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Conserved domains on  [gi|2410728031|ref|WP_268541260|]
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transcription initiation factor IIB family protein [Candidatus Nitrosotenuis cloacae]

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
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 4-301 1.20e-154

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


:

Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 434.26  E-value: 1.20e-154
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031   4 QINTERRCKRCKGL-MVTDSATGERFCTTCGFVISEQVEDSGPE-RHFSKDERDDKSRSGIPTSLAIHDMGLATVIGTVN 81
Cdd:COG1405     7 EEEETSVCPECGGEnLVTDTERGETVCEDCGLVVEEDVIDRGPEwRAFDSEERDERSRTGAPLTLARHDKGLSTEIGWQD 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031  82 KDATGKPLSAHMKHDMTRLRTWDSRSQMHEQTDRNLRQAFTHLDKLKDKLALSDAVVEKAAYIYRKALSKSLVRGRSIEG 161
Cdd:COG1405    87 KDAYGKSLSGRKRRQLARLRKWQNRSRVSSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEKGLLRGRSIEG 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031 162 VLAAAVYAACRDAETPRTLSDVSDAINVKRKDLTKNYRLLVIELDLRMPVVNSISCMSKIASKVGLSEKVKRGALAILKE 241
Cdd:COG1405   167 VAAAALYAACRQAGVPRTLDEIAEVSRVDRKEIARAYRLLNRELGLKVPPIDPIEYIPRIASELGLSEEVERRAREILEK 246

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031 242 ANDMRITAGKDPMGMAATALYISCMKYNEDVSQREIAHAAGVTEVTIRNRYKDLKKSLNL 301
Cdd:COG1405   247 AKEKGLTSGKNPAGLAAAALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRYKELLEALGI 306
 
Name Accession Description Interval E-value
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 4-301 1.20e-154

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 434.26  E-value: 1.20e-154
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031   4 QINTERRCKRCKGL-MVTDSATGERFCTTCGFVISEQVEDSGPE-RHFSKDERDDKSRSGIPTSLAIHDMGLATVIGTVN 81
Cdd:COG1405     7 EEEETSVCPECGGEnLVTDTERGETVCEDCGLVVEEDVIDRGPEwRAFDSEERDERSRTGAPLTLARHDKGLSTEIGWQD 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031  82 KDATGKPLSAHMKHDMTRLRTWDSRSQMHEQTDRNLRQAFTHLDKLKDKLALSDAVVEKAAYIYRKALSKSLVRGRSIEG 161
Cdd:COG1405    87 KDAYGKSLSGRKRRQLARLRKWQNRSRVSSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEKGLLRGRSIEG 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031 162 VLAAAVYAACRDAETPRTLSDVSDAINVKRKDLTKNYRLLVIELDLRMPVVNSISCMSKIASKVGLSEKVKRGALAILKE 241
Cdd:COG1405   167 VAAAALYAACRQAGVPRTLDEIAEVSRVDRKEIARAYRLLNRELGLKVPPIDPIEYIPRIASELGLSEEVERRAREILEK 246

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031 242 ANDMRITAGKDPMGMAATALYISCMKYNEDVSQREIAHAAGVTEVTIRNRYKDLKKSLNL 301
Cdd:COG1405   247 AKEKGLTSGKNPAGLAAAALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRYKELLEALGI 306
tfb PRK00423
transcription initiation factor IIB; Reviewed
 1-301 7.11e-112

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 325.81  E-value: 7.11e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031   1 MVMQINTERRCKRC-KGLMVTDSATGERFCTTCGFVISEQVEDSGPE-RHFSKDERDDKSRSGIPTSLAIHDMGLATVIG 78
Cdd:PRK00423    4 LVLEEEEKLVCPECgSDKLIYDYERGEIVCADCGLVIEENIIDQGPEwRAFDPEQREKRSRVGAPMTYTIHDKGLSTDID 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031  79 TVNKDATGKPLSAHMKHDMTRLRTWDSRSQMHEQTDRNLRQAFTHLDKLKDKLALSDAVVEKAAYIYRKALSKSLVRGRS 158
Cdd:PRK00423   84 WRNKDSYGKSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRS 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031 159 IEGVLAAAVYAACRDAETPRTLSDVSDAINVKRKDLTKNYRLLVIELDLRMPVVNSISCMSKIASKVGLSEKVKRGALAI 238
Cdd:PRK00423  164 IEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSGEVQKKAIEI 243

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2410728031 239 LKEANDMRITAGKDPMGMAATALYISCMKYNEDVSQREIAHAAGVTEVTIRNRYKDLKKSLNL 301
Cdd:PRK00423  244 LQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAEKLDI 306
CYCLIN_TFIIB_archaea_like_rpt2 cd20550
second cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 214-299 1.16e-35

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: 123.47  E-value: 1.16e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031 214 SISCMSKIASKVGLSEKVKRGALAILKEANDMRITAGKDPMGMAATALYISCMKYNEDVSQREIAHAAGVTEVTIRNRYK 293
Cdd:cd20550     2 PADYVPRFASKLGLSGEVQRKAIEILEKAKKKGLTSGKGPAGLAAAAIYIASLLTGERRTQKEIAEVAGVTEVTIRNRYK 81


                  ....*.
gi 2410728031 294 DLKKSL 299
Cdd:cd20550    82 ELLEAL 87
TFIIB pfam00382
Transcription factor TFIIB repeat;
209-297 2.98e-17

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 75.37  E-value: 2.98e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031 209 MPVVNSISCMSKIASKVGLSEKVKRGALAILKEANDMRITAGKDPMGMAATALYISCMKYNEDVSQREIAHAAGVTEVTI 288
Cdd:pfam00382   3 QTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEYTI 82


                  ....*....
gi 2410728031 289 RNRYKDLKK 297
Cdd:pfam00382  83 GKTFKELKK 91
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 130-202 5.39e-05

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: 41.04  E-value: 5.39e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2410728031  130 KLALSDAVVEKAAYIYRKALSKSLVRGRSIEGVLAAAVYAACRDAETPRTLSDVSDAINV-KRKDLTKNYRLLV 202
Cdd:smart00385   9 ALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYfTEEEILRMERLLL 82
 
Name Accession Description Interval E-value
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 4-301 1.20e-154

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 434.26  E-value: 1.20e-154
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031   4 QINTERRCKRCKGL-MVTDSATGERFCTTCGFVISEQVEDSGPE-RHFSKDERDDKSRSGIPTSLAIHDMGLATVIGTVN 81
Cdd:COG1405     7 EEEETSVCPECGGEnLVTDTERGETVCEDCGLVVEEDVIDRGPEwRAFDSEERDERSRTGAPLTLARHDKGLSTEIGWQD 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031  82 KDATGKPLSAHMKHDMTRLRTWDSRSQMHEQTDRNLRQAFTHLDKLKDKLALSDAVVEKAAYIYRKALSKSLVRGRSIEG 161
Cdd:COG1405    87 KDAYGKSLSGRKRRQLARLRKWQNRSRVSSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEKGLLRGRSIEG 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031 162 VLAAAVYAACRDAETPRTLSDVSDAINVKRKDLTKNYRLLVIELDLRMPVVNSISCMSKIASKVGLSEKVKRGALAILKE 241
Cdd:COG1405   167 VAAAALYAACRQAGVPRTLDEIAEVSRVDRKEIARAYRLLNRELGLKVPPIDPIEYIPRIASELGLSEEVERRAREILEK 246

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031 242 ANDMRITAGKDPMGMAATALYISCMKYNEDVSQREIAHAAGVTEVTIRNRYKDLKKSLNL 301
Cdd:COG1405   247 AKEKGLTSGKNPAGLAAAALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRYKELLEALGI 306
tfb PRK00423
transcription initiation factor IIB; Reviewed
 1-301 7.11e-112

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 325.81  E-value: 7.11e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031   1 MVMQINTERRCKRC-KGLMVTDSATGERFCTTCGFVISEQVEDSGPE-RHFSKDERDDKSRSGIPTSLAIHDMGLATVIG 78
Cdd:PRK00423    4 LVLEEEEKLVCPECgSDKLIYDYERGEIVCADCGLVIEENIIDQGPEwRAFDPEQREKRSRVGAPMTYTIHDKGLSTDID 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031  79 TVNKDATGKPLSAHMKHDMTRLRTWDSRSQMHEQTDRNLRQAFTHLDKLKDKLALSDAVVEKAAYIYRKALSKSLVRGRS 158
Cdd:PRK00423   84 WRNKDSYGKSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRS 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031 159 IEGVLAAAVYAACRDAETPRTLSDVSDAINVKRKDLTKNYRLLVIELDLRMPVVNSISCMSKIASKVGLSEKVKRGALAI 238
Cdd:PRK00423  164 IEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSGEVQKKAIEI 243

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2410728031 239 LKEANDMRITAGKDPMGMAATALYISCMKYNEDVSQREIAHAAGVTEVTIRNRYKDLKKSLNL 301
Cdd:PRK00423  244 LQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAEKLDI 306
CYCLIN_TFIIB_archaea_like_rpt2 cd20550
second cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 214-299 1.16e-35

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: 123.47  E-value: 1.16e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031 214 SISCMSKIASKVGLSEKVKRGALAILKEANDMRITAGKDPMGMAATALYISCMKYNEDVSQREIAHAAGVTEVTIRNRYK 293
Cdd:cd20550     2 PADYVPRFASKLGLSGEVQRKAIEILEKAKKKGLTSGKGPAGLAAAAIYIASLLTGERRTQKEIAEVAGVTEVTIRNRYK 81


                  ....*.
gi 2410728031 294 DLKKSL 299
Cdd:cd20550    82 ELLEAL 87
CYCLIN_TFIIB_archaea_like_rpt1 cd20549
first cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 113-207 2.89e-32

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: 115.07  E-value: 2.89e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031 113 TDRNLRQAFTHLDKLKDKLALSDAVVEKAAYIYRKALSKSLVRGRSIEGVLAAAVYAACRDAETPRTLSDVSDAINVKRK 192
Cdd:cd20549     5 AERNLAQALSELDRMASKLGLPRSVREEAAVIYRKAVEKGLVRGRSIESVVAAALYAACRICNVPRTLDEIAEATRVSRK 84

                          90
                  ....*....|....*
gi 2410728031 193 DLTKNYRLLVIELDL 207
Cdd:cd20549    85 EIARCYRLLARELNL 99
TFIIB pfam00382
Transcription factor TFIIB repeat;
209-297 2.98e-17

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 75.37  E-value: 2.98e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031 209 MPVVNSISCMSKIASKVGLSEKVKRGALAILKEANDMRITAGKDPMGMAATALYISCMKYNEDVSQREIAHAAGVTEVTI 288
Cdd:pfam00382   3 QTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEYTI 82


                  ....*....
gi 2410728031 289 RNRYKDLKK 297
Cdd:pfam00382  83 GKTFKELKK 91
TFIIB pfam00382
Transcription factor TFIIB repeat;
113-202 1.36e-16

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 73.45  E-value: 1.36e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031 113 TDRNLRQAFTHLDKLKDKLALSDAVVEKAAYIYRKALSKSLVRGRSIEGVLAAAVYAACRDAETPRTLSDVSDAINVKRK 192
Cdd:pfam00382   1 RDQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEY 80

                          90
                  ....*....|
gi 2410728031 193 DLTKNYRLLV 202
Cdd:pfam00382  81 TIGKTFKELK 90
CYCLIN_TFIIB_rpt2 cd20552
second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 218-295 2.77e-16

second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; TFIIB, also called B-related factor 2 (BRF-2) or S300-II, is a general transcription factor that plays a role in transcription initiation by RNA polymerase II (Pol II). It is involved in the pre-initiation complex (PIC) formation and Pol II recruitment at promoter DNA. TFIIB contains two cyclin boxes. This model corresponds to the second one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIB.


Pssm-ID: 410255 [Multi-domain]  Cd Length: 97  Bit Score: 72.70  E-value: 2.77e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2410728031 218 MSKIASKVGLSEKVKRGALAILKEANDMRITAGKDPMGMAATALYISCMKYNEDVSQREIAHAAGVTEVTIRNRYKDL 295
Cdd:cd20552     6 MSRFCSNLGLPNQVQKAATHIAKKAVELDLVAGRSPISVAAAAIYMASQLSEEKKTQKEIGDVAGVAEVTIRQSYKLL 83
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 119-200 7.51e-15

Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in cell-cycle and transcriptional control. It is about 100 amino acids in length, composed of five helices, and is present in cyclins, transcription initiation factor IIB (TFIIB), and retinoblastoma tumour suppressor protein (Rb). Cyclins consist of 8 classes of cell cycle regulators that function as regulatory subunits of cyclin-dependent kinases (CDKs), which are serine/threonine kinases. The catalytic activities of CDKs are modulated not only by their interactions with cyclins but also by CDK inhibitors (CKIs). CDKs, cyclins and CKIs play key roles in transcription, epigenetic regulation, metabolism, stem cell self-renewal, neuronal functions, and spermatogenesis. TFIIB is a transcription factor that binds the TATA box. Members in this superfamily contain one or two copies of the cyclin box.


Pssm-ID: 410207 [Multi-domain]  Cd Length: 82  Bit Score: 68.59  E-value: 7.51e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031 119 QAFTHLDKLKDKLALSDAVVEKAAYIYRKALSKSLVRGRSIEGVLAAAVYAACRDAETPRTLSDVSDAINVKRKDLTKNY 198
Cdd:cd00043     1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEKELRKAE 80


                  ..
gi 2410728031 199 RL 200
Cdd:cd00043    81 KE 82
CYCLIN_TFIIB_rpt1 cd20551
first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 120-206 1.40e-12

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: 62.22  E-value: 1.40e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031 120 AFTHLDKLKDKLALSDAVVEKAAYIYRKALSKSLVRGRSIEGVLAAAVYAACRDAETPRTLSDVSDAINVKRKDLTKNYR 199
Cdd:cd20551     2 AFKEIGEMADRMNLPRTIKDRAKELFKQVHDQKSLKGRSNDAIAAACLYIACRQEGVPRTFKEICAVSNVSKKEIGRCFK 81


                  ....*..
gi 2410728031 200 LLVIELD 206
Cdd:cd20551    82 LILKALE 88
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 218-294 1.49e-12

Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in cell-cycle and transcriptional control. It is about 100 amino acids in length, composed of five helices, and is present in cyclins, transcription initiation factor IIB (TFIIB), and retinoblastoma tumour suppressor protein (Rb). Cyclins consist of 8 classes of cell cycle regulators that function as regulatory subunits of cyclin-dependent kinases (CDKs), which are serine/threonine kinases. The catalytic activities of CDKs are modulated not only by their interactions with cyclins but also by CDK inhibitors (CKIs). CDKs, cyclins and CKIs play key roles in transcription, epigenetic regulation, metabolism, stem cell self-renewal, neuronal functions, and spermatogenesis. TFIIB is a transcription factor that binds the TATA box. Members in this superfamily contain one or two copies of the cyclin box.


Pssm-ID: 410207 [Multi-domain]  Cd Length: 82  Bit Score: 62.04  E-value: 1.49e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2410728031 218 MSKIASKVGLSEKVKRGALAILKEANDMRITAGKDPMGMAATALYISCMKYNEDVSQREIAHAAGVTEVTIRNRYKD 294
Cdd:cd00043     6 IRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEKELRKAEKE 82
CYCLIN_TFIIIB90_rpt1 cd20553
first cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 117-205 1.33e-10

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: 56.77  E-value: 1.33e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031 117 LRQAFTHLDKLKDKLALSDAVVEKAAYIYRKALSKSLVRGRSIEGVLAAAVYAACRDAETPRTLSDVSDAINVKRKDLTK 196
Cdd:cd20553     3 LQNGRRKIQQLGSQLKLNQHHIDTAFRFYKLAVQRNFTRGRKTSHVAAACLYIVCRREKTPHMLIDFSDVLQVNVYVLGK 82


                  ....*....
gi 2410728031 197 NYRLLVIEL 205
Cdd:cd20553    83 TFLKLCKLL 91
CYCLIN_BRF2 cd20555
cyclin box found in B-related factor 2 (BRF-2) and similar proteins; BRF-2, also called ...
 115-207 1.54e-10

cyclin box found in B-related factor 2 (BRF-2) and similar proteins; BRF-2, also called transcription factor IIIB 50 kDa subunit (TFIIIB50), or BRFU, is a general activator of RNA polymerase (Pol) III transcription and is required for Pol III transcription of genes with promoter elements upstream of the initiation sites. It recruits Pol III to type III gene-external promoters, including the U6 spliceosomal RNA and selenocysteine tRNA genes. BRF-2 contains one cyclin box. The cyclin box fold is generally a protein binding domain, but binds DNA in BRF-2.


Pssm-ID: 410258 [Multi-domain]  Cd Length: 97  Bit Score: 56.90  E-value: 1.54e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031 115 RNLRQAFTHLDKLKDKLALSDAVVEKAAYIYRKALSKSLVRGRSIEG--VLA-AAVYAACRDAETPRTLSDVSDAINVKR 191
Cdd:cd20555     2 RGLKQGLKRVRDLCRVLRLSSVMEETAVELFEQAFKHPDFRHIRLEKkeVLVgCCVYIVCRQNNWPVTMGDICSLLQCDV 81

                          90
                  ....*....|....*.
gi 2410728031 192 KDLTKNYRLLVIELDL 207
Cdd:cd20555    82 SDFSSVYKELLKELNI 97
CYCLIN_TFIIB_rpt2 cd20552
second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 131-201 8.29e-06

second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; TFIIB, also called B-related factor 2 (BRF-2) or S300-II, is a general transcription factor that plays a role in transcription initiation by RNA polymerase II (Pol II). It is involved in the pre-initiation complex (PIC) formation and Pol II recruitment at promoter DNA. TFIIB contains two cyclin boxes. This model corresponds to the second one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIB.


Pssm-ID: 410255 [Multi-domain]  Cd Length: 97  Bit Score: 43.81  E-value: 8.29e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2410728031 131 LALSDAVVEKAAYIYRKALSKSLVRGRSIEGVLAAAVYAACRDAETPRTLSDVSDAINVKRKDLTKNYRLL 201
Cdd:cd20552    13 LGLPNQVQKAATHIAKKAVELDLVAGRSPISVAAAAIYMASQLSEEKKTQKEIGDVAGVAEVTIRQSYKLL 83
TF_Zn_Ribbon pfam08271
TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the ...
 9-49 9.26e-06

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: 41.91  E-value: 9.26e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2410728031   9 RRCKRCKG-LMVTDSATGERFCTTCGFVISEQVEDSGPE-RHF 49
Cdd:pfam08271   1 YKCPNCGStNLVEDYERGELVCTDCGLVLEDNSIDEGPEwREF 43
CYCLIN_TFIIIB90_rpt2 cd20554
second cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 228-297 1.02e-05

second cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar proteins; TFIIIB90, also called B-related factor 1 (BRF-1), or TATA box-binding protein-associated factor, RNA polymerase III, subunit 2 (TAF3B2), is a general activator of RNA polymerase which utilizes different TFIIIB complexes at structurally distinct promoters. TFIIIB90 contains two cyclin boxes. This model corresponds to the second one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIIB90.


Pssm-ID: 410257 [Multi-domain]  Cd Length: 92  Bit Score: 43.27  E-value: 1.02e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031 228 SEKVKRGALAILKEANDMRITAGKDPMGMAATALYISCMKYNEDVSQREIAHAAGVTEVTIRNRYKDLKK 297
Cdd:cd20554    22 THEVANTALRLVQRMKRDWIHTGRRPSGICGAALLIAARMHGFKRTVEEIVRVVRVCESTLRKRLREFEK 91
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 130-202 5.39e-05

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: 41.04  E-value: 5.39e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2410728031  130 KLALSDAVVEKAAYIYRKALSKSLVRGRSIEGVLAAAVYAACRDAETPRTLSDVSDAINV-KRKDLTKNYRLLV 202
Cdd:smart00385   9 ALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYfTEEEILRMERLLL 82
CYCLIN_TFIIB_rpt1 cd20551
first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 219-300 1.68e-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: 39.88  E-value: 1.68e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2410728031 219 SKIASKVGLSEKVKRGALAILKEANDMRITAGKDPMGMAATALYISCMKYNEDVSQREIAHAAGVTEVTIRNRYKDLKKS 298
Cdd:cd20551     7 GEMADRMNLPRTIKDRAKELFKQVHDQKSLKGRSNDAIAAACLYIACRQEGVPRTFKEICAVSNVSKKEIGRCFKLILKA 86


                  ..
gi 2410728031 299 LN 300
Cdd:cd20551    87 LE 88
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 218-295 5.73e-03

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: 35.26  E-value: 5.73e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2410728031  218 MSKIASKVGLSEKVKRGALAILKEANDMRITAGKDPMGMAATALYISCMKYNEDVSQREIAHAAGV-TEVTIRNRYKDL 295
Cdd:smart00385   3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYfTEEEILRMERLL 81
 
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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