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Conserved domains on  [gi|397739073|ref|NP_001257558|]
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mediator of RNA polymerase II transcription subunit 4 isoform 2 [Homo sapiens]

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 ...
 18-143 2.07e-32

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: 115.98  E-value: 2.07e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 397739073   18 QVLELLIHRDGEFQELMKLALNQGKIHHEMQVLEKEVEKRDSDIQQLQKQLKEAEQILATAVYQAKEKLKSIEKARKGAI 97
Cdd:pfam10018   2 KLAEKLLDADDELTKTLKELEEHQKNEARILQLRAEAESLDEKIKEIVKTLKEYEKELRALPFQANQKLASINLANKREV 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 397739073   98 SSEEIIKYAHRISASNAVC--------APLTWVPGDPRRPYPTDLEMRSGLLGQ 143
Cdd:pfam10018  82 DSEELLDYAHRISKYTHVPpaepvaskAPTTWLRGDYFRPWPAEDEIRMGLLAM 135
 
Name Accession Description Interval E-value
Med4 pfam10018
Vitamin-D-receptor interacting Mediator subunit 4; Members of this family function as part of ...
 18-143 2.07e-32

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: 115.98  E-value: 2.07e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 397739073   18 QVLELLIHRDGEFQELMKLALNQGKIHHEMQVLEKEVEKRDSDIQQLQKQLKEAEQILATAVYQAKEKLKSIEKARKGAI 97
Cdd:pfam10018   2 KLAEKLLDADDELTKTLKELEEHQKNEARILQLRAEAESLDEKIKEIVKTLKEYEKELRALPFQANQKLASINLANKREV 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 397739073   98 SSEEIIKYAHRISASNAVC--------APLTWVPGDPRRPYPTDLEMRSGLLGQ 143
Cdd:pfam10018  82 DSEELLDYAHRISKYTHVPpaepvaskAPTTWLRGDYFRPWPAEDEIRMGLLAM 135
PRK12704 PRK12704
phosphodiesterase; Provisional
 29-104 2.46e-04

phosphodiesterase; Provisional


Pssm-ID: 237177 [Multi-domain]  Cd Length: 520  Bit Score: 41.30  E-value: 2.46e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 397739073  29 EFQELMKLALNQGK--IHHEMQVLEKEVEKRDSDIQQLQKQLKEAEQILatavyqaKEKLKSIEKARKGAISSEEIIK 104
Cdd:PRK12704  50 EAEAIKKEALLEAKeeIHKLRNEFEKELRERRNELQKLEKRLLQKEENL-------DRKLELLEKREEELEKKEKELE 120
COG2433 COG2433
Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];
15-102 1.03e-03

Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];


Pssm-ID: 441980 [Multi-domain]  Cd Length: 644  Bit Score: 39.46  E-value: 1.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 397739073  15 EENQVLELLIH-RDGEFQEL-MKLALNQGKIHHEMQVlEKEVEKRDSDIQQLQKQLKEAEQILAtavyQAKEKLKSIEKA 92
Cdd:COG2433  427 AEVEELEAELEeKDERIERLeRELSEARSEERREIRK-DREISRLDREIERLERELEEERERIE----ELKRKLERLKEL 501

                         90
                 ....*....|
gi 397739073  93 RKGAISSEEI 102
Cdd:COG2433  502 WKLEHSGELV 511
 
Name Accession Description Interval E-value
Med4 pfam10018
Vitamin-D-receptor interacting Mediator subunit 4; Members of this family function as part of ...
 18-143 2.07e-32

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: 115.98  E-value: 2.07e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 397739073   18 QVLELLIHRDGEFQELMKLALNQGKIHHEMQVLEKEVEKRDSDIQQLQKQLKEAEQILATAVYQAKEKLKSIEKARKGAI 97
Cdd:pfam10018   2 KLAEKLLDADDELTKTLKELEEHQKNEARILQLRAEAESLDEKIKEIVKTLKEYEKELRALPFQANQKLASINLANKREV 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 397739073   98 SSEEIIKYAHRISASNAVC--------APLTWVPGDPRRPYPTDLEMRSGLLGQ 143
Cdd:pfam10018  82 DSEELLDYAHRISKYTHVPpaepvaskAPTTWLRGDYFRPWPAEDEIRMGLLAM 135
PRK12704 PRK12704
phosphodiesterase; Provisional
 29-104 2.46e-04

phosphodiesterase; Provisional


Pssm-ID: 237177 [Multi-domain]  Cd Length: 520  Bit Score: 41.30  E-value: 2.46e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 397739073  29 EFQELMKLALNQGK--IHHEMQVLEKEVEKRDSDIQQLQKQLKEAEQILatavyqaKEKLKSIEKARKGAISSEEIIK 104
Cdd:PRK12704  50 EAEAIKKEALLEAKeeIHKLRNEFEKELRERRNELQKLEKRLLQKEENL-------DRKLELLEKREEELEKKEKELE 120
COG2433 COG2433
Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];
15-102 1.03e-03

Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];


Pssm-ID: 441980 [Multi-domain]  Cd Length: 644  Bit Score: 39.46  E-value: 1.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 397739073  15 EENQVLELLIH-RDGEFQEL-MKLALNQGKIHHEMQVlEKEVEKRDSDIQQLQKQLKEAEQILAtavyQAKEKLKSIEKA 92
Cdd:COG2433  427 AEVEELEAELEeKDERIERLeRELSEARSEERREIRK-DREISRLDREIERLERELEEERERIE----ELKRKLERLKEL 501

                         90
                 ....*....|
gi 397739073  93 RKGAISSEEI 102
Cdd:COG2433  502 WKLEHSGELV 511
PRK12704 PRK12704
phosphodiesterase; Provisional
 8-109 9.67e-03

phosphodiesterase; Provisional


Pssm-ID: 237177 [Multi-domain]  Cd Length: 520  Bit Score: 36.68  E-value: 9.67e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 397739073   8 QKLLQAGEENQVLELLIHRD-----GEFQELMK-LALNQGKIHHEMQVLEK---EVEKRDSDIQQLQKQLKEAEQILATA 78
Cdd:PRK12704  57 EALLEAKEEIHKLRNEFEKElrerrNELQKLEKrLLQKEENLDRKLELLEKreeELEKKEKELEQKQQELEKKEEELEEL 136

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 397739073  79 VYQAKEKLKSI-----EKARKGAISS------EEIIKYAHRI 109
Cdd:PRK12704 137 IEEQLQELERIsgltaEEAKEILLEKveeearHEAAVLIKEI 178
 
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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