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Conserved domains on  [gi|117949797|sp|Q8N8B7|]
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RecName: Full=Transcription elongation factor A N-terminal and central domain-containing protein; AltName: Full=TFIIS central domain-containing protein 1

Protein Classification

transcription factor S-II family protein( domain architecture ID 13520976)

transcription factor S-II (TFS II) family protein similar to Drosophila melanogaster transcription elongation factor S-II, which is necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites

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 ...
 172-281 4.70e-38

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: 131.94  E-value: 4.70e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117949797  172 PMRTKCIELLYAALTSSSTDQPKADLWQnFAREIEEHVFTLYSKNIKKYKTCIRSKVANLKNPRNSHLQQNLLSGTTSPR 251
Cdd:pfam07500   4 KVRDKCRELLYDALAKDSTEASEEDALE-LAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGEISPE 82

                          90       100       110
                  ....*....|....*....|....*....|
gi 117949797  252 EFAEMTVMEMANKELKQLRASYTESCIQEH 281
Cdd:pfam07500  83 KLVTMSPEEMASEELKKEREKIEKEALKEA 112
TFSII super family cl36890
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 6-343 2.35e-36

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.


The actual alignment was detected with superfamily member TIGR01385:

Pssm-ID: 273592 [Multi-domain]  Cd Length: 299  Bit Score: 133.43  E-value: 2.35e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117949797    6 QIAARASLIEQLMSKRNFEDLGNHLTELETIYVTKEHLQETDVVRAVyRVLKNCPSVALKKKAKCLLSKWKAVykqthsk 85
Cdd:TIGR01385   3 EVASHAKALDKNKSSKNVEQCLDILHQLKEFPPTEELLQETKVGVKV-NKLRKHPNEDISKLAKKIIKSWKKV------- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117949797   86 arnspklfpVRGNKEENSGPShdPSQNETLGicSSNSLSSQDVAKLSEMIVpenraiqlKPKeehfgdgDPESTGKRSSE 165
Cdd:TIGR01385  75 ---------VDKNKSDHPGGN--PEDKTTVG--ESVNSVKQEAKSQSDKIE--------QPK-------YVSSSPRNAKN 126

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117949797  166 LLDPTT----PMRTKCIELLYAALTSSSTDQPKADLWQNFAREIEEHVFTLYSKNIKKYKTCIRSKVANLKNPRNSHLQQ 241
Cdd:TIGR01385 127 DFVPTAvtndKVRDKCRELLYDALAKDSDHPPQSIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRH 206

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117949797  242 NLLSGTTSPREFAEMTVMEMANKELKQLRASYTESCIQEHYLpQVIDGTQTNKIKCRRCEKYNCKVTvidrgtlflpsWV 321
Cdd:TIGR01385 207 NVLTGEITPEKLATMTAEEMASAELKQEREEITKENLFEAQG-AKIQKAVTDLFTCGKCKQKKCTYY-----------QL 274

                         330       340
                  ....*....|....*....|..
gi 117949797  322 RNSNPDEQMMTYVICNECGEQW 343
Cdd:TIGR01385 275 QTRSADEPMTTFVTCEECGNRW 296
 
Name Accession Description Interval E-value
TFIIS_M pfam07500
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ...
 172-281 4.70e-38

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: 131.94  E-value: 4.70e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117949797  172 PMRTKCIELLYAALTSSSTDQPKADLWQnFAREIEEHVFTLYSKNIKKYKTCIRSKVANLKNPRNSHLQQNLLSGTTSPR 251
Cdd:pfam07500   4 KVRDKCRELLYDALAKDSTEASEEDALE-LAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGEISPE 82

                          90       100       110
                  ....*....|....*....|....*....|
gi 117949797  252 EFAEMTVMEMANKELKQLRASYTESCIQEH 281
Cdd:pfam07500  83 KLVTMSPEEMASEELKKEREKIEKEALKEA 112
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 6-343 2.35e-36

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: 133.43  E-value: 2.35e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117949797    6 QIAARASLIEQLMSKRNFEDLGNHLTELETIYVTKEHLQETDVVRAVyRVLKNCPSVALKKKAKCLLSKWKAVykqthsk 85
Cdd:TIGR01385   3 EVASHAKALDKNKSSKNVEQCLDILHQLKEFPPTEELLQETKVGVKV-NKLRKHPNEDISKLAKKIIKSWKKV------- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117949797   86 arnspklfpVRGNKEENSGPShdPSQNETLGicSSNSLSSQDVAKLSEMIVpenraiqlKPKeehfgdgDPESTGKRSSE 165
Cdd:TIGR01385  75 ---------VDKNKSDHPGGN--PEDKTTVG--ESVNSVKQEAKSQSDKIE--------QPK-------YVSSSPRNAKN 126

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117949797  166 LLDPTT----PMRTKCIELLYAALTSSSTDQPKADLWQNFAREIEEHVFTLYSKNIKKYKTCIRSKVANLKNPRNSHLQQ 241
Cdd:TIGR01385 127 DFVPTAvtndKVRDKCRELLYDALAKDSDHPPQSIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRH 206

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117949797  242 NLLSGTTSPREFAEMTVMEMANKELKQLRASYTESCIQEHYLpQVIDGTQTNKIKCRRCEKYNCKVTvidrgtlflpsWV 321
Cdd:TIGR01385 207 NVLTGEITPEKLATMTAEEMASAELKQEREEITKENLFEAQG-AKIQKAVTDLFTCGKCKQKKCTYY-----------QL 274

                         330       340
                  ....*....|....*....|..
gi 117949797  322 RNSNPDEQMMTYVICNECGEQW 343
Cdd:TIGR01385 275 QTRSADEPMTTFVTCEECGNRW 296
TFS2M smart00510
Domain in the central regions of transcription elongation factor S-II (and elsewhere);
172-270 4.70e-17

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


Pssm-ID: 128786 [Multi-domain]  Cd Length: 102  Bit Score: 75.81  E-value: 4.70e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117949797   172 PMRTKCIELLYAALTSSSTDQPKADLWQNFAREIEEHVFTLYSKNIKKYKTCIRSKVANLKNPRNSHLQQNLLSGTTSPR 251
Cdd:smart00510   2 KVRDKCQEMLYKALQKISDPEEIELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITPE 81

                           90
                   ....*....|....*....
gi 117949797   252 EFAEMTVMEMANKELKQLR 270
Cdd:smart00510  82 KLATMTAEELASAELKEKR 100
Med26 pfam08711
TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is ...
 29-78 2.19e-12

TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species {1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. Notably, the 'small' and 'large' Mediator complexes differ in their subunit composition: the Med26 subunit preferentially associates with the small, active complex, whereas cdk8, cyclin C, Med12 and Med13 associate with the large Mediator complex. This family includesthe C terminal region of a number of eukaryotic hypothetical proteins which are homologous to the Saccharomyces cerevisiae protein IWS1. IWS1 is known to be an Pol II transcription elongation factor and interacts with Spt6 and Spt5.


Pssm-ID: 462573 [Multi-domain]  Cd Length: 52  Bit Score: 60.99  E-value: 2.19e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 117949797   29 HLTELETIYVTKEHLQETDVVRAVYRVLKNCPSVALKKKAKCLLSKWKAV 78
Cdd:pfam08711   2 LLKKLEKLPVTLELLKSTGIGKVVNKLRKHKENPEIKKLAKELVKKWKRL 51
Zn-ribbon_TFIIS cd13749
domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing ...
 289-343 6.82e-04

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: 37.20  E-value: 6.82e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 117949797 289 GTQTNKIKCRRCEKYNCkvTVIDRGTlflpswvRNSnpDEQMMTYVICNECGEQW 343
Cdd:cd13749    2 GTTTDLFKCGKCKKRKC--TYYQLQT-------RSA--DEPMTTFVTCLNCGNRW 45
 
Name Accession Description Interval E-value
TFIIS_M pfam07500
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ...
 172-281 4.70e-38

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: 131.94  E-value: 4.70e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117949797  172 PMRTKCIELLYAALTSSSTDQPKADLWQnFAREIEEHVFTLYSKNIKKYKTCIRSKVANLKNPRNSHLQQNLLSGTTSPR 251
Cdd:pfam07500   4 KVRDKCRELLYDALAKDSTEASEEDALE-LAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGEISPE 82

                          90       100       110
                  ....*....|....*....|....*....|
gi 117949797  252 EFAEMTVMEMANKELKQLRASYTESCIQEH 281
Cdd:pfam07500  83 KLVTMSPEEMASEELKKEREKIEKEALKEA 112
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 6-343 2.35e-36

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: 133.43  E-value: 2.35e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117949797    6 QIAARASLIEQLMSKRNFEDLGNHLTELETIYVTKEHLQETDVVRAVyRVLKNCPSVALKKKAKCLLSKWKAVykqthsk 85
Cdd:TIGR01385   3 EVASHAKALDKNKSSKNVEQCLDILHQLKEFPPTEELLQETKVGVKV-NKLRKHPNEDISKLAKKIIKSWKKV------- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117949797   86 arnspklfpVRGNKEENSGPShdPSQNETLGicSSNSLSSQDVAKLSEMIVpenraiqlKPKeehfgdgDPESTGKRSSE 165
Cdd:TIGR01385  75 ---------VDKNKSDHPGGN--PEDKTTVG--ESVNSVKQEAKSQSDKIE--------QPK-------YVSSSPRNAKN 126

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117949797  166 LLDPTT----PMRTKCIELLYAALTSSSTDQPKADLWQNFAREIEEHVFTLYSKNIKKYKTCIRSKVANLKNPRNSHLQQ 241
Cdd:TIGR01385 127 DFVPTAvtndKVRDKCRELLYDALAKDSDHPPQSIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRH 206

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117949797  242 NLLSGTTSPREFAEMTVMEMANKELKQLRASYTESCIQEHYLpQVIDGTQTNKIKCRRCEKYNCKVTvidrgtlflpsWV 321
Cdd:TIGR01385 207 NVLTGEITPEKLATMTAEEMASAELKQEREEITKENLFEAQG-AKIQKAVTDLFTCGKCKQKKCTYY-----------QL 274

                         330       340
                  ....*....|....*....|..
gi 117949797  322 RNSNPDEQMMTYVICNECGEQW 343
Cdd:TIGR01385 275 QTRSADEPMTTFVTCEECGNRW 296
TFS2M smart00510
Domain in the central regions of transcription elongation factor S-II (and elsewhere);
172-270 4.70e-17

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


Pssm-ID: 128786 [Multi-domain]  Cd Length: 102  Bit Score: 75.81  E-value: 4.70e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117949797   172 PMRTKCIELLYAALTSSSTDQPKADLWQNFAREIEEHVFTLYSKNIKKYKTCIRSKVANLKNPRNSHLQQNLLSGTTSPR 251
Cdd:smart00510   2 KVRDKCQEMLYKALQKISDPEEIELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITPE 81

                           90
                   ....*....|....*....
gi 117949797   252 EFAEMTVMEMANKELKQLR 270
Cdd:smart00510  82 KLATMTAEELASAELKEKR 100
Med26 pfam08711
TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is ...
 29-78 2.19e-12

TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species {1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. Notably, the 'small' and 'large' Mediator complexes differ in their subunit composition: the Med26 subunit preferentially associates with the small, active complex, whereas cdk8, cyclin C, Med12 and Med13 associate with the large Mediator complex. This family includesthe C terminal region of a number of eukaryotic hypothetical proteins which are homologous to the Saccharomyces cerevisiae protein IWS1. IWS1 is known to be an Pol II transcription elongation factor and interacts with Spt6 and Spt5.


Pssm-ID: 462573 [Multi-domain]  Cd Length: 52  Bit Score: 60.99  E-value: 2.19e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 117949797   29 HLTELETIYVTKEHLQETDVVRAVYRVLKNCPSVALKKKAKCLLSKWKAV 78
Cdd:pfam08711   2 LLKKLEKLPVTLELLKSTGIGKVVNKLRKHKENPEIKKLAKELVKKWKRL 51
Zn-ribbon_TFIIS cd13749
domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing ...
 289-343 6.82e-04

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: 37.20  E-value: 6.82e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 117949797 289 GTQTNKIKCRRCEKYNCkvTVIDRGTlflpswvRNSnpDEQMMTYVICNECGEQW 343
Cdd:cd13749    2 GTTTDLFKCGKCKKRKC--TYYQLQT-------RSA--DEPMTTFVTCLNCGNRW 45
TFIIS_I cd00183
N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a ...
 30-78 2.33e-03

N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme


Pssm-ID: 238107  Cd Length: 76  Bit Score: 36.52  E-value: 2.33e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 117949797  30 LTELETIYVTKEHLQETDVVRAVYRVLKNcPSVALKKKAKCLLSKWKAV 78
Cdd:cd00183   27 LRLLKKLPLTVEILKETRIGKKVNSLRKH-SNEKIRKLAKALIKSWKKL 74
 
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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