<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 MDP29945

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMDKNFVRIGKWFVRPYEKDEKPVNKSEHLSCAFTFFLHGESNVCTSVEIAQHQPIYLINEEHIHMAQSSPAPFQVLVSPYGLNGTLTGQAYKMSDPATRKLIEEWQYFYPMVLKKKEELKEEEELGYDDDFPVAVEVIVGGVRLVYPSAFVLISQNDIPVPQSVAGAGGHITVGQQGLGSGKDPSNCGMPLTPPTSPEQAVIGESGGTQSAVSHLGSQDGGMITMHSPKRSGKIPPKLHNHMVHRVWKECILNRAQSKRSQMSTPTLEEEPANNPATWDFVDPTQRVSCSCSRHKLLKRCAVGPNRPPAISQPGFSAGPSSSSSLPPPASKHKTTERPEKGDKLQKRPLIPFHHRPSVADEFCMEQDTPGQKLGLAGIDSSLEVSSSRKYDKQMAVPSRNTSKQMNLNPMDSPHSPISPLPPTLSPQPRGQETESLDPPSVPVNPALYGNGLELQQLSTLDDRTVLVGQRLPLMAEVSETALYCGVRPSNPESSDKWWHSYRLPPIDDAEFRPPELQGDRCDAKMEVNSESTALQRLLAQPNKRFKIWQEKQPQMQPLHFLDPLPLSQQPGDSLGEINDPYTFEDGDIKYIFTANKKCKQGTEKDSLKKNKSEDGFGTKDVTTPGHSTPVPDGKNAMSIFSSATKTDVRQDNAAGRAGSSSLTQVTDLAPSLHDLDNIFDNSDDDELGAVSPALRSSKMPAVGAEDRPLGKDGRAAVPYPPTVADLQRMFPTPPSLEQHPAFSPVMNYKDGISSETVTALGMMESPMVSMVSTQLTEFKMEVEDGLGSPKPEEVKDFSYVHKVPTFQPLVGSSMFAPLKMLPSQCLLPLKIPDACLFRPSWAIPPKIEQLPMPPAAIFNRDGYNNVPSVGSLADPDYLNTPQMNTPVTLNSAAPASNSGAGVLPSPATPRFSVPTPRTPRTPRTPRGGGTASGQGSVKYDSTDQGSPASTPSTTRPLNSVEPATMQPIPEAHSLYVTLILSDSVMNIFKDRNFDSCCICACNMNIKGADVGLYIPDSSNEDQYRCTCGFSAIMNRKLGYNSGLFLEDELDIFGKNSDIGQAAERRLMMCQTTFLPQMEGARKSQEPPISLLLLLQNQHTQPFASLSFLDYISSNSRQTLPCVSWSYDRVQADNNDYWTECFNALEQGRQYVDNPTGGKVDEALVRSATVHSWPHSNVLDISMLSSQDVVRMLLSLQPFLQDAIQKKRTGRTWENIQHVQGPLTWQQFHKMAGRGTYGSEESPEPLPIPTLLVGYDKDFLTISPFSLPFWERLLLDPYGGHRDVAYIVVCPENEALLEGAKTFFRDLSAVYEMCRLGQHKPICKVLRDGIMRVGKTVAQKLTDELVSEWFNQPWSSEENDNHSRLKLYAQVCRHHLAPYLATLQLDSSLLIPPKYQSPPAAAPGQATPGNAGPLASNAGSTVSSAGSAFNPTSSSSSGNPAASSSASGSSVPPVSSSAPAPVINQISTTSSSGFSASVVGQNPGTGASSADRTQGNLGCVGDPEPGQSSSQSLQDGQESVTERERIGIPTEPDSADSQAYPPAVVIYMVDPFTYTADEDSTSGNFWLLSLMRCYTEMLDNLPEHMRNSFILQIVPCQYMLQTMKDEQVFYIQYLKSMAFSVYCQCRRPLPTQIHIKSLTGFGPAASIEMTLKNPERPSPIQLYSPPFILAPIKDKQTELGETFGEASQKYNVLFVGYCLSHDQRWLLASCTDLHGELLETCIVNIALPNRSRRSKVSARKIGLQKLWEWCIGIVQMTSLPWRVVIGRLGRLGHGELKDWSILLGECSLQTISKRLKDVCRMCGISAADSPSILSACLVAMEPQGSFVVMPDAVTMGSVFGRSTALNMQSSQLNTPQDASCTHILVFPTSSTIQVAPANYPNEDGFSPNNDDMFVDLPFPDDMDNDIGILMTGNLHSSPNSSPVPSPGSPSGIGVGSHFQHSRSQGERLLSREAPEELKQQPLALGYFVSTAKAENLPQWFWSSCPQAQNQCPLFLKASLHHHISVAQTDELLPARNSQRVPHPLDSKTTSDVLRFVLEQYNALSWLTCNPATQDRTSCLPVHFVVLTQLYNAIMNIL
Length2076
PositionMiddle
OrganismCanis lupus familiaris (Dog) (Canis familiaris)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Mammalia> Eutheria> Laurasiatheria> Carnivora> Caniformia> Canidae> Canis.
Aromaticity0.07
Grand average of hydropathy-0.395
Instability index59.48
Isoelectric point5.67
Molecular weight227386.63
Publications
PubMed=16341006

Function

Annotated function Component of the Mediator complex, a coactivator involved in the 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

>MDP29945
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     681.30|     201|     628|     175|     391|       1
---------------------------------------------------------------------------
  184-  391 (342.55/163.17)	PSNCGMPLTPPTSPeqaVIGESGGTQS.AVSHLGSQDGGMITMHSPKRS...GKIPPKLHNHMVHRVWKECILNRAQSKR....SQMSTPTLEEEPANNP..ATWDFVDPT.....QRVSCSCSRHKLLKRC.AVGPN.....RPPA..ISQPGFSAGPSSSSSLPP.....PASKHKTTERPEKGDKLQKRPLIPFHHRPSVADEFCMEQDTPGQKLGlAGIDSSlevSSSRKYD
  731-  940 (282.44/115.59)	PTPPSLEQHPAFSP...VMNYKDGISSeTVTALGMMESPMVSMVSTQLTefkMEVEDGLGSPKPEEVKDFSYVHKVPTFQplvgSSMFAP.LKMLPS........QCLLPL......KIPDAC....LFRPSwAIPPKieqlpMPPAaiFNRDGYNNVPSVGSLADPdylntPQMNTPVTLNSAAPASNSGAGVLPSPATPRFSVPTPRTPRTPRTPRG.GGTASG...QGSVKYD
 1378- 1460 (56.31/14.82)	.......................................................................YLATLQLDS....SLLIPPKYQSPPAAAPgqATPGNAGPLasnagSTVSSAGSAFNPTSSS.SSG.......NPAA..SSSASGSSVPPVSSSAPA.....P...............................................................
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     170.94|      54|     626|    1315|    1375|       2
---------------------------------------------------------------------------
 1315- 1375 (77.37/67.26)	LGQHKPicKVLRDGIMRVGKTVAQKLTDELvSEWFnqpWSS.EENDNHSRLKLYAQVcRHHL
 1948- 2002 (93.57/54.67)	LSREAP..EELKQQPLALGYFVSTAKAENL.PQWF...WSScPQAQNQCPLFLKASL.HHHI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      67.12|      20|      24|    1837|    1856|       5
---------------------------------------------------------------------------
 1837- 1856 (33.45/20.72)	VFGRSTALNMQSSQLNTPQD
 1862- 1881 (33.67/20.91)	ILVFPTSSTIQVAPANYPNE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      38.25|      10|      62|     978|     994|       6
---------------------------------------------------------------------------
  978-  987 (16.12/22.70)	LILSDSVMNI
  996- 1005 (22.13/ 7.32)	CCICACNMNI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      58.35|      18|      27|    1732|    1758|       9
---------------------------------------------------------------------------
 1732- 1750 (30.47/30.63)	RSkVSAR..KIGLQKLWEWCI
 1761- 1780 (27.88/ 9.03)	RV.VIGRlgRLGHGELKDWSI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      56.09|      16|      16|     394|     409|      10
---------------------------------------------------------------------------
  394-  409 (28.86/13.36)	MAVPSRNTSK.QMNLNP
  410-  426 (27.23/12.13)	MDSPHSPISPlPPTLSP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      65.86|      19|      20|    1563|    1582|      11
---------------------------------------------------------------------------
 1563- 1582 (31.05/27.79)	NFWLLSLMRCyTEMLDNLPE
 1586- 1604 (34.81/24.68)	NSFILQIVPC.QYMLQTMKD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      63.49|      21|      27|    2022|    2042|      13
---------------------------------------------------------------------------
 2022- 2042 (37.12/25.21)	PLDSKTTSDV.LRF.VLEQ.YNAL
 2049- 2072 (26.37/15.61)	PATQDRTSCLpVHFvVLTQlYNAI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      39.55|      10|     911|      46|      55|      14
---------------------------------------------------------------------------
   46-   55 (19.55/12.00)	SVEIAQHQPI
  959-  968 (20.00/12.48)	SVEPATMQPI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      58.76|      19|      22|     651|     672|      17
---------------------------------------------------------------------------
  651-  672 (26.19/22.64)	DNAAGRAGSSSLTQVTdlaPSL
  676-  694 (32.57/19.35)	DNIFDNSDDDELGAVS...PAL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      64.39|      19|      22|    1896|    1915|      20
---------------------------------------------------------------------------
 1896- 1915 (31.76/19.12)	PFPDDmDNDIGILMTGNL.HS
 1921- 1940 (32.63/15.10)	PVPSP.GSPSGIGVGSHFqHS
---------------------------------------------------------------------------




































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 MDP29945 with Med13 domain of Kingdom Metazoa
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