<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 MDP31648

Description Mediator of RNA polymerase II transcription subunit 29
SequenceMSGQGPPSNLTPQQQHMIMQQQQQQQMMRQQQIQQQQLHQRQLQQQQAQQSYQRSRTPQMQQHPGGGSPGSHLQMHPHLQSQGHMQPRSPLVGQHHPAPGSIPPGNPATPQMMQQQMGMNQPMSLPAPHVSRPGSVAPPASVPPNMHTGPSSNQMDQMGGQSQYSHHLQPQQPLSRPGSQQSHIAGGHGGPHSVQQPGSVLAPGSIQQPGSLLAPGSMHQPGSVQQPGSLGAPLSHTGAGGPQSVQGYGPGSVQPPGSAQAPSSVQPGSTFAPGSLQAPASQQPPASIQPPPSAASGSVAGPASAAPAKVEPLKPNEEQIRMVQDPVDLVRNLVQKDLRMSVVEMNKRGAELLHQKEEGAIKEEDRQQYKRATNDFHAVCDEIDRTLTTIMETAKQITKLDKVFQDRTSKEIDGEAMVNSVQKFVDETGIVQKMFDDTVNSVTSTMEKMRRRQKKWKDQQQQQENAEDAEMAE
Length473
PositionTail
OrganismCaenorhabditis briggsae
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Chromadorea> Rhabditida> Rhabditina> Rhabditomorpha> Rhabditoidea> Rhabditidae> Peloderinae> Caenorhabditis.
Aromaticity0.02
Grand average of hydropathy-0.920
Instability index74.69
Isoelectric point7.39
Molecular weight51146.58
Publications
PubMed=14624247

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). 
ECO:0000250
GO - Cellular Component
mediator complex	GO:0016592	IEA:InterPro
nucleus	GO:0005634	IBA:GO_Central
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
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central

Interaction

Binary Interactions











Repeat regions





Repeats

>MDP31648
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      82.62|      16|      16|     197|     212|       1
---------------------------------------------------------------------------
  191-  208 (26.82/ 7.83)	PHSVqqPGSVLAPGSIQQ
  209-  226 (30.03/ 9.79)	PGSLlaPGSMHQPGSVQQ
  273-  290 (25.77/ 7.19)	PGSLqaPASQQPPASIQP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      57.10|      16|      18|      60|      77|       2
---------------------------------------------------------------------------
   60-   77 (27.44/14.65)	MQQHPGGGSPGShLQmHP
  113-  128 (29.67/ 8.37)	MQQQMGMNQPMS.LP.AP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      76.29|      21|      21|     401|     421|       7
---------------------------------------------------------------------------
  394-  414 (31.03/25.96)	AKQITKL..........DKVFQDRT...SKEIDG
  415-  437 (28.39/23.00)	EAMVNSV..........QK.FVDETgivQKMFDD
  438-  466 (16.86/10.08)	..TVNSVtstmekmrrrQKKWKDQQ...QQQENA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      44.13|      15|      22|     347|     366|       9
---------------------------------------------------------------------------
  347-  366 (19.96/30.28)	KRGAELLHqkeegAIKEE.DR
  370-  385 (24.17/18.61)	KRATNDFH.....AVCDEiDR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      48.24|      14|      56|     253|     267|      12
---------------------------------------------------------------------------
  253-  267 (23.81/13.27)	VQPPGSAqAPSSVQP
  299-  312 (24.43/ 8.92)	VAGPASA.APAKVEP
---------------------------------------------------------------------------




































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 MDP31648 with Med29 domain of Kingdom Metazoa


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) EMNKRGAELLHQKEEGAIKEEDRQQYKRATNDFHA
2) MSGQGPPSNLTPQQQHMIMQQQQQQQMMRQQQIQQQQLHQRQLQQQQAQQSYQRSRTPQMQQHPGGGSPGSHLQMHPHLQSQGHMQPRSPLVGQHHPAPGSIPPGNPATPQMMQQQMGMNQPMSLPAPHVSRPGSVAPPASVPPNMHTGPSSNQMDQMGGQSQYSHHLQPQQPLSRPGSQQSHIAGGHGGPHSVQQPGSVLAPGSIQQPGSLLAPGSMHQPGSVQQPGSLGAPLSHTGAGGPQSVQGYGPGSVQPPGSAQAPSSVQPGSTFAPGSLQAPASQQPPASIQPPPSAASGSVAGPASAAPAKVEPLKPNEEQIRMVQDPVD
3) SVTSTMEKMRRRQKKWKDQQQQQENAEDAEMAE
344
1
441
378
328
473










Molecular Recognition Features






MoRF SequenceStartStop




1) LTPQQQH
2) SYQRSRTPQMQ
10
51
16
61