<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 MDP29166

Description Mediator of RNA polymerase II transcription subunit 1
SequenceNDTLSFISEEEKESRSAVLLERLHAKYIASRPWQETFKVVRQTMDKRGPTNAPSHQLMHSCLENLQRAMKVSSLSAMTDRLESIARQNMLGSHLSPSGTECYITSDMFYVEVQLDNSGQLVDVKVAHQGENPTSCPELIQHLREKNFDEFSKHLKGLVELYKLPGDNKLKTKMYIALQSLELDLTKMMHMYRLATSANTLETLLHGSVGLLSARSGGHLVSLHCYLSPYDLLEEKTCSPLSLTDNNIPRSLGLGVSVSVTIEGTSAIYKLPIAPLITGSHPVDNKGLRTPSFSTVTNSNCVDLPACFFLKLNRPMPFSLAFIQRMANTTAIPVFESPPMLSPLYQLIVQSELRLQEDGNITPTLCPHNMTFYSVLPGQLHCYFLNGDAPVQDGQSLQGVIVSKIPFRHPAQVPLLLDIVRHQAAYNSLIGSCVKRTSIDEDGAGLLQFEVCPLTDSSFSVSFQHPVNESLVCVVMDVIDSRQVSCKLYKGPSDALICTDEFITKVVHRCMSIPVTMRAIRRKAETIQADTPALSLIAQTVEIMVKNNLPPSGSPTYNMASCDGPNPMGLPGLTGGNTPTAGGPPGGPNFAGPITSLFGMSRTERQVQGGQGHSEDYNKVTQNPILTSLLQITGSVGSSPNSQNAPTPHQTPPPTSSPASNTKNHPMLMNLLKDNPAQDFAALYSSSPLERQNSSSGSPRTEGMGGTCPGGNPKGMKSQQSSSMSQQHQHHPVTHEDDFHRELLSMDVDASQNSIFDVNLTGDGLDTPHSITPAPSQCGTPPSGSSIPYSQSHVQSQQQQPQAAAPPHMARLPSSDSIGPDITEILSDLPEQTGKGNSGSHGQNPIGGGGEEGGTLGTPIRDSSSSGQGSAVFDSADIFNTNSNENPFTDAVDLIAEAAATAATPTSDSSSTNFFPDAADFNPDLLTSGHGFSQNYFDDSSPSADGDMDIVKSFGGNSQQNTPSGTPQNPASQGQSTPEPSLKDPFDMGIVFGGNSGGAKTLLGQASDMSDTHSGGSQSPLIMGAGCGDFKSAEPKLKPQQSHMRPKEENGSSGSSNAGIGMGSSSTDCKQVKRSRTPSSEGKCKEKPPKRKKVDSDGKSPSHSSGGRPYTPPSGGSGSGGSMSGGGSKSPGSSGRSQTPPGGATPPIPKITIQITKGTITGGKTSSLSGYTSSSSATGSTGGTGGSSSKSHHSHSSSGKIKSKESSATPGSTSKPGSAGLAGGVPSQSKSASQGIGVGKPGSSPITKHGLSGPGSSSSGMVGGNKTKPPGGKPPGSLMNPNMKPNISPSHSRSSTSGEKMSSPLKMQQSQVPGTPPSFKAKSPIGSGGSSSAGSKLSSGPGMCSQKPMGGISSSGTTLSSSSSSSTSSSSSSSSGGGTVAGQNNANNPNAKGKSPSRNKKPSLTAVIDKLKSVGPPVSGPGSGTVPTGGGPGNVPSSGPLNICPSKHISTSQSGEYKREKSEKEAKAKVSVSGGNSGDKKLMDPKAGGVGTSGLAKIIISKPDGGSPSIKAKGPLQKAGEGSGDSVRPQISSVKASPLFSGSTPKHDRSSPSHSRSPGYTPLNHDSESESGSSSVAEKSHQNSPSSDDDQTMRPLPPQDYLSSIPLSSGEKHKKHSSMSMVPSSHPIKADSWSRSPISASDSSLSMLGPERQTRPSPLYMRNEDDDLMDSALTGN
Length1675
PositionMiddle
OrganismTetraodon nigroviridis (Spotted green pufferfish) (Chelonodon nigroviridis)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Actinopterygii> Neopterygii> Teleostei> Neoteleostei> Acanthomorphata> Eupercaria> Tetraodontiformes> Tetradontoidea> Tetraodontidae> Tetraodon.
Aromaticity0.04
Grand average of hydropathy-0.563
Instability index57.94
Isoelectric point8.24
Molecular weight174141.78
Publications
PubMed=15496914

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

>MDP29166
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
            10|     633.24|      72|      74|    1269|    1340|       1
---------------------------------------------------------------------------
  612-  676 (60.04/11.29)	HS.EDYNkvTQNPI...LTSLLQ.........ITG...........S.VGS...S.P.......NS...Q.NAPTPHQTP........P........P.T...S.SP...ASNT.K.......NHPMLMNlLKDN.....PA
  677-  761 (44.30/ 6.09)	QDfAALY..SSSPL...ERQNSS.........S.G...........SPRTE...GmG....gtcPG...G.NPKG..MKSQQSS.SMSQ........Q.H...QHHP...VTHE.DdfhrelLSMDVDAS.QNSIfdvnlTG
 1043- 1109 (44.75/ 6.24)	.....MR..PKEEN...GSSGSS.........NAG...........IGMGS...S.S.tdckqvKR...S.RTPSSEGKCKEKP....PkrkkvdsdG.K...SPSH...SSGG.R........................PY
 1110- 1169 (68.46/14.07)	TP.PS......GGS...GSGGSM.........SGG...........GSKSP...G.SsgrsqtpPG...G.ATP.....P.I.P.KITI........Q.I...TKGT...ITGG.K......TSS.........L.....SG
 1171- 1241 (60.67/11.49)	TS.SSSA..TGSTG...GTGGSS.........SKShhshsssgkikSKESS...A.T.......PG...StSKPGSA...GLAG.GV.P........S.Q...SKSA...SQGI.G......VGK...............PG
 1242- 1313 (102.32/25.25)	S..........SPI...TKHGLS.........GPG...........SSSSG...M.VggnktkpPG...G.KPPGSLMNPNMKP.NISP........S.H...SRSS...TSGE.K......MSSPLKMQ.QSQV.....PG
 1314- 1381 (83.99/19.20)	TP.PSFK..AKSPI...GSGGSS.........SAG...........SKLSS...G.........PGmcsQ.KPMGG..........ISS........S.GttlSSSS...SSST.S......SSSSSSSG.GGTV.....AG
 1386- 1463 (49.66/ 7.86)	NN.PNAK..GKSPS...RNKKPSltavidklkSVG...........PPV.S...G.P..gsgtvPT...G.GGPGNV..PSSGPlNICP........SkH...ISTS...QSGEyK......REKSEK..............
 1505- 1558 (51.88/ 8.59)	GS.PSIK..AKGPLqkaGEGSGD.........SVR...........PQISSvkaS.P.....lfSG...S.TPKHDRS.........SP........S.H...SRS..................................PG
 1560- 1623 (67.16/13.64)	TP.LNHD..SESE.....SGSSS.........VAE...........KS.................H...Q.NSPSSDDDQTMRP..LPP........Q.D...YLSSiplSSGE.K......HKKHSSM...SMV.....PS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     236.49|      48|     233|     549|     611|       2
---------------------------------------------------------------------------
  549-  591 (78.63/24.18)	................PPSG...SPTYNMASCDGPNPMGLPGLTGGNTP..TAGGPPGG...PNFAG
  824-  866 (54.48/16.15)	ILSDL...............peqTGKGNSGS.HGQNPIGGGGEEGG.....TLGTPIRD...SSSSG
  924-  973 (44.84/16.85)	LLTSGhgfsqnyfddsSPSA............DG..DMDIVKSFGGNSQqnTPSGTPQN...PASQG
  977- 1023 (58.54/17.95)	P...............EPSL...KDPFDMGIVFGGNSGGAKTLLGQASD..MSDTHSGGsqsPLIMG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      57.76|      18|     233|     119|     136|       3
---------------------------------------------------------------------------
  119-  136 (33.91/24.08)	QLV...DVKVAHQGE.NPTSCP
  345-  366 (23.85/14.16)	QLIvqsELRLQEDGNiTPTLCP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      45.39|      12|      74|     303|     314|       8
---------------------------------------------------------------------------
  303-  314 (24.67/16.59)	LPA...CFFLKLNRP
  375-  389 (20.72/12.58)	LPGqlhCYFLNGDAP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      38.99|      13|      17|     767|     780|       9
---------------------------------------------------------------------------
  776-  795 (14.52/ 9.62)	QCGTPpsgssiPYsQSHVQS
  801-  813 (24.47/13.10)	QAAAP......PH.MARLPS
---------------------------------------------------------------------------




































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 MDP29166 with Med1 domain of Kingdom Metazoa
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