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Conserved domains on  [gi|2463217765|ref|NP_001405474|]
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general transcription factor IIF subunit 2 isoform 3 [Mus musculus]

Protein Classification

TFIIF_beta domain-containing protein( domain architecture ID 10910399)

TFIIF_beta domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TFIIF_beta pfam02270
TFIIF, beta subunit HTH domain; Accurate transcription in vivo requires at least six general ...
 94-158 2.68e-31

TFIIF, beta subunit HTH domain; Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter.


:

Pssm-ID: 426691  Cd Length: 65  Bit Score: 107.32  E-value: 2.68e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2463217765  94 ARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVGYLKEILKEIGIQNVKGIHKNTWELKPEYR 158
Cdd:pfam02270   1 ARMPRNELLDALFSLFEEHQYWSLKDLRERTRQPEAYLKETLEEIAVLNRSGPFAGMWELKPEYR 65
TFIIF_beta super family cl02122
Transcription initiation factor IIF, beta subunit; The TFIIF-beta subunit, also called RNA ...
 5-64 1.06e-12

Transcription initiation factor IIF, beta subunit; The TFIIF-beta subunit, also called RNA Polymerase II-associating Protein 30 (RAP30), forms a heteromeric complex of RAP30/74 (TFIIF, beta/gamma) that is involved in both initiation and elongation of RNA chains by RNA polymerase II. Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. TFIIF-beta binds directly to RNA polymerase II and helps bring polymerase into a pre-initiation complex.


The actual alignment was detected with superfamily member cd07980:

Pssm-ID: 445677  Cd Length: 123  Bit Score: 61.19  E-value: 1.06e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2463217765   5 GELDLTGAKQNtgVWLVKVPKYLSQQWAKASGRG-EVGKLRIAKlqiEESSKPVRLSQQLD 64
Cdd:cd07980     2 LDLDTSNADRS--VWLVKVPKFLSERWSKLDDDGiELGTLRVYK---DPPSGKPRVSLTLP 57
 
Name Accession Description Interval E-value
TFIIF_beta pfam02270
TFIIF, beta subunit HTH domain; Accurate transcription in vivo requires at least six general ...
 94-158 2.68e-31

TFIIF, beta subunit HTH domain; Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter.


Pssm-ID: 426691  Cd Length: 65  Bit Score: 107.32  E-value: 2.68e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2463217765  94 ARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVGYLKEILKEIGIQNVKGIHKNTWELKPEYR 158
Cdd:pfam02270   1 ARMPRNELLDALFSLFEEHQYWSLKDLRERTRQPEAYLKETLEEIAVLNRSGPFAGMWELKPEYR 65
TFG2 COG5090
Transcription initiation factor IIF, small subunit (RAP30) [Transcription];
85-165 1.34e-20

Transcription initiation factor IIF, small subunit (RAP30) [Transcription];


Pssm-ID: 227421 [Multi-domain]  Cd Length: 297  Bit Score: 85.79  E-value: 1.34e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2463217765  85 RKKKEDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVGYLKEILKEIGIQNVKGIHKNTWELKPEYRHYQTEE 164
Cdd:COG5090   180 KKMLMDKKRERLPKNEVLDMLFKAFEKYPYWTLKGLAEFCGQPEAFLKEILDDIAVLNKKGPYANKYELRPEYKQTMDEL 259


                  .
gi 2463217765 165 K 165
Cdd:COG5090   260 R 260
TFIIF_beta cd07980
Transcription initiation factor IIF, beta subunit; The TFIIF-beta subunit, also called RNA ...
 5-64 1.06e-12

Transcription initiation factor IIF, beta subunit; The TFIIF-beta subunit, also called RNA Polymerase II-associating Protein 30 (RAP30), forms a heteromeric complex of RAP30/74 (TFIIF, beta/gamma) that is involved in both initiation and elongation of RNA chains by RNA polymerase II. Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. TFIIF-beta binds directly to RNA polymerase II and helps bring polymerase into a pre-initiation complex.


Pssm-ID: 259828  Cd Length: 123  Bit Score: 61.19  E-value: 1.06e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2463217765   5 GELDLTGAKQNtgVWLVKVPKYLSQQWAKASGRG-EVGKLRIAKlqiEESSKPVRLSQQLD 64
Cdd:cd07980     2 LDLDTSNADRS--VWLVKVPKFLSERWSKLDDDGiELGTLRVYK---DPPSGKPRVSLTLP 57
TFIIF_beta_N pfam17683
TFIIF, beta subunit N-terminus; Accurate transcription in vivo requires at least six general ...
 15-59 1.36e-07

TFIIF, beta subunit N-terminus; Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter.


Pssm-ID: 465458  Cd Length: 104  Bit Score: 47.34  E-value: 1.36e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2463217765  15 NTGVWLVKVPKYLSQQWAKA---SGRGEVGKLRIAKLQIEESSKPVRL 59
Cdd:pfam17683   1 NSKVWLVKVPKFLWEKWSKPdddNEGIELGTLRVYKNPDPGGKQRVKL 48
 
Name Accession Description Interval E-value
TFIIF_beta pfam02270
TFIIF, beta subunit HTH domain; Accurate transcription in vivo requires at least six general ...
 94-158 2.68e-31

TFIIF, beta subunit HTH domain; Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter.


Pssm-ID: 426691  Cd Length: 65  Bit Score: 107.32  E-value: 2.68e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2463217765  94 ARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVGYLKEILKEIGIQNVKGIHKNTWELKPEYR 158
Cdd:pfam02270   1 ARMPRNELLDALFSLFEEHQYWSLKDLRERTRQPEAYLKETLEEIAVLNRSGPFAGMWELKPEYR 65
TFG2 COG5090
Transcription initiation factor IIF, small subunit (RAP30) [Transcription];
85-165 1.34e-20

Transcription initiation factor IIF, small subunit (RAP30) [Transcription];


Pssm-ID: 227421 [Multi-domain]  Cd Length: 297  Bit Score: 85.79  E-value: 1.34e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2463217765  85 RKKKEDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVGYLKEILKEIGIQNVKGIHKNTWELKPEYRHYQTEE 164
Cdd:COG5090   180 KKMLMDKKRERLPKNEVLDMLFKAFEKYPYWTLKGLAEFCGQPEAFLKEILDDIAVLNKKGPYANKYELRPEYKQTMDEL 259


                  .
gi 2463217765 165 K 165
Cdd:COG5090   260 R 260
TFIIF_beta cd07980
Transcription initiation factor IIF, beta subunit; The TFIIF-beta subunit, also called RNA ...
 5-64 1.06e-12

Transcription initiation factor IIF, beta subunit; The TFIIF-beta subunit, also called RNA Polymerase II-associating Protein 30 (RAP30), forms a heteromeric complex of RAP30/74 (TFIIF, beta/gamma) that is involved in both initiation and elongation of RNA chains by RNA polymerase II. Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. TFIIF-beta binds directly to RNA polymerase II and helps bring polymerase into a pre-initiation complex.


Pssm-ID: 259828  Cd Length: 123  Bit Score: 61.19  E-value: 1.06e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2463217765   5 GELDLTGAKQNtgVWLVKVPKYLSQQWAKASGRG-EVGKLRIAKlqiEESSKPVRLSQQLD 64
Cdd:cd07980     2 LDLDTSNADRS--VWLVKVPKFLSERWSKLDDDGiELGTLRVYK---DPPSGKPRVSLTLP 57
TFIIF_beta_N pfam17683
TFIIF, beta subunit N-terminus; Accurate transcription in vivo requires at least six general ...
 15-59 1.36e-07

TFIIF, beta subunit N-terminus; Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter.


Pssm-ID: 465458  Cd Length: 104  Bit Score: 47.34  E-value: 1.36e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2463217765  15 NTGVWLVKVPKYLSQQWAKA---SGRGEVGKLRIAKLQIEESSKPVRL 59
Cdd:pfam17683   1 NSKVWLVKVPKFLWEKWSKPdddNEGIELGTLRVYKNPDPGGKQRVKL 48
 
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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