<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 MDP28766

Description Mediator of RNA polymerase II transcription subunit 1
SequenceMKAQGETEESEKLNKMSSLLERLHAKFNQNRPWSETIKLVRQVMEKRVVMSSGGHQHLVSCLETLQKALKVTSLPAMTDRLESIARQNGLGSHLSASGTECYITSDMFYVEVQLDPAGQLCDVKVAHHGENPVSCPELVQQLREKNFDEFSKHLKGLVNLYNLPGDNKLKTKMYLALQSLEQDLSKMAVMYWKATNAGPLDKILHGSVGYLTPRSGGHLMNLKYYASPSDLLDDKTASPIILHENNVPRSLGMNASVTVEGTSAMYKLPIAPLIMGSHPADNKWTPSFSAITSANSVDLPACFFLKFPQPIPVSRAFVQKLQNCTGIPLFESQPTYVPLYELITQFELSKDPDPIPLNHNMRFYAALPGQQHCYFLNKDAPLPDGRSLQGILVSKITFQHPGRVPLILNMIRHQVAYNTLIGSCVKRTILKEDSPGLLQFEVCPLSESRFSVSFQHPVNDSLVCVVMDVQDSTHVSCKLYKGVSDALICTDDFIAKVVQRCMSIPVTMRAIRRKAETIQADTPALSLIAETVEDMVKKNLPPASSPGYGMTTGNNPMSGTTTPTNTFPGGPITTLFNMSMSIKDRHESVGHGEDFSKVSQNPILTSLLQITGNGGSTIGSSPTPPHHTPPPVSSMAGNTKNHPMLMNLLKDNPAQDFSTLYGSSPLERQNSSSGSPRMDMCSGSNKTKKKKSSRLPPDKPKHQTEDDFQRELFSMDVDSQNPIFDVNMTADTLDTPHITPAPSQCSTPPTTYPQPVPHPQPSIQRMVRLSSSDSIGPDVTDILSDIAEEASKLPSTSDDCPPIGTPVRDSSSSGHSQSALFDSDVFQTNNNENPYTDPADLIADAAGSPSSDSPSNHFFPDGVDFNPDLLNSQSQSGFGEEYFDESSQSGDNDDFKGFASQALNTLGVPMLGGDNGETKFKGNTQVDTVDFSIISVAGKALGAAELIEHHSGSQSPLLTTGDLGKEKTPKRVKEGNGTSSSSLSGPGSDSKPGKRSRTPSNDGKSKDRPPKRKKGDTEGRSPSHSSNRPFTPPTSTGGSRSPGSAGRSQTPPGVTTPPIPKITIQIPKGTVMVGKPSSHSQYTSSGSVSSSGSKSHHSHSSSSSSSSSASTSGKMKSSKSEGSSSSKLTSSVYSSQGSSGSSQSKNSSQSGGKPGSSPITKHGLSSGSGSTKMKPQGKPSSLMNPLSKPNISPSHSRPPGASDKLASPMKPVPGTPPTSKAKSPISSGSGGSHMSGTSSGSGMKSSSGLGSSGSLSQKTPPSSNSCTASSSFPSSGSSMSSSQNQHGSSKGKSPSRNKKPSLTAVIDKLKHGVVTGGPGGEDAMDGQMGVSANSASHLMSSKHNMSGGEFQGKREKSEKDKSKVSTSGGSGDSSKKTSESKNVGSTGVAKIIISKHDGGSPSIKAKVTLQKPGESSGEGLRPQMASSKNYGSPLISGSTPKHERGSPSHSKSPAYTPQNLDSESESGSSIAEKSYQNSPSSDDGIRPLPEYSTEKHKKHKKEKKKVKDRDRDRDKDRDKKKSHSIKPESWSKSPISSDQSLSMTSNTILSADRPSRLSPDFMIGEEDDDLMDVALIGN
Length1578
PositionMiddle
OrganismCavia porcellus (Guinea pig)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Mammalia> Eutheria> Euarchontoglires> Glires> Rodentia> Hystricomorpha> Caviidae> Cavia.
Aromaticity0.04
Grand average of hydropathy-0.667
Instability index54.70
Isoelectric point8.89
Molecular weight167899.60
Publications
PubMed=21993624

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

>MDP28766
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
            10|     467.92|      50|      51|     992|    1041|       1
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  650-  692 (37.59/ 6.87)	KDNPA..Q.....DFSTLY..................GSSPLERQN......S.SSG.SPR............mdmcSGS...NK....T.....KK..K..KS
  965- 1005 (57.02/14.46)	KEKTP..K....RVK...E..................GNGTSSSS...LSGP....G.SDSK...............PGK..RSR....T.....PS..NDGKS
 1006- 1055 (80.71/23.72)	KDRPP..K....RKKGDTE..................GRSPSHSSNRPFTPPT.STG.GSRS...............PGSagRSQ....T.....PP....GVT
 1056- 1108 (41.32/ 8.33)	TPPIP..KitiqIPKGTVM..................VGKPSSHSQ.....YT.SSG.SVSS...............SGS..KSHhshsS.....SS..SSSSS
 1109- 1171 (44.45/ 9.55)	ASTSG..K....MKSSKSE..................GSSSSKLTSSVYSSQG.SSG.SSQS......knssqsggkPGS..SPI....T.khglSS..GSGST
 1172- 1212 (47.46/10.73)	KMKP..............Q..................GK.PSSLMN.PLSKPNiSPS.HSRP...............PGA..SDK....L.....AS..PMKPV
 1213- 1278 (35.75/ 6.15)	PGTPPtsK....AKSPISS..................GSGGSHMS......GT.SSGsGMKSssglgssgslsqktpPSS..NSC....TasssfPS..S.GSS
 1367- 1433 (36.62/ 6.49)	SGGSG..D....SSKKTSEsknvgstgvakiiiskhdGGSPSIKAKVTLQKP....G.ESSG...............EGL..RPQ....M.....ASskNYGSP
 1436- 1485 (45.71/10.05)	SGSTP..K....HERG.......................SPSHSKSPAYTPQN.LDS.ESES..........gssiaEKS..YQN....S.....PS..SDDGI
 1507- 1550 (41.30/ 8.32)	KDRDR..D....RDK.DRD...................KKKSH.SIK....PE.S...WSKS...............PIS..SDQ....S..lsmTS..NTILS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      61.73|      13|      26|     327|     339|       2
---------------------------------------------------------------------------
  299-  313 (17.07/ 6.52)	LPacFFLKFPQPIPV
  327-  339 (23.98/12.48)	IP..LFESQPTYVPL
  355-  367 (20.67/ 9.63)	IP..LNHNMRFYAAL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     156.47|      38|      50|     146|     183|       3
---------------------------------------------------------------------------
  146-  183 (64.88/46.88)	NFD.EFSKHLKGLVNLYNL..........P..GDNKLKTKMYLALQSLEQD
  196-  234 (56.76/39.84)	NAG.PLDKILHGSVG.YLT..........PrsGGHLMNLKYYASPSDLLDD
  250-  293 (34.82/20.82)	SLGmNASVTVEGTSAMYKLpiaplimgshP..ADNKW.TPSFSAITS....
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             5|     282.55|      50|      52|     696|     745|       4
---------------------------------------------------------------------------
  583-  635 (39.63/13.81)	............KD.......RHESvghGEDFSK......V.....SQ...NPILTslL.QITGNGGSTigssptpPHHTPPPvS.SM
  696-  745 (94.69/43.70)	P......P...DKP.......KHQT...EDDFQRELFSMDV....DSQ...NPIFD..V.NMTADTLDT.......PHITPAP.S.QC
  748-  800 (60.05/24.89)	P......PttyPQP.......VPHP...QPSIQRMVRLSSS....DSI...GP..D..VtDILSDIAEE.......ASKLPST.SdDC
  801-  857 (52.48/20.78)	P......P..iGTPvrdssssGHS........QSALFDSDVfqtnNNE...NPYTD.pA.DLIADAAGS.......PS.SDSP.S.NH
  860-  909 (35.70/11.68)	PdgvdfnP...DLL.......NSQS...QSGFGEEYF..DE....SSQsgdNDDFKgfA.SQALNTLGV.......P...........
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      65.03|      17|      22|     541|     558|       6
---------------------------------------------------------------------------
  541-  558 (30.58/24.07)	PPASSPGYGMTTGNNpMS
  563-  579 (34.45/21.21)	PTNTFPGGPITTLFN.MS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      53.46|      15|      32|    1246|    1260|       7
---------------------------------------------------------------------------
 1246- 1260 (26.04/11.85)	SSGLGSSGSLSQKTP
 1280- 1294 (27.42/12.99)	SSSQNQHGSSKGKSP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      96.97|      30|     340|     101|     135|       8
---------------------------------------------------------------------------
  101-  135 (48.66/40.38)	CYITSDMFYVEVQlDPAGQ..LC...DVKVAHHgenpVSC
  443-  477 (48.31/26.35)	CPLSESRFSVSFQ.HPVNDslVCvvmDVQDSTH....VSC
---------------------------------------------------------------------------




































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 MDP28766 with Med1 domain of Kingdom Metazoa
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