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Conserved domains on  [gi|1063730945|ref|NP_001331544|]
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Transcription elongation factor (TFIIS) family protein [Arabidopsis thaliana]

Protein Classification

TFIIS_I domain-containing protein( domain architecture ID 10075868)

TFIIS_I domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TFIIS_I cd00183
N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a ...
 124-197 3.11e-22

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: 88.90  E-value: 3.11e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063730945 124 QKSIVEIKEKLEDPDLSEE--SLVELLQNLEDMDITFQALQETDIGRHVNRVRKHPSNNVRRLAKQLVKKWKETVD 197
Cdd:cd00183     1 SEEVLRAKKKLEKKDSNEEvsRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSNEKIRKLAKALIKSWKKLVD 76
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 257-303 3.24e-03

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 39.54  E-value: 3.24e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1063730945  257 EPERKPRPVAPQPRRESPSPAKPSRPSPSQQTIPRDKEHKEVDFDTA 303
Cdd:PHA03247  2904 QPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPA 2950
 
Name Accession Description Interval E-value
TFIIS_I cd00183
N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a ...
 124-197 3.11e-22

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: 88.90  E-value: 3.11e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063730945 124 QKSIVEIKEKLEDPDLSEE--SLVELLQNLEDMDITFQALQETDIGRHVNRVRKHPSNNVRRLAKQLVKKWKETVD 197
Cdd:cd00183     1 SEEVLRAKKKLEKKDSNEEvsRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSNEKIRKLAKALIKSWKKLVD 76
Med26 pfam08711
TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is ...
 146-196 1.12e-17

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: 75.63  E-value: 1.12e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1063730945 146 ELLQNLEDMDITFQALQETDIGRHVNRVRKHPSN-NVRRLAKQLVKKWKETV 196
Cdd:pfam08711   1 KLLKKLEKLPVTLELLKSTGIGKVVNKLRKHKENpEIKKLAKELVKKWKRLV 52
TFS2N smart00509
Domain in the N-terminus of transcription elongation factor S-II (and elsewhere);
142-198 1.73e-11

Domain in the N-terminus of transcription elongation factor S-II (and elsewhere);


Pssm-ID: 197766 [Multi-domain]  Cd Length: 75  Bit Score: 59.25  E-value: 1.73e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1063730945  142 ESLVELLQNLEDMDITFQALQETDIGRHVNRVRKHPSNNVRRLAKQLVKKWKETVDE 198
Cdd:smart00509  19 SRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHKNEEIRKLAKKLIKSWKKLVYS 75
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 125-206 5.13e-10

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: 59.85  E-value: 5.13e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063730945 125 KSIVEIKEKLEDPDLSE--ESLVELLQNLEDMDITFQALQETDIGRHVNRVRKHPSNNVRRLAKQLVKKWKETVDEWVKF 202
Cdd:TIGR01385   2 AEVASHAKALDKNKSSKnvEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISKLAKKIIKSWKKVVDKNKSD 81


                  ....
gi 1063730945 203 NQPG 206
Cdd:TIGR01385  82 HPGG 85
PHA03247 PHA03247
large tegument protein UL36; Provisional
 257-303 3.24e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 39.54  E-value: 3.24e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1063730945  257 EPERKPRPVAPQPRRESPSPAKPSRPSPSQQTIPRDKEHKEVDFDTA 303
Cdd:PHA03247  2904 QPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPA 2950
 
Name Accession Description Interval E-value
TFIIS_I cd00183
N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a ...
 124-197 3.11e-22

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: 88.90  E-value: 3.11e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063730945 124 QKSIVEIKEKLEDPDLSEE--SLVELLQNLEDMDITFQALQETDIGRHVNRVRKHPSNNVRRLAKQLVKKWKETVD 197
Cdd:cd00183     1 SEEVLRAKKKLEKKDSNEEvsRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSNEKIRKLAKALIKSWKKLVD 76
Med26 pfam08711
TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is ...
 146-196 1.12e-17

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: 75.63  E-value: 1.12e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1063730945 146 ELLQNLEDMDITFQALQETDIGRHVNRVRKHPSN-NVRRLAKQLVKKWKETV 196
Cdd:pfam08711   1 KLLKKLEKLPVTLELLKSTGIGKVVNKLRKHKENpEIKKLAKELVKKWKRLV 52
TFS2N smart00509
Domain in the N-terminus of transcription elongation factor S-II (and elsewhere);
142-198 1.73e-11

Domain in the N-terminus of transcription elongation factor S-II (and elsewhere);


Pssm-ID: 197766 [Multi-domain]  Cd Length: 75  Bit Score: 59.25  E-value: 1.73e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1063730945  142 ESLVELLQNLEDMDITFQALQETDIGRHVNRVRKHPSNNVRRLAKQLVKKWKETVDE 198
Cdd:smart00509  19 SRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHKNEEIRKLAKKLIKSWKKLVYS 75
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 125-206 5.13e-10

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: 59.85  E-value: 5.13e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063730945 125 KSIVEIKEKLEDPDLSE--ESLVELLQNLEDMDITFQALQETDIGRHVNRVRKHPSNNVRRLAKQLVKKWKETVDEWVKF 202
Cdd:TIGR01385   2 AEVASHAKALDKNKSSKnvEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISKLAKKIIKSWKKVVDKNKSD 81


                  ....
gi 1063730945 203 NQPG 206
Cdd:TIGR01385  82 HPGG 85
PHA03247 PHA03247
large tegument protein UL36; Provisional
 257-303 3.24e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 39.54  E-value: 3.24e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1063730945  257 EPERKPRPVAPQPRRESPSPAKPSRPSPSQQTIPRDKEHKEVDFDTA 303
Cdd:PHA03247  2904 QPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPA 2950
 
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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