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Conserved domains on  [gi|1958782717|ref|XP_038968033|]
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transcription factor IIIB 90 kDa subunit isoform X4 [Rattus norvegicus]

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
CYCLIN_TFIIIB90_rpt2 cd20554
second cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 179-270 3.49e-62

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: 193.50  E-value: 3.49e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717 179 PAIDPCLYIPRFAHLLEFGEKNHEVSMTALRLLQRMKRDWMHTGRRPSGLCGAALLVAARMHDFRRTVKEVISVVKVCES 258
Cdd:cd20554     1 PVIDPSLYIHRFASKLEFGDKTHEVANTALRLVQRMKRDWIHTGRRPSGICGAALLIAARMHGFKRTVEEIVRVVRVCES 80

                          90
                  ....*....|..
gi 1958782717 259 TLRKRLTEFEDT 270
Cdd:cd20554    81 TLRKRLREFEKT 92
CYCLIN_TFIIIB90_rpt1 cd20553
first cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 84-174 3.07e-55

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: 175.80  E-value: 3.07e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717  84 QTLQNGRRHIHHLGSQLQLNQHCLDTAFNFFKMAVSKHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVNVYVL 163
Cdd:cd20553     1 ITLQNGRRKIQQLGSQLKLNQHHIDTAFRFYKLAVQRNFTRGRKTSHVAAACLYIVCRREKTPHMLIDFSDVLQVNVYVL 80

                          90
                  ....*....|.
gi 1958782717 164 GKTFLLLAREL 174
Cdd:cd20553    81 GKTFLKLCKLL 91
TF_Zn_Ribbon pfam08271
TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the ...
 4-46 5.76e-13

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: 62.71  E-value: 5.76e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1958782717   4 RVCRGCGGTDIELDAARGDAVCTGCGSVLEDNIIVSEVQFVEN 46
Cdd:pfam08271   1 YKCPNCGSTNLVEDYERGELVCTDCGLVLEDNSIDEGPEWREF 43
 
Name Accession Description Interval E-value
CYCLIN_TFIIIB90_rpt2 cd20554
second cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 179-270 3.49e-62

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: 193.50  E-value: 3.49e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717 179 PAIDPCLYIPRFAHLLEFGEKNHEVSMTALRLLQRMKRDWMHTGRRPSGLCGAALLVAARMHDFRRTVKEVISVVKVCES 258
Cdd:cd20554     1 PVIDPSLYIHRFASKLEFGDKTHEVANTALRLVQRMKRDWIHTGRRPSGICGAALLIAARMHGFKRTVEEIVRVVRVCES 80

                          90
                  ....*....|..
gi 1958782717 259 TLRKRLTEFEDT 270
Cdd:cd20554    81 TLRKRLREFEKT 92
CYCLIN_TFIIIB90_rpt1 cd20553
first cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 84-174 3.07e-55

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: 175.80  E-value: 3.07e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717  84 QTLQNGRRHIHHLGSQLQLNQHCLDTAFNFFKMAVSKHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVNVYVL 163
Cdd:cd20553     1 ITLQNGRRKIQQLGSQLKLNQHHIDTAFRFYKLAVQRNFTRGRKTSHVAAACLYIVCRREKTPHMLIDFSDVLQVNVYVL 80

                          90
                  ....*....|.
gi 1958782717 164 GKTFLLLAREL 174
Cdd:cd20553    81 GKTFLKLCKLL 91
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 4-266 3.87e-49

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 167.31  E-value: 3.87e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717   4 RVCRGCGGTDIELDAARGDAVCTGCGSVLEDNII----------VSEVQFVENSGG---------GSSAVGQFVSLDGAG 64
Cdd:COG1405    12 SVCPECGGENLVTDTERGETVCEDCGLVVEEDVIdrgpewrafdSEERDERSRTGApltlarhdkGLSTEIGWQDKDAYG 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717  65 KTptLGGG--------------FHVnlgKESRAQTLQNGRRHIHHLGSQLQLNQHCLDTAFNFFKMAVSKHLTRGRKMAH 130
Cdd:COG1405    92 KS--LSGRkrrqlarlrkwqnrSRV---SSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEKGLLRGRSIEG 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717 131 VIAACLYLVCRTEGTPHMLLDLSDLLQVNVYVLGKTFLLLARELCINAPAIDPCLYIPRFAHLLEFGEknhEVSMTALRL 210
Cdd:COG1405   167 VAAAALYAACRQAGVPRTLDEIAEVSRVDRKEIARAYRLLNRELGLKVPPIDPIEYIPRIASELGLSE---EVERRAREI 243

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958782717 211 LQRMKRDWMHTGRRPSGLCGAALLVAARMHDFRRTVKEVISVVKVCESTLRKRLTE 266
Cdd:COG1405   244 LEKAKEKGLTSGKNPAGLAAAALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRYKE 299
tfb PRK00423
transcription initiation factor IIB; Reviewed
 4-278 2.08e-39

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 141.68  E-value: 2.08e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717   4 RVCRGCGGTDIELDAARGDAVCTGCGSVLEDNII---------VSEvQFVENS--GG---------GSSAVGQFVSLDGA 63
Cdd:PRK00423   12 LVCPECGSDKLIYDYERGEIVCADCGLVIEENIIdqgpewrafDPE-QREKRSrvGApmtytihdkGLSTDIDWRNKDSY 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717  64 GKTPTL------------------GGGFHVNLgkesrAQTLQNGRRhihhLGSQLQLNQHCLDTAFNFFKMAVSKHLTRG 125
Cdd:PRK00423   91 GKSISGknraqlyrlrkwqrrirvSNAAERNL-----AFALSELDR----IASQLGLPRSVREEAAVIYRKAVEKGLIRG 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717 126 RKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVNVYVLGKTFLLLARELCINAPAIDPCLYIPRFAHLLEFGEknhEVSM 205
Cdd:PRK00423  162 RSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSG---EVQK 238

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958782717 206 TALRLLQRMKRDWMHTGRRPSGLCGAALLVAARMHDFRRTVKEVISVVKVCESTLRKRLTEFedtpTSQLTID 278
Cdd:PRK00423  239 KAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKEL----AEKLDIK 307
TFIIB pfam00382
Transcription factor TFIIB repeat;
82-173 3.71e-35

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 123.91  E-value: 3.71e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717  82 RAQTLQNGRRHIHHLGSQLQLNQHCLDTAFNFFKMAVSKHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVNVY 161
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEY 80

                          90
                  ....*....|..
gi 1958782717 162 VLGKTFLLLARE 173
Cdd:pfam00382  81 TIGKTFKELKKA 92
TFIIB pfam00382
Transcription factor TFIIB repeat;
176-270 2.20e-33

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 119.29  E-value: 2.20e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717 176 INAPAIDPCLYIPRFAHLLEFGEKnheVSMTALRLLQRMKRDWMHTGRRPSGLCGAALLVAARMHDFRRTVKEVISVVKV 255
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEK---VADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQV 77

                          90
                  ....*....|....*
gi 1958782717 256 CESTLRKRLTEFEDT 270
Cdd:pfam00382  78 TEYTIGKTFKELKKA 92
TF_Zn_Ribbon pfam08271
TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the ...
 4-46 5.76e-13

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: 62.71  E-value: 5.76e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1958782717   4 RVCRGCGGTDIELDAARGDAVCTGCGSVLEDNIIVSEVQFVEN 46
Cdd:pfam08271   1 YKCPNCGSTNLVEDYERGELVCTDCGLVLEDNSIDEGPEWREF 43
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 93-158 5.87e-10

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


Pssm-ID: 214641 [Multi-domain]  Cd Length: 83  Bit Score: 55.29  E-value: 5.87e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958782717   93 IHHLGSQLQLNQHCLDTAFNFFKMAVSKHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQV 158
Cdd:smart00385   3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGY 68
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 186-263 1.21e-06

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: 46.05  E-value: 1.21e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958782717  186 YIPRFAHLLEFgekNHEVSMTALRLLQRMKRDWMHTGRRPSGLCGAALLVAARMHDFRRTVKEVISVVKVC-ESTLRKR 263
Cdd:smart00385   2 FLRRVCKALNL---DPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYFtEEEILRM 77
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 93-147 5.28e-03

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: 38.17  E-value: 5.28e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958782717  93 IHHLGSQLQLNQHCLDTAFNFFKMAVSKHLTRGRKMAHVIAACLYLVCRTEGTPH 147
Cdd:COG5333    52 IMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPR 106
 
Name Accession Description Interval E-value
CYCLIN_TFIIIB90_rpt2 cd20554
second cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 179-270 3.49e-62

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: 193.50  E-value: 3.49e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717 179 PAIDPCLYIPRFAHLLEFGEKNHEVSMTALRLLQRMKRDWMHTGRRPSGLCGAALLVAARMHDFRRTVKEVISVVKVCES 258
Cdd:cd20554     1 PVIDPSLYIHRFASKLEFGDKTHEVANTALRLVQRMKRDWIHTGRRPSGICGAALLIAARMHGFKRTVEEIVRVVRVCES 80

                          90
                  ....*....|..
gi 1958782717 259 TLRKRLTEFEDT 270
Cdd:cd20554    81 TLRKRLREFEKT 92
CYCLIN_TFIIIB90_rpt1 cd20553
first cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 84-174 3.07e-55

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: 175.80  E-value: 3.07e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717  84 QTLQNGRRHIHHLGSQLQLNQHCLDTAFNFFKMAVSKHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVNVYVL 163
Cdd:cd20553     1 ITLQNGRRKIQQLGSQLKLNQHHIDTAFRFYKLAVQRNFTRGRKTSHVAAACLYIVCRREKTPHMLIDFSDVLQVNVYVL 80

                          90
                  ....*....|.
gi 1958782717 164 GKTFLLLAREL 174
Cdd:cd20553    81 GKTFLKLCKLL 91
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 4-266 3.87e-49

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 167.31  E-value: 3.87e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717   4 RVCRGCGGTDIELDAARGDAVCTGCGSVLEDNII----------VSEVQFVENSGG---------GSSAVGQFVSLDGAG 64
Cdd:COG1405    12 SVCPECGGENLVTDTERGETVCEDCGLVVEEDVIdrgpewrafdSEERDERSRTGApltlarhdkGLSTEIGWQDKDAYG 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717  65 KTptLGGG--------------FHVnlgKESRAQTLQNGRRHIHHLGSQLQLNQHCLDTAFNFFKMAVSKHLTRGRKMAH 130
Cdd:COG1405    92 KS--LSGRkrrqlarlrkwqnrSRV---SSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEKGLLRGRSIEG 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717 131 VIAACLYLVCRTEGTPHMLLDLSDLLQVNVYVLGKTFLLLARELCINAPAIDPCLYIPRFAHLLEFGEknhEVSMTALRL 210
Cdd:COG1405   167 VAAAALYAACRQAGVPRTLDEIAEVSRVDRKEIARAYRLLNRELGLKVPPIDPIEYIPRIASELGLSE---EVERRAREI 243

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958782717 211 LQRMKRDWMHTGRRPSGLCGAALLVAARMHDFRRTVKEVISVVKVCESTLRKRLTE 266
Cdd:COG1405   244 LEKAKEKGLTSGKNPAGLAAAALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRYKE 299
tfb PRK00423
transcription initiation factor IIB; Reviewed
 4-278 2.08e-39

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 141.68  E-value: 2.08e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717   4 RVCRGCGGTDIELDAARGDAVCTGCGSVLEDNII---------VSEvQFVENS--GG---------GSSAVGQFVSLDGA 63
Cdd:PRK00423   12 LVCPECGSDKLIYDYERGEIVCADCGLVIEENIIdqgpewrafDPE-QREKRSrvGApmtytihdkGLSTDIDWRNKDSY 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717  64 GKTPTL------------------GGGFHVNLgkesrAQTLQNGRRhihhLGSQLQLNQHCLDTAFNFFKMAVSKHLTRG 125
Cdd:PRK00423   91 GKSISGknraqlyrlrkwqrrirvSNAAERNL-----AFALSELDR----IASQLGLPRSVREEAAVIYRKAVEKGLIRG 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717 126 RKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVNVYVLGKTFLLLARELCINAPAIDPCLYIPRFAHLLEFGEknhEVSM 205
Cdd:PRK00423  162 RSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSG---EVQK 238

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958782717 206 TALRLLQRMKRDWMHTGRRPSGLCGAALLVAARMHDFRRTVKEVISVVKVCESTLRKRLTEFedtpTSQLTID 278
Cdd:PRK00423  239 KAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKEL----AEKLDIK 307
TFIIB pfam00382
Transcription factor TFIIB repeat;
82-173 3.71e-35

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 123.91  E-value: 3.71e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717  82 RAQTLQNGRRHIHHLGSQLQLNQHCLDTAFNFFKMAVSKHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVNVY 161
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEY 80

                          90
                  ....*....|..
gi 1958782717 162 VLGKTFLLLARE 173
Cdd:pfam00382  81 TIGKTFKELKKA 92
TFIIB pfam00382
Transcription factor TFIIB repeat;
176-270 2.20e-33

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 119.29  E-value: 2.20e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717 176 INAPAIDPCLYIPRFAHLLEFGEKnheVSMTALRLLQRMKRDWMHTGRRPSGLCGAALLVAARMHDFRRTVKEVISVVKV 255
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEK---VADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQV 77

                          90
                  ....*....|....*
gi 1958782717 256 CESTLRKRLTEFEDT 270
Cdd:pfam00382  78 TEYTIGKTFKELKKA 92
CYCLIN_TFIIB_archaea_like_rpt2 cd20550
second cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 182-269 3.53e-15

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: 69.92  E-value: 3.53e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717 182 DPCLYIPRFAHLLEFGEknhEVSMTALRLLQRMKRDWMHTGRRPSGLCGAALLVAARMHDFRRTVKEVISVVKVCESTLR 261
Cdd:cd20550     1 DPADYVPRFASKLGLSG---EVQRKAIEILEKAKKKGLTSGKGPAGLAAAAIYIASLLTGERRTQKEIAEVAGVTEVTIR 77


                  ....*...
gi 1958782717 262 KRLTEFED 269
Cdd:cd20550    78 NRYKELLE 85
CYCLIN_TFIIB_archaea_like_rpt1 cd20549
first cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 86-174 2.19e-14

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: 68.07  E-value: 2.19e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717  86 LQNGRRHIHHLGSQLQLNQHCLDTAFNFFKMAVSKHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVNVYVLGK 165
Cdd:cd20549     9 LAQALSELDRMASKLGLPRSVREEAAVIYRKAVEKGLVRGRSIESVVAAALYAACRICNVPRTLDEIAEATRVSRKEIAR 88


                  ....*....
gi 1958782717 166 TFLLLAREL 174
Cdd:cd20549    89 CYRLLAREL 97
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 93-169 3.39e-13

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: 64.35  E-value: 3.39e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958782717  93 IHHLGSQLQLNQHCLDTAFNFFKMAVSKHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVNVYVLGKTFLL 169
Cdd:cd00043     6 IRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEKELRKAEKE 82
TF_Zn_Ribbon pfam08271
TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the ...
 4-46 5.76e-13

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: 62.71  E-value: 5.76e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1958782717   4 RVCRGCGGTDIELDAARGDAVCTGCGSVLEDNIIVSEVQFVEN 46
Cdd:pfam08271   1 YKCPNCGSTNLVEDYERGELVCTDCGLVLEDNSIDEGPEWREF 43
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 182-263 9.84e-11

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: 57.42  E-value: 9.84e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717 182 DPCLYIPRFAHLLEFgekNHEVSMTALRLLQRMKRDWMHTGRRPSGLCGAALLVAARMHDFRRTVKEVISVVKVCESTLR 261
Cdd:cd00043     1 KAVDFIRRLCSKLGL---PEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEKELR 77


                  ..
gi 1958782717 262 KR 263
Cdd:cd00043    78 KA 79
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 93-158 5.87e-10

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


Pssm-ID: 214641 [Multi-domain]  Cd Length: 83  Bit Score: 55.29  E-value: 5.87e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958782717   93 IHHLGSQLQLNQHCLDTAFNFFKMAVSKHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQV 158
Cdd:smart00385   3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGY 68
CYCLIN_BRF2 cd20555
cyclin box found in B-related factor 2 (BRF-2) and similar proteins; BRF-2, also called ...
 86-176 2.67e-07

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: 48.04  E-value: 2.67e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717  86 LQNGRRHIHHLGSQLQLNQHCLDTAFNFFKMAVS----KHLTRGRKMAHViAACLYLVCRTEGTPHMLLDLSDLLQVNVY 161
Cdd:cd20555     4 LKQGLKRVRDLCRVLRLSSVMEETAVELFEQAFKhpdfRHIRLEKKEVLV-GCCVYIVCRQNNWPVTMGDICSLLQCDVS 82

                          90
                  ....*....|....*
gi 1958782717 162 VLGKTFLLLARELCI 176
Cdd:cd20555    83 DFSSVYKELLKELNI 97
CYCLIN_TFIIB_rpt1 cd20551
first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 88-174 4.47e-07

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: 47.20  E-value: 4.47e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958782717  88 NGRRHIHHLGSQLQLNQHCLDTAFNFFKMAVSKHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVNVYVLGKTF 167
Cdd:cd20551     1 AAFKEIGEMADRMNLPRTIKDRAKELFKQVHDQKSLKGRSNDAIAAACLYIACRQEGVPRTFKEICAVSNVSKKEIGRCF 80


                  ....*..
gi 1958782717 168 LLLAREL 174
Cdd:cd20551    81 KLILKAL 87
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 186-263 1.21e-06

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: 46.05  E-value: 1.21e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958782717  186 YIPRFAHLLEFgekNHEVSMTALRLLQRMKRDWMHTGRRPSGLCGAALLVAARMHDFRRTVKEVISVVKVC-ESTLRKR 263
Cdd:smart00385   2 FLRRVCKALNL---DPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYFtEEEILRM 77
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 92-146 2.22e-03

first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or SRB11, is a component of the Mediator complex, a coactivator involved in regulated gene transcription of nearly all RNA polymerase II-dependent genes. It mediates stress-induced mitochondrial fission and apoptosis. CCNC contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain.


Pssm-ID: 410217 [Multi-domain]  Cd Length: 101  Bit Score: 37.19  E-value: 2.22e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958782717  92 HIHHLGSQLQLNQHCLDTAFNFFKMAVSKHLTRGRKMAHVIAACLYLVCRTEGTP 146
Cdd:cd20513     8 FIQALGERLKLRQRVIATAIVYFKRFYARNSFKDIDPRLVAPTCLYLASKVEECP 62
CCL1 COG5333
Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision ...
 93-147 5.28e-03

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: 38.17  E-value: 5.28e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958782717  93 IHHLGSQLQLNQHCLDTAFNFFKMAVSKHLTRGRKMAHVIAACLYLVCRTEGTPH 147
Cdd:COG5333    52 IMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPR 106
 
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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