDERSRTGAPLTLARHDKGLSTEIGWQDkDAYG 91

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397  85 DFLSSS-------LGRWQNR---NSNSDRGLIQAFKTIATMSERLGLVATIKDRANELYKRLEDQKSSRGRNQDALYAAC 154
Cdd:COG1405  92 KSLSGRkrrqlarLRKWQNRsrvSSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEKGLLRGRSIEGVAAAA 171

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397 155 LYIACRQEDKPRTIKEICVIANgATKKEIGRAKDYIVKTLGLEPGQsvdlgtIHAGDFMRRFCSNLAMSNHAVKAAQEAV 234
Cdd:COG1405 172 LYAACRQAGVPRTLDEIAEVSR-VDRKEIARAYRLLNRELGLKVPP------IDPIEYIPRIASELGLSEEVERRAREIL 244

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 15227397 235 QKSEEFDIR--RSPISIAAVVIYIITQLSDDKKTLKDISHATGVAEGTIRNSYKDL 288
Cdd:COG1405 245 EKAKEKGLTsgKNPAGLAAAALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRYKEL 300
tfb PRK00423
transcription initiation factor IIB; Reviewed
 6-292 2.06e-59

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 192.53  E-value: 2.06e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397    6 CTDCKkETELVVDHSAGDTLCSECGLVLESHSIDETSEWRTFANESsNSDPNRVGGPTNPLLADSALTTVIAKPN-GSSG 84
Cdd:PRK00423  14 CPECG-SDKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQ-REKRSRVGAPMTYTIHDKGLSTDIDWRNkDSYG 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397   85 DFLSSS-------LGRWQNR---NSNSDRGLIQAFKTIATMSERLGLVATIKDRANELYKRLEDQKSSRGRNQDALYAAC 154
Cdd:PRK00423  92 KSISGKnraqlyrLRKWQRRirvSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAA 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397  155 LYIACRQEDKPRTIKEICVIANgATKKEIGRAKDYIVKTLGLepgqsvDLGTIHAGDFMRRFCSNLAMSNHAVKAAQEAV 234
Cdd:PRK00423 172 LYAACRRCKVPRTLDEIAEVSR-VSRKEIGRCYRFLLRELNL------KLPPTDPIDYVPRFASELGLSGEVQKKAIEIL 244

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397  235 QKSEEFDIR--RSPISIAAVVIYIITQLSDDKKTLKDISHATGVAEGTIRNSYKDLYPHL 292
Cdd:PRK00423 245 QKAKEKGLTsgKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAEKL 304
CYCLIN_TFIIB_rpt1 cd20551
first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 108-195 2.34e-44

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: 146.19  E-value: 2.34e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397 108 AFKTIATMSERLGLVATIKDRANELYKRLEDQKSSRGRNQDALYAACLYIACRQEDKPRTIKEICVIANGaTKKEIGRAK 187
Cdd:cd20551   2 AFKEIGEMADRMNLPRTIKDRAKELFKQVHDQKSLKGRSNDAIAAACLYIACRQEGVPRTFKEICAVSNV-SKKEIGRCF 80


                ....*...
gi 15227397 188 DYIVKTLG 195
Cdd:cd20551  81 KLILKALE 88
TFIIB pfam00382
Transcription factor TFIIB repeat;
101-185 6.69e-18

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 77.30  E-value: 6.69e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397   101 SDRGLIQAFKTIATMSERLGLVATIKDRANELYKRLEDQKSSRGRNQDALYAACLYIACRQEDKPRTIKEICVIANgATK 180
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQ-VTE 79


                  ....*
gi 15227397   181 KEIGR 185
Cdd:pfam00382  80 YTIGK 84
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 112-192 1.45e-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: 56.83  E-value: 1.45e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397    112 IATMSERLGLVATIKDRANELYKRLEDQKSSRGRNQDALYAACLYIACRQEDKPRTIKEICVIANGATKKEIGRAKDYIV 191
Cdd:smart00385   3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYFTEEEILRMERLLL 82


                   .
gi 15227397    192 K 192
Cdd:smart00385  83 E 83
 
Name Accession Description Interval E-value
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 6-288 1.52e-69

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 218.54  E-value: 1.52e-69
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397   6 CTDCKKETeLVVDHSAGDTLCSECGLVLESHSIDETSEWRTFANESsNSDPNRVGGPTNPLLADSALTTVIAKPN-GSSG 84
Cdd:COG1405  14 CPECGGEN-LVTDTERGETVCEDCGLVVEEDVIDRGPEWRAFDSEE-RDERSRTGAPLTLARHDKGLSTEIGWQDkDAYG 91

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397  85 DFLSSS-------LGRWQNR---NSNSDRGLIQAFKTIATMSERLGLVATIKDRANELYKRLEDQKSSRGRNQDALYAAC 154
Cdd:COG1405  92 KSLSGRkrrqlarLRKWQNRsrvSSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEKGLLRGRSIEGVAAAA 171

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397 155 LYIACRQEDKPRTIKEICVIANgATKKEIGRAKDYIVKTLGLEPGQsvdlgtIHAGDFMRRFCSNLAMSNHAVKAAQEAV 234
Cdd:COG1405 172 LYAACRQAGVPRTLDEIAEVSR-VDRKEIARAYRLLNRELGLKVPP------IDPIEYIPRIASELGLSEEVERRAREIL 244

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 15227397 235 QKSEEFDIR--RSPISIAAVVIYIITQLSDDKKTLKDISHATGVAEGTIRNSYKDL 288
Cdd:COG1405 245 EKAKEKGLTsgKNPAGLAAAALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRYKEL 300
tfb PRK00423
transcription initiation factor IIB; Reviewed
 6-292 2.06e-59

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 192.53  E-value: 2.06e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397    6 CTDCKkETELVVDHSAGDTLCSECGLVLESHSIDETSEWRTFANESsNSDPNRVGGPTNPLLADSALTTVIAKPN-GSSG 84
Cdd:PRK00423  14 CPECG-SDKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQ-REKRSRVGAPMTYTIHDKGLSTDIDWRNkDSYG 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397   85 DFLSSS-------LGRWQNR---NSNSDRGLIQAFKTIATMSERLGLVATIKDRANELYKRLEDQKSSRGRNQDALYAAC 154
Cdd:PRK00423  92 KSISGKnraqlyrLRKWQRRirvSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAA 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397  155 LYIACRQEDKPRTIKEICVIANgATKKEIGRAKDYIVKTLGLepgqsvDLGTIHAGDFMRRFCSNLAMSNHAVKAAQEAV 234
Cdd:PRK00423 172 LYAACRRCKVPRTLDEIAEVSR-VSRKEIGRCYRFLLRELNL------KLPPTDPIDYVPRFASELGLSGEVQKKAIEIL 244

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397  235 QKSEEFDIR--RSPISIAAVVIYIITQLSDDKKTLKDISHATGVAEGTIRNSYKDLYPHL 292
Cdd:PRK00423 245 QKAKEKGLTsgKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAEKL 304
CYCLIN_TFIIB_rpt1 cd20551
first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 108-195 2.34e-44

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: 146.19  E-value: 2.34e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397 108 AFKTIATMSERLGLVATIKDRANELYKRLEDQKSSRGRNQDALYAACLYIACRQEDKPRTIKEICVIANGaTKKEIGRAK 187
Cdd:cd20551   2 AFKEIGEMADRMNLPRTIKDRAKELFKQVHDQKSLKGRSNDAIAAACLYIACRQEGVPRTFKEICAVSNV-SKKEIGRCF 80


                ....*...
gi 15227397 188 DYIVKTLG 195
Cdd:cd20551  81 KLILKALE 88
CYCLIN_TFIIB_rpt2 cd20552
second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 209-298 3.35e-33

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: 117.77  E-value: 3.35e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397 209 AGDFMRRFCSNLAMSNHAVKAAQEAVQKSEEFDIR--RSPISIAAVVIYIITQLSDDKKTLKDISHATGVAEGTIRNSYK 286
Cdd:cd20552   2 TEDFMSRFCSNLGLPNQVQKAATHIAKKAVELDLVagRSPISVAAAAIYMASQLSEEKKTQKEIGDVAGVAEVTIRQSYK 81

                        90
                ....*....|..
gi 15227397 287 DLYPHLSKIAPS 298
Cdd:cd20552  82 LLYPRAEKLFPP 93
CYCLIN_TFIIB_archaea_like_rpt2 cd20550
second cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 211-288 4.50e-19

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: 79.94  E-value: 4.50e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397 211 DFMRRFCSNLAMSNHAVKAAQEAVQKSEEFDI--RRSPISIAAVVIYIITQLSDDKKTLKDISHATGVAEGTIRNSYKDL 288
Cdd:cd20550   4 DYVPRFASKLGLSGEVQRKAIEILEKAKKKGLtsGKGPAGLAAAAIYIASLLTGERRTQKEIAEVAGVTEVTIRNRYKEL 83
TFIIB pfam00382
Transcription factor TFIIB repeat;
101-185 6.69e-18

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 77.30  E-value: 6.69e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397   101 SDRGLIQAFKTIATMSERLGLVATIKDRANELYKRLEDQKSSRGRNQDALYAACLYIACRQEDKPRTIKEICVIANgATK 180
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQ-VTE 79


                  ....*
gi 15227397   181 KEIGR 185
Cdd:pfam00382  80 YTIGK 84
CYCLIN_TFIIB_archaea_like_rpt1 cd20549
first cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 101-196 1.50e-17

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: 76.55  E-value: 1.50e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397 101 SDRGLIQAFKTIATMSERLGLVATIKDRANELYKRLEDQKSSRGRNQDALYAACLYIACRQEDKPRTIKEICVIANgATK 180
Cdd:cd20549   5 AERNLAQALSELDRMASKLGLPRSVREEAAVIYRKAVEKGLVRGRSIESVVAAALYAACRICNVPRTLDEIAEATR-VSR 83

                        90
                ....*....|....*.
gi 15227397 181 KEIGRAKDYIVKTLGL 196
Cdd:cd20549  84 KEIARCYRLLARELNL 99
TFIIB pfam00382
Transcription factor TFIIB repeat;
202-291 2.59e-15

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 69.98  E-value: 2.59e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397   202 VDLGTIHAGDFMRRFCSNLAMSNHAVKAAQEAVQKSEEFDIR--RSPISIAAVVIYIITQLSDDKKTLKDISHATGVAEG 279
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLkgRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEY 80

                          90
                  ....*....|..
gi 15227397   280 TIRNSYKDLYPH 291
Cdd:pfam00382  81 TIGKTFKELKKA 92
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 107-186 1.88e-14

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: 67.44  E-value: 1.88e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397 107 QAFKTIATMSERLGLVATIKDRANELYKRLEDQKSSRGRNQDALYAACLYIACRQEDKPRTIKEICVIAnGATKKEIGRA 186
Cdd:cd00043   1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVS-GVSEKELRKA 79
TF_Zn_Ribbon pfam08271
TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the ...
 6-47 1.80e-12

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: 60.78  E-value: 1.80e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 15227397     6 CTDCKkETELVVDHSAGDTLCSECGLVLESHSIDETSEWRTF 47
Cdd:pfam08271   3 CPNCG-STNLVEDYERGELVCTDCGLVLEDNSIDEGPEWREF 43
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 208-287 6.44e-12

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: 60.50  E-value: 6.44e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397 208 HAGDFMRRFCSNLAMSNHAVKAAQEAVQKSEEFDI--RRSPISIAAVVIYIITQLSDDKKTLKDISHATGVAEGTIRNSY 285
Cdd:cd00043   1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLllGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEKELRKAE 80


                ..
gi 15227397 286 KD 287
Cdd:cd00043  81 KE 82
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 112-192 1.45e-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: 56.83  E-value: 1.45e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397    112 IATMSERLGLVATIKDRANELYKRLEDQKSSRGRNQDALYAACLYIACRQEDKPRTIKEICVIANGATKKEIGRAKDYIV 191
Cdd:smart00385   3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYFTEEEILRMERLLL 82


                   .
gi 15227397    192 K 192
Cdd:smart00385  83 E 83
CYCLIN_BRF2 cd20555
cyclin box found in B-related factor 2 (BRF-2) and similar proteins; BRF-2, also called ...
 103-196 7.93e-10

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: 54.98  E-value: 7.93e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397 103 RGLIQAFKTIATMSERLGLVATIKDRANELYKRL---EDQKSSRGRNQDALYAACLYIACRQEDKPRTIKEICVIANgAT 179
Cdd:cd20555   2 RGLKQGLKRVRDLCRVLRLSSVMEETAVELFEQAfkhPDFRHIRLEKKEVLVGCCVYIVCRQNNWPVTMGDICSLLQ-CD 80

                        90
                ....*....|....*..
gi 15227397 180 KKEIGRAKDYIVKTLGL 196
Cdd:cd20555  81 VSDFSSVYKELLKELNI 97
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 211-289 2.42e-08

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: 50.28  E-value: 2.42e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397    211 DFMRRFCSNLAMSNHAVKAAQEAVQKSEEFD--IRRSPISIAAVVIYIITQLSDDKKTLKDISHATGVA-EGTIRNSYKD 287
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYkfLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYFtEEEILRMERL 80


                   ..
gi 15227397    288 LY 289
Cdd:smart00385  81 LL 82
CYCLIN_TFIIIB90_rpt1 cd20553
first cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 107-165 1.62e-07

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: 48.30  E-value: 1.62e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 15227397 107 QAFKTIATMSERLGLVATIKDRANELYKRLEDQKSSRGRNQDALYAACLYIACRQEDKP 165
Cdd:cd20553   5 NGRRKIQQLGSQLKLNQHHIDTAFRFYKLAVQRNFTRGRKTSHVAAACLYIVCRREKTP 63
CYCLIN_TFIIB_archaea_like_rpt2 cd20550
second cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 112-176 6.13e-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: 6.13e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15227397 112 IATMSERLGLVATIKDRANELYKRLEDQKSSRGRNQDALYAACLYIACRQEDKPRTIKEICVIAN 176
Cdd:cd20550   6 VPRFASKLGLSGEVQRKAIEILEKAKKKGLTSGKGPAGLAAAAIYIASLLTGERRTQKEIAEVAG 70
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 106-193 1.44e-04

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: 42.80  E-value: 1.44e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227397 106 IQAFKTIATMSERLGLVATIKDRANELYKRLEDQKSSRGRNQDALYAACLYIACRQEDKPRTIKEICVIANGATKKEIGR 185
Cdd:COG5333  46 IYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEPKS 125


                ....*...
gi 15227397 186 AKDYIVKT 193
Cdd:COG5333 126 SRERILEY 133
Cyclin_N pfam00134
Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a ...
 152-195 7.77e-04

Cyclin, N-terminal domain; Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a Uracil-DNA glycosylase that is related to other cyclins. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain.


Pssm-ID: 459686 [Multi-domain]  Cd Length: 127  Bit Score: 38.65  E-value: 7.77e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 15227397   152 AACLYIACR-QEDKPRTIKEICVIANGA-TKKEIGRAKDYIVKTLG 195
Cdd:pfam00134  78 VTCLFIAAKyEEIYPPTVEDLVYITDNAyTREEILRMERLILETLN 123
 
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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