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Conserved domains on  [gi|45549559|ref|NP_573049|]
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uncharacterized protein Dmel_CG8117 [Drosophila melanogaster]

Protein Classification

transcription factor S-II family protein( domain architecture ID 1002377)

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

CATH:  2.20.25.10
Gene Ontology:  GO:0006351|GO:0003711|GO:0003677|GO:0008270
PubMed:  8855225

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TFSII super family cl36890
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 4-161 2.33e-54

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: 173.49  E-value: 2.33e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549559     4 EIRIKCREMLATAL-KSGNMPPGCGDPDDMAAKLEDAIYGDLNGCKVKYKNRIRSRLANLRDPKNPELRQKFLLGQITPE 82
Cdd:TIGR01385 137 KVRDKCRELLYDALaKDSDHPPQSIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPE 216

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549559    83 ELSKMTPEEMASDDMKQMRQKYVQDSINAAQMAKVQGTKTDQFKCERCDKRNCS--QLHIRDGDEPIITFVICDECGNRW 160
Cdd:TIGR01385 217 KLATMTAEEMASAELKQEREEITKENLFEAQGAKIQKAVTDLFTCGKCKQKKCTyyQLQTRSADEPMTTFVTCEECGNRW 296


                  .
gi 45549559   161 K 161
Cdd:TIGR01385 297 K 297
 
Name Accession Description Interval E-value
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 4-161 2.33e-54

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: 173.49  E-value: 2.33e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549559     4 EIRIKCREMLATAL-KSGNMPPGCGDPDDMAAKLEDAIYGDLNGCKVKYKNRIRSRLANLRDPKNPELRQKFLLGQITPE 82
Cdd:TIGR01385 137 KVRDKCRELLYDALaKDSDHPPQSIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPE 216

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549559    83 ELSKMTPEEMASDDMKQMRQKYVQDSINAAQMAKVQGTKTDQFKCERCDKRNCS--QLHIRDGDEPIITFVICDECGNRW 160
Cdd:TIGR01385 217 KLATMTAEEMASAELKQEREEITKENLFEAQGAKIQKAVTDLFTCGKCKQKKCTyyQLQTRSADEPMTTFVTCEECGNRW 296


                  .
gi 45549559   161 K 161
Cdd:TIGR01385 297 K 297
TFIIS_M pfam07500
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ...
 1-112 4.52e-42

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: 4.52e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549559     1 MSMEIRIKCREMLATALKSGNMPPGCGDPDDMAAKLEDAIYGDLNGCKVKYKNRIRSRLANLRDPKNPELRQKFLLGQIT 80
Cdd:pfam07500   1 TGDKVRDKCRELLYDALAKDSTEASEEDALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGEIS 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 45549559    81 PEELSKMTPEEMASDDMKQMRQKYVQDSINAA 112
Cdd:pfam07500  81 PEKLVTMSPEEMASEELKKEREKIEKEALKEA 112
TFS2M smart00510
Domain in the central regions of transcription elongation factor S-II (and elsewhere);
4-103 3.65e-34

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


Pssm-ID: 128786 [Multi-domain]  Cd Length: 102  Bit Score: 115.49  E-value: 3.65e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549559      4 EIRIKCREMLATALKSGNMPP-GCGDPDDMAAKLEDAIYGDLNGCKVKYKNRIRSRLANLRDPKNPELRQKFLLGQITPE 82
Cdd:smart00510   2 KVRDKCQEMLYKALQKISDPEeIELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITPE 81

                           90       100
                   ....*....|....*....|.
gi 45549559     83 ELSKMTPEEMASDDMKQMRQK 103
Cdd:smart00510  82 KLATMTAEELASAELKEKREK 102
Zn-ribbon_TFIIS cd13749
domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing ...
 118-161 1.72e-14

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: 63.78  E-value: 1.72e-14
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 45549559 118 QGTKTDQFKCERCDKRNCS--QLHIRDGDEPIITFVICDECGNRWK 161
Cdd:cd13749   1 EGTTTDLFKCGKCKKRKCTyyQLQTRSADEPMTTFVTCLNCGNRWK 46
 
Name Accession Description Interval E-value
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 4-161 2.33e-54

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: 173.49  E-value: 2.33e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549559     4 EIRIKCREMLATAL-KSGNMPPGCGDPDDMAAKLEDAIYGDLNGCKVKYKNRIRSRLANLRDPKNPELRQKFLLGQITPE 82
Cdd:TIGR01385 137 KVRDKCRELLYDALaKDSDHPPQSIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPE 216

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549559    83 ELSKMTPEEMASDDMKQMRQKYVQDSINAAQMAKVQGTKTDQFKCERCDKRNCS--QLHIRDGDEPIITFVICDECGNRW 160
Cdd:TIGR01385 217 KLATMTAEEMASAELKQEREEITKENLFEAQGAKIQKAVTDLFTCGKCKQKKCTyyQLQTRSADEPMTTFVTCEECGNRW 296


                  .
gi 45549559   161 K 161
Cdd:TIGR01385 297 K 297
TFIIS_M pfam07500
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ...
 1-112 4.52e-42

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: 4.52e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549559     1 MSMEIRIKCREMLATALKSGNMPPGCGDPDDMAAKLEDAIYGDLNGCKVKYKNRIRSRLANLRDPKNPELRQKFLLGQIT 80
Cdd:pfam07500   1 TGDKVRDKCRELLYDALAKDSTEASEEDALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGEIS 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 45549559    81 PEELSKMTPEEMASDDMKQMRQKYVQDSINAA 112
Cdd:pfam07500  81 PEKLVTMSPEEMASEELKKEREKIEKEALKEA 112
TFS2M smart00510
Domain in the central regions of transcription elongation factor S-II (and elsewhere);
4-103 3.65e-34

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


Pssm-ID: 128786 [Multi-domain]  Cd Length: 102  Bit Score: 115.49  E-value: 3.65e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549559      4 EIRIKCREMLATALKSGNMPP-GCGDPDDMAAKLEDAIYGDLNGCKVKYKNRIRSRLANLRDPKNPELRQKFLLGQITPE 82
Cdd:smart00510   2 KVRDKCQEMLYKALQKISDPEeIELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITPE 81

                           90       100
                   ....*....|....*....|.
gi 45549559     83 ELSKMTPEEMASDDMKQMRQK 103
Cdd:smart00510  82 KLATMTAEELASAELKEKREK 102
Zn-ribbon_TFIIS cd13749
domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing ...
 118-161 1.72e-14

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: 63.78  E-value: 1.72e-14
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 45549559 118 QGTKTDQFKCERCDKRNCS--QLHIRDGDEPIITFVICDECGNRWK 161
Cdd:cd13749   1 EGTTTDLFKCGKCKKRKCTyyQLQTRSADEPMTTFVTCLNCGNRWK 46
TFIIS_C pfam01096
Transcription factor S-II (TFIIS);
125-161 9.30e-12

Transcription factor S-II (TFIIS);


Pssm-ID: 426046  Cd Length: 39  Bit Score: 56.46  E-value: 9.30e-12
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 45549559   125 FKCERCDKRNCS--QLHIRDGDEPIITFVICDECGNRWK 161
Cdd:pfam01096   1 AKCPKCGNREAYffQLQTRSADEPMTVFYVCTKCGHRWR 39
ZnF_C2C2 smart00440
C2C2 Zinc finger; Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and ...
 125-162 4.46e-07

C2C2 Zinc finger; Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.


Pssm-ID: 128717 [Multi-domain]  Cd Length: 40  Bit Score: 44.24  E-value: 4.46e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 45549559    125 FKCERCDKRNCS--QLHIRDGDEPIITFVICDECGNRWKS 162
Cdd:smart00440   1 AECPKCGNREATfyQLQTRSADEPMTVFYVCTKCGHHWRE 40
Zn-ribbon cd00656
C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The ...
 122-161 1.45e-06

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.


Pssm-ID: 259791  Cd Length: 45  Bit Score: 43.07  E-value: 1.45e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 45549559 122 TDQFKCERCDKRNCS--QLHIRDGDEPIITFVICDECGNRWK 161
Cdd:cd00656   4 TTDRTCPKCGHDEAYwwMLQTRSADEPPTRFYKCTKCGHTWR 45
Zn-ribbon_RPC11 cd10509
C-terminal zinc ribbon domain of RPC11 subunit of RNA polymerase III; The C-terminal zinc ...
 126-161 2.47e-04

C-terminal zinc ribbon domain of RPC11 subunit of RNA polymerase III; The C-terminal zinc ribbon domain (C-ribbon) of subunit C11 (Zn-ribbon_RPC11) in RNA polymerase (Pol) III is required for intrinsic transcript cleavage. RPC11 is also involved in Pol III termination. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPC11 has strong homology to RPB9 of Pol II and RPA12 of Pol I. Zn-ribbon_RPC11 is homologous to Pol II elongation factor TFIIS domain III. C11 has two zinc-binding domains separated by a flexible linker.


Pssm-ID: 259794  Cd Length: 46  Bit Score: 37.18  E-value: 2.47e-04
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 45549559 126 KCERCDKRNCS--QLHIRDGDEPIITFVICDECGNRWK 161
Cdd:cd10509   8 TCPKCGHNRAYfmQIQTRSADEPMTTFYKCCKCGHQWR 45
Zn-ribbon_TFS cd10511
C-terminal zinc ribbon domain of archaeal Transcription Factor S (TFS); TFS is an archaeal ...
 122-162 1.48e-03

C-terminal zinc ribbon domain of archaeal Transcription Factor S (TFS); TFS is an archaeal protein that stimulates the intrinsic cleavage activity of archaeal RNA polymerase. TFS C-terminal domain shows sequence similarity to the homologous C-terminal zinc ribbon domain of subunits A12.2, Rpb9, and C11 in eukaryotic RNA Polymerases (Pol) I, II, and III, respectively and domain III of TFIIS. TFS is not a subunit of archaeal RNA polymerase even though its domains arrangement is similar to A12.2, Rpb9, and C1. TFS is a transcription factor with a similar function to eukaryotic TFIIS. TFS has external cleavage induction activity and improves the fidelity of transcription. TFS has two zinc-binding domains.


Pssm-ID: 259795  Cd Length: 47  Bit Score: 35.02  E-value: 1.48e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 45549559 122 TDQFKCERCDKRNCS--QLHIRDGDEPIITFVICDECGNRWKS 162
Cdd:cd10511   4 TTKITCPKCGHDEAYwwMVQTRSADEPPTRFYKCTKCGHTWRE 46
 
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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