<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 MDP29162

Description Mediator of RNA polymerase II transcription subunit 13
SequenceETMNPCFVPNGASLEDCHSNLFCLADLTGIKWRRFVWQGPTSSPILFPVTEEDPILCSFSRCMAADVLSVWRRHHTQGRRELWLFWWGDDPSFAELIHNELSSEEDGEWESGLSYECRTLLFKAIHNLLERCLMNRGFVRIGKWFVKPYQKEEKIINKSEHLSCAFTFFVHGDSNVCTSVEIAQHQPLQRLSEEHLSLAQQSSSPLQVILSPYGLNGTLTGQAFKMSDHPTQKLIEEWRQFYPISPNPKEVQEDKMEDSDWEDDSLAAVEVLVAGVRMVYPSCLVLLPLTDVPAVVPQGSANTSGSMCGPQQGPHRDPAISSVTLTPPTSPEEAQLAQRWLKLSSASDGYSSHNTLHGGKIPCRMAGQMVETVWQEYNLNRTGHKRKFPTLPNGTCEEEPDKTGIWDFVESTHGPHCNCSRHKNQKQRSSSTSGHPPSSGQPSQPIPKHKLGEKPEKSEKQQKRPQTPFHHRSSVSEEQPLEPQTQRLCLRPQEEGSYPSLHHVDAVPSKAPTLHTHGPPADLAGSPPPPPLSPHPCDHTDNEGTPGGMKNSSTPIHQTFYPPSVEPCILPQKGSPEEPQHGNAPLPLPFPPSYSETLEPTLFVGSAVNPNEDTTHNPWKYFNLPRKKASNFPTPQLPVNKMRDDSGGGAESPPSITEVMSGSTHRLKVSQERVKTYAQRRNSHLVTIAGDAEQSDAADPYAFVEGDEEFTFAEKKDKPGTEKDGSKKHKGDEGSGTSADGENSCPVLSFSAYTVDGQGPAGNKPSASTSLIHVNDLAVSYSDLDKIFNSDEDELAFAQPGCKRAGGGSDDKFACKEAKAAALDPHSCISSADLHQMFPTPPSLDQPGYSPMNSGTKDGLEAGAGLTLLDGSLLNNHFKMEVEEGFCSPKPSDVKDFSFVYKPETSQLFVGCSMYAPLKTLPSQCLLPIKLPEECVYTPSWSLGKMELIPPVTNVSLLAKDNSNIPSVEPDYSQTYTPQTHTPFMSSSAPPSNSGTGILPSPATPRFSVPTPRTPRTPRTPRGPSSVQGSLKYDNSDLYSPASTPSTCRPLSSVEPATVPSIPEAHSLYVTLILSESVMNLFKDCNFDSCCVCVCNMNIRGADVGVYLKDNGEAQYPCTCGFSAVANRRFGQSAGLFLEDELDVVGRGSDSGRDTERCFEELRASSVQKAGSLVEKPPDNLILLLQDQCTNPFAPMAGVEHSKTNASPTSFLRVEERDCYNDCYMALEHGRQFMDNMSGGKVDETLVKSTCLHRWPKCKSADMSKLFSQDVLRVLLSLQPVLQDTIQKKRSVRSWGVQGPLTWQQFHKMAGRGSYGGTDESPEPLPIPTFLVGYEFDFLVLSPFVLPYWEKLLLEPFGSQRDVGYVVICPENEALLSRAKTFFKDLSTTYEKQACQLGQHRPICRSHPEGILKFGATEGRSITEQPLSDWFLKMAARDRYNEAFNKLKLFAQVCRYDLAPYLSEQSLDSSLLSQRSPALASSSSPSQTSSSSSITSGPQSTTACGQPAQISSTPPSSSSVSQAIGGMASSKPSSYSPFGNAGLQSGSSQNGPQATPQGAAGPAENGATNQPQGSAEVPESCPLNSTVERDKVGKPTDGESHAVSYPPAIMVYIVDPFSYEAADREAHSSTYTLGLLCCYMEMLKLLPARIRNAVSVQIVPCQYLLQPVHSGERHVYSQHLKSLAFSVYTQCRRPLPNSTNFKALTGFGPGLAIDTALKNPERPECLRLYTPPFILAPVKDKQTELGETFGEASQKYNVLFVGYCLSHDQRWLLASCTDQHGELLETCIISIDVPSSRARRKNGNVRRVGLQKLWDWCLGLVQVTSLPWRVVIGRLGRMGHGELRDWSILLSRRNLQSLSKRLKETCRMCGISAADTPSILSACLVAMEPQGSFVIMPDSVSTGSVFGRSTTLNMQTSQLSTPQDTSCTHILVFPTSAMVQVNTNTSEPIDINFNPINPDGSDGMGIFDLFDNDMVDPDLINILPNSPTTSPVHSPGSHYHHGGDGSKGQSADRMESHEEALNILQQPMALGYFVSTAKTGPLPDWFWSACPQAQNQCPVFLKASLHLHVSSVQSDELLHSKHSHPLDSNHTSDVLRFVLEQYNALSWLTCDPATQDRRSCLPVYFVVLTQMYNFIRNTL
Length2139
PositionMiddle
OrganismTetraodon nigroviridis (Spotted green pufferfish) (Chelonodon nigroviridis)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Actinopterygii> Neopterygii> Teleostei> Neoteleostei> Acanthomorphata> Eupercaria> Tetraodontiformes> Tetradontoidea> Tetraodontidae> Tetraodon.
Aromaticity0.08
Grand average of hydropathy-0.458
Instability index58.07
Isoelectric point5.79
Molecular weight234723.41
Publications
PubMed=15496914

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. 
ECO:0000256	RuleBase:RU364134
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

>MDP29162
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     181.72|      35|      36|     966|    1001|       1
---------------------------------------------------------------------------
  563-  587 (47.46/15.65)	PSVE.P....CILPQK.GS....P.....EEPQH.GNAPLP
  966- 1000 (70.33/31.44)	PSVE.PDYSQTYTPQT.HT....PFMSSSAPPSNSGTGILP
 1004- 1029 (28.46/ 7.46)	...T.PRFS.VPTPRTpRT....P.RTPRGPSSVQG.....
 1485- 1518 (35.48/11.29)	PSQTsSSSSITSGPQS.TTacgqPAQISSTPPSSS......
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     114.30|      32|      36|      32|      66|       2
---------------------------------------------------------------------------
    2-   37 (35.57/17.19)	...TMNPCFVPngASLED...ChSNLFCLA.DltgikWRRFVW
   38-   76 (52.62/39.56)	QGPTSSPILFP..VTEEDPilC.SFSRCMAaD.vlsvWRRHHT
   77-   93 (26.11/10.05)	QGR.RELWLF...WWGDDP....SF..................
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     110.32|      33|      36|     423|     455|       3
---------------------------------------------------------------------------
  423-  455 (61.60/26.94)	KNQK.QRSSSTSGHPPSSGQPSQPI.PK.HKLGEKP
  457-  492 (48.73/19.76)	KSEKqQKRPQTPFHHRSSVSEEQPLePQtQRLCLRP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      93.99|      27|      31|    1799|    1829|       4
---------------------------------------------------------------------------
 1803- 1829 (51.63/35.58)	GNVRRVGLQKLWDWCLGLVQ..VTSLPWR
 1833- 1861 (42.36/19.46)	GRLGRMGHGELRDWSILLSRrnLQSLSKR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     110.49|      33|      33|    1539|    1571|       5
---------------------------------------------------------------------------
 1539- 1571 (57.34/30.49)	GNAGLQSGSSQNGPQATPQ.GAAGPAENGATNQP
 1573- 1606 (53.14/27.64)	GSAEVPESCPLNSTVERDKvGKPTDGESHAVSYP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      82.30|      23|      36|    1725|    1748|       6
---------------------------------------------------------------------------
 1725- 1748 (38.23/24.93)	CLRlYTPPFILAPVKDKQTELGET
 1764- 1786 (44.06/24.86)	CLS.HDQRWLLASCTDQHGELLET
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      68.41|      13|      36|     846|     858|       7
---------------------------------------------------------------------------
  799-  811 (23.77/12.46)	QPGC.KRAGGGSDD
  846-  858 (26.35/14.86)	QPGY.SPMNSGTKD
  883-  896 (18.29/ 7.38)	EEGFcSPKPSDVKD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      39.98|      10|      32|     496|     505|       8
---------------------------------------------------------------------------
  496-  505 (21.43/ 8.94)	GSYP....SLHHVD
  525-  538 (18.55/ 6.58)	GSPPppplSPHPCD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      82.75|      24|      32|     724|     751|       9
---------------------------------------------------------------------------
  724-  747 (44.94/20.04)	DGSKKHKGDEGSGTSADGENSCPV
  756-  779 (37.81/20.28)	DGQGPAGNKPSASTSLIHVNDLAV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      92.10|      27|      42|     181|     208|      13
---------------------------------------------------------------------------
  181-  208 (41.00/23.36)	EIAQHqPLQRLSEEHLSLAQQSSSPLQV
  225-  251 (51.10/25.84)	KMSDH.PTQKLIEEWRQFYPISPNPKEV
---------------------------------------------------------------------------




































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 MDP29162 with Med13 domain of Kingdom Metazoa


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) EEFTFAEKKDKPGTEKDGSKKHKGDEGSGTSADGE
2) INILPNSPTTSPVHSPGSHYHHGGDGSKGQSADRMESHEEA
3) LSQRSPALASSSSPSQTSSSSSITSGPQSTTACGQPAQISSTPPSSSSVSQAIGGMASSKPSSYSPFGNAGLQSGSSQNGPQATPQGAAGPAENGATNQPQGSAEVPESCPLNSTVERDKVGKPTDGES
4) PSVEPDYSQTYTPQTHTPFMSSSAPPSNSGTGILPSPATPRFSVPTPRTPRTPRTPRGPSSVQGSLKYDNS
5) QGSANTSGSMCGPQQGPHRDPAISSVTLTPPTSPEEAQLAQRWLKL
6) WQEYNLNRTGHKRKFPTLPNGTCEEEPDKTGIWDFVESTHGPHCNCSRHKNQKQRSSSTSGHPPSSGQPSQPIPKHKLGEKPEKSEKQQKRPQTPFHHRSSVSEEQPLEPQTQRLCLRPQEEGSYPSLHHVDAVPSKAPTLHTHGPPADLAGSPPPPPLSPHPCDHTDNEGTPGGMKNSSTPIHQTFYPPSVEPCILPQKGSPEEPQHGNAPLPLPFPPSYSETLEPTLFVGSAVNPNEDTTHNPWKYFNLPRKKASNFPTPQLPVNKMRDDSGGGAESPPSITEVMSGSTHRLKVSQERVKTYAQRRNSHLVTIAGDA
708
1980
1472
966
298
374
742
2020
1600
1036
343
692










Molecular Recognition Features






MoRF SequenceStartStop




1) HNPWKYFNLPRKKAS
616
630