<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 MDP04008

Description Mediator of RNA polymerase II transcription subunit 5
SequenceMSEDEAQQLLHKLLLQALARRLPQSKWLSLLHQLVRRINVAHEDASQGGDAPSLAGSHAAGCLVRFILSQSFIDPLLIEYLQALIYGSANRSGITPDQGSVTDVITVTLHLLANVQAAASNVPAIETISSVIGQGLLMTFQAPVPFRVSSPPFLKLLQHLFASFPNEEAISSPSAEESRSQAKDGTSAPAAMAFVVANLRLLALAADPTASSPQNLLAPRVAITVLINLGQALLAHAIQKLSAAQTTKDHKLKPDDILLRQTRSMAKMCVSEIEAVLQPMNPAWKDEIALLRSLTSQIGVIEQISQTLAEATTSKLSTRTPKRKAETLQDAQQRATWDHFLDISAVAVSEKPPVEPEMVFLMHLLVDQHTAWDTKLDAVKTLFLARRNAAAPSLTLEKSLTSFYFELLVAAIDACATVVESPLAYKGAQVYVAIWRHALCGMIPELVLQLEQWLDDRQDLPLRGQRLEAPHVRLEAALRAALLVMASRLDTCESATGQSHAQSSAAAAGGGEESGRANMMTDVLGLDSPPLQPIKAWLLRACIEHSLARPEAIADEFPDGHKLASEVQSLTQSLRMDAQLEGLALNTLFETRVSTDDPIELLHRVASDPGTHYIFARQLVLQMQGWLEQHDLESIARWCKALSEDATQGGAVLDTVMMYIDPVQLLDPLASILDHQDVGQTSDEPSTLSNILLFVQLLCYRYEIAPSRVSRCAVENHEVDGVSAAQDCEPSEPPFLAKYLSASSVCYPLSTLSEEERGLVGRWIHALFGNEGISDDLIQASPPTTLLRLSPLLFSQSVSACQYGVIDLETLRGGLSYFLQDLLSFALPGALVWLLSEIVRTPLQPVLDFLSESGLQASVVDVPSSDGTLANGLPRNASSRTVHLEVMSLLVDTDACPTSVRELIAKAFDAFVAAVERDGPQLGAGCETFSLASLKARMDGAGVTAGGLKLGFRNDGGR
Length958
PositionTail
OrganismSporisorium scitamineum
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Basidiomycota> Ustilaginomycotina> Ustilaginomycetes> Ustilaginales> Ustilaginaceae> Sporisorium.
Aromaticity0.05
Grand average of hydropathy0.077
Instability index55.87
Isoelectric point5.07
Molecular weight103572.27
Publications









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

>MDP04008
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     179.15|      60|      86|     531|     601|       1
---------------------------------------------------------------------------
    7-   49 (39.24/20.04)	QQL.......lhklllqalarrL.PQSKWL...SLLHQLVRRINVAH....................EDASQGG................
  531-  598 (68.62/76.56)	......................LQPIKAWLlraCIEHSLARPEAIADefpDGHKLASeVQSLTQSLRMDAQLEGLALNTLFeTRVstdDP
  599-  662 (71.30/45.16)	IELlhrvasdpgthyifarqlvLQ.MQGWL....................EQHDLES.IARWCKALSEDATQGGAVLDTVM.MYI...DP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      50.45|      15|      15|     813|     827|       2
---------------------------------------------------------------------------
  813-  827 (25.11/11.96)	GGLSYFLQDLLSFAL
  829-  843 (25.34/12.13)	GALVWLLSEIVRTPL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     160.10|      45|     479|     387|     433|      13
---------------------------------------------------------------------------
  387-  433 (66.17/53.84)	RNAAAPSLTLEKSLTSfYFELLVAA..IDACATVVESPLAyKGAQVYVA
  465-  492 (27.66/13.17)	QRLEAPHVRLEAALRA...ALLVMAsrLDTC..................
  875-  913 (66.27/43.29)	RNASSRTVHLE......VMSLLVDT...DACPTSVRELIA.KAFDAFVA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      51.64|      17|      29|     189|     205|      14
---------------------------------------------------------------------------
  189-  205 (28.24/16.16)	PAAMAFVVANL..RLLALA
  219-  237 (23.40/12.25)	PRVAITVLINLgqALLAHA
---------------------------------------------------------------------------




































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 MDP04008 with Med5 domain of Kingdom Fungi
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