<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 MDP28830

Description Mediator of RNA polymerase II transcription subunit 16
SequenceGGMELAYVCEWEKKPKSNHCPSIPLVCAWSCRNSSPFTTDLRNEEEKDLTHMVHIIDTEHPWDVYSVNSGHTEVITCLEWDQSGSRLLSADADGHIKCWGMTDHLANSWENTVGSVVEGDPVVALSWLHNGVKLALHVEKSGASNFGEKFSRVKFSPSLTLFGGKPMEGWIAVTISGLVTVSLLKPNGQVLTATESLCRLRCRVALADVAFTGGGNIVVATSDGSSTSPVQFYKVCVSVVNEKCKIDTEILPSLFMRCTTDPARKDKYPAITHLKFLARDMSEQVLLCASNQNNSIVECWSLRKEGLPVNNIFQQISPVVGDKQPMILKWRILSATNDLDRVSAVALPKLPISLTNTDLKVANDTKFFPGLGLALAFHDGSVHIVHRLSLQMMAVFYGSSSQRPVDEPALKRPRTTGPLVHFKAMQLSWTSLALAGVDSHGKLSMLRISPSMGHVLDMNMSLRHLLFLLEYCMVTGYDWWDILLHVQPSMVQNLVEKLHEEYMRQNAALQQVLSTRIVAMKASLCKLSSSTIARVCDYHAKLFLIAISCTLKSLLRPHFLNTPDKSPGDRLTEICSKITDVDIDKVMINLKTEEFVLEMTTLQSLQQLIQWVGDFVLYLLASLPNQGSPVRPGHSFLRDGASLGMFRELMVVIRIWGLLKPSCLPVYTATSDTQDSMSLLFRLLTKLWLCCREENHITEPDDALIDECCLLPSQLLIPNIDWLPINDGIISKLQNKQLVRLQFGKAPGLVGHTVSSQFDAFVRAPGQPKIDHLRRLHLGAYPTEECKSCTRCGCVTMLKSPNKVTAVKQWEQRWIKNCLCGGLWRKMPLSYS
Length832
PositionTail
OrganismTaeniopygia guttata (Zebra finch) (Poephila guttata)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Archelosauria> Archosauria> Dinosauria> Saurischia> Theropoda> Coelurosauria> Aves> Neognathae> Passeriformes> Passeroidea> Estrildidae> Estrildinae> Taeniopygia.
Aromaticity0.07
Grand average of hydropathy-0.009
Instability index46.98
Isoelectric point8.03
Molecular weight92765.81
Publications
PubMed=20360741

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
mediator complex	GO:0016592	IEA:Ensembl

GO - Biological Function
thyroid hormone receptor binding	GO:0046966	IEA:Ensembl
transcription coactivator activity	GO:0003713	IEA:Ensembl

GO - Biological Process
positive regulation of transcription initiation from RNA polymerase II promoter	GO:0060261	IEA:Ensembl









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP28830
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     400.03|     126|     135|     455|     589|       1
---------------------------------------------------------------------------
  455-  589 (187.94/159.09)	VLDMNmSLRHLLFLLEYcmvTGyDWWDILLHVQPSmvQ.NLVEKLHeEYMRQNAAL....QQVLSTRIVAMKASLCKLSSSTIARVCDYHAKLFLIAISCTLKSLLRPHfLNTPDKSPGDRLTEICSKITDVDIDKVMIN
  596-  726 (212.08/142.70)	VLEMT.TLQSLQQLIQW...VG.DFVLYLLASLPN..QgSPVRPGH.SFLRDGASLgmfrELMVVIRIWGLLKPSCLPVYTATSDTQDSMSLLFRLLTKLWLCCREENH.ITEPDDALIDECCLLPSQLLIPNIDWLPIN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     152.24|      48|     200|      78|     127|       2
---------------------------------------------------------------------------
   78-  127 (82.18/61.49)	LEWDQSGSRLLSADADGH..IKCWGM.TDHL.ANSWENTVGSVVeGD..PVVaLSW
  277-  330 (70.06/43.85)	LARDMSEQVLLCASNQNNsiVECWSLrKEGLpVNNIFQQISPVV.GDkqPMI.LKW
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     115.63|      35|     364|     375|     412|       3
---------------------------------------------------------------------------
  375-  412 (52.86/59.05)	LAFHDGSVHIVHRLSLQMMAvFYGSSSQRPVDEpaLKR
  741-  775 (62.77/54.06)	LQFGKAPGLVGHTVSSQFDA.FVRAPGQPKIDH..LRR
---------------------------------------------------------------------------




































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 MDP28830 with Med16 domain of Kingdom Metazoa
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