<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 MDP25553

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMHQHQIVQSPARLGLTNPTSPSLPVQTPNPPPPKFPNPQPPQHHHPSTTTTTTTTSSALLSLLPPLPRAQSLLLQMASLATKLFELSPNRPHWLSAYRGTLPTFLPSQSQSLDEPTPTSTKEIISLFTSLQTQLFESVAELQEILDLQDSKQRISQEIKSKDSALLNFANKLKEAERVLDILVDDYADYRRRRPIPPNEEEENATNTTTVASQLKLSDILSYAHRISYTTFAPPEFGAGQAPLRGALPPAPQEEQMRASQLYNFAHLDVGLPKDVETKEKTIEAIIEPQHEANPLENLAGLFPPNISVPAGWKPGMPVVLPTDLPVPPPGWKPGDPVSLDSIPLPRAVEQKLPPIAPQGLHKPPETIQVRHVELDIPDQDDDSSDYSSDVESSDDED
Length397
PositionMiddle
OrganismPopulus trichocarpa (Western balsam poplar) (Populus balsamifera subsp. trichocarpa)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> rosids> fabids> Malpighiales> Salicaceae> Saliceae> Populus.
Aromaticity0.05
Grand average of hydropathy-0.551
Instability index71.31
Isoelectric point4.92
Molecular weight43732.64
Publications
PubMed=16973872

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

>MDP25553
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      73.15|      23|      33|     303|     332|       1
---------------------------------------------------------------------------
  303-  327 (40.31/24.09)	PPnISvPAGW.KPGMPV.VLPTDLPVP
  353-  377 (32.83/ 7.40)	PP.IA.PQGLhKPPETIqVRHVELDIP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             5|     249.55|      48|      48|      38|      85|       2
---------------------------------------------------------------------------
    9-   53 (70.22/24.60)	..SPARLGLTN..PTSPSLPVQT.PNPPPPKFP.............nPQPPQHHHPSTTTTTT
   54-  103 (72.01/25.40)	TTSSALLSLLPPLPRAQSLLLQM.ASLATKLFE............lsPNRPHWLSAYRGTLPT
  104-  136 (30.08/ 6.83)	FLPSQSQSLDEPTPTSTKEIISLfTSLQTQLFE..............................
  160-  209 (42.58/12.36)	SKDSALLNFANKLKEAERVL.............dilvddyadyrrrrPIPPNEEEENATNTTT
  210-  242 (34.65/ 8.85)	VASQ..LKLSDILSYAHRI..SY.TTFAPPEFG.............aGQAP............
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      39.73|      12|      70|     267|     278|       4
---------------------------------------------------------------------------
  267-  278 (21.77/12.98)	LD.VGLPKDVETK
  339-  351 (17.96/ 9.42)	LDsIPLPRAVEQK
---------------------------------------------------------------------------




































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 MDP25553 with Med4 domain of Kingdom Viridiplantae
Unable to open file!