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Conserved domains on  [gi|17539794|ref|NP_501924|]
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IWS1-like protein [Caenorhabditis elegans]

Protein Classification

TFIIS N-terminal domain-containing protein( domain architecture ID 2257)

TFIIS (transcription elongation factor S-II) N-terminal domain-containing protein contains structural motifs that are responsible for interacting with RNA polymerase II (RNAPII) and mediating its catalytic activities

PubMed:  17913884

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TFIIS_I super family cl00146
N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a ...
 237-418 4.88e-24

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


The actual alignment was detected with superfamily member COG5139:

Pssm-ID: 469629  Cd Length: 397  Bit Score: 104.01  E-value: 4.88e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17539794 237 DGTVSRLVERMKHAAKSDRNANIERKPAFQKIKMLPEVKAIMLRAGIVEVLIENGFMSALSEWLAPLPDKCLPALDIRIT 316
Cdd:COG5139 155 DEISLRLKKRMQDAAKKDNANNLEGRPATGKIKNLPEVSDVLMKKALQDTILDNNILDSVRGWLEPLPDKSLPNIKIQKS 234

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17539794 317 VLKLLHNprfWKLDRSTLKQSGLGKAVMMLYKHPNETKENKGIANKLIGEWARPIYHLDTDYstvsrQEREERDYSRMPE 396
Cdd:COG5139 235 LLDVLKT---LPIHTEHLVESGVGRIVYFYTISKKEEKEVRRSAKALVQEWTRPIIKPSGNY-----RDKRIMQLEFDSE 306

                       170       180
                ....*....|....*....|...
gi 17539794 397 K-RKKKINSRDEEEPNDDDQPKR 418
Cdd:COG5139 307 KlRKKSVMDSAKNRKKKSSGEDP 329
 
Name Accession Description Interval E-value
COG5139 COG5139
Uncharacterized conserved protein [Function unknown];
237-418 4.88e-24

Uncharacterized conserved protein [Function unknown];


Pssm-ID: 227468  Cd Length: 397  Bit Score: 104.01  E-value: 4.88e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17539794 237 DGTVSRLVERMKHAAKSDRNANIERKPAFQKIKMLPEVKAIMLRAGIVEVLIENGFMSALSEWLAPLPDKCLPALDIRIT 316
Cdd:COG5139 155 DEISLRLKKRMQDAAKKDNANNLEGRPATGKIKNLPEVSDVLMKKALQDTILDNNILDSVRGWLEPLPDKSLPNIKIQKS 234

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17539794 317 VLKLLHNprfWKLDRSTLKQSGLGKAVMMLYKHPNETKENKGIANKLIGEWARPIYHLDTDYstvsrQEREERDYSRMPE 396
Cdd:COG5139 235 LLDVLKT---LPIHTEHLVESGVGRIVYFYTISKKEEKEVRRSAKALVQEWTRPIIKPSGNY-----RDKRIMQLEFDSE 306

                       170       180
                ....*....|....*....|...
gi 17539794 397 K-RKKKINSRDEEEPNDDDQPKR 418
Cdd:COG5139 307 KlRKKSVMDSAKNRKKKSSGEDP 329
Med26 pfam08711
TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is ...
 317-371 1.91e-08

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: 50.59  E-value: 1.91e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 17539794   317 VLKLLHNprfWKLDRSTLKQSGLGKAVMMLYKHPnETKENKGIANKLIGEWARPI 371
Cdd:pfam08711   2 LLKKLEK---LPVTLELLKSTGIGKVVNKLRKHK-ENPEIKKLAKELVKKWKRLV 52
 
Name Accession Description Interval E-value
COG5139 COG5139
Uncharacterized conserved protein [Function unknown];
237-418 4.88e-24

Uncharacterized conserved protein [Function unknown];


Pssm-ID: 227468  Cd Length: 397  Bit Score: 104.01  E-value: 4.88e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17539794 237 DGTVSRLVERMKHAAKSDRNANIERKPAFQKIKMLPEVKAIMLRAGIVEVLIENGFMSALSEWLAPLPDKCLPALDIRIT 316
Cdd:COG5139 155 DEISLRLKKRMQDAAKKDNANNLEGRPATGKIKNLPEVSDVLMKKALQDTILDNNILDSVRGWLEPLPDKSLPNIKIQKS 234

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17539794 317 VLKLLHNprfWKLDRSTLKQSGLGKAVMMLYKHPNETKENKGIANKLIGEWARPIYHLDTDYstvsrQEREERDYSRMPE 396
Cdd:COG5139 235 LLDVLKT---LPIHTEHLVESGVGRIVYFYTISKKEEKEVRRSAKALVQEWTRPIIKPSGNY-----RDKRIMQLEFDSE 306

                       170       180
                ....*....|....*....|...
gi 17539794 397 K-RKKKINSRDEEEPNDDDQPKR 418
Cdd:COG5139 307 KlRKKSVMDSAKNRKKKSSGEDP 329
Med26 pfam08711
TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is ...
 317-371 1.91e-08

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: 50.59  E-value: 1.91e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 17539794   317 VLKLLHNprfWKLDRSTLKQSGLGKAVMMLYKHPnETKENKGIANKLIGEWARPI 371
Cdd:pfam08711   2 LLKKLEK---LPVTLELLKSTGIGKVVNKLRKHK-ENPEIKKLAKELVKKWKRLV 52
 
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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