NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|767980346|ref|XP_011534975|]
View 

transcription factor IIIB 90 kDa subunit isoform X3 [Homo sapiens]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
CYCLIN_TFIIIB90_rpt1 cd20553
first cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 84-174 6.62e-56

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: 183.89  E-value: 6.62e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346  84 QTLQNGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVNVYVL 163
Cdd:cd20553    1 ITLQNGRRKIQQLGSQLKLNQHHIDTAFRFYKLAVQRNFTRGRKTSHVAAACLYIVCRREKTPHMLIDFSDVLQVNVYVL 80

                         90
                 ....*....|.
gi 767980346 164 GKTFLLLAREL 174
Cdd:cd20553   81 GKTFLKLCKLL 91
BRF1 pfam07741
Brf1-like TBP-binding domain; In budding yeasts, Brf1 forms the TFIIIB complex with ...
 400-496 1.16e-38

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: 137.69  E-value: 1.16e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346  400 SGIDDLEIDRYILNESEARVKAELWMRENAEYLREQREKEARIAKEKELGIYKEHKPKKSCKRREPIQASTAREAIEKML 479
Cdd:pfam07741   1 SDLDDDELDNYILSEEEVKIKERIWVELNKDYLEEQAEKRLKAEAAEAAGKPKKKRKRKKKEKKNIGPASTAAEAAKNML 80

                          90
                  ....*....|....*..
gi 767980346  480 EQKKISSKINYSVLRGL 496
Cdd:pfam07741  81 KKKKFSKKINYDALKSL 97
SUA7 super family cl34255
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 4-216 6.24e-20

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


The actual alignment was detected with superfamily member COG1405:

Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 91.04  E-value: 6.24e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346   4 RVCRGCGGTDIELDAARGDAVCTACGSVLEDNII--VSEVQ-FVESSGGGSSAVGQFVSL----------------DGAG 64
Cdd:COG1405   12 SVCPECGGENLVTDTERGETVCEDCGLVVEEDVIdrGPEWRaFDSEERDERSRTGAPLTLarhdkglsteigwqdkDAYG 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346  65 KTptLGGG--------------FHVnlgKESRAQTLQNGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAH 130
Cdd:COG1405   92 KS--LSGRkrrqlarlrkwqnrSRV---SSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEKGLLRGRSIEG 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346 131 VIAACLYLVCRTEGTPHMLLDLSDLLQVNVYVLGKTFLLLARELCINAPAI----------------------------- 181
Cdd:COG1405  167 VAAAALYAACRQAGVPRTLDEIAEVSRVDRKEIARAYRLLNRELGLKVPPIdpieyipriaselglseeverrareilek 246

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 767980346 182 ------------------ALLVAARMHDFRRTVKEVISVVKVCESTLRKRLTE 216
Cdd:COG1405  247 akekgltsgknpaglaaaALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRYKE 299
 
Name Accession Description Interval E-value
CYCLIN_TFIIIB90_rpt1 cd20553
first cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 84-174 6.62e-56

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: 183.89  E-value: 6.62e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346  84 QTLQNGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVNVYVL 163
Cdd:cd20553    1 ITLQNGRRKIQQLGSQLKLNQHHIDTAFRFYKLAVQRNFTRGRKTSHVAAACLYIVCRREKTPHMLIDFSDVLQVNVYVL 80

                         90
                 ....*....|.
gi 767980346 164 GKTFLLLAREL 174
Cdd:cd20553   81 GKTFLKLCKLL 91
BRF1 pfam07741
Brf1-like TBP-binding domain; In budding yeasts, Brf1 forms the TFIIIB complex with ...
 400-496 1.16e-38

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: 137.69  E-value: 1.16e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346  400 SGIDDLEIDRYILNESEARVKAELWMRENAEYLREQREKEARIAKEKELGIYKEHKPKKSCKRREPIQASTAREAIEKML 479
Cdd:pfam07741   1 SDLDDDELDNYILSEEEVKIKERIWVELNKDYLEEQAEKRLKAEAAEAAGKPKKKRKRKKKEKKNIGPASTAAEAAKNML 80

                          90
                  ....*....|....*..
gi 767980346  480 EQKKISSKINYSVLRGL 496
Cdd:pfam07741  81 KKKKFSKKINYDALKSL 97
TFIIB pfam00382
Transcription factor TFIIB repeat;
82-173 2.60e-34

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 125.45  E-value: 2.60e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346   82 RAQTLQNGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVNVY 161
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEY 80

                          90
                  ....*....|..
gi 767980346  162 VLGKTFLLLARE 173
Cdd:pfam00382  81 TIGKTFKELKKA 92
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 4-216 6.24e-20

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 91.04  E-value: 6.24e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346   4 RVCRGCGGTDIELDAARGDAVCTACGSVLEDNII--VSEVQ-FVESSGGGSSAVGQFVSL----------------DGAG 64
Cdd:COG1405   12 SVCPECGGENLVTDTERGETVCEDCGLVVEEDVIdrGPEWRaFDSEERDERSRTGAPLTLarhdkglsteigwqdkDAYG 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346  65 KTptLGGG--------------FHVnlgKESRAQTLQNGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAH 130
Cdd:COG1405   92 KS--LSGRkrrqlarlrkwqnrSRV---SSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEKGLLRGRSIEG 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346 131 VIAACLYLVCRTEGTPHMLLDLSDLLQVNVYVLGKTFLLLARELCINAPAI----------------------------- 181
Cdd:COG1405  167 VAAAALYAACRQAGVPRTLDEIAEVSRVDRKEIARAYRLLNRELGLKVPPIdpieyipriaselglseeverrareilek 246

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 767980346 182 ------------------ALLVAARMHDFRRTVKEVISVVKVCESTLRKRLTE 216
Cdd:COG1405  247 akekgltsgknpaglaaaALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRYKE 299
tfb PRK00423
transcription initiation factor IIB; Reviewed
 4-228 1.37e-17

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 83.90  E-value: 1.37e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346   4 RVCRGCGGTDIELDAARGDAVCTACGSVLEDNIIVSEVQ---FVESSGGGSSAVGQFVSL----------------DGAG 64
Cdd:PRK00423  12 LVCPECGSDKLIYDYERGEIVCADCGLVIEENIIDQGPEwraFDPEQREKRSRVGAPMTYtihdkglstdidwrnkDSYG 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346  65 KTPTLGGGFHV-NLGKESR------------AQTLQNGRRhihhLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHV 131
Cdd:PRK00423  92 KSISGKNRAQLyRLRKWQRrirvsnaaernlAFALSELDR----IASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGV 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346 132 IAACLYLVCRTEGTPHMLLDLSDLLQVNVYVLGKTFLLLARELCINAP-------------------------------- 179
Cdd:PRK00423 168 VAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPptdpidyvprfaselglsgevqkkaieilqka 247

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767980346 180 ---------------AIALLVAARMHDFRRTVKEVISVVKVCESTLRKRLTEFedtpTSQLTID 228
Cdd:PRK00423 248 kekgltsgkgptglaAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKEL----AEKLDIK 307
CYCLIN_TFIIIB90_rpt2 cd20554
second cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 182-220 1.50e-17

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: 77.94  E-value: 1.50e-17
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 767980346 182 ALLVAARMHDFRRTVKEVISVVKVCESTLRKRLTEFEDT 220
Cdd:cd20554   54 ALLIAARMHGFKRTVEEIVRVVRVCESTLRKRLREFEKT 92
TF_Zn_Ribbon pfam08271
TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the ...
 4-45 2.47e-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: 64.25  E-value: 2.47e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 767980346    4 RVCRGCGGTDIELDAARGDAVCTACGSVLEDNIIVSEVQFVE 45
Cdd:pfam08271   1 YKCPNCGSTNLVEDYERGELVCTDCGLVLEDNSIDEGPEWRE 42
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 93-158 8.15e-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: 55.68  E-value: 8.15e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767980346    93 IHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQV 158
Cdd:smart00385   3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGY 68
 
Name Accession Description Interval E-value
CYCLIN_TFIIIB90_rpt1 cd20553
first cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 84-174 6.62e-56

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: 183.89  E-value: 6.62e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346  84 QTLQNGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVNVYVL 163
Cdd:cd20553    1 ITLQNGRRKIQQLGSQLKLNQHHIDTAFRFYKLAVQRNFTRGRKTSHVAAACLYIVCRREKTPHMLIDFSDVLQVNVYVL 80

                         90
                 ....*....|.
gi 767980346 164 GKTFLLLAREL 174
Cdd:cd20553   81 GKTFLKLCKLL 91
BRF1 pfam07741
Brf1-like TBP-binding domain; In budding yeasts, Brf1 forms the TFIIIB complex with ...
 400-496 1.16e-38

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: 137.69  E-value: 1.16e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346  400 SGIDDLEIDRYILNESEARVKAELWMRENAEYLREQREKEARIAKEKELGIYKEHKPKKSCKRREPIQASTAREAIEKML 479
Cdd:pfam07741   1 SDLDDDELDNYILSEEEVKIKERIWVELNKDYLEEQAEKRLKAEAAEAAGKPKKKRKRKKKEKKNIGPASTAAEAAKNML 80

                          90
                  ....*....|....*..
gi 767980346  480 EQKKISSKINYSVLRGL 496
Cdd:pfam07741  81 KKKKFSKKINYDALKSL 97
TFIIB pfam00382
Transcription factor TFIIB repeat;
82-173 2.60e-34

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 125.45  E-value: 2.60e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346   82 RAQTLQNGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVNVY 161
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEY 80

                          90
                  ....*....|..
gi 767980346  162 VLGKTFLLLARE 173
Cdd:pfam00382  81 TIGKTFKELKKA 92
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 4-216 6.24e-20

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 91.04  E-value: 6.24e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346   4 RVCRGCGGTDIELDAARGDAVCTACGSVLEDNII--VSEVQ-FVESSGGGSSAVGQFVSL----------------DGAG 64
Cdd:COG1405   12 SVCPECGGENLVTDTERGETVCEDCGLVVEEDVIdrGPEWRaFDSEERDERSRTGAPLTLarhdkglsteigwqdkDAYG 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346  65 KTptLGGG--------------FHVnlgKESRAQTLQNGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAH 130
Cdd:COG1405   92 KS--LSGRkrrqlarlrkwqnrSRV---SSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEKGLLRGRSIEG 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346 131 VIAACLYLVCRTEGTPHMLLDLSDLLQVNVYVLGKTFLLLARELCINAPAI----------------------------- 181
Cdd:COG1405  167 VAAAALYAACRQAGVPRTLDEIAEVSRVDRKEIARAYRLLNRELGLKVPPIdpieyipriaselglseeverrareilek 246

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 767980346 182 ------------------ALLVAARMHDFRRTVKEVISVVKVCESTLRKRLTE 216
Cdd:COG1405  247 akekgltsgknpaglaaaALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRYKE 299
tfb PRK00423
transcription initiation factor IIB; Reviewed
 4-228 1.37e-17

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 83.90  E-value: 1.37e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346   4 RVCRGCGGTDIELDAARGDAVCTACGSVLEDNIIVSEVQ---FVESSGGGSSAVGQFVSL----------------DGAG 64
Cdd:PRK00423  12 LVCPECGSDKLIYDYERGEIVCADCGLVIEENIIDQGPEwraFDPEQREKRSRVGAPMTYtihdkglstdidwrnkDSYG 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346  65 KTPTLGGGFHV-NLGKESR------------AQTLQNGRRhihhLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHV 131
Cdd:PRK00423  92 KSISGKNRAQLyRLRKWQRrirvsnaaernlAFALSELDR----IASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGV 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346 132 IAACLYLVCRTEGTPHMLLDLSDLLQVNVYVLGKTFLLLARELCINAP-------------------------------- 179
Cdd:PRK00423 168 VAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPptdpidyvprfaselglsgevqkkaieilqka 247

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767980346 180 ---------------AIALLVAARMHDFRRTVKEVISVVKVCESTLRKRLTEFedtpTSQLTID 228
Cdd:PRK00423 248 kekgltsgkgptglaAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKEL----AEKLDIK 307
CYCLIN_TFIIIB90_rpt2 cd20554
second cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 182-220 1.50e-17

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: 77.94  E-value: 1.50e-17
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 767980346 182 ALLVAARMHDFRRTVKEVISVVKVCESTLRKRLTEFEDT 220
Cdd:cd20554   54 ALLIAARMHGFKRTVEEIVRVVRVCESTLRKRLREFEKT 92
TF_Zn_Ribbon pfam08271
TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the ...
 4-45 2.47e-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: 64.25  E-value: 2.47e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 767980346    4 RVCRGCGGTDIELDAARGDAVCTACGSVLEDNIIVSEVQFVE 45
Cdd:pfam08271   1 YKCPNCGSTNLVEDYERGELVCTDCGLVLEDNSIDEGPEWRE 42
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 93-169 4.40e-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: 64.74  E-value: 4.40e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767980346  93 IHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVNVYVLGKTFLL 169
Cdd:cd00043    6 IRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEKELRKAEKE 82
CYCLIN_TFIIB_archaea_like_rpt1 cd20549
first cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 86-174 1.87e-12

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: 63.84  E-value: 1.87e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346  86 LQNGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVNVYVLGK 165
Cdd:cd20549    9 LAQALSELDRMASKLGLPRSVREEAAVIYRKAVEKGLVRGRSIESVVAAALYAACRICNVPRTLDEIAEATRVSRKEIAR 88


                 ....*....
gi 767980346 166 TFLLLAREL 174
Cdd:cd20549   89 CYRLLAREL 97
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 93-158 8.15e-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: 55.68  E-value: 8.15e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767980346    93 IHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQV 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 2.00e-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: 49.20  E-value: 2.00e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346  86 LQNGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVS----RHLTRGRKMAHViAACLYLVCRTEGTPHMLLDLSDLLQVNVY 161
Cdd:cd20555    4 LKQGLKRVRDLCRVLRLSSVMEETAVELFEQAFKhpdfRHIRLEKKEVLV-GCCVYIVCRQNNWPVTMGDICSLLQCDVS 82

                         90
                 ....*....|....*
gi 767980346 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 2.93e-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: 48.35  E-value: 2.93e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767980346  88 NGRRHIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTPHMLLDLSDLLQVNVYVLGKTF 167
Cdd:cd20551    1 AAFKEIGEMADRMNLPRTIKDRAKELFKQVHDQKSLKGRSNDAIAAACLYIACRQEGVPRTFKEICAVSNVSKKEIGRCF 80


                 ....*..
gi 767980346 168 LLLAREL 174
Cdd:cd20551   81 KLILKAL 87
CYCLIN_CCNC_rpt1 cd20513
first cyclin box found in cyclin-C (CCNC) and similar proteins; CCNC, also termed CycC, or ...
 92-146 1.11e-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: 38.73  E-value: 1.11e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 767980346  92 HIHHLGNQLQLNQHCLDTAFNFFKMAVSRHLTRGRKMAHVIAACLYLVCRTEGTP 146
Cdd:cd20513    8 FIQALGERLKLRQRVIATAIVYFKRFYARNSFKDIDPRLVAPTCLYLASKVEECP 62
CYCLIN_TFIIB_archaea_like_rpt2 cd20550
second cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 180-219 2.95e-03

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: 37.18  E-value: 2.95e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 767980346 180 AIALLVAARMHDFRRTVKEVISVVKVCESTLRKRLTEFED 219
Cdd:cd20550   46 AAAIYIASLLTGERRTQKEIAEVAGVTEVTIRNRYKELLE 85
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH