<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 MDP00936

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMWTNVFKIGGLHQISWFQFLPNEFDPSSLSDKSVKVDARDAATSVVLSSHLQLQKEGFLSTWTNSFVGPWDPSQGLHNPDEKIKLWLFLPGNHSSVVEKAQPTVSKLRVLASGLWVAPGDSEEVAAALSQALRNCVERALKGFSFMRFGDVFSRYHPSSQSEELYRKGQPVVEFIFAATEEAIFVHAVISAKHIRALSSGDIEMTLKHSTDHFSNRLPVVISPHGMLGRLTGCCPSDLVKQVYFSSVKLKASNEVVGLPYHALHGSGCHLRGQNCYAEITLGGPIGGNDKILAQNSGLHKNLSRHNLTESMPETKVNQKGPLEPSRVFIYPAEAVLVPVMQTSLARSCLKSRFWLQNWIGPSLFASSFFMHRSTTRSLCCSFYFSSDCKADSKDGSRLESNSLRSQHGYHSSSSSNNSSISSISSSSSDSDYRTSGAGDLEADADSLTCRQSGLSSIDQSHDILKLGSKRVHSGMSESFNQAGAVINPSTSDYGSIEVNNSAIIGGSNHPVGWGWDDDDRGMGMDIQALLSEFGDFGDLFEDDVLPFGEPPGTAESQAVVISAQDCGDFGSSPSTSMMDVSDQMLLPVGFPSFESFHSPPAPVAMDDSLTQNQDLTKTVSVPGKVNCPPASTSGEFDHVVKAEALMTFAPEYGAVETPSVEVTSSIFRSPYLPKSRKTETENSCSNKYVYSATPPSPCVDDSDEKSGITVNMKICSGRQDKIAVPQSKKYYTHIDGGIHKSNGMSSTCDDGTAAHEPVTMSSSLGLNSLNAVKSVSSKGSDGSLRVESFVPSLKPMLATELECLMCQAFMCRIRHTLLSSRCHLPVGLNRLSAVNILNQPHVDSSILSDNLSSKSEVKKKETIPVRIAGDMDAVLLDGNLSAPVGVWRPVTKGAKSTTHPMELCPSIPQNSFVEENLLSYGLRQPLQELLDGLALLVQQATSFVDVALDSDCGDGVHGWLALQEQLRRGFSCGPSMVHAGCGGVLSSCHSVDIAGVELVDPLSVDVQPSFTISLLQSDIKAALKTAFGTLDGPLFVSDWCKGRSLSCEAGSMCDEFYAESTASASECQDSSNGARAEEASDRKSLQEACLSESEQQAGSKLRPTLAVVPFPAILVGYQDDWLKTSASSLQLWEKAPLEPYATQKHMTYHVVCPDIEPLTTAAADFFQQLGTVYETCNLGTHSPQNFGSEMDLDSGKSSCSGFVVLDCPQSMKIDSSSASILGSISDYFLSLSNGWDLASYLKSLSKVLKTLNLSSCMTTSTKEGNSGPYTVVYVVCPFPEPLAILRTVVESSIAVGSSVLSSDKEKRSMMHNQVGKALNHSAAVDETLSNVLTISGFSIPKLVLQIVTVDAIFRVTNPPLNELVVLKEIAFTVYNKARRVLRGSNCDVVPSSTSLSGRSHSVLMQMASPLTGMWKDCVGPRLAASSLQRESDLDASLRSSTWENSWQTRSGALGCDPNRGGDFLIQDESRCMFEPLFILADPGSLERGVTPPVFGNPASESSKVLADDGTSGSLMQSSASSGSGDTGPSSQHDSSESDGFGSGNQKTLPSLHCCYGWTEDWRWLVCIWTDSRGELLDSYIYPFGGISSRQDTKGLQSLFIQILQQGCQILQSCSADAGKPRDFVIARIGCFFELECQEWQKALYAIGGSEVKKWSLQLRRSVPDGMPTNSNGTSMQQQEMTLLQERTLPSSPSPLYSPHSKSSTFMKSGLGQPSNRKQLMGGVDSSRGLLQWVQSISFISLSVDHSLQLVFQADSLASGSTQSNGFLNQPSYLEGYTPVRSLGLTSASYVLIPSPSIRFLPPAPLQLPTCLTAESPPLAHLLHSKGSAIPLCTGFVVSKAVPSMRKDSRSISKEEWPSILSVSLVDYYGGNNMAQDKIVKGMGKLGGRGLSSEAREFELETHLVLESVAAELHALSWMTVSPAYLERRSALPFHCDMVLRLRRLLHFADKELSRQPEESPS
Length1961
PositionKinase
OrganismCoffea canephora (Robusta coffee)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> asterids> lamiids> Gentianales> Rubiaceae> Ixoroideae> Gardenieae complex> Bertiereae - Coffeeae clade> Coffeeae> Coffea.
Aromaticity0.07
Grand average of hydropathy-0.196
Instability index55.12
Isoelectric point5.55
Molecular weight211884.57
Publications
PubMed=25190796

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

>MDP00936
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     218.67|      94|     252|      47|     161|       1
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   56-   99 (35.27/41.96)	..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................EGFLStwtnSFVGPWDP.SQGLHNPDEKIKLWLFLPGNhsSVVEK
  100-  158 (67.86/48.19)	AQPTVSKLRVLASGL.WVAPGDSEEVAAALSQALRNCVERALKGFSFMRFGdvFSrYHPS...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
  877-  915 (41.14/15.42)	............................................................sqseelyrkgqpvvefifaateeaifvhavisakhiralssgdiemtlkhstdhfsnrlpvvisphgmlgrltgccpsdlvkqvyfssvklkasnevvglpyhalhgsgchlrgqncyaeitlggpiggndkilaqnsglhknlsrhnltesmpetkvnqkgplepsrvfiypaeavlvpvmqtslarsclksrfwlqnwigpslfassffmhrsttrslccsfyfssdckadskdgsrlesnslrsqhgyhsssssnnssississsssdsdyrtsgagdleadadsltcrqsglssidqshdilklgskrvhsgmsesfnqagavinpstsdygsievnnsaiiggsnhpvgwgwddddrgmgmdiqallsefgdfgdlfeddvlpfgeppgtaesqavvisaqdcgdfgsspstsmmdvsdqmllpvgfpsfesfhsppapvamddsltqnqdltktvsvpgkvncppastsgefdhvvkaealmtfapeygavetpsvevtssifrspylpksrktetenscsnkyvysatppspcvddsdeksgitvnmkicsgrqdkiavpqskkyythidggihksngmsstcddgtaahepvtmssslglnslnavksvsskgsdgslrvesfvpslkpmlateleclmcqafmcrirhtllssrchlpvglnrlsavnilnqphvdssilsdnlssksevkkketipvriagdmdavllDGNLS....APVGVWRPvTKGAKSTTHPMELCPSIPQN..SFVEE
  919-  975 (74.39/38.05)	SYGLRQPLQELLDGLaLLVQQATSFVDVALDSDCGDGVHGWLALQEQLRRG..FS.CGPS...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     191.48|      48|     121|    1149|    1196|       2
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 1149- 1196 (86.15/58.60)	HVVCPDIEPLTTA..AADFFQQLGTVYETC.NLGT...HSPQNFGSEMDLDSGK
 1222- 1263 (47.62/28.35)	GSISDYFLSLSNGwdLASYLKSLSKVLKTL.NL......SSCMTTSTKE.....
 1273- 1316 (57.71/36.27)	YVVCPFPEPLAI..........LRTVVESSiAVGSsvlSSDKEKRSMMHNQVGK
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     590.16|     185|     756|     626|     827|       3
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  626-  827 (295.26/146.47)	NCP..PAST..SGEfDHVVkaeaLMTFA.PEYGAVET...PSVeVTSSIFRSPYLPKSRKTET.ENSCSNKYVYSATPPSPCVD..DSDEKSGITVNMKIcsgrqdkIAVPQS.KKYYTHIDGGIHKSNGMSSTCDDGTAAHEpVTMSSSLGLNSLNAVKSVSSKGSDG.SLRVESFVPSLKPMLA.TE.LECLMCqaFMCRIRHTLLSSRCHlPVG
 1385- 1584 (294.90/118.16)	NCDvvPSSTslSGR.SHSV....LMQMAsPLTGMWKDcvgPRL.AASSLQRESDLDASLRSSTwENSWQTRSGALGCDPNRGGDflIQDESRCMFEPLFI.......LADPGSlERGVTPPVFGNPASESSKVLADDGTSGSL.MQSSASSGSGDTGPSSQHDSSESDGfGSGNQKTLPSLHCCYGwTEdWRWLVC..IWTDSRGELLDSYIY.PFG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     302.01|      99|     631|     381|     506|       4
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  381-  506 (139.26/117.83)	SFYFS...SDCKADSK......DGSRLESNSLRSQhgyhsssssnnsSISSISSSSSDSDYRTSGAGDLEADaDSltcrqSGLSSIDQSHDILKLGskrvHSGMSESFNQAGAVINPSTSdygsiEVNNSAIIGG
 1009- 1116 (162.75/84.24)	SFTISllqSDIKAALKtafgtlDGPLFVSDWCKGR............SLSCEAGSMCDEFYAESTASASECQ.DS.....SNGARAEEASDRKSLQ....EACLSESEQQAGSKLRPTLA.....VVPFPAILVG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      81.79|      23|     632|    1199|    1221|       8
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 1199- 1221 (44.32/21.58)	CSGFVVLDCPQSMKIDSSS......ASIL
 1832- 1860 (37.47/17.20)	CTGFVVSKAVPSMRKDSRSiskeewPSIL
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      63.92|      18|     816|     307|     324|       9
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  307-  324 (32.50/19.74)	LTESMPETKVNQKGPLEP
 1122- 1139 (31.42/18.81)	LKTSASSLQLWEKAPLEP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      68.19|      18|     816|      11|      43|      10
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   11-   28 (35.31/42.97)	LHQISWFQFLPNEFDPSS
 1912- 1929 (32.88/10.71)	LHALSWMTVSPAYLERRS
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      41.78|      11|      25|     571|     581|      11
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  571-  581 (20.36/12.70)	SSPSTSMMDVS
  598-  608 (21.43/13.91)	SPPAPVAMDDS
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      37.52|      11|     623|     980|     992|      14
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  980-  992 (14.19/15.01)	GCgGVLSSChSVD
 1606- 1616 (23.33/11.43)	GC.QILQSC.SAD
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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 MDP00936 with Med13 domain of Kingdom Viridiplantae
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