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Conserved domains on  [gi|1519956849|gb|RPI84191|]
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MAG: transcription initiation factor IIB [Nitrosopumilales archaeon]

Protein Classification

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 9-299 4.26e-162

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


:

Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 453.13  E-value: 4.26e-162
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849   9 SDRCPRCGKGPMVTDNSSGEMFCGNCGFVVTERIEETGPEWRAFSKEEHEDRSRAGIPTSLAMHDMGLATIIGPVDKDAS 88
Cdd:COG1405    11 TSVCPECGGENLVTDTERGETVCEDCGLVVEEDVIDRGPEWRAFDSEERDERSRTGAPLTLARHDKGLSTEIGWQDKDAY 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849  89 GKPLSASMKSTIERLRTWDSRSQVHEPVDRNFRQAFSELDRLKDKLAVGDAVIEKAAYVYRKALEKGLVRGRSISALVAA 168
Cdd:COG1405    91 GKSLSGRKRRQLARLRKWQNRSRVSSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEKGLLRGRSIEGVAAA 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849 169 ALYAACRDTETPRTLKDIAHASNIKKKDVARCYRLLIRELDLKMPVVDPVKCVARIASKSGLSEKTKRKALEILKKAEQG 248
Cdd:COG1405   171 ALYAACRQAGVPRTLDEIAEVSRVDRKEIARAYRLLNRELGLKVPPIDPIEYIPRIASELGLSEEVERRAREILEKAKEK 250

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1519956849 249 KISAGKDPMGLAAAALYVACVMNGENKTQKDVAEAAGVTEVTIRNRYKGLK 299
Cdd:COG1405   251 GLTSGKNPAGLAAAALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRYKELL 301
 
Name Accession Description Interval E-value
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 9-299 4.26e-162

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 453.13  E-value: 4.26e-162
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849   9 SDRCPRCGKGPMVTDNSSGEMFCGNCGFVVTERIEETGPEWRAFSKEEHEDRSRAGIPTSLAMHDMGLATIIGPVDKDAS 88
Cdd:COG1405    11 TSVCPECGGENLVTDTERGETVCEDCGLVVEEDVIDRGPEWRAFDSEERDERSRTGAPLTLARHDKGLSTEIGWQDKDAY 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849  89 GKPLSASMKSTIERLRTWDSRSQVHEPVDRNFRQAFSELDRLKDKLAVGDAVIEKAAYVYRKALEKGLVRGRSISALVAA 168
Cdd:COG1405    91 GKSLSGRKRRQLARLRKWQNRSRVSSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEKGLLRGRSIEGVAAA 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849 169 ALYAACRDTETPRTLKDIAHASNIKKKDVARCYRLLIRELDLKMPVVDPVKCVARIASKSGLSEKTKRKALEILKKAEQG 248
Cdd:COG1405   171 ALYAACRQAGVPRTLDEIAEVSRVDRKEIARAYRLLNRELGLKVPPIDPIEYIPRIASELGLSEEVERRAREILEKAKEK 250

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1519956849 249 KISAGKDPMGLAAAALYVACVMNGENKTQKDVAEAAGVTEVTIRNRYKGLK 299
Cdd:COG1405   251 GLTSGKNPAGLAAAALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRYKELL 301
tfb PRK00423
transcription initiation factor IIB; Reviewed
 11-304 2.77e-123

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 355.08  E-value: 2.77e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849  11 RCPRCGKGPMVTDNSSGEMFCGNCGFVVTERIEETGPEWRAFSKEEHEDRSRAGIPTSLAMHDMGLATIIGPVDKDASGK 90
Cdd:PRK00423   13 VCPECGSDKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQREKRSRVGAPMTYTIHDKGLSTDIDWRNKDSYGK 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849  91 PLSASMKSTIERLRTWDSRSQVHEPVDRNFRQAFSELDRLKDKLAVGDAVIEKAAYVYRKALEKGLVRGRSISALVAAAL 170
Cdd:PRK00423   93 SISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAAL 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849 171 YAACRDTETPRTLKDIAHASNIKKKDVARCYRLLIRELDLKMPVVDPVKCVARIASKSGLSEKTKRKALEILKKAEQGKI 250
Cdd:PRK00423  173 YAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSGEVQKKAIEILQKAKEKGL 252

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1519956849 251 SAGKDPMGLAAAALYVACVMNGENKTQKDVAEAAGVTEVTIRNRYKGLKIHLKL 304
Cdd:PRK00423  253 TSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAEKLDI 306
CYCLIN_TFIIB_archaea_like_rpt2 cd20550
second cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 216-302 4.51e-42

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: 140.03  E-value: 4.51e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849 216 DPVKCVARIASKSGLSEKTKRKALEILKKAEQGKISAGKDPMGLAAAALYVACVMNGENKTQKDVAEAAGVTEVTIRNRY 295
Cdd:cd20550     1 DPADYVPRFASKLGLSGEVQRKAIEILEKAKKKGLTSGKGPAGLAAAAIYIASLLTGERRTQKEIAEVAGVTEVTIRNRY 80


                  ....*..
gi 1519956849 296 KGLKIHL 302
Cdd:cd20550    81 KELLEAL 87
TFIIB pfam00382
Transcription factor TFIIB repeat;
211-301 1.60e-21

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 86.54  E-value: 1.60e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849 211 KMPVVDPVKCVARIASKSGLSEKTKRKALEILKKAEQGKISAGKDPMGLAAAALYVACVMNGENKTQKDVAEAAGVTEVT 290
Cdd:pfam00382   2 DQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEYT 81

                          90
                  ....*....|.
gi 1519956849 291 IRNRYKGLKIH 301
Cdd:pfam00382  82 IGKTFKELKKA 92
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 223-296 1.03e-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: 45.66  E-value: 1.03e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1519956849  223 RIASKSGLSEKTKRKALEILKKAEQGKISAGKDPMGLAAAALYVACVMNGENKTQKDVAEAAGV-TEVTIRNRYK 296
Cdd:smart00385   5 RVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYfTEEEILRMER 79
 
Name Accession Description Interval E-value
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 9-299 4.26e-162

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 453.13  E-value: 4.26e-162
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849   9 SDRCPRCGKGPMVTDNSSGEMFCGNCGFVVTERIEETGPEWRAFSKEEHEDRSRAGIPTSLAMHDMGLATIIGPVDKDAS 88
Cdd:COG1405    11 TSVCPECGGENLVTDTERGETVCEDCGLVVEEDVIDRGPEWRAFDSEERDERSRTGAPLTLARHDKGLSTEIGWQDKDAY 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849  89 GKPLSASMKSTIERLRTWDSRSQVHEPVDRNFRQAFSELDRLKDKLAVGDAVIEKAAYVYRKALEKGLVRGRSISALVAA 168
Cdd:COG1405    91 GKSLSGRKRRQLARLRKWQNRSRVSSSKERNLVQALSEIDRLASALGLPDSVRETAAVIYRKAVEKGLLRGRSIEGVAAA 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849 169 ALYAACRDTETPRTLKDIAHASNIKKKDVARCYRLLIRELDLKMPVVDPVKCVARIASKSGLSEKTKRKALEILKKAEQG 248
Cdd:COG1405   171 ALYAACRQAGVPRTLDEIAEVSRVDRKEIARAYRLLNRELGLKVPPIDPIEYIPRIASELGLSEEVERRAREILEKAKEK 250

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1519956849 249 KISAGKDPMGLAAAALYVACVMNGENKTQKDVAEAAGVTEVTIRNRYKGLK 299
Cdd:COG1405   251 GLTSGKNPAGLAAAALYLAALLLGEKVTQKEVAEVAGVTEVTIRNRYKELL 301
tfb PRK00423
transcription initiation factor IIB; Reviewed
 11-304 2.77e-123

transcription initiation factor IIB; Reviewed


Pssm-ID: 234758 [Multi-domain]  Cd Length: 310  Bit Score: 355.08  E-value: 2.77e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849  11 RCPRCGKGPMVTDNSSGEMFCGNCGFVVTERIEETGPEWRAFSKEEHEDRSRAGIPTSLAMHDMGLATIIGPVDKDASGK 90
Cdd:PRK00423   13 VCPECGSDKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQREKRSRVGAPMTYTIHDKGLSTDIDWRNKDSYGK 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849  91 PLSASMKSTIERLRTWDSRSQVHEPVDRNFRQAFSELDRLKDKLAVGDAVIEKAAYVYRKALEKGLVRGRSISALVAAAL 170
Cdd:PRK00423   93 SISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAAL 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849 171 YAACRDTETPRTLKDIAHASNIKKKDVARCYRLLIRELDLKMPVVDPVKCVARIASKSGLSEKTKRKALEILKKAEQGKI 250
Cdd:PRK00423  173 YAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSGEVQKKAIEILQKAKEKGL 252

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1519956849 251 SAGKDPMGLAAAALYVACVMNGENKTQKDVAEAAGVTEVTIRNRYKGLKIHLKL 304
Cdd:PRK00423  253 TSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAEKLDI 306
CYCLIN_TFIIB_archaea_like_rpt2 cd20550
second cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 216-302 4.51e-42

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: 140.03  E-value: 4.51e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849 216 DPVKCVARIASKSGLSEKTKRKALEILKKAEQGKISAGKDPMGLAAAALYVACVMNGENKTQKDVAEAAGVTEVTIRNRY 295
Cdd:cd20550     1 DPADYVPRFASKLGLSGEVQRKAIEILEKAKKKGLTSGKGPAGLAAAAIYIASLLTGERRTQKEIAEVAGVTEVTIRNRY 80


                  ....*..
gi 1519956849 296 KGLKIHL 302
Cdd:cd20550    81 KELLEAL 87
CYCLIN_TFIIB_archaea_like_rpt1 cd20549
first cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar ...
 116-210 3.88e-30

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: 109.67  E-value: 3.88e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849 116 VDRNFRQAFSELDRLKDKLAVGDAVIEKAAYVYRKALEKGLVRGRSISALVAAALYAACRDTETPRTLKDIAHASNIKKK 195
Cdd:cd20549     5 AERNLAQALSELDRMASKLGLPRSVREEAAVIYRKAVEKGLVRGRSIESVVAAALYAACRICNVPRTLDEIAEATRVSRK 84

                          90
                  ....*....|....*
gi 1519956849 196 DVARCYRLLIRELDL 210
Cdd:cd20549    85 EIARCYRLLARELNL 99
TFIIB pfam00382
Transcription factor TFIIB repeat;
211-301 1.60e-21

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 86.54  E-value: 1.60e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849 211 KMPVVDPVKCVARIASKSGLSEKTKRKALEILKKAEQGKISAGKDPMGLAAAALYVACVMNGENKTQKDVAEAAGVTEVT 290
Cdd:pfam00382   2 DQTLIDARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEYT 81

                          90
                  ....*....|.
gi 1519956849 291 IRNRYKGLKIH 301
Cdd:pfam00382  82 IGKTFKELKKA 92
CYCLIN_TFIIB_rpt2 cd20552
second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 222-298 7.06e-17

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: 74.24  E-value: 7.06e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1519956849 222 ARIASKSGLSEKTKRKALEILKKAEQGKISAGKDPMGLAAAALYVACVMNGENKTQKDVAEAAGVTEVTIRNRYKGL 298
Cdd:cd20552     7 SRFCSNLGLPNQVQKAATHIAKKAVELDLVAGRSPISVAAAAIYMASQLSEEKKTQKEIGDVAGVAEVTIRQSYKLL 83
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 216-296 4.70e-16

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: 71.67  E-value: 4.70e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849 216 DPVKCVARIASKSGLSEKTKRKALEILKKAEQGKISAGKDPMGLAAAALYVACVMNGENKTQKDVAEAAGVTEVTIRNRY 295
Cdd:cd00043     1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEKELRKAE 80


                  .
gi 1519956849 296 K 296
Cdd:cd00043    81 K 81
CYCLIN_TFIIIB90_rpt2 cd20554
second cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 213-294 1.31e-12

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: 62.53  E-value: 1.31e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849 213 PVVDPVKCVARIASKSGLSEKTKR---KALEILKKAEQGKISAGKDPMGLAAAALYVACVMNGENKTQKDVAEAAGVTEV 289
Cdd:cd20554     1 PVIDPSLYIHRFASKLEFGDKTHEvanTALRLVQRMKRDWIHTGRRPSGICGAALLIAARMHGFKRTVEEIVRVVRVCES 80


                  ....*
gi 1519956849 290 TIRNR 294
Cdd:cd20554    81 TLRKR 85
CYCLIN_TFIIB_rpt1 cd20551
first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 123-209 2.09e-10

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: 56.44  E-value: 2.09e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849 123 AFSELDRLKDKLAVGDAVIEKAAYVYRKALEKGLVRGRSISALVAAALYAACRDTETPRTLKDIAHASNIKKKDVARCYR 202
Cdd:cd20551     2 AFKEIGEMADRMNLPRTIKDRAKELFKQVHDQKSLKGRSNDAIAAACLYIACRQEGVPRTFKEICAVSNVSKKEIGRCFK 81


                  ....*..
gi 1519956849 203 LLIRELD 209
Cdd:cd20551    82 LILKALE 88
TF_Zn_Ribbon pfam08271
TFIIB zinc-binding; The transcription factor TFIIB contains a zinc-binding motif near the ...
 11-52 3.36e-10

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: 54.62  E-value: 3.36e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1519956849  11 RCPRCGKGPMVTDNSSGEMFCGNCGFVVTERIEETGPEWRAF 52
Cdd:pfam08271   2 KCPNCGSTNLVEDYERGELVCTDCGLVLEDNSIDEGPEWREF 43
TFIIB pfam00382
Transcription factor TFIIB repeat;
123-207 5.08e-08

Transcription factor TFIIB repeat;


Pssm-ID: 425652 [Multi-domain]  Cd Length: 92  Bit Score: 49.95  E-value: 5.08e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849 123 AFSELDRLKDKLAVGDAVIEKAAYVYRKALEKGLVRGRSISALVAAALYAACRDTETPRTLKDIAHASNIKKKDVARCYR 202
Cdd:pfam00382   8 ARRFIPRFADALELPEKVADAAFEIAKLAVDDNLLKGRSPAGIAAACLYIACRLEGTKRTLKEISSVLQVTEYTIGKTFK 87


                  ....*
gi 1519956849 203 LLIRE 207
Cdd:pfam00382  88 ELKKA 92
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 122-203 6.01e-07

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: 46.63  E-value: 6.01e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849 122 QAFSELDRLKDKLAVGDAVIEKAAYVYRKALEKGLVRGRSISALVAAALYAACRDTETPRTLKDIAHASNIKKKDVARCY 201
Cdd:cd00043     1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPELIAAACLYLACKLEELPRTLKEIAKVSGVSEKELRKAE 80


                  ..
gi 1519956849 202 RL 203
Cdd:cd00043    81 KE 82
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 223-296 1.03e-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: 45.66  E-value: 1.03e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1519956849  223 RIASKSGLSEKTKRKALEILKKAEQGKISAGKDPMGLAAAALYVACVMNGENKTQKDVAEAAGV-TEVTIRNRYK 296
Cdd:smart00385   5 RVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKELVHYTGYfTEEEILRMER 79
CYCLIN_TFIIB_rpt1 cd20551
first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 219-303 1.82e-05

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: 42.57  E-value: 1.82e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849 219 KCVARIASKSGLSEKTKRKALEILKKAEQGKISAGKDPMGLAAAALYVACVMNGENKTQKDVAEAAGVTEVTIRNRYKGL 298
Cdd:cd20551     4 KEIGEMADRMNLPRTIKDRAKELFKQVHDQKSLKGRSNDAIAAACLYIACRQEGVPRTFKEICAVSNVSKKEIGRCFKLI 83


                  ....*
gi 1519956849 299 KIHLK 303
Cdd:cd20551    84 LKALE 88
CYCLIN_BRF2 cd20555
cyclin box found in B-related factor 2 (BRF-2) and similar proteins; BRF-2, also called ...
 118-210 1.93e-04

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: 39.95  E-value: 1.93e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849 118 RNFRQAFSELDRLKDKLAVGDAVIEKAAYVYRKALEKGLVRGRSISALVAAAL---YAACRDTETPRTLKDIAHASNIKK 194
Cdd:cd20555     2 RGLKQGLKRVRDLCRVLRLSSVMEETAVELFEQAFKHPDFRHIRLEKKEVLVGccvYIVCRQNNWPVTMGDICSLLQCDV 81

                          90
                  ....*....|....*.
gi 1519956849 195 KDVARCYRLLIRELDL 210
Cdd:cd20555    82 SDFSSVYKELLKELNI 97
CYCLIN_TFIIIB90_rpt1 cd20553
first cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 120-208 2.99e-03

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: 36.36  E-value: 2.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519956849 120 FRQAFSELDRLKDKLAVGDAVIEKAAYVYRKALEKGLVRGRSISALVAAALYAACRDTETPRTLKDIAHASNIKKKDVAR 199
Cdd:cd20553     3 LQNGRRKIQQLGSQLKLNQHHIDTAFRFYKLAVQRNFTRGRKTSHVAAACLYIVCRREKTPHMLIDFSDVLQVNVYVLGK 82


                  ....*....
gi 1519956849 200 CYRLLIREL 208
Cdd:cd20553    83 TFLKLCKLL 91
DZR pfam12773
Double zinc ribbon; This family consists of a pair of zinc ribbon domains.
 6-35 7.53e-03

Double zinc ribbon; This family consists of a pair of zinc ribbon domains.


Pssm-ID: 432773 [Multi-domain]  Cd Length: 45  Bit Score: 33.89  E-value: 7.53e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 1519956849   6 SLFSDRCPRCGkgpmvTDNSSGEMFCGNCG 35
Cdd:pfam12773  21 PLKPDRCPNCG-----APVPPNARFCPYCG 45
 
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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