<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 MDP26030

Description Mediator of RNA polymerase II transcription subunit 5
SequenceMEGRASRSAQQIGLSRWQKFIANSLAKRLDPERFESYAPILYSKHPLPPAIIADLFLRPRSGNRQFLDPRIPQYLQSLSKLRYIDIPSVLKGLYRYSTSHTQAHPTNGQGLEGDGEATRLIRWGSSYGSEEVMFYRLTKAVAQGAAIQNAAVALEIAKIMSKWMTLFTDASTAFAVDPMGQMQANQARDEMDCARAAFVALLLGVCENQVVLKALSRPQAAAARKAMSEGLATFVPTIMHNAGPVTTRLDHFRTRTLTNFEPAEAGKPLAAPELDQLFDSGVELNNFVIPELPVANSRAGLYIYLNAALVGRPLIDDTAVFNYLNNRYQGDVQSTTIDLILASFDVLANAVFRNEGNKAAHMLRSYLMNKLPILISNLSKHMYPPLTAEYCITEALSHVDTNAFPTLSSMFDESRNNNPYTDSVREEFCWACCLHGLLRESSIETILGETPYQSLPSRGRYVKDTLVAECLDDPERMQALVKELDNMDGNVGAVCHALTEVLAQLCRNKETMSLKNLCSQLSRRPLSLDVILLFEKPTAILQPLCDLLDDWKYDEDQGEYQPVYEEFGSVLLLLLAFAYRYNLTASDIGARSPDSFVAKFLGQGHLSRSSEELSDLEKSHLGGWIHGLFDQEAGGLTDDLISSCPPQEFYLLIPTLFQNVVTAFATGHLSEESLKGGVEYLVDTFLLPSLVTAITYLANSLWVERHNQNTIIRVLHLVLQPSAISEEAKTMLSSVLNIVAKPLEHSLRASQRQDPKNQKIDPLLGVLKDNIPLSRRTGGADHNELETWTSTQGEGLATALRHTMQGFVQWSLHPGINITPTSYSHRQVLAALRLLGAKRVLRLICEEVKQQTEAGGGSVVYDVATALVCAPEVTNNPQTPGLTFFEDSGNVPAPVQRRLTLRDVLKAEAEDSRRLQRTDMSQAELVVRLHRRVEAQMAVSEAEAIHAEAILQGDLGLGLDDAAGSLSEAMAAAAANAGPTGGAMTVDSVGLDLGMGGVGGDLDLGDATGNGGSLDLGADDIFSGLSAGGDFEWDTMDLG
Length1039
PositionTail
OrganismVerticillium alfalfae (strain VaMs.102 / ATCC MYA-4576 / FGSC 10136) (Verticillium wilt of alfalfa) (Verticillium albo-atrum)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Pezizomycotina> Sordariomycetes> Hypocreomycetidae> Glomerellales> Plectosphaerellaceae> Verticillium.
Aromaticity0.07
Grand average of hydropathy-0.125
Instability index44.94
Isoelectric point5.13
Molecular weight113640.71
Publications
PubMed=21829347

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

>MDP26030
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      77.57|      29|      35|     973|    1005|       1
---------------------------------------------------------------------------
  955- 1001 (35.01/27.07)	LGLGlddaagslseamaaAAANAGPTG.GAmtvDSV..GLDLGmGGVGGD
 1002- 1034 (42.56/20.72)	LDLG.............dATGNGGSLDlGA...DDIfsGLSAG.GDFEWD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      59.95|      17|      36|     183|     199|       2
---------------------------------------------------------------------------
  183-  199 (31.30/22.06)	QANQARDEMDCARAAFV
  219-  235 (28.65/19.53)	QAAAARKAMSEGLATFV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      52.14|      17|      23|     843|     862|       4
---------------------------------------------------------------------------
  843-  859 (30.17/23.48)	LIC.EEVKQQTEAGG.......GSV
  867-  891 (21.96/ 6.79)	LVCaPEVTNNPQTPGltffedsGNV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     120.03|      30|      34|     664|     697|       5
---------------------------------------------------------------------------
  269-  295 (46.28/23.53)	LAAPEL.DQLFDS..GVE...LNNFVIPEL....PVA
  633-  663 (22.83/ 6.57)	..AGGLTDDLISScpPQEfYL....LIPTLfqnvVTA
  664-  693 (50.91/37.27)	FATGHLSEESLKG..GVE.YLVDTFLLPSL....VTA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      61.13|      17|      25|     505|     521|       6
---------------------------------------------------------------------------
  505-  521 (31.00/16.79)	LCRNKETMSLKNLCSQL
  532-  548 (30.14/16.16)	LLFEKPTAILQPLCDLL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      43.14|      13|      23|     319|     331|       7
---------------------------------------------------------------------------
  319-  331 (25.11/14.70)	AVFNYLNN...RYQGD
  342-  357 (18.03/ 8.70)	ASFDVLANavfRNEGN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      75.12|      23|      36|     369|     391|       8
---------------------------------------------------------------------------
  369-  391 (43.02/33.64)	NKLPILIS..NLSKHMYP...PLTAEYC
  402-  429 (32.10/22.96)	NAFPTLSSmfDESRNNNPytdSVREEFC
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      33.14|      10|      23|     938|     947|      10
---------------------------------------------------------------------------
  938-  947 (16.53/ 8.83)	AVSEAEAIHA
  963-  972 (16.61/ 8.90)	AGSLSEAMAA
---------------------------------------------------------------------------




































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 MDP26030 with Med5 domain of Kingdom Fungi
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