<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 MDP27503

Description Mediator of RNA polymerase II transcription subunit 5
SequenceMPRGPATAGLSAAVGQWTKFLGRAEAKRLDPSDFARFVPILSSDFYPLPPIVIANLLLKPTKQSSYSLDPRRLQYLTILLNQKLVNIQSVLKVLHQYSTSHAKIQSQHHADATHEAATANKGDQGQQGDKKPKRVFWQNSFNDEEVIFLQLSKVITHGQGIRHASDAYEMAANLSKWITLYIDVIAAFSRDTFGNIQNMRTRQDMENSLQAFSLLLVHFLGNQRVVSAFSRPDAKGHRKRLAASIDQLIPYILQNPNTSGIAVKLEFSRGQTLAGEESSDLKDAAVAEMHSYMDNMIGLDAWQIPDIPLVNSRAGLYIYINAALVGRPLIDDHSLYTYLHNRYQGDLQTTAIHLILASFDVLANAVFRYEGSKTGHLLKSYVVNKVPLILGNFAASSSPMYPFDAEFCISQALGQVDTNVFPTLSNMFDMSNTSSSFQDSVRQDFCFACQLHGLLSSSAIETLLGEITYQTLPDEGRYVKETLVQACLGDFERSQKLIGELDNMNGNVGAAAQAIVEVIGTLCRNKETMTLKQLCSRLASKPSSLDILLLFDKPYKILHPLCELLDNWGGYDEDQGEYQPVYEEFGSILLLLLAFVHRYSLTPTDLAIRSPDSFVGKLLGRGSLSRPLDELSEQEKSHLNGWVHGLFDSEAGGLGDDLMSSCPPQDFYLLMPTLFDQIVMALNLLDTLLLPSLVPALLFLANNLRTDKQAGQAAVIKILQLTLRPNSISNEASIMLSSVLNIVAKPLELSLRSYQRQVPASQQVEPLLRALKENLAVSGRTGGADHSELENWTGTHHNGSGSVGGLYGAIRHTVQNLVQWAQNSPGNGVPTTYTHRQILVALQICGAKRVLSALLKELKVQTEAGNGPVAYDVVTAIICAPDVHNSPVMDDDPASTRGADANHNHTVQRKQRRITLREALKFEAEDFKKIQKSDPLMAETVVRLHRRVEAQMTLPPPPPPPAQHLHHHQQAMLQPELSALGVVAGDTMGDSMMNAAAVAVSSGDHHQSVDAMSLDAAGMGVGGLDVGGAGGMDLSGMGDMGMGGMGGLMVNTNTGGSVTGIQSGGGAAGGGRGGAGGAGAGTAGNVGGGAGGGAGGGSGAGGAGGDLSGDDIFSGLGTGDFTTDFGNWDTMELG
Length1134
PositionTail
OrganismSordaria macrospora (strain ATCC MYA-333 / DSM 997 / K(L3346) / K-hell)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Pezizomycotina> Sordariomycetes> Sordariomycetidae> Sordariales> Sordariaceae> Sordaria.
Aromaticity0.07
Grand average of hydropathy-0.125
Instability index38.34
Isoelectric point5.74
Molecular weight121855.78
Publications
PubMed=20386741

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

>MDP27503
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             5|     158.93|      24|      25|    1056|    1079|       1
---------------------------------------------------------------------------
  779-  804 (23.07/ 7.76)	...GR...TGGADhselEN..WTG..THhNGSGSVG
 1024- 1041 (26.30/10.03)	LDVGG...AGG........mdL.......SGMGDMG
 1043- 1069 (39.92/19.66)	GGMGGlmvNTNTG....GS..VTG..IQ.SGGGAAG
 1070- 1095 (40.37/19.98)	GGRGG...AGGAGagtaGN..VGG...G.AGGGA.G
 1096- 1117 (29.28/12.14)	GG.SG...AGGAG....GD..LSGddIF.SGLG...
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     138.30|      37|      37|     387|     423|       2
---------------------------------------------------------------------------
  354-  385 (40.86/26.54)	.LILASFDVLANAVFRYEG....SKTG.HLLKSYVVNK
  387-  423 (63.04/45.30)	PLILGNFAASSSPMYPFDAEFCISQAL.GQVDTNVFPT
  425-  453 (34.40/21.07)	SNMFDMSNTSSSFQDSVRQDFCFACQLhG.........
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      58.84|      18|      18|     670|     687|       4
---------------------------------------------------------------------------
  670-  687 (31.64/16.85)	LMPTLFDQIVMALNLLDT
  689-  706 (27.20/13.50)	LLPSLVPALLFLANNLRT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      59.21|      19|      37|     822|     845|       5
---------------------------------------------------------------------------
  822-  845 (24.26/30.14)	QNSPGNGvPTTYthrQILVALqIC
  861-  879 (34.95/20.16)	QTEAGNG.PVAY...DVVTAI.IC
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      46.93|      15|      37|     612|     627|       8
---------------------------------------------------------------------------
  612-  627 (23.32/17.02)	DSFVGKlLGRGSLSR.P
  648-  663 (23.61/12.16)	DSEAGG.LGDDLMSScP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     112.36|      35|      38|     156|     190|       9
---------------------------------------------------------------------------
  156-  190 (61.79/41.45)	THG..QGIRHASDAYEMAANLSKWITLYID...VIAAFSR
  192-  231 (50.56/32.59)	TFGniQNMRTRQDMENSLQAFSLLLVHFLGnqrVVSAFSR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     257.16|      83|     269|     242|     335|      10
---------------------------------------------------------------------------
  242-  335 (124.42/99.96)	AASIDQLIPYILQNPNTsgIAVKLEFSRgqtLAGEESS.D...LKDAAVAEMH...SYMDNMIGLDAWQIPDIPlVNSRAGLYIYINAALVGRpliddHSL
  512-  601 (132.74/78.61)	AQAIVEVIGTLCRNKET..MTLKQLCSR...LASKPSSlDillLFDKPYKILHplcELLDNWGGYDEDQGEYQP.VYEEFGSILLLLLAFVHR.....YSL
---------------------------------------------------------------------------




































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 MDP27503 with Med5 domain of Kingdom Fungi
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