<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Detailed information on MDP15068

Description Mediator of RNA polymerase II transcription subunit 4
SequenceHWIPQSAAPAAAMMQHMPSPARLGVTASSPSLPPNQSPANPTSSPPQANPPSASAAAAAAGAGAAVPTLTTSPALLPLLPPLPRAQSLLHLISSLASNLFELSPNRAAWISSYRGSLPNFLASSSASAAPTPLPAPVSTTKEAMSMLTSLQTQLFETVAELQETLDLQDARAKLAREARAKDASLLAFAKKLREAHHVLDRLVDDYADYRRDPKRPRGAAAVDEPEPVSQGDFGASLHSKLKLDDILTYAHRISYTTFAPPEHGAGLPLRGALPPAPQDNELRMSQLYQFADLDVGVPKKPLETKEGLTAEMESMPLFELPEEEPPRPSMLPITVPPGWQKGLPALLPAFPMPPPGWKPGDPIXXXXXXXXXXXXXXXXXXXLLSSLMNNDPVYQFLLGCNQWCQGPKSQYRSRL
Length415
PositionMiddle
OrganismHordeum vulgare subsp. vulgare (Domesticated barley)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> Liliopsida> Poales> Poaceae> BOP clade> Pooideae> Triticodae> Triticeae> Hordeinae> Hordeum.
Aromaticity0.06
Grand average of hydropathy-0.274
Instability index61.25
Isoelectric point6.28
Molecular weight42405.99
Publications
PubMed=23075845

Function

Annotated function Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene- specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. 
GO - Cellular Component
core mediator complex	GO:0070847	IBA:GO_Central
mediator complex	GO:0016592	IEA:InterPro

GO - Biological Function
transcription coregulator activity	GO:0003712	IBA:GO_Central

GO - Biological Process
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP15068
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      59.04|      15|      15|     328|     342|       1
---------------------------------------------------------------------------
  328-  342 (30.32/11.84)	PSMLPI..TVPPGWQKG
  344-  360 (28.73/10.82)	PALLPAfpMPPPGWKPG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     334.55|      86|     216|       4|     105|       2
---------------------------------------------------------------------------
    4-   56 (75.65/18.80)	.................................................................................PQSAAPAAAMMQHMP.SPARLGVTASSP.SLPPNQS.PANPTSSP....PQANPPSASAA
   70-  138 (100.74/40.64)	TTSPALLPL...LPPLPRAQSLLHLISSLASNLfELS............................................PNRAAWISSYRGSLP.N....FLASSSA.SAAPTPL.PA..............PVS....
  139-  266 (100.51/28.32)	TTKEAM.SM...LTSL.QTQ.LFETVAELQETL.DLQdaraklarearakdasllafakklreahhvldrlvddyadyrrdPKRPRGAAAVDEPEPvSQGDFGASLHSKlKLDDILT.YAHRISYT....TFA.PPEHGAG
  267-  326 (57.65/12.74)	......LPLrgaLPPAPQDNE....................................................................LRMSQLY.QFADLDVGVPKK.PLETKEGlTAEMESMPlfelPEEEPP.....
---------------------------------------------------------------------------




































Explaination for Stockholm format
  The  "Stockholm" format is a system for marking up features in a multiple alignment. These mark-up annotations are preceded by a 'magic' label, of which there are four types. The Stockholm format is used by HMMER, Pfam, and Belvu. Mark-up lines include any characters except whitespace. Underscore ("_") is used instead of space. 

 #=GR (seqname) PP (Generic per-Sequence AND per-Column markup, exactly 1 char per column) where PP is Posterior Probability  [0-9*], (0=0.00-0.05; 1=0.05-0.15; *=0.95-1.00) 
 
 #=GC PP_cons line is Stockholm-format consensus posterior probability annotation for the entire column.  It’s calculated simply as the arithmetic mean of the per-residue posterior probabilities in that column.  This should prove useful in phylogenetic inference applications, for example, where it’s common to mask away non confidently aligned columns of a multiple alignment. The PP_cons line provides an objective measure of the confidence assigned to each column.
 
 #=GC RF line is Stockholm-format reference coordinate annotation, with an x marking each column that the profile considered to be consensus.





Alignment of MDP15068 with Med4 domain of Kingdom Viridiplantae
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