<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 MDP05935

Description Mediator of RNA polymerase II transcription subunit 13 (Fragment)
SequenceLLCEMSHVNLNSTNGASLEDCHTNVFVLTELNGLKWCRWCCSNSSIVYADIPDDAVLCGYGRCVTQGFLCVWRRAPPVHSSNRVDLRLAVEKELWIFWYGDEPDWALLCTGLTKIEEGSWEKGVEYETRTMLFKALHNQIDRVLLNANFLRFGNWYVNPLNYPKTKNKSNRPKYVIAFSLSFFVHGENNVCVTVSVQRHVPVYRLCRQLMLANRKLPVLLSPWSLSGELVFDPDKASEPGESQFQQQLWKDWCRFYASLDSGGAESTTGVGSGSPFKEANSSSTSSSTTTDKLPKMMDVFVCGVRLKVPTRFVCVVDPDNVATSPQQPGSLLAGFRQWLCEKTMENLMCHQRRQSGPTSPSAGESDSFGLAGSWNIVDPGQRERCCCSVGQSTSCCGTGAAGSVRFTSKCKSSDVSPKRVGCFHRRVAASRKLMTSAGLDGSSTAAGDDDDQQHQTMVEEAGTSTTSALLNSTTTATATVTATTASTASAAAAAAPVASAVCSSASMTSSAMFLDHCSADEVGCNAAVEPKSKMRRSVEPSELLQQQQTPDPLVIPPKYTGLESIEVDQRLLSMKRRYNVNANYDTDGEFQLMKLSFSRYHSHHQEQIPLLHIQQQQQQQQQQQQQQQQQNQSNSFISRVSSSSVKNFGKPTDQFTEKFYRALTSYSWCHAMETNRKRRFFVQNVLLLFSEAVLNCRSIAPVGQRHLAQSNARQVEKIYGYKNKNKRKDNTTNDHDRTDDVLSGDMCKREEEKACVKSDAEFQLTDDSSAIVHHQMMEEGPSPSSGISDCENEIHAFLSPPPSLGTEEERLNATEKIVAVKMDATNQNNEHANSSSSSSNNNNNNNNNNKNNSSTTTSNSNNVAVLSCSQRSSASSAYPSSSTQVVAVAGAVVDHLGIIYPTPPSQEALQQLSPESHAGTGTTAVAGTQTGACSSGSYGQGSTMKAATYLSGCSDCKDAPEVQVVIPYVLASEFFGAVPASSRRSAVRFEKILCYKPSRLLPALYHHHHHHHHHHHHHHQSASVGHLASLPTYGLGAIPHHSWSNCGSFGSWFGSSSVRLGSQASIGLDSSSSATGRSIISAPASVRSVAEPSPVNNNPPSVSSPHFVRTPRTPGMELASPMSNASSAYAKNLSSIEPASSVLHPEGHSLVMMLLLSDTFVHLYRDSNFDSCPLCVCNMNIRGLEMGHYVNLRRCDDNMSVLYHSSARNTFTNKCTCGFSASRHRYLSYKSGVFYEDEDDATGAVWERLTASHLETVPFSREIVELVRHQSLLQDLTCSLMLFRTSPFGCLNAEASGAIGGGGGGGGGGGSMSTSLLSVTSSSWSMFDDVEKIIPLGLPNAVYNAVELRDFTELCQLALEQSMLSLDCNNVALYVEQVPAAKRSATSSYINGWGYAKTVEPSNSLETMALLRSLLPLLQESLQKPRGLWQAKHSVEGPLTWRQLHRKCTHRPGSNGREDLSGPEPIPELLVCSDRDWIQVSPFSIRLWDRMCLEPFTQPKDVAFIAVVPDTQYVVRKARGFFRELSRTYEGMRLGRHCPITRVLKDGIMRVGKTHAKQLDQKPVDPWFDRFESASDGRSIIGAKLKLYAQVCRHYLAPHIFSPVWNAFDRSIFREIGRECPASTPTTTCTSSSLSNVDSVGTAVSSQSAELANTTISASGSGASCVSAGTTGMTTTTTTATAVTTSVADSSSSTAISYGLNNNNNNTNNSSNNSINMMNTSSSNNSNDSRMSESSANGNDNNGLLSPTSDGPNFPHVVVIYLVNPFNFGPDDQHVRDLNRLVTTGLFRCYLEILQEVPATFRSSMQLQIIPLQTVLDTSLLDDWELQQNGIVDEDRRLKSMPRAAMNSNSSNVGGGIGQQRVPLSSSTHLRSLALNVFMQIRSVAYSCLHSCLPKVMTGFGPAASRHELLRRKQNSAGFRLYSAPVVLAPIQDRTSCLNGTTGSNGSFGSSSSNSASSFCGGGSESRDDHGQVLFLAYCLSAKQQWLLCTVTDQQGAVLDSCVINMMLNNRHNVVKRELIWSALRRLWDYVVGILASSCRPWRIVIGRLGRLGHEELKAWAHLLSKSQLRSTSRLLREQCAVCQPMPTIFETPAILSACLISTELDPNMRIFPDSFVHDDRFGQGAKQCPLSSPEDVSSSHIMVFPTSALIQISQCCIMTGGLPGADETDGDFESIWKDLMISPEGDGLESGLNDIFGSMSEANLMNDSTVGFDANSSHTRGLAISESSDESIQLQPLALGFLVSTAPTGPVPEWFWTVRPSARDLLPVHLRSALHIHTSGVQQSDDHLLAGGANRSTSGTVHPLDSSLTTDVLRYVLETYNALSWLCLDFRTGDRVSCFPLHIQALSRLYRAMDALL
Length2358
PositionMiddle
OrganismTrichinella nelsoni
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Enoplea> Dorylaimia> Trichinellida> Trichinellidae> Trichinella.
Aromaticity0.07
Grand average of hydropathy-0.315
Instability index51.67
Isoelectric point6.53
Molecular weight257552.28
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

>MDP05935
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     422.52|     103|     192|    1853|    1962|       1
---------------------------------------------------------------------------
 1853- 1955 (179.10/127.21)	VG..GGIGQQRVPLSSSTHLRSLALNVF.....MQIRSVAY....SC.........LHSCLPKVMTGF.GPAASRHELLRRKQN.SA.....GFRLYSAPV.VLAPIQD.RTSCLNGTTGS.......NGSFGSSSSNS
 1964- 2039 (68.34/36.95)	.......SESR.....DDHGQVLFLAYC.....LSAKQQWL....LCtvtdqqgavLDSCVINMMLN......NRHNVVKRELIwSA.....LRRLWDYVVgILA......SSC.........................
 2046- 2117 (74.17/41.08)	IGrlGRLGHEE..LKAWAHLLSKS..........QLRSTSRllreQC..........AVCQP.MPTIFeTPAILSACLISTELD..P.....NMRIFPDSF.V....................................
 2123- 2217 (100.91/57.20)	.....GQGAKQCPLSSPEDVSSSHIMVFptsalIQIS........QC............C...IMTGG.LPGA..............detdgDFESIWKDL.MISPEGDgLESGLNDIFGSmseanlmNDSTVGFDANS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             5|     141.11|      17|     192|     631|     647|       2
---------------------------------------------------------------------------
  631-  647 (23.51/ 8.62)	NQSNSFISR..VSSSSVKN
  826-  842 (32.84/15.04)	NQNNEHANS..SSSSSNNN
  845-  861 (31.67/14.23)	NNNNNKNNS..STTTSNSN
 1702- 1718 (30.05/13.12)	NNNNNTNNS..SNNSINMM
 1721- 1739 (23.03/ 8.29)	SSSNNSNDSrmSESSANGN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     104.67|      34|      42|    1617|    1652|       3
---------------------------------------------------------------------------
 1617- 1652 (48.84/37.50)	GRECpASTPTTTCTSSSlSNVDSVGTAVSSQSAELA
 1662- 1695 (55.84/33.06)	GASC.VSAGTTGMTTTT.TTATAVTTSVADSSSSTA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     103.43|      31|     922|     668|     701|       4
---------------------------------------------------------------------------
  668-  701 (52.10/41.12)	WCHAMETNRKRRFFVQNVLLLFSEAvlnCRS.IAP
 1567- 1598 (51.33/32.51)	WFDRFESASDGRSIIGAKLKLYAQV...CRHyLAP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      44.92|      14|      45|    1485|    1501|       5
---------------------------------------------------------------------------
 1485- 1501 (20.38/25.33)	IRLwDRMClePFTQP.KD
 1532- 1546 (24.54/14.19)	MRL.GRHC..PITRVlKD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     156.55|      47|     192|     869|     954|       7
---------------------------------------------------------------------------
  503-  551 (76.67/28.15)	SSASMTSSAMflDHCSADEVGCNAAVEPKSKMRRSVEPSELLQQQQTPD
  869-  915 (79.88/90.38)	SQRSSASSAY..PSSSTQVVAVAGAVVDHLGIIYPTPPSQEALQQLSPE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      63.45|      21|      44|    1312|    1335|      10
---------------------------------------------------------------------------
 1312- 1335 (27.16/24.25)	MSTSLLSVTSSSWSMFddVEKiIP
 1359- 1379 (36.29/19.91)	LEQSMLSLDCNNVALY..VEQ.VP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      59.54|      16|      17|     919|     934|      12
---------------------------------------------------------------------------
  919-  934 (29.37/17.01)	GTGTTAVAGTQTGACS
  939-  954 (30.18/17.70)	GQGSTMKAATYLSGCS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      55.69|      14|      15|    1744|    1757|      13
---------------------------------------------------------------------------
 1744- 1757 (27.55/15.29)	LLSPTSDGPNFPHV
 1762- 1775 (28.15/15.81)	LVNPFNFGPDDQHV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      47.95|      11|      51|      48|      58|      14
---------------------------------------------------------------------------
   48-   58 (22.85/12.20)	YADIPDDAVLC
   99-  109 (25.11/14.13)	YGDEPDWALLC
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      52.57|      15|      19|    1042|    1056|      15
---------------------------------------------------------------------------
 1042- 1056 (32.15/16.20)	SWSNCG..SFGSWFGSS
 1062- 1078 (20.42/ 7.40)	SQASIGldSSSSATGRS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      47.00|      15|      15|     466|     480|      18
---------------------------------------------------------------------------
  466-  480 (23.59/14.96)	TSALLNSTTTATATV
  483-  497 (23.41/14.79)	TTASTASAAAAAAPV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      52.86|      15|      15|     782|     796|      20
---------------------------------------------------------------------------
  782-  796 (26.74/17.99)	SPSSGISDCENEIHA
  799-  813 (26.12/17.33)	SPPPSLGTEEERLNA
---------------------------------------------------------------------------




































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 MDP05935 with Med13 domain of Kingdom Metazoa
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