<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 MDP17957

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMWTNVFKIGGLHHISWFQFLPNESDLNSLPDKSVKVEQKDVATCLVILAHLQLQKEGFLSTWTNSFVGPWDPSQGLHNPDEKIKLWLFLPGRYSSVVEKAQAAVSRLRVVASGIWVAPGDSEEVAAALSQSLRNYIERALARHSYMRFGDVFLKYHPSQSEGLSSKGQPTVEFIFSASEETIFVHVIISAKHIRALSNGDVERVLKHSSTNSSFRLPVIASPHGIRGSLTGCCPSDLVKQVYLSSGKFRTLNGYIGLPYHVSQGPGCQLRGQNCYVEITLGCPRSDSDKALQTNSQSTKNSSKNYIVESIAARRGDQKVSPDHLSAHEKAFIYPAEAVVVPVLQKSFARSSLKRFWLQNWIGPSLPGSSFFMHCGGDTDFLEGSWIESNGVRMQHGYNSSSNSNSSSISSISSGSSDSDYKMTTGELEADADSLSCRQSGLSSNDQMENDGLKLGSKRPRTGMTEPFGQAGMVKNVHMQDFGSVEVNDSAITGIANDQIGSRWDWDDDRGAGMDIQALLSEFGDFGDFFENDDLPFGEPPGTAESQALMFSGPDCGEVANSPIGVMDVVDQMLPPVAFPSFESFNPSPAVVIDESASKSQEDTHGTLALIPVNCTPSSSSGEFDHLIKAEALMTFAPEYGAVETPTSEFSSSIFRSPYCPKSRQVESSNSSSNNYAYGATPPSSPCFEGSNEKTGIQVNLKTGPGRNDTKKYYTLVEGGKVPLDRRTLTSNESRPTSEAMMPSPLLNSNSSNTVKSAQRKMSDGTLGAESFLVSVKTVLATEVECIMFQASMCRMRHTLLSPGNPTSVNLHRLSGSTGLNQVHGDASTMTDNISGRHEVKKKESIPVRIAGDMDGGVLDGHLSSPVGVWRSVGVPKLTKHTSSSNIEVSVSLPHHSFSEEGVLSYRQRQQPLQELLDGMALLVQQATSFVDVALDADCGDGPYGWLALQEHWRRGFSCGPSMIHAGCGGTLASCHFLDIAGVELVDPLSADIHSSAVTTLLQSEIKIALKSAFGNLEGPLCVTDWCKGHIQSGDGATTCDGSSGESTLSECKDSSTVTLSVGEPMSPALSSAAGSSSLKASSTPDGAKVDETSQRKSNQEIEPELLPRIKPTVFVLPLPAILVGYQDDWLKTSASSLQLWEKAPFEPYASPKPITYCVVCPDIDPLTSAAADFFQQLGTVYETCKLGTHSPQSLGNQMEMDAGKSLSSGFVLLDCPQSMKIESSNASLVGSISDYFLSLSNGWDLASYLKSLSKAVKALKIGPSLSTNPKEGNSSPCMVIYVVCPFPEPAAVLQTVIESSVSIGSIIPPANRERRSMLLAQVGKALSSLAAVDEASASNVLVLSGFSIPKLVLQIVTVDAIFRVTSPALNELIILKETAFTVYNKARRISKGSSNDVQPSTSSRSHLTQMSSVPAMWNSLPRETDIDSRLRSGTWDNSWQTARAGGLTCDPNRNGDFSLQDEIRYMFEPLFILSEPGSLDHAVAPTIIGNMVSESSKLQSDDTGGSFMQSASSAGSVDSGSSSQHDGSEPDGYGSSYQKTLPSLHCCYGWTEDWRWLVCIWTDARGELLDSHIFPFGGISSRQDTKGLQCLFVQVLQQGCQILQACSSPDTGGVKPRDFVITRIGNFFELEYIEWQKAIYSVGGSEVKKWPLQLRRSMPDGMAAGANGASLQQQEMGLIQERTLPSSPSPLYSPHSKASGYMKGGLGQTSSRKQLIGGHAAVDNSRGMLQWMLSISFVTISIDHSLHLLLQADTPSPGGSGSGVGTSIYLEGITPVKSLGSTSASYILIPSPSMRFLPSTPLQHPTCLTAESPPLAHLLHSKGSAIPLSTGFVVSKAVPSVRRDYKSNSREEWPSVLSVSLIDYYGGNNMTQDKMFRRIMKQGGRTLGVDGKDFEIRTQVILESVAAELQALSWMTVSPAYLERRTALPFHCDMVLRLRRLLHFADKELSSQPGRSQV
Length1958
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.
Aromaticity0.07
Grand average of hydropathy-0.238
Instability index52.82
Isoelectric point5.71
Molecular weight211399.69
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

>MDP17957
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     188.77|      52|      57|     956|    1012|       1
---------------------------------------------------------------------------
  934-  973 (66.82/31.52)	..............LDADCGDGPYGWLALQE...HWRRGFSC..GPSMIHAGCGGTLAS
  974- 1032 (77.78/50.95)	ChflDIAGVElvDPLSADIHSSAVTTLLQSEIKIALKSAFGNleGPLCVTDWCKGHIQS
 1039- 1072 (44.17/19.11)	C...DGSSGE..STLSECKDSSTVTLSVGEPMSPALSSA....................
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      98.39|      30|      57|    1282|    1313|       2
---------------------------------------------------------------------------
 1282- 1313 (48.68/33.81)	VVCPFPEPAAVLQTVIESSvsIGSIIPPANRE
 1342- 1371 (49.71/28.80)	VLSGFSIPKLVLQIVTVDA..IFRVTSPALNE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     148.02|      48|      54|     425|     478|       4
---------------------------------------------------------------------------
  425-  476 (63.77/53.49)	.....GELEADADSLscrqSGLsSNDQMENDGLKLGSKRPRTGMTEPFGqAGM.VKNV
  477-  518 (60.62/33.29)	HMqdfGSVEVNDSAI....TGI.ANDQ.......IGS...RWDWDDDRG.AGMdIQAL
  521-  542 (23.63/ 7.70)	EFgdfG...................DFFENDDLPFG.EPPGT................
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     160.19|      58|     212|     585|     689|       5
---------------------------------------------------------------------------
  585-  689 (67.25/100.19)	NPSPAVVIDESASKSQEDTHGTLALIPvnctpssssgefdhlikaealmtfapeygavetptsefsssifRSPyCPKSRQVESSNSSSNNYAygATPPsSPCFEG
  691-  748 (92.94/44.69)	NEKTGIQVNLKTGPGRNDTKKYYTLVE...........................................GGK.VPLDRRTLTSNESRPTSE..AMMP.SPLLNS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     202.11|      62|     212|    1435|    1499|       8
---------------------------------------------------------------------------
 1435- 1499 (100.81/69.85)	WDNSWQTARAGGLTcdPNRNGDfSLQDEIRYMFEPLFILSEPGSL..DHAVAPTII.GNMVSESSKLQ
 1650- 1714 (101.31/59.05)	WPLQLRRSMPDGMA..AGANGA.SLQQQEMGLIQERTLPSSPSPLysPHSKASGYMkGGLGQTSSRKQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     167.90|      52|      56|     808|     860|       9
---------------------------------------------------------------------------
  808-  860 (83.54/58.54)	VNLHRLSGSTGLNQvHGDASTMTDNISGRHEVKKKESI.PVRIAGDMDGGVLDG
  866-  918 (84.36/54.70)	VGVWRSVGVPKLTK.HTSSSNIEVSVSLPHHSFSEEGVlSYRQRQQPLQELLDG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     224.07|      71|     103|     237|     316|      10
---------------------------------------------------------------------------
  237-  316 (107.15/82.56)	LVKQVYLSSGKFRTLNGYIGlPyhvsQGPGCQLRgQNCYVEIT.LGCPRSDSDK.ALQ..TNSQSTKNSSKnyiVESIAARRGD
  343-  417 (116.92/65.07)	LQKSFARSSLKRFWLQNWIG.P....SLPGSSFF.MHCGGDTDfLEGSWIESNGvRMQhgYNSSSNSNSSS...ISSISSGSSD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     215.69|      66|     420|    1074|    1150|      14
---------------------------------------------------------------------------
 1074- 1150 (96.74/79.36)	GSSSLKASSTPDGakVDETSqrkSNQEIEPEllPRIKPTVFVLPLPAILV..GYQDDWlktsASSLQLWEKAPFEPYAS
 1504- 1571 (118.95/68.93)	GGSFMQSASSAGS..VDSGS...SSQHDGSE..PDGYGSSYQKTLPSLHCcyGWTEDW....RWLVCIWTDARGELLDS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      88.58|      25|     506|    1407|    1431|      15
---------------------------------------------------------------------------
 1407- 1431 (46.01/29.20)	LTQMSSVPAMW...NSLPRETDIDSRLR
 1912- 1939 (42.57/26.42)	LSWMTVSPAYLerrTALPFHCDMVLRLR
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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 MDP17957 with Med13 domain of Kingdom Viridiplantae
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