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Conserved domains on  [gi|697503463|ref|XP_009680371|]
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PREDICTED: transcription factor IIIB 50 kDa subunit [Struthio camelus australis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CYCLIN_BRF2 cd20555
cyclin box found in B-related factor 2 (BRF-2) and similar proteins; BRF-2, also called ...
 32-128 3.93e-49

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: 160.14  E-value: 3.93e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697503463  32 SRCVQRGIKRVQDLCKVLQLPSVFEETAVSYFQRALQHPSFHLVSLEKKELLGGCCVFVTCRQHNWPLTMGTICSLLYAK 111
Cdd:cd20555    1 SRGLKQGLKRVRDLCRVLRLSSVMEETAVELFEQAFKHPDFRHIRLEKKEVLVGCCVYIVCRQNNWPVTMGDICSLLQCD 80

                         90
                 ....*....|....*..
gi 697503463 112 KELFASVYLSVQKELEL 128
Cdd:cd20555   81 VSDFSSVYKELLKELNI 97
 
Name Accession Description Interval E-value
CYCLIN_BRF2 cd20555
cyclin box found in B-related factor 2 (BRF-2) and similar proteins; BRF-2, also called ...
 32-128 3.93e-49

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: 160.14  E-value: 3.93e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697503463  32 SRCVQRGIKRVQDLCKVLQLPSVFEETAVSYFQRALQHPSFHLVSLEKKELLGGCCVFVTCRQHNWPLTMGTICSLLYAK 111
Cdd:cd20555    1 SRGLKQGLKRVRDLCRVLRLSSVMEETAVELFEQAFKHPDFRHIRLEKKEVLVGCCVYIVCRQNNWPVTMGDICSLLQCD 80

                         90
                 ....*....|....*..
gi 697503463 112 KELFASVYLSVQKELEL 128
Cdd:cd20555   81 VSDFSSVYKELLKELNI 97
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 45-196 1.60e-06

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 49.06  E-value: 1.60e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697503463  45 LCKVLQLPSVFEETAVSYFQRALQhpsfhlvslekKELLGG--------CCVFVTCRQHNWPLTMGTICSLLYAKKELFA 116
Cdd:COG1405  132 LASALGLPDSVRETAAVIYRKAVE-----------KGLLRGrsiegvaaAALYAACRQAGVPRTLDEIAEVSRVDRKEIA 200

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697503463 117 SVYLSVQKELELSVPALSLMD-LAKthLSSfrlfqrAADIPapfvedkEKMVTRTMQIVELASETWLVTGRHPVPLitAA 195
Cdd:COG1405  201 RAYRLLNRELGLKVPPIDPIEyIPR--IAS------ELGLS-------EEVERRAREILEKAKEKGLTSGKNPAGL--AA 263


                 .
gi 697503463 196 A 196
Cdd:COG1405  264 A 264
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 40-105 1.05e-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: 37.57  E-value: 1.05e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 697503463    40 KRVQDLCKVLQLPSVFEETAVSYFQRALQHPSFHLVSLekkELLGGCCVFVTCRQHNWPLTMGTIC 105
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSP---SLIAAAALYLASKTEETPPWTKELV 63
 
Name Accession Description Interval E-value
CYCLIN_BRF2 cd20555
cyclin box found in B-related factor 2 (BRF-2) and similar proteins; BRF-2, also called ...
 32-128 3.93e-49

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: 160.14  E-value: 3.93e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697503463  32 SRCVQRGIKRVQDLCKVLQLPSVFEETAVSYFQRALQHPSFHLVSLEKKELLGGCCVFVTCRQHNWPLTMGTICSLLYAK 111
Cdd:cd20555    1 SRGLKQGLKRVRDLCRVLRLSSVMEETAVELFEQAFKHPDFRHIRLEKKEVLVGCCVYIVCRQNNWPVTMGDICSLLQCD 80

                         90
                 ....*....|....*..
gi 697503463 112 KELFASVYLSVQKELEL 128
Cdd:cd20555   81 VSDFSSVYKELLKELNI 97
CYCLIN_SF cd00043
Cyclin box fold superfamily; The cyclin box is a protein binding domain that functions in ...
 37-120 5.82e-09

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: 52.41  E-value: 5.82e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697503463  37 RGIKRVQDLCKVLQLPSVFEETAVSYFQRALQHPSFHLVSLEkkeLLGGCCVFVTCRQHNWPLTMGTICSLLYAKKELFA 116
Cdd:cd00043    1 KAVDFIRRLCSKLGLPEEVLELAIELLDRFLSKGLLLGRSPE---LIAAACLYLACKLEELPRTLKEIAKVSGVSEKELR 77


                 ....
gi 697503463 117 SVYL 120
Cdd:cd00043   78 KAEK 81
SUA7 COG1405
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB ...
 45-196 1.60e-06

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


Pssm-ID: 441015 [Multi-domain]  Cd Length: 309  Bit Score: 49.06  E-value: 1.60e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697503463  45 LCKVLQLPSVFEETAVSYFQRALQhpsfhlvslekKELLGG--------CCVFVTCRQHNWPLTMGTICSLLYAKKELFA 116
Cdd:COG1405  132 LASALGLPDSVRETAAVIYRKAVE-----------KGLLRGrsiegvaaAALYAACRQAGVPRTLDEIAEVSRVDRKEIA 200

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697503463 117 SVYLSVQKELELSVPALSLMD-LAKthLSSfrlfqrAADIPapfvedkEKMVTRTMQIVELASETWLVTGRHPVPLitAA 195
Cdd:COG1405  201 RAYRLLNRELGLKVPPIDPIEyIPR--IAS------ELGLS-------EEVERRAREILEKAKEKGLTSGKNPAGL--AA 263


                 .
gi 697503463 196 A 196
Cdd:COG1405  264 A 264
CYCLIN smart00385
domain present in cyclins, TFIIB and Retinoblastoma; A helical domain present in cyclins and ...
 40-105 1.05e-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: 37.57  E-value: 1.05e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 697503463    40 KRVQDLCKVLQLPSVFEETAVSYFQRALQHPSFHLVSLekkELLGGCCVFVTCRQHNWPLTMGTIC 105
Cdd:smart00385   1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSP---SLIAAAALYLASKTEETPPWTKELV 63
CYCLIN_TFIIIB90_rpt1 cd20553
first cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar ...
 35-98 1.24e-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: 37.51  E-value: 1.24e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 697503463  35 VQRGIKRVQDLCKVLQLPSVFEETAVSYFQRALQHpsfHLVSLEKKELLGGCCVFVTCRQHNWP 98
Cdd:cd20553    3 LQNGRRKIQQLGSQLKLNQHHIDTAFRFYKLAVQR---NFTRGRKTSHVAAACLYIVCRREKTP 63
CYCLIN_TFIIB_rpt1 cd20551
first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins; ...
 37-127 4.44e-03

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: 36.03  E-value: 4.44e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697503463  37 RGIKRVQDLCKVLQLPSVFEETAVSYFQRALQHPSfhlvsLEKK--ELLGGCCVFVTCRQHNWPLTMGTICSLLYAKKEL 114
Cdd:cd20551    1 AAFKEIGEMADRMNLPRTIKDRAKELFKQVHDQKS-----LKGRsnDAIAAACLYIACRQEGVPRTFKEICAVSNVSKKE 75

                         90
                 ....*....|...
gi 697503463 115 FASVYLSVQKELE 127
Cdd:cd20551   76 IGRCFKLILKALE 88
 
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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