<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 MDP31649

Description Mediator of RNA polymerase II transcription subunit 29
SequenceMSGQGPPPSMTPQQQHMLMQQQQQQQMMRQQQMQQQQMQQQRQQQIQQQAQQPYQRARTPQMVPQGGSPGGAHLQMHPHLQPQGQMQPRSPLVGAQLQAPSSVPTAANPTTPQMMQQQMGMNQPMSLPPTHVSRPGSVAPPSSVPVNLQHTSGAPGLPGSQMEHQYPMHLQPQQQTLSRPGSQQSQHIQQPGSIQRPGSVLAPGSIPPGGPASQTGPQSIQVFGPGSVQPPGSTQAPSSVQPASTFNPGSIQAPASQQPPASVQPPPSAASGSTVAGAQSSKEPLKPNEEQIRMVQDPVDLVRNLVQKDLRNSLVEMNKRGAELVRQKQEGEVNEDGKAQYSRATNDFHAVCDEIDRTLTTVLETAKQLSKLDKVFFDRSSRDLDGEVMVNSVQNFVDNTEIVQRMFDDTIGSVTSSMESMRRRQKKWEDQHKNDDVEMME
Length441
PositionTail
OrganismCaenorhabditis elegans
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Chromadorea> Rhabditida> Rhabditina> Rhabditomorpha> Rhabditoidea> Rhabditidae> Peloderinae> Caenorhabditis.
Aromaticity0.02
Grand average of hydropathy-0.899
Instability index73.15
Isoelectric point6.84
Molecular weight48285.52
Publications
PubMed=9851916
PubMed=15020414

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 (By similarity). 
GO - Cellular Component
mediator complex	GO:0016592	IEA:InterPro
nucleus	GO:0005634	ISS:WormBase

GO - Biological Function
DNA-binding transcription factor activity, RNA polymerase II-specific	GO:0000981	IBA:GO_Central
RNA polymerase II transcription regulatory region sequence-specific DNA binding	GO:0000977	IBA:GO_Central

GO - Biological Process
lateral inhibition	GO:0046331	IGI:WormBase
positive regulation of Notch signaling pathway	GO:0045747	IGI:WormBase
regulation of cell fate specification	GO:0042659	IGI:WormBase
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP31649
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     127.06|      20|      20|     223|     242|       1
---------------------------------------------------------------------------
  106-  129 (28.54/ 6.40)	AAnpttPQMMQQQMGMNQPMSLP.P
  133-  150 (28.03/ 6.13)	SR....PGSVAPPSS..VPVNLQ.H
  178-  197 (29.52/ 6.92)	SR....PGS.QQSQHIQQPGSIQrP
  223-  242 (40.97/13.02)	FG....PGSVQPPGSTQAPSSVQ.P
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      32.86|      16|      42|     199|     221|       3
---------------------------------------------------------------------------
   60-   77 (23.89/10.83)	P...Q......................MVPQGGSpgGAHLQMH
  217-  259 ( 8.97/ 6.94)	PqsiQvfgpgsvqppgstqapssvqpaSTFNPGSiqAPASQQP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      41.61|      10|      54|     152|     161|       4
---------------------------------------------------------------------------
  152-  161 (20.48/ 9.15)	SGAPGLPGSQ
  205-  214 (21.12/ 9.68)	SIPPGGPASQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     163.16|      51|      54|     330|     383|       5
---------------------------------------------------------------------------
  330-  383 (76.32/82.87)	EGEVNEDGKAQYSRATNdfhAVCDEIDRTLTTVLETAKQLSKLDKVFFDRSSRD
  385-  435 (86.84/81.27)	DGEVMVNSVQNFVDNTE...IVQRMFDDTIGSVTSSMESMRRRQKKWEDQHKND
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      42.83|      12|      15|      30|      42|       6
---------------------------------------------------------------------------
   30-   42 (20.04/ 9.60)	QQQmQQQQMQQQR
   47-   58 (22.78/ 7.00)	QQQ.AQQPYQRAR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      43.84|      13|      20|     292|     304|       7
---------------------------------------------------------------------------
  292-  304 (22.40/15.58)	IRMVQDPVDLVRN
  315-  327 (21.44/14.60)	VEMNKRGAELVRQ
---------------------------------------------------------------------------




































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 MDP31649 with Med29 domain of Kingdom Metazoa
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