<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 MDP26029

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMDEFIDARFERVEKALASLVESVSKYHPYAKQALDLQEADKELSRGLELVQQHQNNHLRLQELRTTSSALDAQIRETLSTLASTRRDITTTHITVHGDEDHYPIKYEELLNYARRISKTTLPPAGVTNGVMFEPATSEDPPAGAVTNGVQSAVTSAAPTPSGAPTPGAPTPGAQTPAAPTPTPQQLPDPSGLNGAPSQPPEQPGAAPGDNPSGAPLGITTALPSGLRDHLDANHGTIFLPWPNEYQIGGGALAACQDLSERGIDPRGYDPVAVAAEAKRREEEDKAAKAELERRKAEETRRKREEWEANQRRRAAEAAQKPEPSATSPAPRRGQECAVPVY
Length341
PositionMiddle
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.
Aromaticity0.04
Grand average of hydropathy-0.753
Instability index63.92
Isoelectric point5.33
Molecular weight36680.13
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. 
ECO:0000256	RuleBase:RU364141
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

>MDP26029
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      64.49|      16|      16|     122|     137|       1
---------------------------------------------------------------------------
  127-  145 (21.63/ 6.85)	TNGVMFEPATS....edP.PAGaV
  146-  163 (20.92/ 6.41)	TNGVQ.SAVTS...aapT.PSG.A
  170-  192 (21.95/ 7.05)	TPGAQTPAAPTptpqqlPdPSG.L
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      41.70|      12|      16|     293|     304|       2
---------------------------------------------------------------------------
  293-  304 (20.53/12.08)	RRKAEETRRKRE
  311-  322 (21.17/12.70)	RRRAAEAAQKPE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      50.19|      13|      26|     196|     208|       4
---------------------------------------------------------------------------
  196-  208 (27.09/13.73)	PSQPPEQPGAAPG
  223-  235 (23.11/10.65)	PSGLRDHLDANHG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      42.61|      12|      25|      86|      97|       5
---------------------------------------------------------------------------
   86-   97 (21.52/12.85)	RDITTTHITVHG
  114-  125 (21.08/12.46)	RRISKTTLPPAG
---------------------------------------------------------------------------




































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 MDP26029 with Med4 domain of Kingdom Fungi


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) ARRISKTTLPPAGVTNGVMFEPATSEDPPAGAVTNGVQSAVTSAAPTPSGAPTPGAPTPGAQTPAAPTPTPQQLPDPSGLNGAPSQPPEQPGAAPGDNPSGAPLGITTALPSGLRDHLDANHGTIFLPWPNEYQ
2) DAQIRETLSTLASTRRDITTTHITVHGDEDH
3) GGGALAACQDLSERGIDPRGYDPVAVAAEAKRREEEDKAAKAELERRKAEETRRKREEWEANQRRRAAEAAQKPEPSATSPAPRRGQECAVPV
113
71
248
246
101
340










Molecular Recognition Features






MoRF SequenceStartStop




1) RRKREEWEANQRRRAAEAAQKPEPSATSPAPRRGQECAVPVY
300
341