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Conserved domains on  [gi|568929484|ref|XP_006503337|]
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transcription elongation factor A N-terminal and central domain-containing protein 2 isoform X1 [Mus musculus]

Protein Classification

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 ...
 38-111 2.72e-18

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: 75.42  E-value: 2.72e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568929484  38 IEDIKRWKTMLELPDQTKE--NLVAALQELKKKMPSREVLRSTRIGHAVNKMRRHSDPEVAGLAKEVYTEWKTFIE 111
Cdd:cd00183    1 SEEVLRAKKKLEKKDSNEEvsRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSNEKIRKLAKALIKSWKKLVD 76
TFIIS_M super family cl47972
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ...
 126-202 3.29e-03

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.


The actual alignment was detected with superfamily member pfam07500:

Pssm-ID: 462184  Cd Length: 112  Bit Score: 36.03  E-value: 3.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929484  126 KTESFRKNAQKLLSEALELKMDHL-------LVENIERETFHLCSRLiNGPYRRTVRALVFTLKHR--AEIREQVKSGAL 196
Cdd:pfam07500   1 TGDKVRDKCRELLYDALAKDSTEAseedaleLAVEIEEALFKKFGGT-NKKYKNKIRSLLFNLKDKknPDLRRRVLSGEI 79


                  ....*.
gi 568929484  197 PVGTFV 202
Cdd:pfam07500  80 SPEKLV 85
 
Name Accession Description Interval E-value
TFIIS_I cd00183
N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a ...
 38-111 2.72e-18

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: 75.42  E-value: 2.72e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568929484  38 IEDIKRWKTMLELPDQTKE--NLVAALQELKKKMPSREVLRSTRIGHAVNKMRRHSDPEVAGLAKEVYTEWKTFIE 111
Cdd:cd00183    1 SEEVLRAKKKLEKKDSNEEvsRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSNEKIRKLAKALIKSWKKLVD 76
Med26 pfam08711
TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is ...
 60-110 3.85e-11

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: 55.98  E-value: 3.85e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 568929484   60 AALQELKKKMPSREVLRSTRIGHAVNKMRRHS-DPEVAGLAKEVYTEWKTFI 110
Cdd:pfam08711   1 KLLKKLEKLPVTLELLKSTGIGKVVNKLRKHKeNPEIKKLAKELVKKWKRLV 52
TFS2N smart00509
Domain in the N-terminus of transcription elongation factor S-II (and elsewhere);
56-112 1.63e-07

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


Pssm-ID: 197766 [Multi-domain]  Cd Length: 75  Bit Score: 46.92  E-value: 1.63e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 568929484    56 ENLVAALQELKKKMPSREVLRSTRIGHAVNKMRRHSDPEVAGLAKEVYTEWKTFIEK 112
Cdd:smart00509  19 SRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHKNEEIRKLAKKLIKSWKKLVYS 75
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 61-112 4.93e-07

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: 49.07  E-value: 4.93e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 568929484   61 ALQELKKKMPSREVLRSTRIGHAVNKMRRHSDPEVAGLAKEVYTEWKTFIEK 112
Cdd:TIGR01385  26 ILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISKLAKKIIKSWKKVVDK 77
TFIIS_M pfam07500
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ...
 126-202 3.29e-03

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: 36.03  E-value: 3.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929484  126 KTESFRKNAQKLLSEALELKMDHL-------LVENIERETFHLCSRLiNGPYRRTVRALVFTLKHR--AEIREQVKSGAL 196
Cdd:pfam07500   1 TGDKVRDKCRELLYDALAKDSTEAseedaleLAVEIEEALFKKFGGT-NKKYKNKIRSLLFNLKDKknPDLRRRVLSGEI 79


                  ....*.
gi 568929484  197 PVGTFV 202
Cdd:pfam07500  80 SPEKLV 85
 
Name Accession Description Interval E-value
TFIIS_I cd00183
N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a ...
 38-111 2.72e-18

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: 75.42  E-value: 2.72e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568929484  38 IEDIKRWKTMLELPDQTKE--NLVAALQELKKKMPSREVLRSTRIGHAVNKMRRHSDPEVAGLAKEVYTEWKTFIE 111
Cdd:cd00183    1 SEEVLRAKKKLEKKDSNEEvsRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSNEKIRKLAKALIKSWKKLVD 76
Med26 pfam08711
TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is ...
 60-110 3.85e-11

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: 55.98  E-value: 3.85e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 568929484   60 AALQELKKKMPSREVLRSTRIGHAVNKMRRHS-DPEVAGLAKEVYTEWKTFI 110
Cdd:pfam08711   1 KLLKKLEKLPVTLELLKSTGIGKVVNKLRKHKeNPEIKKLAKELVKKWKRLV 52
TFS2N smart00509
Domain in the N-terminus of transcription elongation factor S-II (and elsewhere);
56-112 1.63e-07

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


Pssm-ID: 197766 [Multi-domain]  Cd Length: 75  Bit Score: 46.92  E-value: 1.63e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 568929484    56 ENLVAALQELKKKMPSREVLRSTRIGHAVNKMRRHSDPEVAGLAKEVYTEWKTFIEK 112
Cdd:smart00509  19 SRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHKNEEIRKLAKKLIKSWKKLVYS 75
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 61-112 4.93e-07

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: 49.07  E-value: 4.93e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 568929484   61 ALQELKKKMPSREVLRSTRIGHAVNKMRRHSDPEVAGLAKEVYTEWKTFIEK 112
Cdd:TIGR01385  26 ILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISKLAKKIIKSWKKVVDK 77
TFIIS_M pfam07500
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ...
 126-202 3.29e-03

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: 36.03  E-value: 3.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568929484  126 KTESFRKNAQKLLSEALELKMDHL-------LVENIERETFHLCSRLiNGPYRRTVRALVFTLKHR--AEIREQVKSGAL 196
Cdd:pfam07500   1 TGDKVRDKCRELLYDALAKDSTEAseedaleLAVEIEEALFKKFGGT-NKKYKNKIRSLLFNLKDKknPDLRRRVLSGEI 79


                  ....*.
gi 568929484  197 PVGTFV 202
Cdd:pfam07500  80 SPEKLV 85
 
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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