<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 MDP06164

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMSHVNLNSTNGASLEDCHTNVFVLTELNGLKWCRWCCSNSSIVYADIPDDAVLCGYGRCVTQGFLCVWRRAPPVHSSNRVDLRLAVEKELWIFWYGDEPDWALLCTGLTKIEEGSWEKGVEYETRTMLFKALHNQIDRVLLNANFLRFGNWYVNPLNYPKTKNKSNRPKYVIAFSLSFFVHGENNVCVTVSVQRHVPVYRLCRQLMLANRKLPVLLSPWSLSGELVFDPDKASEPGESQFQQQLWKDWCRFYASLDSGGAESTTGVGSGSPFKEANSSSTTTTTTTDKLPKMMDVFVCGVRLKVPTRFVCVVDPDNVASSPQQPGSLLAGFRQWLCEKTMENLMCHQRRQSGPTSPSAGESDSFGLAGSWNIVDPGQRERCCCSVGQSTSCCGTGAAGSVRFTSKCKSSDVSPKRIGCFHRRVAASRKLMTSAGLDGSSTAAGDDDDQQHQTMVEEAGTSTTSALLNSTTTAPATVTATAASTASAAAAAAPVASAVCSSASMTSSTMFLDHCSANVVGCNVAVEPKSKMRRSVEQSELLQQQQTPDPLVIPPKYTGLESIEVDQRLLSMKRRYNVSTNYDTDGELQLMKLSFSRYHSHHQEQIHLLHIQQQQQQQQQQQQQHQQQQNQSNSFISRVSSSSVKNFGKPTDQFTEKFYRALTSYSWCQAMETNRKRRFFVQNVLLLFSEAVLNCRSIAPVGQRHLAQSNARQVEKIYGYKNKNKRKDITTNDHDRTDDVLSGDMCKREEEKACVKSDAEFHLTDDSSAIVHHQMMEEGPSPSSGISDCENEIHAFLSPPPSLGTEEERLNATEKIVAVKMDATNQNNEHANSSSSSNNNNNNNNNNNNNSSTTTTTNSNNVAVLSCSQRSSASSAYPSSTQVVAVAGAVVDHLGIIYPTPPSQEALQQLSPESHAGTGTTAVAGTQTGACSSGSYGQGSTMKAASYLSGSRDCKDAPEVQVVIPYVLASEFFGAIPASSRRSAVRFEKILCYKPSRLLPALYHHHHHHHHHHHHHHHQSASVGHLASLPTYGLGAIPHHSWSNCGSFGSWFGSSSVRLGSQASIGLDSSSSATGRSIISAPASVRSVAEPSPVNNNPPSVSSPHFVRTPRTPGMELASPMSNASSAYAKNLSSIEPASSVLHPEGHSLVMMLLLSDTFVHLYRDSNFDSCPLCVCNMNIRGLEMGHYVNLRRCDDNMSVLYHSSARNTFTNKCTCGFSASRHRYLSYKSGVFYEDEDDATGAVWERLTASHLETVPFSREIVELVRHQSLLQDLTCSLMLFRTSPFGCLNAEASGAIGGGGGGGGGGGGGGGGGGSLSTSLLSVTSSSWSMFDDLEKNIPLGLPNAVYNAVELRDFTELCQLALEQSMLSLDCNNVALYVEQVPAAKRSATSSYINGWGYAKTVEPSNSLETMALLRSLLPLLQESLQKPRGLWQAKHSVEGPLTWRQLHRKCTHRPGSNGREDLSGPEPIPELLVCSDRDWIQVSPFSIRLWDRMCLEPFTQPKDVAFIAVVPDTQYVVRKARGFFRELSRTYEGMRLGRHCPITRVLKDGIMRVGKTHAKQLDQKPVDPWFDRFESASDGRNIIGAKLKLYAQVCRHYLAPHIFSPVWNAFDRSIFREIGRECPASTPTTTCTSSSLSNVDSVGTALSSQSAELANTTVSASGSGASCVSAGTTGMTTTTTTATAVTTSVADSSSSTAISYGLNNNNNNNNNTNNSSNNSMNMMNTSSSNNSNDSRMSESSANGNDNNGLLSPTSDGPNFPHVVVIYLVNPFNFGPDDQHVRDLNRLVTTGLFRCYLEILQEVPATFRSSMQLQIIPLQTVLDTSLLDDWELQQNGIVDEDRRLKSMPRAAVNSNSSNVGGGIGQQRVPLSSSTHLRSLALNVFMQIRSVAYSCLHSCLPKVMTGFGPAASRHELLRRKQNSAGFRLYSAPVVLAPIQDRTSCLNGTTGSNGSFGSSSSNSASSFCGGGSESRDDHGQVLFLAYCLSAKQQWLLCTVTDQQGAVLDSCVINMMLNNRHNVVKRELIWSALRRLWDYVVGILASSCRPWRIVIGRLGRLGHEELKAWAHLLSKSQLRSTSRLLREQCAVCQPMPTIFETPAILSACLISTELDPNMRIFPDSFVHDDRFGQGAKQCPLSSPEDVSSSHIMVFPTSALIQISQCCIMTGGLPGADETDGDFESIWKDLMISPEGDGLESGLNDIFGSMSEANLMNDSTVGFDANSSHTRGLAISESSDESIQLQPLALGFLVSTAPTGPVPEWFWTVRPSARDLLPVHLRSALHIHTSGVQQSDDHLLAGGANRSTSGTVHPLDSSLTTDVLRYVLETYNALSWLCLDFRTGDRVSCFPLHIQALSRLYRAMDALL
Length2365
PositionMiddle
OrganismTrichinella patagoniensis
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Enoplea> Dorylaimia> Trichinellida> Trichinellidae> Trichinella.
Aromaticity0.07
Grand average of hydropathy-0.325
Instability index51.84
Isoelectric point6.64
Molecular weight258173.79
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. 


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

>MDP06164
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|      91.39|      19|      19|     823|     841|       1
---------------------------------------------------------------------------
  823-  837 (20.17/ 6.64)	..........NQ.NNEHAN...S....SSSSNN
  838-  855 (25.29/10.40)	NNNN........nNNNNNN...S....STTTTT
 1708- 1731 (25.13/10.27)	NNNN.....nNT.NNSSNN...SmnmmNTSSSN
 1732- 1759 (20.80/ 7.10)	NSNDsrmsesSA.NGNDNNgllS....PTSDGP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     131.87|      41|     543|     353|     428|       2
---------------------------------------------------------------------------
  311-  351 (77.02/63.77)	VVDPD.......NVASSPQQPGSLLAGFRQWL..CEK...TMENLMCHQRR..QS
  372-  426 (54.85/53.63)	IVDPGqrercccSVGQSTSCCGTGAAGSVRFTskCKSsdvSPKRIGCFHRRvaAS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     515.49|     165|     543|    1310|    1694|       3
---------------------------------------------------------------------------
 1312- 1489 (264.28/201.52)	GGGS...............LSTS....LLSVTSSSWSMFDDLEKNIPLglpNAVYNAVElrdfTELCQLALEQ......SMLSLDCNNVALYVEQVpaaKRSAtSSYINGWgyAKTVEPSNSLETMALLRSLLPLLQES...LQKPRGLWQAKHSVEGPLTWRQLHRKCTH..RPGSNGRE.DLSGPEPI..PELLVCSDRDWIQVSPFSI
 1968- 2165 (251.21/73.45)	GGGSesrddhgqvlflaycLSAKqqwlLCTVTDQQGAVLDSCVINMML...NNRHNVVK....RELIWSALRRlwdyvvGILASSCRPWRIVIGRL...GRLG.HEELKAW..AHLLSKSQLRSTSRLLREQCAVCQPMptiFETPAILSACLISTELDPNMRIFPDSFVHddRFGQGAKQcPLSSPEDVssSHIMVFPTSALIQISQCCI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      72.05|      20|      20|    1077|    1096|       4
---------------------------------------------------------------------------
 1077- 1096 (35.77/18.04)	ISAPASVRSVAEPSPVNNNP
 1099- 1118 (36.28/18.40)	VSSPHFVRTPRTPGMELASP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      60.45|      17|     541|    1284|    1301|       5
---------------------------------------------------------------------------
 1284- 1301 (29.28/20.79)	PFGCLNAEASGaIGGGGG
 1849- 1865 (31.17/17.45)	PRAAVNSNSSN.VGGGIG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      98.59|      30|      44|    1621|    1650|       7
---------------------------------------------------------------------------
 1621- 1650 (52.31/24.95)	GREC..PASTPTTTCTSSSLSNVDSVGTALSS
 1666- 1697 (46.28/21.26)	GASCvsAGTTGMTTTTTTATAVTTSVADSSSS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      45.57|      14|      18|     766|     783|       9
---------------------------------------------------------------------------
  766-  783 (18.25/21.35)	SAIvhHQMMeeGPSPSSG
  789-  802 (27.33/14.80)	NEI..HAFL..SPPPSLG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      56.62|      15|      19|    1015|    1031|      10
---------------------------------------------------------------------------
 1015- 1031 (22.90/14.97)	HHQSASVGHLASLptYG
 1037- 1051 (33.72/16.17)	HHSWSNCGSFGSW..FG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      84.18|      25|     248|     869|     893|      11
---------------------------------------------------------------------------
  869-  893 (41.60/28.19)	SSASSAYPSSTQVVAVAGAVVDHLG
 1120- 1144 (42.58/29.07)	SNASSAYAKNLSSIEPASSVLHPEG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      69.61|      21|      50|      46|      70|      13
---------------------------------------------------------------------------
   46-   70 (32.31/33.45)	DIPDDAVLC.GYGRcVTQGflcVWRR
   97-  118 (37.30/21.57)	DEPDWALLCtGLTK.IEEG...SWEK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     129.12|      39|     539|    1782|    1820|      14
---------------------------------------------------------------------------
 1782- 1820 (66.53/40.25)	VRDLNRLVTTGLFRCYLEILQEVP...ATFRSSMQLQIIPLQ
 2309- 2350 (62.58/37.42)	VHPLDSSLTTDVLRYVLETYNALSwlcLDFRTGDRVSCFPLH
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     146.81|      49|     902|     634|     698|      16
---------------------------------------------------------------------------
  634-  698 (70.56/79.13)	ISRVSSSSVKNFGK.........PTDQFTEKFyraltsyswcqamETNRKRRFFVQNVLLLFSEAvlnCRS.IAP
 1544- 1602 (76.24/48.43)	ITRVLKDGIMRVGKthakqldqkPVDPWFDRF.............ESASDGRNIIGAKLKLYAQV...CRHyLAP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      47.82|      10|     215|      32|      41|      17
---------------------------------------------------------------------------
   32-   41 (25.82/11.79)	WCRWCCSNSS
  248-  257 (22.01/ 9.04)	WCRFYASLDS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      43.75|      13|     403|     596|     608|      21
---------------------------------------------------------------------------
  580-  592 (19.97/11.70)	YDTDGELQLMKLS
  596-  608 (23.78/15.45)	YHSHHQEQIHLLH
---------------------------------------------------------------------------




































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 MDP06164 with Med13 domain of Kingdom Metazoa
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