<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 MDP09338

Description Mediator of RNA polymerase II transcription subunit 5
SequenceMDEWATFFAHALDRRLPTDKLEQFAKVLSTKSPLATPLIAELLLRPSESRNYDLDPQVSLYVQALLRIDILDVPSVLRALLRHSTSRPVDATKEDQEVASGSQTRWTKSYGHEERLVYGLSKIVAAGDRPKSAQEALVMANALTEWMRLLVMSNAADDMMREIGAGNDTHNQETMAVRVAVGALLVALAENSTVNDALKNRCPKDTLKGFSQSLANFTPLLINGSSMFAERLELYTKTLVALEPMDKKAQKAGAEIDQIIDSAMALGMDNIPVVEIPTMNSRAGLYVYLNSLLTGRPMVDDNQLLNFLHNRYQGDIQTTCIDLIVSSFDILANAIFRSESPQTTFLLRSFLINKVPLLISMISAPMFPPLSPELCITEALSHVDTNAFPTFSSMFDDTSAGDMFSDSVRQDFCFSCCLHGLIPEESIERLLGEIPMQTLPAGGRYTKDEVLEQCLSDSEKIEAFTDELEHMDGNVGAVSQAITELLRRLCESKDTMALKSLCAHLARKPSSLDVLLIFDKPLTILPPICQLLDAWRYDDDQGEYQPVYEEFGSILLLVLAFVYRYDLSATELGVQTPDSFIAKLLVRGSTARLLDDLSSVESSQLDGWIKGLFNAEGGGLGDEPMALCPPQDFYLLVPTLFSQIVLASQHGHLTDDVLRGGLEYLLDPSLLPSLIPALLSLASNILTAPPPSSLLQALILPQSISAEASLLHNAILPIPAPHLSRSLRALQRSVPTRTDLDPLIAALRPHLHFSRSAIDLTTDFPVPPNIPTAVRHAARALINWNPPAAPPNYSPRLPVLAVRMLGARRALLTLLEELAHQCALGNSGTAYDVVASLVCAPPKAAAGVQGRITLREALASEAAKVGAEVGKEGPEAERAEVVVRLYRRVEALSAGGGIDEQAGLMGADLGIAGVGGEGLVGEDMMGVLSGEGMMGLEGGMLDDMKLDF
Length948
PositionTail
OrganismPseudogymnoascus verrucosus
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Pezizomycotina> Leotiomycetes> Leotiomycetes incertae sedis> Pseudeurotiaceae> Pseudogymnoascus.
Aromaticity0.06
Grand average of hydropathy0.069
Instability index44.01
Isoelectric point4.82
Molecular weight102950.18
Publications
PubMed=29295979

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

>MDP09338
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      97.76|      27|      27|     665|     691|       1
---------------------------------------------------------------------------
  665-  688 (34.31/14.14)	...................LLDPSLLPSLIPALLSLASN.ILTA
  689-  718 (30.62/11.86)	P.PP.............ssLLQALILPQSISAEASLLHNaILPI
  765-  807 (32.84/13.23)	PvPPniptavrhaaralinWNPPAAPPNYSPRLPVLAVR.MLGA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      48.50|      14|      18|     905|     922|       2
---------------------------------------------------------------------------
  905-  918 (25.07/18.42)	MGADLGIAGVGGEG
  925-  938 (23.43/ 7.42)	MGVLSGEGMMGLEG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      26.52|      13|      15|     852|     865|       3
---------------------------------------------------------------------------
  845-  861 (11.23/ 9.44)	AAGVqgrITlREALASE
  862-  877 (15.28/ 7.90)	AAKVgaeVG.KEGPEAE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      43.01|      13|      16|     210|     222|       4
---------------------------------------------------------------------------
  210-  222 (21.96/12.44)	FSQSLANFTPLLI
  228-  240 (21.04/11.65)	FAERLELYTKTLV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      53.58|      16|      18|     356|     371|       5
---------------------------------------------------------------------------
  356-  371 (31.39/22.32)	PLL.....ISMISAPMFPPLS
  372-  392 (22.19/13.27)	PELciteaLSHVDTNAFPTFS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      71.57|      21|      40|      34|      58|       7
---------------------------------------------------------------------------
   34-   54 (36.20/14.64)	LATPLIAELLLRPSESRNYDL
   71-   91 (35.36/17.30)	LDVPSVLRALLRHSTSRPVDA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      72.40|      22|      35|     410|     434|       8
---------------------------------------------------------------------------
  410-  434 (35.97/25.36)	QDFCFSCCLHGlipEESIERLLGEI
  447-  468 (36.43/18.33)	KDEVLEQCLSD...SEKIEAFTDEL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      82.17|      26|     293|     176|     202|      11
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  176-  202 (37.77/28.70)	AVRVAVGALLVALAENSTVNdALKNRC
  477-  502 (44.41/28.88)	AVSQAITELLRRLCESKDTM.ALKSLC
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      69.80|      24|      27|     556|     581|      14
---------------------------------------------------------------------------
  556-  581 (32.88/31.15)	LLVLAFVYRY..DLSATElGVQTpDSFI
  584-  609 (36.91/23.58)	LLVRGSTARLldDLSSVE.SSQL.DGWI
---------------------------------------------------------------------------




































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 MDP09338 with Med5 domain of Kingdom Fungi
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