<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 MDP28866

Description Mediator of RNA polymerase II transcription subunit 5
SequenceMDGRVIRGVQRAALEQWSEFIAKSLAHRLDPDKFETYVPFLQAKHPLPPAAVADLFLRPQPHNHESLDPRVPRYLQVLSNLNYIDTPSILKALFRYSTSRAHSRDAAQPADGDVQRPNMLHWGSSYAAEEVMFYRLTKSVAQGTAIQNTGSGLEIASIMAKWIALFTDAATAFTVDVMGQLHNSQVREEMESARAAFVALLLGVCENQVVLKAMSKPEAQGTRKALSESLANFVPTIMQSAGPIATRLDMFRTSTLAGFEPVDEQKNKSNAEIEDLFDSTVALENFVISELPIVNSRAGLYIYLNAALVGRPLIDDHAIFNYLNNRYQGDVQTTTVDLILASFDVLANAASRNEGHQAAHLLRSFLMNKLPILIESLSKHMYGPVNAEYCITEALGRVDTTTFPTLSSMFDETRSNNPFTDSVREEFCWACCLHGLVRESSIETLLGETPYQSLPAGGRYLKENLVAECLADPERMQALIGELDNKDGNAGAVCQALTEVLGQLCRNKETMSLKLLCSQLAQKPLSLDVMLMFEKPATILHPLCDLLDSWKYDEDQGEYQPVYEEFGSILLLVMAFAYRYGLSASDMGVTSSDSFVARLLGQGHQSRPFDELSDQEKGHLNGWIHGLFDSEAGGLGDELMSSCPPQDFYLLVSTLFQNIVLAFGTGHLAEESLRGGIEYLVDTFLLPSLVVAIAYLANSLWIERSDCQKAIVRVLSSVLAPTSISNEAQAMLTSVMNIVAKPLEHSLRAYQRSDPKSQEVEPLLKAIKDSIPLSRRTGAADHTELDAWSLGGFSNSIRQTLQQLVQWSIHPTMDRMPPAYTHRQMLVALKLLGAKRLLQLLYEDIRQQTDTGSGSIIYDVVTAIVCAPDVVNTPSNPVNFLDNSGNVPVPTQRKLTLREVLKSDAEDCKRLQKTDMNLAEIVVRLYRKVESQMAVSQAQAMQADTMLQSDLGLSLDPGAGSLDDAMAAATANVVQGDGISVDNVSLDLGLGGVGGDLGLGGSSNNGGGSLDLGADDIFSGLGAGDDFQWDNMDLS
Length1035
PositionTail
OrganismColletotrichum higginsianum (strain IMI 349063) (Crucifer anthracnose fungus)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Pezizomycotina> Sordariomycetes> Hypocreomycetidae> Glomerellales> Glomerellaceae> Colletotrichum> Colletotrichum destructivum species complex.
Aromaticity0.07
Grand average of hydropathy-0.093
Instability index40.71
Isoelectric point4.86
Molecular weight113261.31
Publications
PubMed=22885923

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

>MDP28866
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     125.18|      37|      45|     950|     986|       1
---------------------------------------------------------------------------
  950-  986 (64.25/35.33)	DLGL..SLDPGAGSLDDAMAAATANVVQGDGISVDNVSL
  996- 1034 (60.93/33.15)	DLGLggSSNNGGGSLDLGADDIFSGLGAGDDFQWDNMDL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     276.11|      93|     218|       7|     115|       2
---------------------------------------------------------------------------
    7-  115 (141.82/176.17)	RGVQRAALEQWSEFI......AKSLAHRLDPDKFETYVPF..LQAKHPLPPAAVADLFlrpqpHNHESLD...........PRVPRYLQVLSNLnyIDTPSI.LKALFRYSTSRahsrdaAQpadGDVQ
  220-  332 (134.30/117.27)	QGTRKALSESLANFVptimqsAGPIATRLDMFRTSTLAGFepVDEQKNKSNAEIEDLF.....DSTVALEnfviselpivnSRAGLYIYLNAAL..VGRPLIdDHAIFNYLNNR......YQ...GDVQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      75.99|      22|      37|     385|     406|       4
---------------------------------------------------------------------------
  385-  406 (38.96/24.66)	VNAEYCITEAL.GRVDTTTFPTL
  423-  445 (37.03/23.10)	VREEFCWACCLhGLVRESSIETL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      77.86|      25|     216|     711|     736|       5
---------------------------------------------------------------------------
  711-  736 (35.66/31.21)	IVRVLSSVLAPTSISnEAQAMLTSVM
  922-  946 (42.20/31.40)	VVRLYRKVESQMAVS.QAQAMQADTM
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      80.19|      15|     216|     447|     461|       6
---------------------------------------------------------------------------
  447-  461 (27.69/15.83)	GETPYQSLPAGGRYL
  636-  650 (27.82/15.94)	GDELMSSCPPQDFYL
  666-  680 (24.67/13.27)	GHLAEESLRGGIEYL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      89.54|      30|     395|     483|     513|       7
---------------------------------------------------------------------------
  483-  513 (50.04/31.35)	LDNkDGNAGAVCQ...ALTEVL...GQLCR..NKETMSL
  881-  918 (39.50/20.26)	LDN.SGNVPVPTQrklTLREVLksdAEDCKrlQKTDMNL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      52.33|      15|      16|     744|     758|       8
---------------------------------------------------------------------------
  744-  758 (27.12/17.58)	EHSLRAYQRSDPKSQ
  761-  775 (25.22/15.84)	EPLLKAIKDSIPLSR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     106.44|      24|      25|     172|     195|       9
---------------------------------------------------------------------------
  172-  195 (38.98/23.36)	AFTVDVMGQLHNSQVREEMESARA
  196-  219 (38.60/23.06)	AFVALLLGVCENQVVLKAMSKPEA
  595-  616 (28.87/15.54)	.FVARLLGQGHQSRPFDELSDQE.
---------------------------------------------------------------------------




































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 MDP28866 with Med5 domain of Kingdom Fungi
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