<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 MDP00277

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMLQHQISHSPARLGLTSPTSSSSPSLSNPNPAKFAAAVAAAAHQQPHHHPNLPPASSSSAAAAAAAAAVPATSSTLLSLLPPLPRAQSLLLQMSALASKLFDVSPNRALWLSSFRGSLPSFLSAQSPPPPPAQSHGAALPEPPPSSTKEILALFTSLQTQLFKAVAELQEILDLQDARQKLTREIRSNDSALLSFANRLKDAEHVLDVLVDDYADYRRPKRSRSASAAAEDDGDDDLGGGSTTTVASRLNLSNIVSYAHRISYTTFAPPDFGAGQAPLRGALPPAPQDEQMRISQLYNVEDIQLPKSAVQDDHKESISMVEPANPDVPAIPGLPTNIIIPSGWKPGMPVELPTDLPVPPPGWKPGDPIALPPMDTLPVRRPEEPQLQPVGPPGLHKEPETIQVRHVDLELPDNFDDSSDYSSDDASSEDDE
Length431
PositionMiddle
OrganismEucalyptus grandis (Flooded gum)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> rosids> malvids> Myrtales> Myrtaceae> Myrtoideae> Eucalypteae> Eucalyptus.
Aromaticity0.04
Grand average of hydropathy-0.380
Instability index74.69
Isoelectric point4.92
Molecular weight45863.75
Publications
PubMed=24919147

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:EnsemblPlants

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

>MDP00277
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      73.42|      18|      20|     338|     357|       1
---------------------------------------------------------------------------
  340-  357 (40.93/23.49)	PSGWKPGMPVELP.TD.LPV
  359-  378 (32.49/12.02)	PPGWKPGDPIALPpMDtLPV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      46.11|      14|      20|      29|      42|       2
---------------------------------------------------------------------------
   29-   42 (25.61/14.96)	PN..PAKFAAAVAAAA
   50-   65 (20.50/10.36)	PNlpPASSSSAAAAAA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      37.43|      11|      19|     113|     128|       3
---------------------------------------------------------------------------
  113-  128 (16.17/12.32)	SFRGSLPsflsaQSPP
  134-  144 (21.26/ 6.61)	SHGAALP.....EPPP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      39.78|      11|      19|     379|     389|       4
---------------------------------------------------------------------------
  379-  389 (20.54/11.73)	RRPEEPQLQPV
  396-  406 (19.24/10.52)	KEPETIQVRHV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      60.61|      19|      32|     169|     187|       6
---------------------------------------------------------------------------
  169-  187 (31.16/22.04)	QEILD.LQDARQKLTREIRS
  203-  222 (29.46/20.45)	EHVLDvLVDDYADYRRPKRS
---------------------------------------------------------------------------




































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 MDP00277 with Med4 domain of Kingdom Viridiplantae
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