<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 MDP09560

Description Mediator of RNA polymerase II transcription subunit 1
SequenceMYFLGAVISTNALMEQLYLKYQQRPWSETLKLVHFCMDKPRRSPVGNASDGLLLSCMEKLQRTLNRSLFSVMNRLESLSKQKGLNSHVSPSGTACYITSNMFYIEVQLEKDGRVMDAKLAHLGEAPVICDDLVQHLRMKNYDAFGKILEDLSNLYQIPGNSEMKAKGYLALQSLEKDLYSMSLLHRTQDVNRVTEVLHGKVGHLVPRTGGTPMNTEFYISPYQILEAELNPGSLVCGTKAVVTVEGTDTLHKLPLSPLLVDSQAGEDGNPTFLPLTNELSMDLSAYFLLKFHQPIPLSLSNIEEIQMLTGIQITALKLAPLYELIIQSTLKEKCSEDLSVHKSCFFVSLPDCPKHCYFINKGPEKSNLVGALVSKIPFTHPKCVPPVIEILRHQVAYNSLISSCVSDKYINEDDSELLYFEVAPYKNTSISVFFIHPMRENLACVTIDVVTSREVQCSLHLHPQDPTLNSSDGFISRSLKRCMSVPVVMRAIFRNAAQVEADSGTQGTEVDNKQKPELPSEQIIDSNRLEESLSVAGQQDLVKTNKESVPDSPEQGLSTTKLETLGDETEKSNTTVNTETLSRVEESNSTASTEVVMKDK
Length600
PositionMiddle
OrganismGallus gallus (Chicken)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Archelosauria> Archosauria> Dinosauria> Saurischia> Theropoda> Coelurosauria> Aves> Neognathae> Galloanserae> Galliformes> Phasianidae> Phasianinae> Gallus.
Aromaticity0.06
Grand average of hydropathy-0.225
Instability index47.25
Isoelectric point5.54
Molecular weight66802.72
Publications
PubMed=15592404

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. 
ECO:0000256	RuleBase:RU364059
GO - Cellular Component
mediator complex	GO:0016592	IBA:GO_Central
GO - Biological Function
retinoic acid receptor binding	GO:0042974	IBA:GO_Central
thyroid hormone receptor binding	GO:0046966	IBA:GO_Central
transcription coregulator activity	GO:0003712	IBA:GO_Central
vitamin D receptor binding	GO:0042809	IBA:GO_Central
GO - Biological Process
cellular response to thyroid hormone stimulus	GO:0097067	IBA:GO_Central
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central

Interaction

Binary Interactions











Repeat regions





Repeats

>MDP09560
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      48.25|      15|      18|     538|     555|       1
---------------------------------------------------------------------------
  541-  555 (26.60/20.54)	LVKTNKESVPDSPEQ
  557-  571 (21.65/ 6.95)	LSTTKLETLGDETEK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      53.47|      16|      24|     136|     151|       3
---------------------------------------------------------------------------
  136-  151 (27.74/23.26)	LRMKNYDAFGKILEDL
  163-  178 (25.74/21.01)	MKAKGYLALQSLEKDL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      54.01|      18|      23|     234|     255|       5
---------------------------------------------------------------------------
  234-  255 (21.81/29.08)	LVCGTKAvvTVEGTDTLhkLPL
  258-  275 (32.20/23.02)	LLVDSQA..GEDGNPTF..LPL
---------------------------------------------------------------------------




































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 MDP09560 with Med1 domain of Kingdom Metazoa


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) QVEADSGTQGTEVDNKQKPELPSEQIIDSNRLE
2) SVAGQQDLVKTNKESVPDSPEQGLSTTKLETLGDETEKSNTTVNTETLSRVEESNSTASTEVVMKDK
515
551
547
617










Molecular Recognition Features






MoRF SequenceStartStop




1) KLETL
578
582