<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 MDP05942

Description Mediator of RNA polymerase II transcription subunit 13 (Fragment)
SequenceLLCEMSHVNLNSTNGASLEDCHTNVFVLVTMLKIFSMRMRSFTELNGLKWCRWCCSNSSIVYADIPDDAVLCGYGRCVTQGFLCVWRRAPPVHSSNRVDLRLAVEKELWIFWYGDEPDWALLCTGLTKIEEGSWEKGVEYETRTMLFKALHNQIDRVLLNANFLRFGNWYVNPLNYPKTKNKSNRPKYVIAFSLSFFVHGENNVCVTVSVQRHVPVYRLCRQLMLANRKLPVLLSPWSLSGELVFDPDKASESGESQFQQQLWKDWCRFYASLDSGGAESTTGVGSGSPFKEANSSSTTTTTTTDKLPKMMDVFVCGVRLKVPTRFVCVVDPDNVASSPQQSGSLLAGFRQWLCEKTMENLICHQRRQSGPTSPSAGESDSFGLAGSWNIVDPGQRERCCCSVGQSTSCCGTGAAGSVRFTSKCKSSDVSPKRVGCFHRRVAASRKLMTSAGLDGSSTAAGDDDDQQHQTMVEEAGTSTTSALLNSTTTATATVTATAASTASAAAAAAAPVASAVCSSASMTSSTMFLDHCSANVVGCNVAVEPKSKMRRSVEQSELLQQQQTPDPLVIPPKYTGLESIEVDQRLLSMKRRYNVSTNYDTDGDLQLMKLSFSRYHSHHQEQIHLLHIQQQQQQQQQQNQSNSFISRVSSSSVKNFGKPTDQFTEKFYRALTSYSWCQAMETNRKRRFFVQNVLLLFSEAVLNCRSIAPVGQRHLAQSNARQVEKIYGYKNKNKRKDITTNDHDRTDDVLSGDMCKREEEKACVKSDAEFHMTDDSSAIVHHQMMEEGPSPSSGISDCENEIHAFLSPPPSLGTEEERLNATEKIVAVKMDATNQNNEHANSSSSSNNNNNNNNNSSSTTTTNSNNVAVLSCSQRSSASSAYPSSTQVVAVAGAVVDHLGIIYPTPPSQEALQQLSPESHAGTGTTAVAGTQTGACSSGSYGQGSTMKAASYLSGYRDCKDAPEVQVVIPYVLASEFFGAVPASSRRSAVRFEKILCYKPSRLLPALYHHHHHHHHHHHHHHHHHQSASVGHLASLPTYGLGAISHHSWSNCGSFGSWFGSSSVRLGSQASIGLDSSSSATGRSIISAPASVRSVAEPSPVNNNPPSVSSPHFVRTPRTPGMELASPMSNASSAYAKNLSSIEPASSVLHPEGHSLVMMLLLSDTFVHLYRDSNFDSCPLCVCNMNIRGLEMGHYVNLRRCDDNMSVLYHSSARNTFTNKCTCGFSASRHRYLSYKSGVFYEDEDDATGAVWERLTASHLETVPFSREIVELVRHQSLLQDLTCSLMLFRTSPFGCLNAEASGAIGGGGGGGGGGGGGGSLSTSLLSVTSSSWSMFDDVEKNIPLGLPNAVYNAVELRDFTELCQLALEQSMLSLDCNNVALYVEQVPAAKRSATSSYINGWGYAKTVEPSNSLETMALLRSLLPLLQESLQKPRGLWQAKHSVEGPLTWRQLHRKCTHRPGSNGREDLSGPEPIPELLVCSDRDWIQVSPFSIRLWDRMCLEPFTQPKDVAFIAVVPDTQYVVRKARGFFRELSRTYEGMRLGRHCPITRVLKDGIMRVGKTHAKQLDQKPVDPWFDRFESASDGRNIIGAKLKLYAQVCRHYLAPHIFSPVWNAFDRSIFREIGRECPASTPTTTCTSSSLSNVDSVGTAVSSQSAELANTTVSASGSGASCVSAGTTGMTTTTTTATAVTTSVADSSSSTAISYGLNNNNNNNNNTNNSSNNSMNMMNTSSSNNSNDSRMSESSTNGNDNNGLLSPTSDGPNFPHVVVIYLVNPFNFGPDDQHVRDLNRLVTTGLFRCYLEILQEVPATFRSSMQLQIIPLQTVLDTSLLDDWELQHNGIVDEDRRLKSMPRAAVNSNSSSVGGGIGQQRVSLSSSTHLRSLALNVFMQIRSVAYSCLHSCLPKVMTGFGPAASRHELLRRKQNSAGFRLYSAPVVLAPIQDRTSCLNGTTGSNGSFGSSSSNSASSFCGGGSESRDDHGQVLFLAYCLSAKQQWLLCTVTDQQGAVLDSCVINMMLNNRHNVVKRELIWSALRRLWDYVVGILASSCRPWRIVIGRLGRLGHEELKAWAHLLSKSQLRSTSRLLREQCAVCQPMPTIFETPAILSACLISTELDPNMRIFPDSFVHDDRFGQGAKQCPLSSPEDVSSSHIMVFPTSALIQISQCCIMTGGLPGADETDGDFESIWKDLMISPEGDGLESGLNDIFGSMSEANLMNDSTVGFDANSSHTRGLAISESSDESIQLQPLALGFLVSTAPTGPVPEWFWTVRPSARDLLPVHLRSALHIHTSGVQQSDDHLLASGANRSTSGTVHPLDSSLTTDVLRYVLETYNALSWLCLDFRTGDRVSCFPLHIQALSRLYRAMDALL
Length2370
PositionMiddle
OrganismTrichinella murrelli
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Enoplea> Dorylaimia> Trichinellida> Trichinellidae> Trichinella.
Aromaticity0.07
Grand average of hydropathy-0.300
Instability index50.89
Isoelectric point6.73
Molecular weight258986.05
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

>MDP05942
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      47.43|      12|      19|    1024|    1035|       2
---------------------------------------------------------------------------
 1024- 1035 (21.67/ 9.13)	HHQSASVGHLAS
 1046- 1057 (25.76/12.27)	HHSWSNCGSFGS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     136.97|      41|     542|     936|    1004|       3
---------------------------------------------------------------------------
  937-  979 (69.71/65.21)	SSGSYGQGSTMKAAS........YLSGYRDCKDAPevQVVIPYVLASEFFG
 1733- 1781 (67.26/20.83)	SSSNNSNDSRMSESStngndnngLLSPTSDGPNFP..HVVVIYLVNPFNFG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      50.07|      14|      44|    1626|    1639|       4
---------------------------------------------------------------------------
 1626- 1639 (28.49/18.14)	GREC..PASTPTTTCT
 1671- 1686 (21.58/11.47)	GASCvsAGTTGMTTTT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     103.53|      23|      44|    1321|    1344|       5
---------------------------------------------------------------------------
 1321- 1344 (33.06/21.87)	LSTSLLSVTSSSWSMFDDVEKnIP
 1368- 1388 (35.01/18.58)	LEQSMLSLDCNNVALY..VEQ.VP
 1390- 1410 (35.46/18.92)	AKRSATSSYINGWGYAKTVE...P
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      87.05|      18|     542|    1293|    1310|       7
---------------------------------------------------------------------------
 1293- 1310 (35.18/17.51)	PFGCLNAEASGAIGGGGG
 1854- 1870 (30.98/14.44)	PRAAVNSNSS.SVGGGIG
 1960- 1975 (20.89/ 7.07)	.FGSSSSNSASSFCGGG.
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     120.77|      35|     861|     832|     866|       8
---------------------------------------------------------------------------
  832-  866 (64.13/34.98)	ATNQNNEHANSSSSSN.....NNNNNNNNSSSTTTTNSNN
 1689- 1728 (56.64/30.00)	ATAVTTSVADSSSSTAisyglNNNNNNNNNTNNSSNNSMN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      68.15|      23|     542|    1495|    1545|      10
---------------------------------------------------------------------------
 1495- 1545 (21.90/46.24)	RLWDrmclepftqpkdvafiavvpdtqYVVrkarGFFRELSRTYEgMRLGR
 2038- 2060 (46.25/30.45)	RLWD.......................YVV....GILASSCRPWR.IVIGR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      47.82|      10|     215|      50|      59|      14
---------------------------------------------------------------------------
   50-   59 (25.82/12.78)	WCRWCCSNSS
  266-  275 (22.01/ 9.78)	WCRFYASLDS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      67.11|      19|      53|      62|      81|      16
---------------------------------------------------------------------------
   62-   81 (33.22/27.11)	YADIPDDAVLC.GYGRcVTQG
  113-  132 (33.88/21.07)	YGDEPDWALLCtGLTK.IEEG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      71.46|      23|      54|    1074|    1098|      20
---------------------------------------------------------------------------
 1074- 1098 (34.31/27.66)	LDSSSSATGRSIIS.APASvrSVAEP
 1128- 1151 (37.15/22.98)	MSNASSAYAKNLSSiEPAS..SVLHP
---------------------------------------------------------------------------




































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 MDP05942 with Med13 domain of Kingdom Metazoa
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