<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 MDP04540

Description Mediator of RNA polymerase II transcription subunit 13 (Fragment)
SequenceRANHPVKRFKPNEISKQCRVMCTKKLYEGHTHTKPRMPSPRSVYGSQLSIDPTAAMACNSGNIDPNVNMGTGLVGIAASGISSSLGNNQIDCKNNDSSMSSGIGGGGMMGGGVNSSVSGNFFEELDIKTEMMSGMGTSSTSPCKDSKSGIGGNLFTVEGLNPSPNDLEQLFETSSNDECGSVQIHTPPDSNNPSNGCAITTNTIDELKRTTNTALVGNAGVQGNSSAATNAVVMAALQNCNNTNTSAAVVTSLNNSAGSLSSGLGGGIVGGANTIQAEDLTKMFPTPPSHEQHHPNSSPCQMDIQMTDLSVITSSTIMGQTLDTCLGISGMLKMKQEYSIELGSPVEEPIEDWSYVFRPPQQAKFVGSSKYAPLTNLPSLTMPPLVIPPNCLYKPSWQQPRNTHQQQQQQQQQQQHQLQQQQLQHHQQQQQQQQQQHQQLHELLSAAPRTPLQQQQPRTPLGPMSSSPMHNTVPTPLNSGGGGGSLLLNQLNCPQAALTNTPPTMQQLMQRPGMSPISPATHVPFPHTSPMMHQQQQRQTPIHPPPPYEVAVSSPALSTASSTPAYLNRPYHSQEPPQTPQSVNNQMQTIGGPHSVPGGNRETPSLGYYAGAGSSNSNSNSNSITHGLPEVSSVIVNILLYDTALNVFRDHNFDSSTVCVCNADNQHFGNIRGSDSGVYVPLPGTTFNPTSSSSLATSSNALRALSAFGSVGLGGGLGGGGIANSLDSPASLAGAGSSSSTTPSTTTPANNAQQYITGYVDDDAVECTCGFSAVINRRLACKAGLFYEDEMEITGIAEDPGRHKKHSLLTLITTLTSKAINNNNNNNGVIDKSVEQVAYSIFDLLLEQCSIIQTSSSAIHRSLQRHRRRLAKKSQKPQSVAAIANVLEYIDANDIIALALEQARLAFDSTRMDIMEQQVVPFSTHRKQTGNNQLALTLTGRINVHKWPYISVGFSRSNKDIVSTMKSVQPMLQNAFHSKSRNAAGAKDATYIVNGPLTWRQFHRLAGRASGQCEPQPIPSVIVGHDKDWISVAPLAIHYWDKFLLEPYSYARDVVYLVMVPDNDYILSKTKTYFKELSSTYEMCKLGKHAPICGWNGMLTVQQRSPTEKPFTTTIDNWLRSIDDTVLAEQLRLYAYAFQHQLAPYLNRVPNDKTLLNPLDNNTRNSSAGSNVTASSTSSSLSGNGGGSNTGQDNSEQRGNMAASDHSTSMDHSGGDHSQHSSHSGTDAQGNLNENKPTTEKPDVKPPLILGDPLGVAECLEEVNPTAIVLYVVEPFTYGSDSPDLERMACIALLRMYSELLKTIPESVRSHINIQIISLESILELGCSRNRKRFSDEIKCLALNIFSQCKRHMVHAQAVKSLTGFGTAANVEAFLKTKDEKNRRPYKMYTPPYILAPMHEKNDKTDFSRAALGGMRGNPNDQKYSVMYCNYCLSEDQSWLLATVTDDRGEMLEKRCINIDVPNRTRRRRAPARRIGLKKLMDYILGLISQTTQTWRLVVGRIGRIGHNELKSWSYLLGKSNLQKVTKQLKDMCKQCQLMYPPTILSACLVTLEPDAKLRVMPDQFTPDERFSQISIQNPLSTPQDVTCTHILVFPTSAVCLSFTRQFQNETQVDLDEDFINFGNDEDENDVFKDADLMDDLLGQWDNGGGTGRGMSNHNSPDRIEDNRSWQSVGGNNFNSAQHQDIEEVS
Length1690
PositionMiddle
OrganismLucilia cuprina (Green bottle fly) (Australian sheep blowfly)
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Arthropoda> Hexapoda> Insecta> Pterygota> Neoptera> Endopterygota> Diptera> Brachycera> Muscomorpha> Oestroidea> Calliphoridae> Luciliinae> Lucilia.
Aromaticity0.06
Grand average of hydropathy-0.495
Instability index53.08
Isoelectric point6.41
Molecular weight184203.42
Publications
PubMed=26108605

Function

Annotated function Component of the Mediator complex, a coactivator involved in 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

>MDP04540
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      73.02|      18|      20|     398|     417|       1
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  398-  415 (37.55/16.17)	QQPRNTHQQQQQQQQQQQ
  419-  436 (35.46/18.74)	QQQQLQHHQQQQQQQQQQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             5|     723.63|     301|     607|      51|     372|       2
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   51-  259 (247.29/175.19)	..................................................................................................................................................................................................DPTAAMACNSGNID.PNVNMGTGLVGIAASGI......SSSLGNNqidckNNDSSMSSGIG....GGGMMGGGVNSSvsgnffeeLDiKTEMMSGMGTSS......TSPCKDSKSGIGGNL..FTVE...GLNPSPND....LEQLFETSSNDECGSVQihTPPDSNNPSNGCAITTNTIDELKRTTNtalvGNaGVQGNS.SAATNAVVMAALQNCNNTNTSA.AVVTSLNNSAGS
  260-  372 (117.38/54.65)	LS..SGLGGG..IVGGANTIQAEDLTKMFPTPPSHEQ..HHPNSSPCQMDIQMTDLSVITSSTIMGQTLDT..CLGISGMLKMKQ.EYSIELG.SPVEEPIEDW.SYVFR......PPQ.......QAKFVGSSKYA......................................................................................................................................................................................................................................................................................................
  477-  596 (72.00/28.24)	LN..SGGGGGslLLNQLNCPQAA.LTN...TPPTMQQlmQRPGMSPIS...PATHVPFPHTSPMMHQQQQR..QTPI....HPPP.PYEVAVS.SPALSTASSTpAYLNRpyhsqePPQtpqsvnnQMQTIGGPHSV......................................................................................................................................................................................................................................................................................................
  654-  869 (220.04/119.28)	.........................................................................................................................................pggnretpslgyyagagssnsnsnsnsithglpevssvivnillydtalnvfrdhnfDSSTVCVCNADNQHfGNIRGSDSGVYVPLPGTtfnptsSSSLATS.....SNALRALSAFGsvglGGGLGGGGIANS........LD.SPASLAGAGSSSsttpstTTPANNAQQYITGYVddDAVEctcGFSAVINRrlacKAGLFYEDEMEITGIAE..DPGRHKKHSLLTLITTLTSKAINNNNN....NN.GVIDKSvEQVAYSIFDLLLEQCSIIQTSSsAIHRSLQRHRRR
  870-  983 (66.91/25.27)	LAkkSQKPQS..VAAIANVLEYIDANDIIAL..ALEQ..ARLAFDSTRMDIM..EQQVVPFSTHRKQTGNNqlALTLTGRINVHKwPY.ISVGfSRSNKDIVST.MKSVQ......PML.......QNAFHSKSRNA......................................................................................................................................................................................................................................................................................................
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     133.36|      37|     462|    1184|    1223|       3
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 1184- 1223 (63.96/33.21)	NGGGSNTGQDNSEQRGNMaasDHSTSMDHSGGDHSQHSSH
 1647- 1683 (69.40/30.84)	NGGGTGRGMSNHNSPDRI...EDNRSWQSVGGNNFNSAQH
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      33.46|       9|      15|     451|     460|       5
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  451-  460 (14.14/10.48)	PLQQQQPrTP
  468-  476 (19.32/ 9.48)	PMHNTVP.TP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     129.72|      41|    1524|       7|      50|       7
---------------------------------------------------------------------------
    7-   50 (66.57/50.58)	KRFKpnEISKQCRVM........CTKKLY.EGHTHTKPRMPSPRSVYgSQLSI
 1527- 1576 (63.14/36.89)	KQLK..DMCKQCQLMypptilsaCLVTLEpDAKLRVMPDQFTPDERF.SQISI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     105.25|      31|     531|    1046|    1076|       8
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 1046- 1076 (54.74/32.61)	EPYSYARDV..VYLVMVPDNDYILSKTKTYFKE
 1578- 1610 (50.52/29.56)	NPLSTPQDVtcTHILVFPTSAVCLSFTRQFQNE
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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 MDP04540 with Med13 domain of Kingdom Metazoa
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