<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 MDP26825

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMAHPNSQTNGASLEDCHTNFFALTDLCGIRWRKLTSEGYSPQPGGGGPWDYLNDPVLLSYWRCLSNDILCVWRRIPSASSASSPGGSSAFPPSFPSGFPNPQSSTQQGSNGLSTLSGAKELWIFWYGDTSPDLSSLVVPEILNMEGEHGSWENGLSYECRSLLFKALHNLIERCLLSRDFIRLGKWFVQPQEGVDSACTQQQQHQQPDSSNPTTTIPARNGHLSFSFSFFVHGESTVCASIDVRQHPVVRKTTHRHLAAAQATSGGVHVMLAPYGLAGALTGVSYRSATDHVTRKLMEEWRQYYPVECGLEAASDTEDMVEVIVGNVRMRYPTCYVMVCDADRMLMTPPASPPLTSNPASISRSISHSAVVSSLTSSSAVTSAHHSSTTPTTDKDSTVNLWDFVDPTTKNSCICMASTTPLNTSSSSSSSSSIPSSSSSSSSSSGKRGGGVHPFHHRPTYAAPTRAQSTVASVGQKLLPDNNNAAAALPPGNSSLPLSSPHPPASNDPSSNFIPSTPSASDHNMTSQDQNCSRATPGGAAHTPGGGPKSNQAAYSPYVALPSPRSSAGQQPASCGPATSVAPTTPNVGSGGGCSGERANGGGSTCSTADLYGIKKIVLPQKEYEEELKEGETAPGLLYDYSNMTAWLFHPVKRMKVGNNSSNGDRPTDSSDGGSSCSGKQINGNLMVSDGVHNGQSRKRKEPDSGRDEDSNSLNSANAAGGAAKPVNPSSLFTSEGLQASYQDLDKIFDNSDESNDTCPVPTPPGSNKPAGLPEDTALMGHGHHKAPRVNILASAEFSNMFPTPPSHEHPMQSPCGQMEGSVDLLGGDMNNSGHNGIKSEPGSGHSLNGCSPTYLQEDSANKDWSYVYRPPTVWKVANSSKYAPLPILPSQTMSPLFLPAPYRPSSSSNSSANHSSGIVEGQPPGFPQHQPGFPHHHPPQQQLQLQIQQQQQQHHHHHQQQPQSVNNSNNMSNHSNLPECHSLMVNIVLGDSMLNIFRDHNFDSCTVCVCSDGQNWVGTIRGQDAVFYLPESSNARSSSMRACRCNCGFSALVNRHLAHQAGLFYEDEVEIVGANATRDPGQFKRGSLYASIAAVVMEASAPLVDTLPVALMELLREQCLLVHHSSSPLYRAEQLQAATRKASLLHALDYSDGCETARNALTQPHPSHGAHGHSTNHPSTLSAGNNGPIVHYWPFLHVQGPNSSQDVIRVMRTLQPLLQDSIQKKRAASLWRAPFAVQGPLTWRQFHRMAVRGTEDRCEPQPIPSVMAGYDRDWVAIGPLAIPHWDRLLLEPYSRQRDVAYIVLAPEMDYVLSRTKIFFKELSATYEMCRFGRHVPYKGLRDGILRVGKSAAAKLANDAVDDWFSNIGDSPIASLLRLYAKVCRYHLAPTLINMPMDRTLLDPPAPPSSNRPMNAVPSPMAPPSTTPIHPGDFGSATQSGMGPPNPGGSTPLQGSSTFGVHHTSTPSSGITSSDGKPTSPKTEDGADGTSGHGASGATDGSAADDEEVDPPSIVIYIVDPFSFGSDNLDLGRLTALGLLRCYHQMLSLLSETVQLNVSLQLISADAILQLGKDLTGASRYDSLRSLALNVFSQCKKLISQPSNVKSLTGFGPAAASDTFLKAKDERNRAPYRVYIPAYVLAPTKDRTVCDLDPGVSTNGGPGSGPLSFLARPDKYSVLYVSYCLSEDQRWLIAACTDERGELVDSCTIGIDVPNRTKRKRVSVRRFGLQRLMDFILGVISTGVHPWRLVIGRVGRMGHGELKSWSALLSRKNLLRASRHLADICGQCSLVFPSQAPTLVSACLVSLEPDSHFRMMPDQVTPDERFGQQSANSHLSTPEDASCTHILVFPTSATTRSPQTTFHEENINGPDLGDDDLLSALNDDMGDGFEGMSGFDDIFMTWPETDQVNDGTDDLTSDITGGNNGGMNNMGGCGTSRSPGASHGGGGGGSPGRGGMRSNMNPESPSGMGGHHHAGGSGRQSPRAEQEEVGTLLQQPLALGYYVSTAPTGDMPSWFWSSCPHLARACPAFLKCALHLHNHAVQQNSDDILLQQQQQQVNNSSKVHPLDSQVTTDVLRYVMEGYNALSWLSLDPKSRDRRSCLPIHIQLLVQLYHALAALV
Length2118
PositionMiddle
OrganismDaphnia pulex (Water flea)
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Arthropoda> Crustacea> Branchiopoda> Diplostraca> Cladocera> Anomopoda> Daphniidae> Daphnia.
Aromaticity0.06
Grand average of hydropathy-0.433
Instability index54.09
Isoelectric point6.19
Molecular weight227514.16
Publications
PubMed=21292972

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	IBA:GO_Central

GO - Biological Function
transcription coregulator activity	GO:0003712	IBA:GO_Central

GO - Biological Process
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP26825
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             5|     239.26|      42|      44|     527|     568|       1
---------------------------------------------------------------------------
  483-  529 (51.54/17.42)	NAAAALPPGNSSLPLS.....SPHP....................................P.ASNDP...SS.......NfIPST..PSASDhnmtsQDQ
  530-  572 (66.18/24.91)	NCSRATPGGAAHTPGG.....GPKS....................................NQAAYSP...YV.......A.LPSP..RSSAG....qQPA
  828-  910 (31.75/ 7.29)	DMNNSGHNGIKSEPGSghslnGCSPtylqedsankdwsyvyrpptvwkvansskyaplpilPSQTMSP....L.......F.LPAPyrPSSSS......NS
 1432- 1478 (41.38/12.22)	DFGSATQSG......M.....GPPN....................................P.GGSTPlqgSStfgvhhtS.TPSSgiTSSDG.....KPT
 1932- 1967 (48.40/15.81)	.CGTSRSPGASHGGGG.....GGSP....................................GRGGMRS...NM.......N.PESP..SGM..........
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     368.27|     129|     477|      82|     221|       2
---------------------------------------------------------------------------
   27-  173 (209.38/100.43)	CGIRwRKLTSEG.YSPQPGGGgpWDYLNDPVLLSYWRCLSNDILCVWRRIPsassaSS..PGGSSAFPPSFP.SGFPNPQSSTQQGSNGLSTLSGAKELWIFWYGdtspdlsSLVVPEILNM.EGEHGSWENGLSyecRSLLFKALHNLIER
  174-  275 (123.04/48.42)	CLLS.RDFIRLGkWFVQPQEG..VDSACTQQQQHQQPDSSNPTTTIPARNGhlsfsFSffVHGESTVCASIDvRQHPVVRKTTHRHLAAAQATSGGVHVMLAPYG...............................................
 1740- 1783 (35.85/ 8.61)	.............................................................................................STGVHPW............RLVIGRVGRMgHGELKSWSALLS...RKNLLRASRHLADI
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     322.91|     110|     477|    1491|    1630|       3
---------------------------------------------------------------------------
 1167- 1297 (168.31/94.96)	SHGAHG.........HSTNHPStlsagnngpIVHYW..PF......LHVqGPNSSQDVIRVMRTLQPLLQDSIQKKRAASLWRAPFAVQ......GPLTWRQFHRMAVrGTEDRC.....EPQPIPSvMAGYdrdwvaiGPLAIPhwDRLLLEPYSRQR
 1491- 1628 (154.60/141.74)	GHGASGatdgsaaddEEVDPPS.........IVIYIvdPFsfgsdnLDL.GRLTALGLLRCYHQMLSLLSETVQLNVSLQLISADAILQlgkdltGASRYDSLRSLAL.NVFSQCkklisQPSNVKS.LTGF.......GPAAAS..DTFLKAKDERNR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     158.85|      42|      43|     649|     690|       4
---------------------------------------------------------------------------
  428-  450 (23.32/ 6.65)	...........SSSSSIPSSSSSSSSS.SG..KRGG.G.......
  649-  690 (76.94/44.78)	HPVKRMKVGNNSSNGDRPTDSSDGGSSCSG..KQIN.GNLMVSDG
  692-  736 (58.59/31.73)	HNGQSRKRKEPDSGRDEDSNSLNSANAAGGaaKPVNpSSLFTSEG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      56.29|      14|      15|    1393|    1407|       5
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 1393- 1407 (27.21/14.46)	NMPMDrTLLDPPAPP
 1410- 1423 (29.09/11.42)	NRPMN.AVPSPMAPP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      69.49|      16|      16|     929|     944|       6
---------------------------------------------------------------------------
  929-  944 (35.54/16.51)	HQPGFPHHHPPQQQLQ
  948-  963 (33.95/15.42)	QQQQQQHHHHHQQQPQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      56.10|      13|      40|     761|     773|       7
---------------------------------------------------------------------------
  761-  773 (27.07/13.39)	PTPPGSNKPAGLP
  802-  814 (29.03/15.05)	PTPPSHEHPMQSP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      65.33|      17|      41|     338|     357|       8
---------------------------------------------------------------------------
  338-  354 (35.42/20.45)	VCDADRMLMT..PPASPPL
 1648- 1666 (29.91/ 9.17)	VCDLDPGVSTngGPGSGPL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     118.68|      38|     747|     278|     335|      11
---------------------------------------------------------------------------
  286-  335 (55.47/72.59)	RSATdhvtrklMEEWRqyypVECGLEAASDT..........EDMVEvIVGNVRMRYPTCY
 1036- 1083 (63.21/32.73)	RSSS.......MRACR....CNCGFSALVNRhlahqaglfyEDEVE.IVGANATRDPGQF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      43.22|      13|      15|    1310|    1322|      12
---------------------------------------------------------------------------
 1310- 1322 (21.89/16.18)	YVLSR..TKIFFKEL
 1326- 1340 (21.33/15.53)	YEMCRfgRHVPYKGL
---------------------------------------------------------------------------




































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 MDP26825 with Med13 domain of Kingdom Metazoa
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