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Conserved domains on  [gi|31543847|ref|NP_038764|]
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elongin-A [Mus musculus]

Protein Classification

TFIIS_I domain-containing protein( domain architecture ID 12897059)

TFIIS_I domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Elongin_A pfam06881
RNA polymerase II transcription factor SIII (Elongin) subunit A; This family represents a ...
 565-663 1.02e-33

RNA polymerase II transcription factor SIII (Elongin) subunit A; This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin.


:

Pssm-ID: 462026  Cd Length: 105  Bit Score: 124.64  E-value: 1.02e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 31543847   565 IFEVGGVPYSVLEPVLERCTPDQLYRIEECNHVLIEETDQLWKVHCHRDFKEE------RPEEYESWREMYLRLQDAREQ 638
Cdd:pfam06881   1 IDDVGDVPYHLLRPILLKCSPEQLRRIEENSPHLAGDTDELWKRFIKRDFPNWaeekdyEPKNPKSWRKLYEKLKEEREE 80

                          90       100
                  ....*....|....*....|....*
gi 31543847   639 RLRLLTNNIRSAHANKPKGRQAKMA 663
Cdd:pfam06881  81 KLKAAAERLRQAYAGLQKEKQSKQI 105
TFIIS_I cd00183
N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a ...
 37-76 6.30e-13

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: 64.64  E-value: 6.30e-13
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 31543847  37 PITVDILVETGVGKTVNSFRKH--EQVGNFARDLVAQWKKLV 76
Cdd:cd00183  34 PLTVEILKETRIGKKVNSLRKHsnEKIRKLAKALIKSWKKLV 75
TFSII super family cl36890
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 37-119 2.24e-06

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: 50.22  E-value: 2.24e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 31543847    37 PITVDILVETGVGKTVNSFRKH--EQVGNFARDLVAQWKKLVpverNSEAEDQDfeknnsRKRPRDALQREEELEGNYQE 114
Cdd:TIGR01385  34 PPTEELLQETKVGVKVNKLRKHpnEDISKLAKKIIKSWKKVV----DKNKSDHP------GGNPEDKTTVGESVNSVKQE 103


                  ....*
gi 31543847   115 SWKPS 119
Cdd:TIGR01385 104 AKSQS 108
 
Name Accession Description Interval E-value
Elongin_A pfam06881
RNA polymerase II transcription factor SIII (Elongin) subunit A; This family represents a ...
 565-663 1.02e-33

RNA polymerase II transcription factor SIII (Elongin) subunit A; This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin.


Pssm-ID: 462026  Cd Length: 105  Bit Score: 124.64  E-value: 1.02e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 31543847   565 IFEVGGVPYSVLEPVLERCTPDQLYRIEECNHVLIEETDQLWKVHCHRDFKEE------RPEEYESWREMYLRLQDAREQ 638
Cdd:pfam06881   1 IDDVGDVPYHLLRPILLKCSPEQLRRIEENSPHLAGDTDELWKRFIKRDFPNWaeekdyEPKNPKSWRKLYEKLKEEREE 80

                          90       100
                  ....*....|....*....|....*
gi 31543847   639 RLRLLTNNIRSAHANKPKGRQAKMA 663
Cdd:pfam06881  81 KLKAAAERLRQAYAGLQKEKQSKQI 105
TFIIS_I cd00183
N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a ...
 37-76 6.30e-13

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: 64.64  E-value: 6.30e-13
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 31543847  37 PITVDILVETGVGKTVNSFRKH--EQVGNFARDLVAQWKKLV 76
Cdd:cd00183  34 PLTVEILKETRIGKKVNSLRKHsnEKIRKLAKALIKSWKKLV 75
TFS2N smart00509
Domain in the N-terminus of transcription elongation factor S-II (and elsewhere);
7-78 2.09e-12

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


Pssm-ID: 197766 [Multi-domain]  Cd Length: 75  Bit Score: 63.10  E-value: 2.09e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 31543847      7 LQVVEKLQARLAANPD-PKKLLKYLKKLSILPITVDILVETGVGKTVNSFRKH--EQVGNFARDLVAQWKKLVPV 78
Cdd:smart00509   1 LLRAAKKLDKVANNGKeVSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHknEEIRKLAKKLIKSWKKLVYS 75
Med26 pfam08711
TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is ...
 37-76 6.15e-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: 57.91  E-value: 6.15e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 31543847    37 PITVDILVETGVGKTVNSFRKH---EQVGNFARDLVAQWKKLV 76
Cdd:pfam08711  10 PVTLELLKSTGIGKVVNKLRKHkenPEIKKLAKELVKKWKRLV 52
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 37-119 2.24e-06

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: 50.22  E-value: 2.24e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 31543847    37 PITVDILVETGVGKTVNSFRKH--EQVGNFARDLVAQWKKLVpverNSEAEDQDfeknnsRKRPRDALQREEELEGNYQE 114
Cdd:TIGR01385  34 PPTEELLQETKVGVKVNKLRKHpnEDISKLAKKIIKSWKKVV----DKNKSDHP------GGNPEDKTTVGESVNSVKQE 103


                  ....*
gi 31543847   115 SWKPS 119
Cdd:TIGR01385 104 AKSQS 108
 
Name Accession Description Interval E-value
Elongin_A pfam06881
RNA polymerase II transcription factor SIII (Elongin) subunit A; This family represents a ...
 565-663 1.02e-33

RNA polymerase II transcription factor SIII (Elongin) subunit A; This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin.


Pssm-ID: 462026  Cd Length: 105  Bit Score: 124.64  E-value: 1.02e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 31543847   565 IFEVGGVPYSVLEPVLERCTPDQLYRIEECNHVLIEETDQLWKVHCHRDFKEE------RPEEYESWREMYLRLQDAREQ 638
Cdd:pfam06881   1 IDDVGDVPYHLLRPILLKCSPEQLRRIEENSPHLAGDTDELWKRFIKRDFPNWaeekdyEPKNPKSWRKLYEKLKEEREE 80

                          90       100
                  ....*....|....*....|....*
gi 31543847   639 RLRLLTNNIRSAHANKPKGRQAKMA 663
Cdd:pfam06881  81 KLKAAAERLRQAYAGLQKEKQSKQI 105
TFIIS_I cd00183
N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a ...
 37-76 6.30e-13

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: 64.64  E-value: 6.30e-13
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 31543847  37 PITVDILVETGVGKTVNSFRKH--EQVGNFARDLVAQWKKLV 76
Cdd:cd00183  34 PLTVEILKETRIGKKVNSLRKHsnEKIRKLAKALIKSWKKLV 75
TFS2N smart00509
Domain in the N-terminus of transcription elongation factor S-II (and elsewhere);
7-78 2.09e-12

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


Pssm-ID: 197766 [Multi-domain]  Cd Length: 75  Bit Score: 63.10  E-value: 2.09e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 31543847      7 LQVVEKLQARLAANPD-PKKLLKYLKKLSILPITVDILVETGVGKTVNSFRKH--EQVGNFARDLVAQWKKLVPV 78
Cdd:smart00509   1 LLRAAKKLDKVANNGKeVSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHknEEIRKLAKKLIKSWKKLVYS 75
Med26 pfam08711
TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is ...
 37-76 6.15e-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: 57.91  E-value: 6.15e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 31543847    37 PITVDILVETGVGKTVNSFRKH---EQVGNFARDLVAQWKKLV 76
Cdd:pfam08711  10 PVTLELLKSTGIGKVVNKLRKHkenPEIKKLAKELVKKWKRLV 52
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 37-119 2.24e-06

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: 50.22  E-value: 2.24e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 31543847    37 PITVDILVETGVGKTVNSFRKH--EQVGNFARDLVAQWKKLVpverNSEAEDQDfeknnsRKRPRDALQREEELEGNYQE 114
Cdd:TIGR01385  34 PPTEELLQETKVGVKVNKLRKHpnEDISKLAKKIIKSWKKVV----DKNKSDHP------GGNPEDKTTVGESVNSVKQE 103


                  ....*
gi 31543847   115 SWKPS 119
Cdd:TIGR01385 104 AKSQS 108
 
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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