<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 MDP17953

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMWTNVFKIGGLHHVSWFQFLPNESDLNSLPDKSVKVEQKDFATWLVLSAHFQLQKEGFLSTWTNSFVGPWDPSQGLHNPDEKIKLWLFLPGRYSSVVDKAQAAVSRLRVVASGVWVAPGDSEEVAAALSQSLRNYIERALTGHSYVRFGDVFLKYHPSQSEGLSRKGRPTVEFIFSASEEAIFVHAIISAKHIRALSNGDVERVLKQSSSNSSYRLPVIASPHGIRGSLTGCCPNDLVKQVFMSSGKSKTSNGFIGMPYHVSQGPGCQLREQNCYVEITLGCPRSESDKELETNLQSTKNSSKNHIAESPAVRRGDQKVSPDHLSAYEKAFIYPVEAIVVPVLPKSFARSSLKRFWLQNWIGPSLPGSSFFMHCGGDTDFLEGSWIESNGLRMQHSYNSSSNSNSSSISSIISGSSDSDYKMTTGELEADGDSLSCRQSGLSSNDQMEIDDLKLGSKRPRTGMNEPYGQVGTVKNAPMQEFGSVEVNASAITGIANEQIGSRWDWDDDRGAGMDIQALLSEFGDFGDFFENDDLPFGEPPGTAESQALMFSGPDCGEVANTPIGVMDVVDQMLLPAAFPSFESFNPSPAVAIDESASKSQEATHGALALVPVNCTPPSSSGEFDYLIKAEALLTFAPEYGAVETPTSEFSSSIFRRPYCPKSRQVESSNPSSNKYAYGATPPPSPFFEGSNEKTGMQVNLKTGAGRNDTKKYYTLVESGKVHLDRRTFIFNESHPTSEVMVPSPLLTSNSSNTVQRKMSDCILGAENFLFSMKTVLATEVECIMFQASMCSMRHMLLSYGNPTPVNLSRLSGSTVLNQLHGDASTMTDSISARYEVKKKESIPVRIAGDMDGGLLDGHLNAPVGVWRSVGVPKLTKHTSSPNIEVSASLPHHSFSEEGILSYRQRQQPLQELLDGMALLVQQATSFVDVALDADCGDGPYGWLALQEHWRRGFSCGPSMVHAGCGGALAACHSLDIAGVELVDPLSADIHSSAVISLLQSEIKTALKSAFGNLDGPLCVTDWCKGRFQSGDGATTCDGLIGESTLSGCKDSSSIVTLPVGEPMSPALSCAAGSSSLKASSTLDGAKVDETSQRRSNQEIEPELRFRIKPTVFVLPSPAILVGYQDDWLKTSASSLQLWEKAPFEPYASPKPISYYVVCPDIDPLTSAAADFFQQLGTVYETCKLGTHSPQSLGNHMEMDAGKSLYTGFVLLDCPQSMKIESSNASLVGSISDYFLSLSNGWDLASYLKSLSKAVKALKIGPSLLTNPKEGSSSSCMVIYVVCPFPEPAAVLQTVIESSVAIGSIIPPADRERRSMLLGQVRKALSSLAAVDDASASNVLVLSGFSTPKLVLQIVTVDAIFRVTSPALNELIILKETAFTVYNKARRISKGSSNDVQSSSASSRSHSALTQMSSVPAMWNSLPREADIDSRLRAGTWDNSWQTMRTGSLTCDPNRNGDFSLQDEIHYMFEPLFILSEPGSLEHAVTPAVFGNLGSESLKMQSDDSSGSFMQSASSAGSVDTGSSSQHDGSEPTGFGSSHQKALPSLHCCYGWTEDWRWLVCIWTDARGELLDSHIFPFGGISSRQDTKGLQCLFVQVLQQGCQILQSCSSPDTGSVKPRDFVITRIGSFFELEYIEWQRAIYSVGGSEVKKWPLQLRRSMPDGMAASTNGASLQQQEMSLIQERTLPSSPSLLYSPLLKASGYMKGGLGQPSSRKQLMGGYTVVDNSRGMLQWVQSITLVTISVDHSLHLMFQADMPSPGGNGSSVGPSIYREGISPVKSLGSTSASYILIPSPSMRFLPPTPLQHPTCLTAESPPLAHLLHSKGSAIPLSTGFVVSKAVPSMRNDYRSDAREEWPSVLSVSLIDYYGDNNMTEDKMYRGIMKQGGRTLGTDGKDLEIGTQLILENIAAELQALSWMTVSPAYLERRTALPFHCDMVLRLRRLLHFADKELSSQPGRSQV
Length1959
PositionKinase
OrganismPopulus trichocarpa (Western balsam poplar) (Populus balsamifera subsp. trichocarpa)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> rosids> fabids> Malpighiales> Salicaceae> Saliceae> Populus.
Aromaticity0.08
Grand average of hydropathy-0.223
Instability index53.57
Isoelectric point5.57
Molecular weight212507.33
Publications
PubMed=16973872

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	IBA:GO_Central

GO - Biological Function
transcription coregulator activity	GO:0003712	IBA:GO_Central

GO - Biological Process
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP17953
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     105.42|      32|      57|    1278|    1311|       1
---------------------------------------------------------------------------
 1278- 1311 (52.48/37.20)	IYVVCPFPEPAAVLQTVieSSVAIGSIIPPADRE
 1338- 1369 (52.94/31.59)	VLVLSGFSTPKLVLQIV..TVDAIFRVTSPALNE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     198.09|      55|      57|     518|     574|       2
---------------------------------------------------------------------------
  445-  492 (56.58/31.91)	.......DQMEIDDLKLGsKRPRTGM............................NEPY...G.QVGTVKNAPMqefGSVEVNASAIT
  520-  574 (99.46/65.89)	SEFGDFGDFFENDDLPFG.EPPGTAE............................SQALMFSGPDCGEVANTPI...GVMDVVDQMLL
  576-  645 (42.05/18.43)	AAFPSFESFNPSPAVAID.ESASKSQeathgalalvpvnctppsssgefdylikAEALLTFAPEYGAV.ETP...............
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     213.34|      53|      85|     836|     889|       3
---------------------------------------------------------------------------
  792-  832 (49.58/22.06)	..............MRHMLLSYGNP..TPVNLSR...LSGSTVLNQlHGDASTMTDSISA
  836-  889 (84.94/47.48)	VKKKESIpVRIAGDMDGGLLDGHLN..APVGVWR...SVGVPKLTK.HTSSPNIEVSASL
  920-  974 (78.82/39.66)	VQQATSF.VDVALDADCG..DGPYGwlALQEHWRrgfSCG.PSMVH.AGCGGALAACHSL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     130.90|      41|      89|     194|     237|       4
---------------------------------------------------------------------------
  194-  237 (60.38/54.44)	RALSNGDVERVLkQSSSNSSyRLPVIASPHGIRGSlTGCCPNDL
  284-  324 (70.53/47.47)	RSESDKELETNL.QSTKNSS.KNHIAESPAVRRGD.QKVSPDHL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     222.53|      66|      90|    1519|    1589|       5
---------------------------------------------------------------------------
 1519- 1589 (114.51/86.51)	DTGSSSQHDgSEPTGFGSSHQ.KALPSLHCCY..GWTEDWRWLVCIwtdaRGELLDSHIFPFGGISSRQDTKGL
 1611- 1679 (108.02/67.15)	DTGSVKPRD.FVITRIGSFFElEYIEWQRAIYsvGGSEVKKWPLQL....RRSMPDGMAASTNGASLQQQEMSL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      58.13|      18|      54|    1057|    1082|       6
---------------------------------------------------------------------------
 1057- 1079 (25.61/19.99)	LPvgepmSPALSCAAGSSSLKAS
 1114- 1131 (32.53/ 8.12)	LP.....SPAILVGYQDDWLKTS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     395.81|     111|     623|    1145|    1264|       9
---------------------------------------------------------------------------
 1145- 1264 (173.22/138.10)	PYASPKPIS.YYVVCPdidpltSAAADFFQQLGTVYETCkLGTHSPqSLGnHMEMDAGKS..LYTGFVLLDCPQSMKIE.SSNA.....SLVG.SIS.DYFLSLSNGWD......LASYLKSLSKAVKALKIGPSLL
 1714- 1770 (66.20/34.64)	..........................................................KQ..LMGGYTVVDNSRGMLQW.VQSI.....TLV..TISvDHSLHLMFQAD......MPSPGGNGS......SVGPSIY
 1776- 1902 (156.39/100.54)	PVKSLGSTSaSYILIP......SPSMRFLPPTPLQHPTC.LTAESP.PLA.HLLHSKGSAipLSTGFVVSKAVPSMRNDyRSDAreewpSVLSvSLI.DYYGDNNMTEDkmyrgiMKQGGRTLGTDGKDLEIGTQLI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     158.63|      46|     311|      29|      77|      10
---------------------------------------------------------------------------
   29-   76 (80.41/42.67)	LPDKSVKVEQKDFatWLVLSAHFQLQKEGFL...STWTNSFVGPWDPSQGL
  343-  391 (78.21/33.10)	LPKSFARSSLKRF..WLQNWIGPSLPGSSFFmhcGGDTDFLEGSWIESNGL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      87.72|      25|     412|    1012|    1037|      16
---------------------------------------------------------------------------
 1012- 1037 (44.38/36.32)	NLDGPLCVTDWcKGRFQS.GDGATTCD
 1426- 1451 (43.35/28.81)	DIDSRLRAGTW.DNSWQTmRTGSLTCD
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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 MDP17953 with Med13 domain of Kingdom Viridiplantae
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