<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 MDP06340

Description Mediator of RNA polymerase II transcription subunit 13 (Fragment)
SequenceLLCEMSHVNLNSTNGASLEDCHTNVFVLTELNGLKWCRWCCSNSSIVYADIPDDAVLCGYGRCVTQGFLCVWRRAPPVHSSNRVDLRLAVEKELWIFWYGDEPDWALLCTGLTKIEEGSWEKGVEYETRTMLFKALHNQIDRVLLNANFLRFGNWYVNPLNYPKTKNKSNRPKYVIAFSLSFFVHGENNVCVTVSVQRHVPVYRLCRQLMLANRKLPVLLSPWSLSGELVFDPDKASEPGESQFQQQLWKDWCRFYASLDSGGAESTTGVGSGSPFKEANSSSTTTTTTTDKLPKMMDVFVCGVRLKVPTRFVCVVDPDNVASSPQQPGSLLAGFRQWLCEKTMENLICHQRRQSGPTSPSAGESDSFGLAGSWNIVDPGQRERCCCSVGQSTSCCGTGAAGSVRFTSKCKSSDVSPKRVGCFHRRVAASRKLMTSAGLDGSSTAAGDDDDQQHQTMVEEAGTSTTSALLNSTTTATATVTATAASTASAAAAAAAPVASAVCSSASMTLSTMFLDHCSANVVGCNVAVEPKSKMRRSVEQSELLQQQQTPDPLVIPPKYTGLESIEVDQRLLSMKRRYNVSTNYDTDGDLQLMKLSFSRYHSHHQEQIHLLHIQQKQQQQQQQQQQQQNQSNSFISRVSSSSVKNFGKPTDQFTEKFYRALTSYSWCQAMETNRKRRFFVQNVLLLFSEAVLNCRSIAPVGQRHLAQSNARQVEKIYGYKNKNKRKDITTNDHDRTDDVLSGDMCKREEEKACVKSDAEFHLTDDSSAIVHHQMMEEGPSPSSGISDCENEIHAFLSPPPSLGTEEERSNATEKIVTVKMDATNQNNEHANSSSSSNNNNNNNNNSSTTTTTNSNNVAVLSCSQRSSASSAYPSSTQVVAVAGAVVDHLGIIYPTPPSQEALQQLSPESHAGTGTTAVAGTQTGASSSGSYGQGSTMKAASYLSGYRDCKDAPEVQVVIPYVLASEFFGAVPASSRRSAARFEKILCYKPSRLLPALYHHHHHHHHHHHHHHHHHHQSASVGHLASLPTYGLGAISHHSWSNCGSFGSWFGSSSVRLGSQASIGLDSSSSATGRSIISAPASVRSVAEPSPVNNNPPSVSSPHFVRTPRTPGMELASPMSNASSAYAKNLSSIEPASSVLHPEGHSLVMMLLLSDTFVHLYRDSNFDSCPLCVCNMNIRGLEMGHYVNLRRCDDNMSVLYHSSARNTFTNKCTCGFSASRHRYLSYKSGVFYEDEDDATGAVWERLTASHLETVPFSREIVELVRHQSLLQDLTCSLMLFRTSPFGCLNAEASGAIGGGGGGGGGGSLSASLLSVTSSSWSMFDDVEKNIPLGLPNAVYNAVELRDFTELCQLALEQSMLSLDCNNVALYVEQVPAAKRSATSSYINGWGYAKTVEPSNSLETMALLRSLLPLLQESLQKPRGLWQAKHSVEGPLTWRQLHRKCTHRPGSNGREDLSGPEPIPELLVCSDRDWIQVSPFSIRLWDRMCLEPFTQPKDVAFIAVVPDTQYVVRKARGFFRELSRTYEGMRLGRHCPITRVLKDGIMRVGKTHAKQLDQKPVDPWFDRFESASDGRNIIGAKLKLYAQVCRHYLAPHIFSPVWNAFDRSIFREIGRECPASTPTATCTSSSLSNVDSVGTAVSSQSAELANTTVSASGSGASCVSAGTTGMTTTTTTATAVTTSVADSSSSTAISYGLNNNNNNNNTNNSSNNSMNMMNTSSSNNSNDSRMSESSANGNDNNGLLSPTSDGPNFPHVVVIYLVNPFNFGPDDQHVRDLNRLVTTGLFRCYLEILQEVPATFRSSMQLQIIPLQTVLDTSLLDDWELQHNGIVDEDRRLKSMPRAAVNSNSSSVGGGIGQQRVPLSSSTHLRSLALNVFMQIRSVAYSCLHSCLPKVMTGFGPAASRHELLRRKQNSAGFRLYSAPVVLAPIQDRTSCLNGTTGSNGSFGSSSSNSASSFCGGGSESRDDHGQVLFLSYCLSAKQQWLLCTVTDQQGAVLDSCVINMMLNNRHNVVKRELIWSALRRLWDYVVGILASSCRPWRIVIGRLGRLGHEELKAWAHLLSKSQLRSTSRLLREQCAVCQPMPTIFETPAILSACLISTELDPNMRIFPDSFVHDDRFGQGAKQCPLSSPEDVSSSHIMVFPTSALIQISQCCIMTGGLPGADETDGDFESIWKDLMISPEGDGLESGLNDIFGSMSEANLMNDSTVGFDANSSHTRGLAISESSDESIQLQPLALGFLVSTAPTGPVPEWFWTVRPSARDLLPVHLRSALHIHTSGVQQSDDHLLAGGANRSTSGTVHPLDSSLTTDVLRYVLETYNALSWLCLDFRTGDRVSCFPLHIQALSRLYRAMDALL
Length2357
PositionMiddle
OrganismTrichinella nativa
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Enoplea> Dorylaimia> Trichinellida> Trichinellidae> Trichinella.
Aromaticity0.07
Grand average of hydropathy-0.313
Instability index51.23
Isoelectric point6.67
Molecular weight257600.30
Publications









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

>MDP06340
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      52.26|      18|     241|      51|     109|       1
---------------------------------------------------------------------------
   59-   80 (23.38/24.00)	GYGRcVTQGflcVWRRAPPVHS
  111-  128 (28.88/53.75)	GLTK.IEEG...SWEKGVEYET
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     146.06|      44|     240|    1677|    1727|       2
---------------------------------------------------------------------------
  823-  869 (72.70/41.86)	ATNQNNEHANSSSSS.......NNNNNNNNNSStttTTNSNNVAVLSCSQRSSA
 1677- 1727 (73.35/55.98)	ATAVTTSVADSSSSTaisyglnNNNNNNNTNNS...SNNSMNMMNTSSSNNSND
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      33.64|       9|      18|     773|     783|       4
---------------------------------------------------------------------------
  773-  783 (14.88/11.36)	HQMMeeGPSPS
  794-  802 (18.76/ 7.88)	HAFL..SPPPS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     162.26|      45|     242|     979|    1071|       7
---------------------------------------------------------------------------
  601-  645 (79.85/23.76)	YHSHHQEQIHLLHIQQKQQQQQQ..Q............QQQQQNQSNSFISRVSSSSVK
  999- 1057 (82.41/90.18)	YHHHHHHHHHHHHHHHHHHQSASvgHlaslptyglgaiSHHSWSNCGSFGSWFGSSSVR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     164.01|      51|     541|     504|     564|       9
---------------------------------------------------------------------------
  176-  227 (86.40/52.51)	IAFSLSFFVHGENNV..CvTVSVQRHVPVYRLCRQ.LMLANRKLP.VLLSPWSLSG
  508-  562 (77.60/64.87)	MTLSTMFLDHCSANVvgC.NVAVEPKSKMRRSVEQsELLQQQQTPdPLVIPPKYTG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      84.47|      26|     541|     944|     969|      10
---------------------------------------------------------------------------
  944-  969 (47.58/30.24)	LSGYRDCKDAPEVQVV..IPYVL..ASEFF
 1490- 1519 (36.89/21.83)	LEPFTQPKDVAFIAVVpdTQYVVrkARGFF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      47.95|      11|      54|      48|      58|      11
---------------------------------------------------------------------------
   48-   58 (22.85/12.18)	YADIPDDAVLC
   99-  109 (25.11/14.09)	YGDEPDWALLC
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     102.99|      25|      54|    1066|    1090|      12
---------------------------------------------------------------------------
 1066- 1090 (41.05/22.73)	LDSSSSATGRSIIS.APASVRSVAEP
 1094- 1112 (28.13/12.93)	.....NNNPPS.VS.SPHFVRTPRTP
 1120- 1143 (33.81/17.24)	MSNASSAYAKNLSSiEPAS..SVLHP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      63.95|      17|     104|    1839|    1855|      13
---------------------------------------------------------------------------
 1839- 1855 (31.39/16.10)	SMPRAAVNSNSSSVGGG
 1946- 1962 (32.56/17.02)	SFGSSSSNSASSFCGGG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      55.69|      14|      16|    1743|    1756|      16
---------------------------------------------------------------------------
 1743- 1756 (27.55/13.81)	LLSPTSDGPNFPHV
 1761- 1774 (28.15/14.28)	LVNPFNFGPDDQHV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     101.07|      31|     915|     667|     700|      17
---------------------------------------------------------------------------
  667-  700 (50.50/46.65)	WCQAMETNRKRRFFVQNVLLLFSEAvlnCRS.IAP
 1564- 1595 (50.57/37.43)	WFDRFESASDGRNIIGAKLKLYAQV...CRHyLAP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     100.07|      29|     681|    1198|    1228|      20
---------------------------------------------------------------------------
 1198- 1228 (50.49/38.65)	SVLYhsSARNTFTNKCTCGF..SASRHRYLSYK
 1882- 1912 (49.58/30.83)	SVAY..SCLHSCLPKVMTGFgpAASRHELLRRK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     167.10|      51|      84|     230|     283|      21
---------------------------------------------------------------------------
  230-  283 (82.21/60.74)	VFDPDK.ASEPGESQFQQQLWKDW.CRfyASLDSGGAESTTGVGSGSPfKEANSSS
  315-  367 (84.88/51.01)	VVDPDNvASSPQQPGSLLAGFRQWlCE..KTMENLICHQRRQSGPTSP.SAGESDS
---------------------------------------------------------------------------




































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 MDP06340 with Med13 domain of Kingdom Metazoa


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) DDSSAIVHHQMMEEGPSPSSGISDCENEIHAFLSPPPSLGTEEERSNATEKIVTVKMDATNQNNEHANSSSSSNNNNNNNNNSSTTTTTNSNNVAVL
2) GLDGSSTAAGDDDDQQHQTMVEEAGTSTTSALL
3) PPSQEALQQLSPESHAGTGTTAVAGTQTGASSSGSY
4) SVRSVAEPSPVNNNPPSVSSPHFVRTPRTPGMELASP
5) TAISYGLNNNNNNNNTNNSSNNSMNMMNTSSSNNSNDSRMSESSANGNDNNGLLSPTS
6) VEPKSKMRRSVEQSELLQQQQTPDPLVIPPKY
765
438
897
1083
1691
529
861
470
932
1119
1748
560










Molecular Recognition Features






MoRF SequenceStartStop




NANANA