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Conserved domains on  [gi|62955741|ref|NP_001017883|]
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mediator of RNA polymerase II transcription subunit 4 [Danio rerio]

Protein Classification

mediator of RNA polymerase II transcription subunit 4( domain architecture ID 4324)

mediator of RNA polymerase II transcription subunit 4 (Med4) is a component of the mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes

Gene Symbol:  MED4
Gene Ontology:  GO:0061629|GO:0016592
PubMed:  15175151|16263706

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Med4 super family cl10818
Vitamin-D-receptor interacting Mediator subunit 4; Members of this family function as part of ...
 49-175 1.92e-34

Vitamin-D-receptor interacting Mediator subunit 4; Members of this family function as part of the Mediator (Med) complex, which links DNA-bound transcriptional regulators and the general transcription machinery, particularly the RNA polymerase II enzyme. They play a role in basal transcription by mediating activation or repression according to the specific complement of transcriptional regulators bound to the promoter.


The actual alignment was detected with superfamily member pfam10018:

Pssm-ID: 401849  Cd Length: 184  Bit Score: 122.15  E-value: 1.92e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62955741    49 ILELLIQRDKEFQELMQTALEQGRVHQEMQSLEKEVEKRDSDIQQLQKQLKEAEHILATAVYQAKEKLKSIDKARKGSIS 128
Cdd:pfam10018   3 LAEKLLDADDELTKTLKELEEHQKNEARILQLRAEAESLDEKIKEIVKTLKEYEKELRALPFQANQKLASINLANKREVD 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 62955741   129 SKEIIKYAHRISASNAVC--------APLNWVPGDPRRPYPTDLEMRSGMLGNMS 175
Cdd:pfam10018  83 SEELLDYAHRISKYTHVPpaepvaskAPTTWLRGDYFRPWPAEDEIRMGLLAMSQ 137
 
Name Accession Description Interval E-value
Med4 pfam10018
Vitamin-D-receptor interacting Mediator subunit 4; Members of this family function as part of ...
 49-175 1.92e-34

Vitamin-D-receptor interacting Mediator subunit 4; Members of this family function as part of the Mediator (Med) complex, which links DNA-bound transcriptional regulators and the general transcription machinery, particularly the RNA polymerase II enzyme. They play a role in basal transcription by mediating activation or repression according to the specific complement of transcriptional regulators bound to the promoter.


Pssm-ID: 401849  Cd Length: 184  Bit Score: 122.15  E-value: 1.92e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62955741    49 ILELLIQRDKEFQELMQTALEQGRVHQEMQSLEKEVEKRDSDIQQLQKQLKEAEHILATAVYQAKEKLKSIDKARKGSIS 128
Cdd:pfam10018   3 LAEKLLDADDELTKTLKELEEHQKNEARILQLRAEAESLDEKIKEIVKTLKEYEKELRALPFQANQKLASINLANKREVD 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 62955741   129 SKEIIKYAHRISASNAVC--------APLNWVPGDPRRPYPTDLEMRSGMLGNMS 175
Cdd:pfam10018  83 SEELLDYAHRISKYTHVPpaepvaskAPTTWLRGDYFRPWPAEDEIRMGLLAMSQ 137
ClpA COG0542
ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein ...
 16-114 5.26e-03

ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440308 [Multi-domain]  Cd Length: 836  Bit Score: 37.75  E-value: 5.26e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62955741  16 STLDDLEVLSREL----IEMLALSRSQKLPPPGEDTLILELLIQRDKEFQELMQTALEQGRVHQEMQSLEKEVEKRDSDI 91
Cdd:COG0542 408 SKPEELDELERRLeqleIEKEALKKEQDEASFERLAELRDELAELEEELEALKARWEAEKELIEEIQELKEELEQRYGKI 487

                        90       100
                ....*....|....*....|...
gi 62955741  92 QQLQKQLKEAEHILATAVYQAKE 114
Cdd:COG0542 488 PELEKELAELEEELAELAPLLRE 510
 
Name Accession Description Interval E-value
Med4 pfam10018
Vitamin-D-receptor interacting Mediator subunit 4; Members of this family function as part of ...
 49-175 1.92e-34

Vitamin-D-receptor interacting Mediator subunit 4; Members of this family function as part of the Mediator (Med) complex, which links DNA-bound transcriptional regulators and the general transcription machinery, particularly the RNA polymerase II enzyme. They play a role in basal transcription by mediating activation or repression according to the specific complement of transcriptional regulators bound to the promoter.


Pssm-ID: 401849  Cd Length: 184  Bit Score: 122.15  E-value: 1.92e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62955741    49 ILELLIQRDKEFQELMQTALEQGRVHQEMQSLEKEVEKRDSDIQQLQKQLKEAEHILATAVYQAKEKLKSIDKARKGSIS 128
Cdd:pfam10018   3 LAEKLLDADDELTKTLKELEEHQKNEARILQLRAEAESLDEKIKEIVKTLKEYEKELRALPFQANQKLASINLANKREVD 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 62955741   129 SKEIIKYAHRISASNAVC--------APLNWVPGDPRRPYPTDLEMRSGMLGNMS 175
Cdd:pfam10018  83 SEELLDYAHRISKYTHVPpaepvaskAPTTWLRGDYFRPWPAEDEIRMGLLAMSQ 137
ClpA COG0542
ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein ...
 16-114 5.26e-03

ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440308 [Multi-domain]  Cd Length: 836  Bit Score: 37.75  E-value: 5.26e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62955741  16 STLDDLEVLSREL----IEMLALSRSQKLPPPGEDTLILELLIQRDKEFQELMQTALEQGRVHQEMQSLEKEVEKRDSDI 91
Cdd:COG0542 408 SKPEELDELERRLeqleIEKEALKKEQDEASFERLAELRDELAELEEELEALKARWEAEKELIEEIQELKEELEQRYGKI 487

                        90       100
                ....*....|....*....|...
gi 62955741  92 QQLQKQLKEAEHILATAVYQAKE 114
Cdd:COG0542 488 PELEKELAELEEELAELAPLLRE 510
 
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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