<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 MDP26006

Description Mediator of RNA polymerase II transcription subunit 5
SequenceMDSRTAAQGALRATIDFWKKFVSRCIARRVDTDRFEVLVQQVYAEHPLPPAVIADFFLRPQPSNDNSLDPRIPPYLQALTRLGYIDTPSVLQALYKYSSSHAQAQQPNDGDDKNEAAQPPRTPHIKHWKSSYWAEEAIFYSLTKAVVEGRAIPDSTIALDVVKIISKYMTLFTAASTAFAADMLGQLHSPQIRDEMESARAGLVALLLRLCENDVLVKAVSKPFAKDARKELAASLASFVPTLQLVPELTEKLELFRTETLASLDPADKKKQVANAAMDELLDSTVGLENFVIPEIPISNTRAGLYIYLNAALIGRPILDDNALFSYMNNKYQGDVQSSAIDLILASFDILANAVFRNEGQKDAHLLRSYLINKLPLLLYQLCPPEFPGTSAEFCITEALHHVDTSLFPTASLMFDESRNNNPYTESVREEFCASCVLHGLVQRDHVERILGEISLSDEPSLQKYSKEKLVQDCLSDMDKIQGLILELDKMDGNVGAVCQALIELLRQYCHSKETMSLKLLCSQLAAKPQSLDVILLFEKLPTILEPLCQLLDNWRYEEDQGEYQPVYEEFGSILLLVLAFAYRYNLTATDAGAIGPDSCVAKIIGRGHIARQGNELTEQENGHLGGWIHGLFDTEAGGLGDELMSSCPPQEFYLLVATLFQNIVVAYAHGYLNDESLKGGVEYLVDTFLLPSLVPAIRFLSDYLWVDQKEAKSVIKVLQLILLPSSISGEASTMLSSVKNLIARPLEHALRTYQRRDPKNQDIEPLLRTLKDSIPLSRRTGGADINELESWTSTATNGLASAIKHNIQGLVHWSMHPAINSMPTSYTHRQMLAALKLLGSKRLLHIILDEVRQQTEAGNANSVYDVATSLICAPDAAKDAPVGMLDVNGNMPPTLQRPRTLREMLKAEAEGCKKLQKKDAALAEIVVRLHRRVEMLMVMPEAQAMLQTADMALGDAMAAAASGVQGDSMSVDNMLDVGMGGVPSDLGLGPASAGGSLDPSGDNELFGAFGSQELDNFDWDMDNMV
Length1026
PositionTail
OrganismNectria haematococca (strain 77-13-4 / ATCC MYA-4622 / FGSC 9596 / MPVI) (Fusarium solani subsp. pisi)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Pezizomycotina> Sordariomycetes> Hypocreomycetidae> Hypocreales> Nectriaceae> Fusarium> Fusarium solani species complex> Fusarium vanettenii.
Aromaticity0.07
Grand average of hydropathy-0.099
Instability index43.46
Isoelectric point5.02
Molecular weight113109.11
Publications
PubMed=19714214

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

>MDP26006
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      71.69|      23|      30|     614|     643|       1
---------------------------------------------------------------------------
  618-  643 (36.68/36.50)	TEQENGHLggwIHGLFDT.....EAGGLGDE
  649-  676 (35.01/15.15)	PPQEFYLL...VATLFQNivvayAHGYLNDE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      89.87|      27|      29|     538|     566|       2
---------------------------------------------------------------------------
  538-  566 (47.19/40.05)	FEKLPTILepLCQLLDNWRYE...EDQGEYQP
  568-  597 (42.68/28.41)	YEEFGSIL..LLVLAFAYRYNltaTDAGAIGP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      61.32|      18|      19|     297|     315|       3
---------------------------------------------------------------------------
  297-  315 (27.13/25.94)	PISNTRAgLYIYLNAALIG
  317-  334 (34.19/26.38)	PILDDNA.LFSYMNNKYQG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      54.91|      18|      19|     948|     965|       4
---------------------------------------------------------------------------
  948-  965 (28.85/16.20)	QTADMALGDAMAAAASGV
  966-  983 (26.07/13.94)	QGDSMSVDNMLDVGMGGV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      47.93|      16|      19|     786|     804|       5
---------------------------------------------------------------------------
  786-  801 (28.90/30.63)	INELESW..........TS.TATNGLA
  808-  834 (19.03/ 7.20)	IQGLVHWsmhpainsmpTSyTHRQMLA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     145.15|      39|     136|     205|     265|       7
---------------------------------------------------------------------------
  205-  243 (61.91/34.43)	ALLLRLCENDVLVKAVSK...PFA.KDARKELAAS..LASFVPTL
  340-  378 (53.13/26.67)	AIDLILASFDILANAVFR...NEGqKDA.HLLRSY..LINKLPLL
  406-  442 (30.11/48.42)	....SLFPTASLMFDESRnnnPYT.ESVREEFCAScvLHGLV...
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      42.72|      15|      29|     735|     753|       8
---------------------------------------------------------------------------
  735-  753 (17.09/19.99)	MLSSVKNLIarPLEHalRT
  767-  781 (25.63/13.94)	LLRTLKDSI..PLSR..RT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      37.28|      11|      15|     677|     687|       9
---------------------------------------------------------------------------
  677-  687 (18.64/10.19)	SLKGGVEYLVD
  693-  703 (18.63/10.18)	SLVPAIRFLSD
---------------------------------------------------------------------------




































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 MDP26006 with Med5 domain of Kingdom Fungi
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