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Conserved domains on  [gi|145361010|ref|NP_182035|]
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Cyclin/Brf1-like TBP-binding protein [Arabidopsis thaliana]

Protein Classification

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 ...
 172-263 1.52e-44

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: 152.67  E-value: 1.52e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010 172 KLVDPSIFIPRFSNMLLKGAHNNKLVLTATHIIASMKRDWMQTGRKPSGICGAALYTAALSHGIKCSKTDIVNIVHICEA 251
Cdd:cd20554    1 PVIDPSLYIHRFASKLEFGDKTHEVANTALRLVQRMKRDWIHTGRRPSGICGAALLIAARMHGFKRTVEEIVRVVRVCES 80

                         90
                 ....*....|..
gi 145361010 252 TLTKRLIEFGDT 263
Cdd:cd20554   81 TLRKRLREFEKT 92
CYCLIN_SF super family cl40454
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 71-162 4.86e-30

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.


The actual alignment was detected with superfamily member cd20553:

Pssm-ID: 477360 [Multi-domain]  Cd Length: 91  Bit Score: 113.01  E-value: 4.86e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010  71 IRKATDELMNLRDALGIGDDrddVIVMASNFFRIALDHNFTKGRSKELVFSSCLYLTCRQFKLAVLLIDFSSYLRVSVYD 150
Cdd:cd20553    3 LQNGRRKIQQLGSQLKLNQH---HIDTAFRFYKLAVQRNFTRGRKTSHVAAACLYIVCRREKTPHMLIDFSDVLQVNVYV 79

                         90
                 ....*....|..
gi 145361010 151 LGSVYLQLCDML 162
Cdd:cd20553   80 LGKTFLKLCKLL 91
BRF1 pfam07741
Brf1-like TBP-binding domain; In budding yeasts, Brf1 forms the TFIIIB complex with ...
 371-480 4.63e-23

Brf1-like TBP-binding domain; In budding yeasts, Brf1 forms the TFIIIB complex with TATA-binding protein (TBP) and Bdp1. The TFIIIB complex can be recruited to the Pol III promoters and form an exceptionally kinetically stable TFIIIB-DNA complex, which then recruits the Pol III enzymatic complex and helps maintain it for multiple transcription cycles in a process called facilitated recycling. This entry represents the TATA binding protein (TBP) binding domain of Brf1 that covers both the Brf homology II and III regions.


:

Pssm-ID: 462250 [Multi-domain]  Cd Length: 98  Bit Score: 93.78  E-value: 4.63e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010  371 SDVDDRELDCYFRTPEEVRLVKIFFDHENPGYDEKEAAKKAAGLNACNNASNifeaskaaaaksrKEKRQQRAEEEKNAP 450
Cdd:pfam07741   1 SDLDDDELDNYILSEEEVKIKERIWVELNKDYLEEQAEKRLKAEAAEAAGKP-------------KKKRKRKKKEKKNIG 67

                          90       100       110
                  ....*....|....*....|....*....|.
gi 145361010  451 PPATGIEAVDSMVKRKKF-RDINCDYLEELF 480
Cdd:pfam07741  68 PASTAAEAAKNMLKKKKFsKKINYDALKSLF 98
 
Name Accession Description Interval E-value
CYCLIN_TFIIIB90_rpt2 cd20554
second cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 172-263 1.52e-44

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: 152.67  E-value: 1.52e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010 172 KLVDPSIFIPRFSNMLLKGAHNNKLVLTATHIIASMKRDWMQTGRKPSGICGAALYTAALSHGIKCSKTDIVNIVHICEA 251
Cdd:cd20554    1 PVIDPSLYIHRFASKLEFGDKTHEVANTALRLVQRMKRDWIHTGRRPSGICGAALLIAARMHGFKRTVEEIVRVVRVCES 80

                         90
                 ....*....|..
gi 145361010 252 TLTKRLIEFGDT 263
Cdd:cd20554   81 TLRKRLREFEKT 92
CYCLIN_TFIIIB90_rpt1 cd20553
first cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 71-162 4.86e-30

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: 113.01  E-value: 4.86e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010  71 IRKATDELMNLRDALGIGDDrddVIVMASNFFRIALDHNFTKGRSKELVFSSCLYLTCRQFKLAVLLIDFSSYLRVSVYD 150
Cdd:cd20553    3 LQNGRRKIQQLGSQLKLNQH---HIDTAFRFYKLAVQRNFTRGRKTSHVAAACLYIVCRREKTPHMLIDFSDVLQVNVYV 79

                         90
                 ....*....|..
gi 145361010 151 LGSVYLQLCDML 162
Cdd:cd20553   80 LGKTFLKLCKLL 91
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 63-264 2.46e-23

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 100.67  E-value: 2.46e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010  63 MSSSRERIIRKATDELMNLRDALGIGDDrddVIVMASNFFRIALDHNFTKGRSKELVFSSCLYLTCRQFKLAVLLIDFSS 142
Cdd:COG1405  114 VSSSKERNLVQALSEIDRLASALGLPDS---VRETAAVIYRKAVEKGLLRGRSIEGVAAAALYAACRQAGVPRTLDEIAE 190

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010 143 YLRVSVYDLGSVY------LQLcDMlyitenhnyeKLVDPSIFIPRFSNML-LKGahnnKLVLTATHIIASMKRDWMQTG 215
Cdd:COG1405  191 VSRVDRKEIARAYrllnreLGL-KV----------PPIDPIEYIPRIASELgLSE----EVERRAREILEKAKEKGLTSG 255

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 145361010 216 RKPSGICGAALYTAALSHGIKCSKTDIVNIVHICEATLTKR---LIEFGDTE 264
Cdd:COG1405  256 KNPAGLAAAALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRykeLLEALGIE 307
BRF1 pfam07741
Brf1-like TBP-binding domain; In budding yeasts, Brf1 forms the TFIIIB complex with ...
 371-480 4.63e-23

Brf1-like TBP-binding domain; In budding yeasts, Brf1 forms the TFIIIB complex with TATA-binding protein (TBP) and Bdp1. The TFIIIB complex can be recruited to the Pol III promoters and form an exceptionally kinetically stable TFIIIB-DNA complex, which then recruits the Pol III enzymatic complex and helps maintain it for multiple transcription cycles in a process called facilitated recycling. This entry represents the TATA binding protein (TBP) binding domain of Brf1 that covers both the Brf homology II and III regions.


Pssm-ID: 462250 [Multi-domain]  Cd Length: 98  Bit Score: 93.78  E-value: 4.63e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010  371 SDVDDRELDCYFRTPEEVRLVKIFFDHENPGYDEKEAAKKAAGLNACNNASNifeaskaaaaksrKEKRQQRAEEEKNAP 450
Cdd:pfam07741   1 SDLDDDELDNYILSEEEVKIKERIWVELNKDYLEEQAEKRLKAEAAEAAGKP-------------KKKRKRKKKEKKNIG 67

                          90       100       110
                  ....*....|....*....|....*....|.
gi 145361010  451 PPATGIEAVDSMVKRKKF-RDINCDYLEELF 480
Cdd:pfam07741  68 PASTAAEAAKNMLKKKKFsKKINYDALKSLF 98
tfb PRK00423
transcription initiation factor IIB; Reviewed
 64-259 4.62e-17

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 81.98  E-value: 4.62e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010  64 SSSRERIIRKATDELMNLRDALGIGDDrddVIVMASNFFRIALDHNFTKGRSKELVFSSCLYLTCRQFKLAVLLIDFSSY 143
Cdd:PRK00423 115 SNAAERNLAFALSELDRIASQLGLPRS---VREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEV 191

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010 144 LRVSVYDLGSVYLQLCDMLYITenhnyEKLVDPSIFIPRFSNML-LKGAHNNKlvltATHIIASMKRDWMQTGRKPSGIC 222
Cdd:PRK00423 192 SRVSRKEIGRCYRFLLRELNLK-----LPPTDPIDYVPRFASELgLSGEVQKK----AIEILQKAKEKGLTSGKGPTGLA 262

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 145361010 223 GAALYTAALSHGIKCSKTDIVNIVHICEATLTKRLIE 259
Cdd:PRK00423 263 AAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKE 299
TFIIB pfam00382
Transcription factor TFIIB repeat;
173-263 3.44e-16

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 73.83  E-value: 3.44e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010  173 LVDPSIFIPRFSNMLlkgAHNNKLVLTATHIIASMKRDWMQTGRKPSGICGAALYTAALSHGIKCSKTDIVNIVHICEAT 252
Cdd:pfam00382   5 LIDARRFIPRFADAL---ELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEYT 81

                          90
                  ....*....|.
gi 145361010  253 LTKRLIEFGDT 263
Cdd:pfam00382  82 IGKTFKELKKA 92
TFIIB pfam00382
Transcription factor TFIIB repeat;
67-158 2.62e-10

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 57.27  E-value: 2.62e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010   67 RERIIRKATDELMNLRDALGIGDDrddVIVMASNFFRIALDHNFTKGRSKELVFSSCLYLTCRQFKLAVLLIDFSSYLRV 146
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEK---VADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQV 77

                          90
                  ....*....|..
gi 145361010  147 SVYDLGSVYLQL 158
Cdd:pfam00382  78 TEYTIGKTFKEL 89
 
Name Accession Description Interval E-value
CYCLIN_TFIIIB90_rpt2 cd20554
second cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 172-263 1.52e-44

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: 152.67  E-value: 1.52e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010 172 KLVDPSIFIPRFSNMLLKGAHNNKLVLTATHIIASMKRDWMQTGRKPSGICGAALYTAALSHGIKCSKTDIVNIVHICEA 251
Cdd:cd20554    1 PVIDPSLYIHRFASKLEFGDKTHEVANTALRLVQRMKRDWIHTGRRPSGICGAALLIAARMHGFKRTVEEIVRVVRVCES 80

                         90
                 ....*....|..
gi 145361010 252 TLTKRLIEFGDT 263
Cdd:cd20554   81 TLRKRLREFEKT 92
CYCLIN_TFIIIB90_rpt1 cd20553
first cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 71-162 4.86e-30

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: 113.01  E-value: 4.86e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010  71 IRKATDELMNLRDALGIGDDrddVIVMASNFFRIALDHNFTKGRSKELVFSSCLYLTCRQFKLAVLLIDFSSYLRVSVYD 150
Cdd:cd20553    3 LQNGRRKIQQLGSQLKLNQH---HIDTAFRFYKLAVQRNFTRGRKTSHVAAACLYIVCRREKTPHMLIDFSDVLQVNVYV 79

                         90
                 ....*....|..
gi 145361010 151 LGSVYLQLCDML 162
Cdd:cd20553   80 LGKTFLKLCKLL 91
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 63-264 2.46e-23

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 100.67  E-value: 2.46e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010  63 MSSSRERIIRKATDELMNLRDALGIGDDrddVIVMASNFFRIALDHNFTKGRSKELVFSSCLYLTCRQFKLAVLLIDFSS 142
Cdd:COG1405  114 VSSSKERNLVQALSEIDRLASALGLPDS---VRETAAVIYRKAVEKGLLRGRSIEGVAAAALYAACRQAGVPRTLDEIAE 190

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010 143 YLRVSVYDLGSVY------LQLcDMlyitenhnyeKLVDPSIFIPRFSNML-LKGahnnKLVLTATHIIASMKRDWMQTG 215
Cdd:COG1405  191 VSRVDRKEIARAYrllnreLGL-KV----------PPIDPIEYIPRIASELgLSE----EVERRAREILEKAKEKGLTSG 255

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 145361010 216 RKPSGICGAALYTAALSHGIKCSKTDIVNIVHICEATLTKR---LIEFGDTE 264
Cdd:COG1405  256 KNPAGLAAAALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRykeLLEALGIE 307
BRF1 pfam07741
Brf1-like TBP-binding domain; In budding yeasts, Brf1 forms the TFIIIB complex with ...
 371-480 4.63e-23

Brf1-like TBP-binding domain; In budding yeasts, Brf1 forms the TFIIIB complex with TATA-binding protein (TBP) and Bdp1. The TFIIIB complex can be recruited to the Pol III promoters and form an exceptionally kinetically stable TFIIIB-DNA complex, which then recruits the Pol III enzymatic complex and helps maintain it for multiple transcription cycles in a process called facilitated recycling. This entry represents the TATA binding protein (TBP) binding domain of Brf1 that covers both the Brf homology II and III regions.


Pssm-ID: 462250 [Multi-domain]  Cd Length: 98  Bit Score: 93.78  E-value: 4.63e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010  371 SDVDDRELDCYFRTPEEVRLVKIFFDHENPGYDEKEAAKKAAGLNACNNASNifeaskaaaaksrKEKRQQRAEEEKNAP 450
Cdd:pfam07741   1 SDLDDDELDNYILSEEEVKIKERIWVELNKDYLEEQAEKRLKAEAAEAAGKP-------------KKKRKRKKKEKKNIG 67

                          90       100       110
                  ....*....|....*....|....*....|.
gi 145361010  451 PPATGIEAVDSMVKRKKF-RDINCDYLEELF 480
Cdd:pfam07741  68 PASTAAEAAKNMLKKKKFsKKINYDALKSLF 98
tfb PRK00423
transcription initiation factor IIB; Reviewed
 64-259 4.62e-17

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 81.98  E-value: 4.62e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010  64 SSSRERIIRKATDELMNLRDALGIGDDrddVIVMASNFFRIALDHNFTKGRSKELVFSSCLYLTCRQFKLAVLLIDFSSY 143
Cdd:PRK00423 115 SNAAERNLAFALSELDRIASQLGLPRS---VREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEV 191

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010 144 LRVSVYDLGSVYLQLCDMLYITenhnyEKLVDPSIFIPRFSNML-LKGAHNNKlvltATHIIASMKRDWMQTGRKPSGIC 222
Cdd:PRK00423 192 SRVSRKEIGRCYRFLLRELNLK-----LPPTDPIDYVPRFASELgLSGEVQKK----AIEILQKAKEKGLTSGKGPTGLA 262

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 145361010 223 GAALYTAALSHGIKCSKTDIVNIVHICEATLTKRLIE 259
Cdd:PRK00423 263 AAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKE 299
TFIIB pfam00382
Transcription factor TFIIB repeat;
173-263 3.44e-16

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 73.83  E-value: 3.44e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010  173 LVDPSIFIPRFSNMLlkgAHNNKLVLTATHIIASMKRDWMQTGRKPSGICGAALYTAALSHGIKCSKTDIVNIVHICEAT 252
Cdd:pfam00382   5 LIDARRFIPRFADAL---ELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEYT 81

                          90
                  ....*....|.
gi 145361010  253 LTKRLIEFGDT 263
Cdd:pfam00382  82 IGKTFKELKKA 92
TFIIB pfam00382
Transcription factor TFIIB repeat;
67-158 2.62e-10

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 57.27  E-value: 2.62e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010   67 RERIIRKATDELMNLRDALGIGDDrddVIVMASNFFRIALDHNFTKGRSKELVFSSCLYLTCRQFKLAVLLIDFSSYLRV 146
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEK---VADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQV 77

                          90
                  ....*....|..
gi 145361010  147 SVYDLGSVYLQL 158
Cdd:pfam00382  78 TEYTIGKTFKEL 89
CYCLIN_TFIIB_archaea_like_rpt2 cd20550
second cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 175-259 1.48e-09

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: 54.90  E-value: 1.48e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010 175 DPSIFIPRFSNML-LKGahnnKLVLTATHIIASMKRDWMQTGRKPSGICGAALYTAALSHGIKCSKTDIVNIVHICEATL 253
Cdd:cd20550    1 DPADYVPRFASKLgLSG----EVQRKAIEILEKAKKKGLTSGKGPAGLAAAAIYIASLLTGERRTQKEIAEVAGVTEVTI 76


                 ....*.
gi 145361010 254 TKRLIE 259
Cdd:cd20550   77 RNRYKE 82
CYCLIN_TFIIB_archaea_like_rpt1 cd20549
first cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 64-155 1.15e-08

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: 52.66  E-value: 1.15e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010  64 SSSRERIIRKATDELMNLRDALGIGDDrddVIVMASNFFRIALDHNFTKGRSKELVFSSCLYLTCRQFKLAVLLIDFSSY 143
Cdd:cd20549    2 STAAERNLAQALSELDRMASKLGLPRS---VREEAAVIYRKAVEKGLVRGRSIESVVAAALYAACRICNVPRTLDEIAEA 78

                         90
                 ....*....|..
gi 145361010 144 LRVSVYDLGSVY 155
Cdd:cd20549   79 TRVSRKEIARCY 90
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 73-157 1.26e-08

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: 52.03  E-value: 1.26e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145361010  73 KATDELMNLRDALGIGDDrddVIVMASNFFRIALDHNFTKGRSKELVFSSCLYLTCRQFKLAVLLIDFSSYLRVSVYDLG 152
Cdd:cd00043    1 KAVDFIRRLCSKLGLPEE---VLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEKELR 77


                 ....*
gi 145361010 153 SVYLQ 157
Cdd:cd00043   78 KAEKE 82
CYCLIN_BRF2 cd20555
cyclin box found in B-related factor 2 (BRF-2) and similar proteins; BRF-2, also called ...
 98-158 5.71e-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: 47.66  E-value: 5.71e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 145361010  98 ASNFFRIALDHNFTKGRS---KELVFSSCLYLTCRQFKLAVLLIDFSSYLRVSVYDLGSVYLQL 158
Cdd:cd20555   28 AVELFEQAFKHPDFRHIRlekKEVLVGCCVYIVCRQNNWPVTMGDICSLLQCDVSDFSSVYKEL 91
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 179-256 2.48e-04

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: 40.09  E-value: 2.48e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 145361010 179 FIPRFSNMLLkgaHNNKLVLTATHIIASMKRDWMQTGRKPSGICGAALYTAALSHGIKCSKTDIVNIVHICEATLTKR 256
Cdd:cd00043    5 FIRRLCSKLG---LPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEKELRKA 79
CYCLIN_TFIIB_rpt1 cd20551
first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 98-155 5.14e-04

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: 39.11  E-value: 5.14e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 145361010  98 ASNFFRIALDHNFTKGRSKELVFSSCLYLTCRQFKLAVLLIDFSSYLRVSVYDLGSVY 155
Cdd:cd20551   23 AKELFKQVHDQKSLKGRSNDAIAAACLYIACRQEGVPRTFKEICAVSNVSKKEIGRCF 80
 
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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