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Conserved domains on  [gi|215694411|dbj|BAG89404|]
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unnamed protein product [Oryza sativa Japonica Group]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TOA2 super family cl34913
Transcription initiation factor IIA, gamma subunit [Transcription];
4-103 9.74e-34

Transcription initiation factor IIA, gamma subunit [Transcription];


The actual alignment was detected with superfamily member COG5123:

Pssm-ID: 227452 [Multi-domain]  Cd Length: 113  Bit Score: 112.74  E-value: 9.74e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215694411   4 FELYRRSTIGMCLTETLDEMVSSGTLSPELAIQVLVQFDKSMTEALENQVKSKVSIKGHLHTYRFCDNVWTFILTEASFK 83
Cdd:COG5123    5 YELYRRSMIGKVLEDALDELISAGVISPNLAMHVLETFDKSVPEVLNKSVTSSLTFKGKLDTYNFCDGVWTFITKNFVMS 84

                         90       100
                 ....*....|....*....|
gi 215694411  84 NEETTEQVGKVKIVACDSKL 103
Cdd:COG5123   85 LNNEYFNAGEVNIVACKARI 104
 
Name Accession Description Interval E-value
TOA2 COG5123
Transcription initiation factor IIA, gamma subunit [Transcription];
4-103 9.74e-34

Transcription initiation factor IIA, gamma subunit [Transcription];


Pssm-ID: 227452 [Multi-domain]  Cd Length: 113  Bit Score: 112.74  E-value: 9.74e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215694411   4 FELYRRSTIGMCLTETLDEMVSSGTLSPELAIQVLVQFDKSMTEALENQVKSKVSIKGHLHTYRFCDNVWTFILTEASFK 83
Cdd:COG5123    5 YELYRRSMIGKVLEDALDELISAGVISPNLAMHVLETFDKSVPEVLNKSVTSSLTFKGKLDTYNFCDGVWTFITKNFVMS 84

                         90       100
                 ....*....|....*....|
gi 215694411  84 NEETTEQVGKVKIVACDSKL 103
Cdd:COG5123   85 LNNEYFNAGEVNIVACKARI 104
TFIIA_gamma_N pfam02268
Transcription initiation factor IIA, gamma subunit, helical domain; Accurate transcription in ...
 4-49 1.25e-23

Transcription initiation factor IIA, gamma subunit, helical domain; Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA box. The N-terminal domain of the gamma subunit is a 4 helix bundle.


Pssm-ID: 460518  Cd Length: 46  Bit Score: 85.20  E-value: 1.25e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 215694411    4 FELYRRSTIGMCLTETLDEMVSSGTLSPELAIQVLVQFDKSMTEAL 49
Cdd:pfam02268   1 YELYRRTTLGMALTDTLDELIQDGRITPQLAMKVLEQFDKSINEAL 46
TFIIA_gamma_N cd10145
Gamma subunit of transcription initiation factor IIA, N-terminal helical domain; Transcription ...
 4-51 6.76e-22

Gamma subunit of transcription initiation factor IIA, N-terminal helical domain; Transcription factor II A (TFIIA) is one of the general transcription factors for RNA polymerase II. TFIIA increases the affinity of the TATA-binding protein (TBP) for DNA, in order to assemble the initiation complex. TFIIA also functions as an activator during development and differentiation, and is involved in transcription from TATA-less promoters. TFIIA is composed of more than one subunit in various organisms. Mammalian TFIIA large subunits (TFIIA alpha and beta), and the smaller subunit (TFIIA gamma) form a heterotrimer. TFIIA alpha and beta are encoded by a single TFIIA_alpha_beta gene and post-translationally processed and cleaved. TOA1 and TOA2 are the two subunits of Yeast TFIIA which correspond to Mammalian TFIIA_alpha_beta and TFIIA gamma, respectively. TOA1 and TOA2 form a heterodimeric protein complex. The TFIIA gamma subunit is highly conserved between humans, Drosophila and yeast and it is required for TFIIA function. The N-terminal domain of the gamma subunit forms a 4-helix bundle together with the alpha subunit.


Pssm-ID: 199901  Cd Length: 49  Bit Score: 80.69  E-value: 6.76e-22
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 215694411   4 FELYRRSTIGMCLTETLDEMVSSGTLSPELAIQVLVQFDKSMTEALEN 51
Cdd:cd10145    2 YELYRNTTLGIALQDALDELIQDGQITPQLAMKVLLQFDKSINEALAN 49
 
Name Accession Description Interval E-value
TOA2 COG5123
Transcription initiation factor IIA, gamma subunit [Transcription];
4-103 9.74e-34

Transcription initiation factor IIA, gamma subunit [Transcription];


Pssm-ID: 227452 [Multi-domain]  Cd Length: 113  Bit Score: 112.74  E-value: 9.74e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215694411   4 FELYRRSTIGMCLTETLDEMVSSGTLSPELAIQVLVQFDKSMTEALENQVKSKVSIKGHLHTYRFCDNVWTFILTEASFK 83
Cdd:COG5123    5 YELYRRSMIGKVLEDALDELISAGVISPNLAMHVLETFDKSVPEVLNKSVTSSLTFKGKLDTYNFCDGVWTFITKNFVMS 84

                         90       100
                 ....*....|....*....|
gi 215694411  84 NEETTEQVGKVKIVACDSKL 103
Cdd:COG5123   85 LNNEYFNAGEVNIVACKARI 104
TFIIA_gamma_N pfam02268
Transcription initiation factor IIA, gamma subunit, helical domain; Accurate transcription in ...
 4-49 1.25e-23

Transcription initiation factor IIA, gamma subunit, helical domain; Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA box. The N-terminal domain of the gamma subunit is a 4 helix bundle.


Pssm-ID: 460518  Cd Length: 46  Bit Score: 85.20  E-value: 1.25e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 215694411    4 FELYRRSTIGMCLTETLDEMVSSGTLSPELAIQVLVQFDKSMTEAL 49
Cdd:pfam02268   1 YELYRRTTLGMALTDTLDELIQDGRITPQLAMKVLEQFDKSINEAL 46
TFIIA_gamma_C pfam02751
Transcription initiation factor IIA, gamma subunit; Accurate transcription in vivo requires at ...
 60-101 5.54e-22

Transcription initiation factor IIA, gamma subunit; Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA box. The C-terminal domain of the gamma subunit is a 12 stranded beta-barrel.


Pssm-ID: 460675  Cd Length: 43  Bit Score: 80.66  E-value: 5.54e-22
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 215694411   60 KGHLHTYRFCDNVWTFILTEASFK-NEETTEQVGKVKIVACDS 101
Cdd:pfam02751   1 KGHLDTYRFCDNVWTFILKDVTFKlDNNETVKVDKVKIVACDA 43
TFIIA_gamma_N cd10145
Gamma subunit of transcription initiation factor IIA, N-terminal helical domain; Transcription ...
 4-51 6.76e-22

Gamma subunit of transcription initiation factor IIA, N-terminal helical domain; Transcription factor II A (TFIIA) is one of the general transcription factors for RNA polymerase II. TFIIA increases the affinity of the TATA-binding protein (TBP) for DNA, in order to assemble the initiation complex. TFIIA also functions as an activator during development and differentiation, and is involved in transcription from TATA-less promoters. TFIIA is composed of more than one subunit in various organisms. Mammalian TFIIA large subunits (TFIIA alpha and beta), and the smaller subunit (TFIIA gamma) form a heterotrimer. TFIIA alpha and beta are encoded by a single TFIIA_alpha_beta gene and post-translationally processed and cleaved. TOA1 and TOA2 are the two subunits of Yeast TFIIA which correspond to Mammalian TFIIA_alpha_beta and TFIIA gamma, respectively. TOA1 and TOA2 form a heterodimeric protein complex. The TFIIA gamma subunit is highly conserved between humans, Drosophila and yeast and it is required for TFIIA function. The N-terminal domain of the gamma subunit forms a 4-helix bundle together with the alpha subunit.


Pssm-ID: 199901  Cd Length: 49  Bit Score: 80.69  E-value: 6.76e-22
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 215694411   4 FELYRRSTIGMCLTETLDEMVSSGTLSPELAIQVLVQFDKSMTEALEN 51
Cdd:cd10145    2 YELYRNTTLGIALQDALDELIQDGQITPQLAMKVLLQFDKSINEALAN 49
TFIIA_gamma_C cd10014
Gamma subunit of transcription initiation factor IIA, C-terminal domain; Transcription factor ...
 57-102 3.83e-21

Gamma subunit of transcription initiation factor IIA, C-terminal domain; Transcription factor II A (TFIIA) is one of the general transcription factors for RNA polymerase II. TFIIA increases the affinity of the TATA-binding protein (TBP) for DNA, in order to assemble the initiation complex. TFIIA also functions as an activator during development and differentiation, and is involved in transcription from TATA-less promoters. TFIIA is composed of more than one subunit in various organisms. Mammalian TFIIA large subunits (TFIIA alpha and beta), and the smaller subunit (TFIIA gamma) form a heterotrimer. TFIIA alpha and beta are encoded by a single TFIIA_alpha_beta gene and post-translationally processed and cleaved. TOA1 and TOA2 are the two subunits of Yeast TFIIA which correspond to Mammalian TFIIA_alpha_beta and TFIIA gamma, respectively. TOA1 and TOA2 form a heterodimeric protein complex. The TFIIA gamma subunit is highly conserved between humans, Drosophila and yeast and it is required for TFIIA function. The C-terminal domain of the gamma (TFIIA_gamma_C) subunit forms a beta-barrel structure together with TFIIA beta.


Pssm-ID: 199900  Cd Length: 47  Bit Score: 78.83  E-value: 3.83e-21
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 215694411  57 VSIKGHLHTYRFCDNVWTFILTEASFKNEET-TEQVGKVKIVACDSK 102
Cdd:cd10014    1 LTFKGHLKTYRFCDNVWTFILNDVEFKESNTeVVTVDKVKIVACDGK 47
 
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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