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Conserved domains on  [gi|1028909952|pdb|5IYD|T]
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Chain T, General transcription factor IIF subunit 2

Protein Classification

general transcription factor IIF subunit 2( domain architecture ID 3765)

general transcription factor IIF subunit 2 (GTF2F2) is a subunit of TFIIF, which is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB

Gene Ontology:  GO:0006366|GO:0006367|GO:0005674

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TFIIF_beta super family cl02122
Transcription initiation factor IIF, beta subunit; The TFIIF-beta subunit, also called RNA ...
 6-247 3.50e-34

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 COG5090:

Pssm-ID: 445677 [Multi-domain]  Cd Length: 297  Bit Score: 124.69  E-value: 3.50e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_T        6 ELDLTGAKQNTGVWLVKVPKYLSQQWAkaSGRGEVGKLRIAKTQGRTEVSFTLNedLANIHDIGGKPASVSAPREHPFVL 85
Cdd:COG5090  19 DADLDLNNRHTKVWLVKVPLFLAEKWL--SREAEIGELLGTKRTSTDPAVISLL--LSNEFCNGGFPSSYDLKIKPKDVN 94

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_T       86 QSVggqtltVFTESSSD----KLSLEGIVVQRAECRPAASENYMRLKRLQIEESSKPVRLSQQLD--KVVTTNYKPVANH 159
Cdd:COG5090  95 NYY------VFRESETSthekNTAVVGTVNHECYVTPEVNDEYLRYKQDRGFKSDSKKSDVQVIDylKGGKRGEKFGSLR 168

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_T      160 QYNIEYERKKKE----DGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYLKEILKEIGVQNVKGIHKNTWEL 235
Cdd:COG5090 169 SSTLEFLARKRKkmlmDKKRERLPKNEVLDMLFKAFEKYPYWTLKGLAEFCGQPEAFLKEILDDIAVLNKKGPYANKYEL 248

                       250
                ....*....|..
5IYD_T      236 KPEYRHYQGEEK 247
Cdd:COG5090 249 RPEYKQTMDELR 260
 
Name Accession Description Interval E-value
TFG2 COG5090
Transcription initiation factor IIF, small subunit (RAP30) [Transcription];
6-247 3.50e-34

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


Pssm-ID: 227421 [Multi-domain]  Cd Length: 297  Bit Score: 124.69  E-value: 3.50e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_T        6 ELDLTGAKQNTGVWLVKVPKYLSQQWAkaSGRGEVGKLRIAKTQGRTEVSFTLNedLANIHDIGGKPASVSAPREHPFVL 85
Cdd:COG5090  19 DADLDLNNRHTKVWLVKVPLFLAEKWL--SREAEIGELLGTKRTSTDPAVISLL--LSNEFCNGGFPSSYDLKIKPKDVN 94

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_T       86 QSVggqtltVFTESSSD----KLSLEGIVVQRAECRPAASENYMRLKRLQIEESSKPVRLSQQLD--KVVTTNYKPVANH 159
Cdd:COG5090  95 NYY------VFRESETSthekNTAVVGTVNHECYVTPEVNDEYLRYKQDRGFKSDSKKSDVQVIDylKGGKRGEKFGSLR 168

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_T      160 QYNIEYERKKKE----DGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYLKEILKEIGVQNVKGIHKNTWEL 235
Cdd:COG5090 169 SSTLEFLARKRKkmlmDKKRERLPKNEVLDMLFKAFEKYPYWTLKGLAEFCGQPEAFLKEILDDIAVLNKKGPYANKYEL 248

                       250
                ....*....|..
5IYD_T      236 KPEYRHYQGEEK 247
Cdd:COG5090 249 RPEYKQTMDELR 260
TFIIF_beta pfam02270
TFIIF, beta subunit HTH domain; Accurate transcription in vivo requires at least six general ...
 176-240 1.91e-32

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: 113.09  E-value: 1.91e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
5IYD_T        176 ARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYLKEILKEIGVQNVKGIHKNTWELKPEYR 240
Cdd:pfam02270   1 ARMPRNELLDALFSLFEEHQYWSLKDLRERTRQPEAYLKETLEEIAVLNRSGPFAGMWELKPEYR 65
TFIIF_beta cd07980
Transcription initiation factor IIF, beta subunit; The TFIIF-beta subunit, also called RNA ...
 5-118 3.05e-32

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: 114.35  E-value: 3.05e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_T        5 GELDLTGAKQNtgVWLVKVPKYLSQQWAKASGRG-EVGKLRIAKTQ--GRTEVSFTLNEDLANIHDIggkpasvsaPREH 81
Cdd:cd07980   2 LDLDTSNADRS--VWLVKVPKFLSERWSKLDDDGiELGTLRVYKDPpsGKPRVSLTLPENLPENANI---------PKEY 70

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
5IYD_T       82 PFVLQSVGGQTLTVFTESSS----------------DKLSLEGIVVQRAECRP 118
Cdd:cd07980  71 ELDMTNESVQNTYVFSEKDLpgfkarsqpyyrksipKKTALEGRVVHECDCRP 123
 
Name Accession Description Interval E-value
TFG2 COG5090
Transcription initiation factor IIF, small subunit (RAP30) [Transcription];
6-247 3.50e-34

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


Pssm-ID: 227421 [Multi-domain]  Cd Length: 297  Bit Score: 124.69  E-value: 3.50e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_T        6 ELDLTGAKQNTGVWLVKVPKYLSQQWAkaSGRGEVGKLRIAKTQGRTEVSFTLNedLANIHDIGGKPASVSAPREHPFVL 85
Cdd:COG5090  19 DADLDLNNRHTKVWLVKVPLFLAEKWL--SREAEIGELLGTKRTSTDPAVISLL--LSNEFCNGGFPSSYDLKIKPKDVN 94

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_T       86 QSVggqtltVFTESSSD----KLSLEGIVVQRAECRPAASENYMRLKRLQIEESSKPVRLSQQLD--KVVTTNYKPVANH 159
Cdd:COG5090  95 NYY------VFRESETSthekNTAVVGTVNHECYVTPEVNDEYLRYKQDRGFKSDSKKSDVQVIDylKGGKRGEKFGSLR 168

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_T      160 QYNIEYERKKKE----DGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYLKEILKEIGVQNVKGIHKNTWEL 235
Cdd:COG5090 169 SSTLEFLARKRKkmlmDKKRERLPKNEVLDMLFKAFEKYPYWTLKGLAEFCGQPEAFLKEILDDIAVLNKKGPYANKYEL 248

                       250
                ....*....|..
5IYD_T      236 KPEYRHYQGEEK 247
Cdd:COG5090 249 RPEYKQTMDELR 260
TFIIF_beta pfam02270
TFIIF, beta subunit HTH domain; Accurate transcription in vivo requires at least six general ...
 176-240 1.91e-32

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: 113.09  E-value: 1.91e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
5IYD_T        176 ARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYLKEILKEIGVQNVKGIHKNTWELKPEYR 240
Cdd:pfam02270   1 ARMPRNELLDALFSLFEEHQYWSLKDLRERTRQPEAYLKETLEEIAVLNRSGPFAGMWELKPEYR 65
TFIIF_beta cd07980
Transcription initiation factor IIF, beta subunit; The TFIIF-beta subunit, also called RNA ...
 5-118 3.05e-32

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: 114.35  E-value: 3.05e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_T        5 GELDLTGAKQNtgVWLVKVPKYLSQQWAKASGRG-EVGKLRIAKTQ--GRTEVSFTLNEDLANIHDIggkpasvsaPREH 81
Cdd:cd07980   2 LDLDTSNADRS--VWLVKVPKFLSERWSKLDDDGiELGTLRVYKDPpsGKPRVSLTLPENLPENANI---------PKEY 70

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
5IYD_T       82 PFVLQSVGGQTLTVFTESSS----------------DKLSLEGIVVQRAECRP 118
Cdd:cd07980  71 ELDMTNESVQNTYVFSEKDLpgfkarsqpyyrksipKKTALEGRVVHECDCRP 123
TFIIF_beta_N pfam17683
TFIIF, beta subunit N-terminus; Accurate transcription in vivo requires at least six general ...
 15-119 7.80e-22

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: 86.63  E-value: 7.80e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IYD_T         15 NTGVWLVKVPKYLSQQWAKA---SGRGEVGKLRIAKT---QGRTEVSFTLNEDLANIHDIggkpasvsaPREHPFVLQSV 88
Cdd:pfam17683   1 NSKVWLVKVPKFLWEKWSKPdddNEGIELGTLRVYKNpdpGGKQRVKLKLNDDLPQHENI---------PKEYNLDVTNT 71

                          90       100       110
                  ....*....|....*....|....*....|...
5IYD_T         89 GGQTLTVFTESSSD--KLSLEGIVVQRAECRPA 119
Cdd:pfam17683  72 RVQNTYVFSEKDLPgfKANLAGRVVHECNVRPV 104
 
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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