<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 MDP00587

Description RNA polymerase II transcription mediators isoform 6 (Fragment)
SequencePVRALDAIEENGVERYPHELSYDEKRVSLIRRIDFAWALETDEERERKKKQKKKNSKDATATWLVENLQLAHQELSVIIDLINTVEANDAVTVAGMTRPKPLPNEVLSDLAVSAATKLQCYRHLGKYFKQSAKALEQQIAREARFYGALIRLQQNWKVKRQRVAAPSSSNEGFTIDLFDNSLYDSATISRPSSLSVIHIEHDSAGMLAINLPSNSCHSLHFGFLGVHSADIPKESSKIKTHGSVDQTTRDSQKESMSDDESVKETHLLLREVHQSIFNDQVFDMVNREAFNQSAGVNVTGIRENYLQLSIGQGTSLFISLVPSSKGDDQAVDTANAQNLESAIVSLDSFDDVKSGEGKHDITEKKWGFPNRISCEIYLQQIVHEHAFIKGKDRPNSSGTRVSGQSGKVCRVPYLHLMTHPTWHSRTSSWTIFMKVPQSILHVESQSQKSDFQNMKDAIKSQFRTKVVVNDDRINVEGEGAPNVVGLFKRSSEDICSVNKYDCDLADLPVIILQQVGCYCQFLGLLQS
Length527
PositionHead
OrganismTheobroma cacao (Cacao) (Cocoa)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> rosids> malvids> Malvales> Malvaceae> Byttnerioideae> Theobroma.
Aromaticity0.07
Grand average of hydropathy-0.457
Instability index44.79
Isoelectric point6.34
Molecular weight59072.82
Publications
PubMed=23731509

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:InterPro

GO - Biological Function
transcription coregulator activity	GO:0003712	IEA:InterPro

GO - Biological Process
regulation of transcription by RNA polymerase II	GO:0006357	IEA:InterPro









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP00587
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     121.88|      37|     155|     166|     202|       1
---------------------------------------------------------------------------
  166-  202 (64.29/52.23)	PSSSNEGFTIDLFDNSLYDSATISRPSSLSVIHIE..HD
  322-  360 (57.59/45.92)	PSSKGDDQAVDTANAQNLESAIVSLDSFDDVKSGEgkHD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     143.14|      48|     395|      77|     125|       3
---------------------------------------------------------------------------
   77-  125 (78.62/60.85)	VII..DLINtVEANDAVTVAGMTRPKPLP....NEV...LSDLAVSAATKLQCY.RHLG
  466-  523 (64.51/44.69)	VVVndDRIN.VEGEGAPNVVGLFKRSSEDicsvNKYdcdLADLPVIILQQVGCYcQFLG
---------------------------------------------------------------------------




































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 MDP00587 with Med17 domain of Kingdom Viridiplantae
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