<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 MDP04353

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMSTNGGSLEDCHTNVFALTELNGLKWKCLTTPLSQRTWTSLEQDPVLSAYARCLQAGILCAWRRQPPQPTGTLAAMQLPDYRIDVVKELWVFWYSHEEPDCLTEYTSHLACSEDGQGNWSVPGIQYETRTLFFKALHNLIERNMLKNGYIRIGKYFTRPYEVPSSDRIHCSPSYVNGISFNFFVHGENIVCATVSVQRQPTLFRLSRRHLDLGKKQPVILGPWSMRAVLLPEQPRIVDSTTPLLQQQSSASQYGNFTSLSSVAHQINPVPSSSIDSDTISNSYDGAGTISKAAVDKLWSEWLQFFCLIVNVERNLGSADTVGYIGYTENTSPAKNSLPKMVLVDVDGVHMWYPSSLIVVQASDDLLLRQNEKTINDDDSDFFNSGSNSSSFTARTPPATGGHARLRSTPSFRKRKKRLSECDTGSNAERHNAMYGTMVNGARAAQRFFEESFIAPASSRRKESTESPSSSGLGLLMSAAANDDDCRWNFTDGMRRKDREEGCGCHHCRLQQSSSATALPNLPSQYTCIDQESNQSCCTPVNFSNSSLEAKKEGPAIFHRRSSSCTRSPSPPRSPPWEKKILATSSETGDSEHNLDWIRESYFRNSRSSSRSGRADLLHEDRHICPKTPDASTIMESPERRRVQRNSVQMFGKIGSCKPIYQNLSPTSRPRSPACDTSQAESLGRMQSKDCLSNDFASSAGKHTPTITDQQPNLINSLRLKKGKKLKGRKRKADEKLEWSGIESLDVSFLTAKVGEDNEDDDNINFTCPSNFKLRECKSEINGEVVESSNAVPHTRSSLNVSTSQSQDVLRSLPVFSQIGSAMPSNAGVNLTPSIFTSDCDTQPLFLDDCNPSAITMVERRSPVDTVVTDSVHLSPPASNERVEPTQILGGTVANVMARVGGPPSVGDYMIYPTPPSVDATQSQQFSPQNTLIQANPTSILYPPTVSYMAAAAAAAVNLCHNIPPVQLPPTVVSETDATTETTPTIKRELENDDERLLGKLHYSIGEKPVYGKFMQLEMALSRKFAGNILAKEFLSLEAKECRMLEGVYADQLKLIKAAVAAREKRKKVGRAPDYLFMRERLRNLAPHSSFTTVRHYRIPYNNGHMFSSHCLPTLQMLPHGMSMNGVPNFVTNGPPFGAASYNGNNSVMSMMMSSGCLPPSGTTIMQPVPSSSRMGVVHMNQQMSMAHLRPLARIPSMPPYASSQTGPLQHPPFMGQSAQFCSPPGMMNAPNPISSFPGGPMCSMSTGPVQSSHMLSGMHGTTPSQPLGANNMHAAGPPNGQFSMQQPQQPFQQLSHFVNNANFNGQVGMTAVNPSQQSIYQQQIMFRCNMNGNLPAQHSIHSSDSYGIDSQGQAPVEPPPPFSQSINQQYAAVHNVQGGSMIYPQSAHMMRPNTLMSQAQNQNMMCGPRTSQNPMMTVSSSIGSPNNGGLFGNRLMNMPHVMDTTTVPPNNIRTHPEGKSLVLAVLLQDTVLDLHYDSVFDACPICSCNGSIRAKELGVYITPPEVLRQPPAQQQLIVSKPTSGFYNSTSNSCNCGFSAVRHRYLSMKAGLFAEDAKEATDINETQSQPAIPHTIWFDSMSGRDMNFIALLREQTLVRDLGGLLDQVTLLSLQCERASQTERIGSDSSKHCEYIISEVDQRELPLVFQAACEVACMEMNCRRPPHDVRSVLLHDWGVQISNEMREPRESECMALLQEIGPILEESLRIARSSPLFGSNNIVEGPLTWRFFDRKALKAAGGTEDDSGPEAVPNIVVASEKDAVITSPQIIRLWEKMSLEPYDQPKDVLYIGVVPDNLICIEKTKKYLMDLSRMYEQCRFGRHIPFSREVLRDGLLRVPTRYPATNPGECDNFLNQVERHIGDNKSLITRLKVYMQYFENEMARILINNDDIFSRDKYRAALAESQIHSVQHISIAAYQCGGYTVSSSDHMPPPSAPGSIIISGQSSDASHGPNSTSGPSSSGITIGESLTPDGSIGDGSAQNMTNFSSFMTEQLVADGIIAEDEPGTLPHVIVIYLVNPFLLGAEENPLVARVVTVALMRAFNALLYRLNNKRRPQLQLEMIALQNIFDYCGASADFLKDERGRLNGYDQGRLEKSQNERLSSSDSLKTIAFSVYTHSRVVLPDIVRGILPKSMTRFGPASAMVDLLNELERKEPIYYKVPSKPFILAPPSPVMQRPNCDLMQINTDEAVLFVSYCLIGNDWLAATVTDHQGHSLDNCLINLRLKPDHKRVNMRYKQSTQIRDSLYRLWSYILGTLANGTRNWRLVIGRVGRIGHGEFKFWTQILSKSYLKQVGTRMKHVCRACHVMPGTSEVPGVLSACLVSLEPEAHLRVFPSSFQHDDRFLKNSRHRALTTPDDTSCTHILVFPTSPELNLDHQGGNGVAELEEDDFSNLLTEEIGEEFSELIGNGEDLMTNGTGPPPQSASFRLGGNTGIPSEYADVSIENQPLATGYYISTAPASDLPEWFWSACPSAKRRNPVHLKSSLHLNTPNVQQGDDISSFGKGTEACHHQLDSQATADVLRYVLEMYNALSWLNMDLVSGERRSCLPIHIQALMWLCNAVNRFIN
Length2565
PositionMiddle
OrganismBrugia malayi (Filarial nematode worm)
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Chromadorea> Rhabditida> Spirurina> Spiruromorpha> Filarioidea> Onchocercidae> Brugia.
Aromaticity0.07
Grand average of hydropathy-0.399
Instability index58.10
Isoelectric point6.42
Molecular weight283664.72
Publications
PubMed=17885136

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

>MDP04353
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     240.46|      46|      49|    1105|    1153|       1
---------------------------------------------------------------------------
 1107- 1152 (89.68/44.53)	SSHCLPTLQMLPHGMS.MN...GVPNFVTNGPPFGAASYNGNNSVMSMMM
 1154- 1185 (44.35/21.54)	.SGCLP.....PSGTTiMQ...PVP....SSSRMGVVHMNQQ...MSM..
 1218- 1254 (71.07/30.54)	AQFCSPP......GM..MN....APNPISSFPG.GPMCSMSTGPVQSSHM
 1406- 1437 (35.36/12.10)	...CGPRTSQNPM.MT.VSssiGSPN...NGGLFGNRLMN..........
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     104.82|      28|    1219|     842|     943|       2
---------------------------------------------------------------------------
  884-  915 (48.08/26.75)	PTQILGgtvANVMaRVGGPPSVGDYMIYPTPP
 1263- 1290 (56.74/58.01)	PSQPLG...ANNM.HAAGPPNGQFSMQQPQQP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      91.33|      21|    1223|    1309|    1329|       3
---------------------------------------------------------------------------
 1306- 1322 (30.39/15.67)	QV....G...MTAVNPS...QQSIYQQ
 1323- 1343 (37.15/21.03)	QIMFRCN...MNGNLPA...QHSIHSS
 1344- 1369 (23.79/10.42)	D.SYGIDsqgQAPVEPPppfSQSINQQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     149.71|      34|    1223|     842|     881|       4
---------------------------------------------------------------------------
  845-  880 (59.18/39.02)	FLDDCNPSAITmvERRSPVDTVVTDSVH.LSPPASNE
 2342- 2370 (47.45/20.54)	FLKNSRHRALT.....TPDDTSCT...HiLVFPTSPE
 2465- 2489 (43.07/17.58)	FWSAC.PSA....KRRNPVH..LKSSLH.LNTP....
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     225.16|      72|    1223|     598|     704|       5
---------------------------------------------------------------------------
  598-  676 (108.39/115.17)	RESYFRNSRSSSR.SGraDLLhEDRHICPKTPdASTIMESPERRRVQRnSVQMFGKIGSCKPIYQ..NLSPTsrPRSPACDT
  767-  841 (116.77/55.10)	CPSNFKLRECKSEiNG..EVV.ESSNAVPHTR.SSLNVSTSQSQDVLR.SLPVFSQIGSAMPSNAgvNLTPS..IFTSDCDT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     135.35|      42|      49|    1574|    1622|       9
---------------------------------------------------------------------------
 1578- 1622 (64.29/57.30)	DSMSGRDMNFIALLREQtlvRDLGGLLD...QVTLLSLQCERASQTER
 1624- 1668 (71.06/43.00)	GSDSSKHCEYIISEVDQ...RELPLVFQaacEVACMEMNCRRPPHDVR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      59.27|      18|    1394|     988|    1007|      11
---------------------------------------------------------------------------
  988- 1007 (27.70/28.13)	ELENDDERLLgkLHYSIGEK
 2383- 2400 (31.57/23.32)	ELEEDDFSNL..LTEEIGEE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      93.38|      25|      49|     498|     522|      12
---------------------------------------------------------------------------
  498-  522 (47.04/22.59)	REEGCGCHHCRLQQSSSATALPNLP
  550-  574 (46.34/22.14)	KKEGPAIFHRRSSSCTRSPSPPRSP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     117.13|      35|     896|     127|     163|      14
---------------------------------------------------------------------------
  127-  163 (57.86/46.70)	ETRTLFFKALHNLIERNMLKNgyIRIGKYFT..RPYEVP
 1063- 1099 (59.27/39.99)	EKRKKVGRAPDYLFMRERLRN..LAPHSSFTtvRHYRIP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      56.54|      15|    1487|     458|     472|      17
---------------------------------------------------------------------------
  458-  472 (27.06/13.29)	SRRKESTESPSSSGL
 1948- 1962 (29.48/15.22)	SHGPNSTSGPSSSGI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      68.00|      22|      49|    1476|    1500|      18
---------------------------------------------------------------------------
 1476- 1500 (35.74/30.24)	YDSVFDAcpiCSCN.GSIRAKEL....GVY
 1526- 1552 (32.26/17.30)	YNSTSNS...CNCGfSAVRHRYLsmkaGLF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     106.77|      31|    1426|     420|     450|      19
---------------------------------------------------------------------------
  420-  450 (55.77/49.80)	ECDTGSN.AERHNAMYGTMVNGARAAQRFFEE
 1847- 1878 (51.00/44.65)	ECDNFLNqVERHIGDNKSLITRLKVYMQYFEN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      55.87|      15|      54|    1448|    1462|      20
---------------------------------------------------------------------------
 1448- 1462 (28.05/15.50)	PPNNIRTHPEGKSLV
 1503- 1517 (27.82/15.30)	PPEVLRQPPAQQQLI
---------------------------------------------------------------------------




































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 MDP04353 with Med13 domain of Kingdom Metazoa
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