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Conserved domains on  [gi|145699116|ref|NP_001007578|]
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transcription elongation factor A N-terminal and central domain-containing protein [Mus musculus]

Protein Classification

zinc ribbon domain-containing protein( domain architecture ID 10539513)

zinc ribbon domain-containing protein is likely to be DNA-binding

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TFIIS_M pfam07500
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ...
 181-290 1.30e-39

Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity.


:

Pssm-ID: 462184  Cd Length: 112  Bit Score: 136.18  E-value: 1.30e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145699116  181 SVRSKCVELLYTALASSCTDHTEVHIWQnLAREIEEHIFTLHSNNIKKYKTSIRSKVANLKNPRNFHLQQNFLSGTMSAR 260
Cdd:pfam07500   4 KVRDKCRELLYDALAKDSTEASEEDALE-LAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGEISPE 82

                          90       100       110
                  ....*....|....*....|....*....|
gi 145699116  261 EFAEMSVLDMASQELKQLRASYTESSIQEH 290
Cdd:pfam07500  83 KLVTMSPEEMASEELKKEREKIEKEALKEA 112
Zn-ribbon super family cl02609
C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The ...
 298-351 3.24e-03

C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The homologous C-terminal zinc ribbon domains of subunits A12.2, Rpb9, and C11 in RNA Polymerases (Pol) I, II, and III, respectively are required for intrinsic transcript cleavage. TFS is a related archaeal protein that is involved in RNA cleavage by archaeal polymerase. These proteins have two zinc-binding beta-ribbon domains, N-terminal zinc ribbon (N-ribbon) and C-terminal zinc ribbon (C-ribbon). Transcription Factor IIS (TFIIS) domain III is homologous to the C-ribbon domain that stimulates the weak cleavage activity of Rpb9 for Pol II.


The actual alignment was detected with superfamily member cd13749:

Pssm-ID: 445850  Cd Length: 47  Bit Score: 35.27  E-value: 3.24e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 145699116 298 GTWTNKIKCRRCDKYNCKVTViargtlflpswVQNSNPDEQMT-YVICNECGEQW 351
Cdd:cd13749    2 GTTTDLFKCGKCKKRKCTYYQ-----------LQTRSADEPMTtFVTCLNCGNRW 45
 
Name Accession Description Interval E-value
TFIIS_M pfam07500
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ...
 181-290 1.30e-39

Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity.


Pssm-ID: 462184  Cd Length: 112  Bit Score: 136.18  E-value: 1.30e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145699116  181 SVRSKCVELLYTALASSCTDHTEVHIWQnLAREIEEHIFTLHSNNIKKYKTSIRSKVANLKNPRNFHLQQNFLSGTMSAR 260
Cdd:pfam07500   4 KVRDKCRELLYDALAKDSTEASEEDALE-LAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGEISPE 82

                          90       100       110
                  ....*....|....*....|....*....|
gi 145699116  261 EFAEMSVLDMASQELKQLRASYTESSIQEH 290
Cdd:pfam07500  83 KLVTMSPEEMASEELKKEREKIEKEALKEA 112
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 181-351 7.66e-27

transcription elongation factor S-II; This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.


Pssm-ID: 273592 [Multi-domain]  Cd Length: 299  Bit Score: 108.00  E-value: 7.66e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145699116  181 SVRSKCVELLYTALA------SSCTDHTEvhiwqnLAREIEEHIFTLHSNNIKKYKTSIRSKVANLKNPRNFHLQQNFLS 254
Cdd:TIGR01385 137 KVRDKCRELLYDALAkdsdhpPQSIDPEA------KAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLT 210

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145699116  255 GTMSAREFAEMSVLDMASQELKQLRASYTESSIQEH--CLPQsvdGTWTNKIKCRRCDKYNCKVTviargtlflpsWVQN 332
Cdd:TIGR01385 211 GEITPEKLATMTAEEMASAELKQEREEITKENLFEAqgAKIQ---KAVTDLFTCGKCKQKKCTYY-----------QLQT 276

                         170       180
                  ....*....|....*....|
gi 145699116  333 SNPDEQM-TYVICNECGEQW 351
Cdd:TIGR01385 277 RSADEPMtTFVTCEECGNRW 296
TFS2M smart00510
Domain in the central regions of transcription elongation factor S-II (and elsewhere);
181-279 2.11e-16

Domain in the central regions of transcription elongation factor S-II (and elsewhere);


Pssm-ID: 128786 [Multi-domain]  Cd Length: 102  Bit Score: 73.89  E-value: 2.11e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145699116   181 SVRSKCVELLYTALASSCtDHTEVHIW-QNLAREIEEHIFTLHSNNIKKYKTSIRSKVANLKNPRNFHLQQNFLSGTMSA 259
Cdd:smart00510   2 KVRDKCQEMLYKALQKIS-DPEEIELDpTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITP 80

                           90       100
                   ....*....|....*....|
gi 145699116   260 REFAEMSVLDMASQELKQLR 279
Cdd:smart00510  81 EKLATMTAEELASAELKEKR 100
Zn-ribbon_TFIIS cd13749
domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing ...
 298-351 3.24e-03

domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing transcription factor. It has been shown in vitro to have distinct biochemical activities, including binding to RNA polymerases, stimulation of transcript elongation, and activation of a nascent RNA cleavage activity in the RNA polymerase II (Pol II) elongation complex. TFIIS consists of three domains. Domain II and III are sufficient for all known TFIIS activities. Domain III is a zinc ribbon that separated from domain II by a long linker and is indispensable for TFIIS function. The TFIIS homologs, subunits A12.2, B9, and C11, of Pol I, II, and III respectively, are required for RNA cleavage by the polymerases. In a single organism, there are tissue-specific TFIIS related proteins.


Pssm-ID: 259796  Cd Length: 47  Bit Score: 35.27  E-value: 3.24e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 145699116 298 GTWTNKIKCRRCDKYNCKVTViargtlflpswVQNSNPDEQMT-YVICNECGEQW 351
Cdd:cd13749    2 GTTTDLFKCGKCKKRKCTYYQ-----------LQTRSADEPMTtFVTCLNCGNRW 45
 
Name Accession Description Interval E-value
TFIIS_M pfam07500
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ...
 181-290 1.30e-39

Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity.


Pssm-ID: 462184  Cd Length: 112  Bit Score: 136.18  E-value: 1.30e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145699116  181 SVRSKCVELLYTALASSCTDHTEVHIWQnLAREIEEHIFTLHSNNIKKYKTSIRSKVANLKNPRNFHLQQNFLSGTMSAR 260
Cdd:pfam07500   4 KVRDKCRELLYDALAKDSTEASEEDALE-LAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGEISPE 82

                          90       100       110
                  ....*....|....*....|....*....|
gi 145699116  261 EFAEMSVLDMASQELKQLRASYTESSIQEH 290
Cdd:pfam07500  83 KLVTMSPEEMASEELKKEREKIEKEALKEA 112
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 181-351 7.66e-27

transcription elongation factor S-II; This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.


Pssm-ID: 273592 [Multi-domain]  Cd Length: 299  Bit Score: 108.00  E-value: 7.66e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145699116  181 SVRSKCVELLYTALA------SSCTDHTEvhiwqnLAREIEEHIFTLHSNNIKKYKTSIRSKVANLKNPRNFHLQQNFLS 254
Cdd:TIGR01385 137 KVRDKCRELLYDALAkdsdhpPQSIDPEA------KAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLT 210

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145699116  255 GTMSAREFAEMSVLDMASQELKQLRASYTESSIQEH--CLPQsvdGTWTNKIKCRRCDKYNCKVTviargtlflpsWVQN 332
Cdd:TIGR01385 211 GEITPEKLATMTAEEMASAELKQEREEITKENLFEAqgAKIQ---KAVTDLFTCGKCKQKKCTYY-----------QLQT 276

                         170       180
                  ....*....|....*....|
gi 145699116  333 SNPDEQM-TYVICNECGEQW 351
Cdd:TIGR01385 277 RSADEPMtTFVTCEECGNRW 296
TFS2M smart00510
Domain in the central regions of transcription elongation factor S-II (and elsewhere);
181-279 2.11e-16

Domain in the central regions of transcription elongation factor S-II (and elsewhere);


Pssm-ID: 128786 [Multi-domain]  Cd Length: 102  Bit Score: 73.89  E-value: 2.11e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145699116   181 SVRSKCVELLYTALASSCtDHTEVHIW-QNLAREIEEHIFTLHSNNIKKYKTSIRSKVANLKNPRNFHLQQNFLSGTMSA 259
Cdd:smart00510   2 KVRDKCQEMLYKALQKIS-DPEEIELDpTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITP 80

                           90       100
                   ....*....|....*....|
gi 145699116   260 REFAEMSVLDMASQELKQLR 279
Cdd:smart00510  81 EKLATMTAEELASAELKEKR 100
Zn-ribbon_TFIIS cd13749
domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing ...
 298-351 3.24e-03

domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing transcription factor. It has been shown in vitro to have distinct biochemical activities, including binding to RNA polymerases, stimulation of transcript elongation, and activation of a nascent RNA cleavage activity in the RNA polymerase II (Pol II) elongation complex. TFIIS consists of three domains. Domain II and III are sufficient for all known TFIIS activities. Domain III is a zinc ribbon that separated from domain II by a long linker and is indispensable for TFIIS function. The TFIIS homologs, subunits A12.2, B9, and C11, of Pol I, II, and III respectively, are required for RNA cleavage by the polymerases. In a single organism, there are tissue-specific TFIIS related proteins.


Pssm-ID: 259796  Cd Length: 47  Bit Score: 35.27  E-value: 3.24e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 145699116 298 GTWTNKIKCRRCDKYNCKVTViargtlflpswVQNSNPDEQMT-YVICNECGEQW 351
Cdd:cd13749    2 GTTTDLFKCGKCKKRKCTYYQ-----------LQTRSADEPMTtFVTCLNCGNRW 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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