<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 MDP08562

Description Mediator of RNA polymerase II transcription subunit 1
SequenceMSAVGARKHSLEDFFDLLPTLRSKFEDYPACLRRTAFCARFATLRNQLDRIALQCDMKINQTGPITTALGQPAGIAWRLSSECFAVVVSAVPIEGYSLPPGTTPPQDDLASVSAVHFEFNQEKPILCEELVDELRKRNYNALLAHITNLLALYNVPGDRSHRCRAFLCLQVLEEDLSVLSAAATVDSEGVAVNPPPVTLSPRNVSEVATLVQSINFSAIGQIEPRSGGRFAALTYFVSPAQEAIARSRILKQAPSHPNLRGLLKGFFAFVGLRATADKIQHNLPFIPLVNLQKDESGLNIAQFATADSIKCGPIAAEFVLFLHPPLIISTEATADVEKITGIPLVCTQNCSPEPVHTLILRRHNQEALRLVDVHMLLPNRSQHVYHLRPEYSNRLQGYCVTEIAFTSPSQLPTLVSLLRRHAAWLSFVESFALHPRNPVSKDEALSFRFDISMSSMDELGVSFAHPCALERKVQVQPKLANHCLSVVQKFIHAMARLSAVCIQFGNFGVKLTRVSGCNLSERLERSTGATTTPPDPTRVLARSHNLPVAMTWLLILLGCPVNRSLSCIFPGATSITPSSCTSTTVASTAASSDAERHFRATFLARARRALQFSDDCDADGLLSGADQISQENLQHLDLLTQPPPPSPTQFDVFVTPVSSSAASCVSSLSLPGVDAFRPVGSPNTMTTTVPIGGSAALRSNAFLASAPLPPGVLVTTPPSCLLDGASAVKPMSMEETITSTSGCFPPPPLVGIGNGGVGNRSALAFSTPLIPGTISVSTAMFASPSSSASASPSPLKTPLFSTPVPTPPLGSRQSCPNIATTTSSSATSSVSAGSMLVSLLDEDIPPQSVHLPTLNTASLQPSRVISSMLPQPQLPQQQTSVHKPSSSDVLNHLLTSGQSEKDSALLRGKNKAPMLSTVSSPSLKTNLPSLSSRSTPSSMGSVGGGISGAYSGQAFTTTTTTTKRQRKRREASPVAAVEPIQFISVLPTRSSVAEATLAGKQSRFSAEAVSASLSTSTSEGGKLMTSTTAASAVSTVVSSEKHKSGRPSSGSSGGGGGVNQPTRHTPSSASSYSYAGATSSLVSKSVYDFEDLPMSLSSTTSLSKQPPSSASGIGAISATIGPYVPTTTNGNVITSCATLATATVSTTKSELRITIRPNWTAASSTSVGGTGPSSGIPNTSTASAKPRVVVDGKPSSFLKQMLHSSPATNSGDVSTDRTLQPSFMTGAVKPKKERKRRASSKSGKSLPLSNSAAVSNMSEISSALNRKVLTGSTSTVASAAMTGTTTGSYKPSHGLTASSSGPFPTSFSSVKPVKGRKKASSMSTFSSSVVFTPSEPVGAAATSVAALKPTTTSGGPTKKIKLSGDDATRSLEVVEPTISATSKGNGLMKGYKIPKKKAASPVQPSPQTSAAATAQPLIRTSPSLSSEVDGAEASIQSSPGAPPLRDQISVSVADTDTLQPKPASLLSVSETTPASADSAWTALPEMLTPQQRLPFPQSSGLQPQVSRKLPKNLTDIVEQLRAKSTREHTIPPGCGGSGPIPGNEDGSVNSSGWQQSETSAFTSLETTAVQEDEKMQEKEVEEEEEAEEKNKKRTTDTIASNGSGRQSRPGCTISPSLASDDTSSSTTAKVATAATVHRQHTVAGAGRVSTGEDQSSALFEGSRSRRGSISQELAFDATVASTETSGESGARTSIRAGQLSDVGVGALIEGPAHMSSRGTAQPGPITRTPGITKAGDVEEPSPSGSTDQLLNTQYTLGRWRCLV
Length1763
PositionMiddle
OrganismSchistocephalus solidus (Tapeworm)
KingdomMetazoa
LineageEukaryota> Metazoa> Spiralia> Lophotrochozoa> Platyhelminthes> Cestoda> Eucestoda> Diphyllobothriidea> Diphyllobothriidae> Schistocephalus.
Aromaticity0.04
Grand average of hydropathy-0.188
Instability index56.80
Isoelectric point9.03
Molecular weight184381.78
Publications









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

>MDP08562
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             8|     586.77|     100|     102|     561|     662|       1
---------------------------------------------------------------------------
  561-  651 (136.10/60.63)	................VNRS...LSCIFPGATSITP..SSCTSTT...VASTAA.SSDAERHFRATFLARARRA....LQFS.......DDCDADGLLSGA......DQISQENLQH...LDLLT.......Q...PPPP............SPTQFD
  654-  766 (96.36/42.49)	VTPVSSSAA.....scVS.S...LS..LPGVDAFRPvgSPNTMTTtvpIGGSAAlRSNA...F....LASAPLPpgvlVTTP.......PSC....LLDGA......SAVKPMSMEE...TITST.......SgcfPPPPlvgignggvgnrSALAFS
  866-  942 (66.45/24.51)	........................SSMLPQPQLPQQ..Q....TS...VHKP.S.SSDVLNHL...............LTSG.......QSEKDSALLRGKnkapmlSTVSSPSLK........TnlpslssR...STPS............SMGSV.
 1006- 1073 (70.14/26.43)	..............................AEAVSA..SLSTSTS...EGGKLM.TSTTA........ASAVST....VVSSekhksgrPSSGSSG...GG......GGVNQ....P.......T.......R...HTPS............SASSYS
 1141- 1201 (68.89/25.78)	...................................................TAT.VSTTKSELRITI..RPNWT....AASS.......TSVGGTGPSSGI......PNTSTASAKP...R.VVV.......D...GKPS............SFLKQM
 1275- 1326 (50.04/16.00)	............................................T...VASAAM.TGTTTGSYK.........................PSHGLTASSSGP......FPTSFSSVKPvkgR...............KKAS............SMSTFS
 1431- 1469 (31.52/ 6.40)	......................................................................AEAS....IQSS.......P..GAPPL...R......DQIS.VSVAD...TDTL........Q...PKPA............SLLSVS
 1471- 1542 (67.26/22.86)	TTPASADSAwtalpemL.TPqqrLP..FPQSSGLQP..Q..VSRK...LPKNLT...DIVEQLR....AKSTRE....HTIP.......PGCGGSGPIPG..........................................................
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     186.91|      35|      55|    1604|    1638|       2
---------------------------------------------------------------------------
 1355- 1383 (31.97/10.69)	......GPTK.KIKLSGDDATRSL.EVVEPTISATSK
 1384- 1419 (48.20/19.97)	GNGLMKGYKIpKKKAASPVQPSPQ.TSAAATAQPLIR
 1604- 1638 (59.25/26.29)	GRQSRPGCTI.SPSLASDDTSSST.TAKVATAATVHR
 1661- 1695 (47.50/19.57)	GSRSRRG.SI.SQELAFDATVASTeTSGESGARTSIR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     198.27|      63|     225|     103|     168|       3
---------------------------------------------------------------------------
  103-  168 (101.85/93.60)	TPPQDDLASVSAVHFEFNQE.KPILCEELVdeLRKRNYNAL.LAHITNLLA.....LYNVPGDRSHRCRAFlC
  330-  399 (96.42/76.06)	TEATADVEKITGIPLVCTQNcSPEPVHTLI..LRRHNQEALrLVDVHMLLPnrsqhVYHLRPEYSNRLQGY.C
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      73.86|      22|     232|    1107|    1130|       4
---------------------------------------------------------------------------
 1107- 1130 (35.51/23.51)	PSSAsgIGAISATIGPYVPTTTNG
 1333- 1354 (38.35/19.29)	PSEP..VGAAATSVAALKPTTTSG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     173.95|      45|     491|    1202|    1250|       9
---------------------------------------------------------------------------
  783-  811 (48.47/17.67)	SP.SSSASASPSPLKTPLFSTPVPTP................PLGS
  944-  982 (55.64/24.24)	......GGISGAYSGQ.AFTTTTTTTKRQRKRREASPVAAVEPIQF
 1205- 1250 (69.84/40.00)	SPaTNSGDVSTDRTLQPSFMTGAVKPKKERKRRASSKSGKSLPLSN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      51.13|      14|      15|    1711|    1724|      11
---------------------------------------------------------------------------
 1711- 1724 (26.38/15.68)	PAHMSSRGTAQPGP
 1729- 1742 (24.74/14.12)	PGITKAGDVEEPSP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     114.64|      35|      56|     405|     460|      14
---------------------------------------------------------------------------
  405-  440 (58.00/65.95)	FTSPSQLPTLVSLLRRHAAW.LSFVESFaLHPRNPVS
  463-  498 (56.64/24.78)	FAHPCALERKVQVQPKLANHcLSVVQKF.IHAMARLS
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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 MDP08562 with Med1 domain of Kingdom Metazoa
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