<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 MDP29208

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMSTANGGSLDDCITNLFALTELNGLQWRQYECPSWNIDSNPRTLLQNEPILVAYSKLQSDGILSVWRRVVKKSPPTVVNLLPTLDGTAPKELWVFWYGATEPEEIEKHCKDLIKKKNEDESEDGTVTGIPYDVRCLLYKSWNTQMEKHYRRKKFLQIGRWFVRPHKLIDPSIAFMIDDFVLAHCHSFNIVGGNSMCMAIKTQLQPNLVHIAPFHIERNKKNKDSRINVLLAPWSLNAHVSLRYSITPITKKEEEEVEKQLTQWKELNMFADQKRKKRRREEGGDTEGEESEDEGWGDIKTPKMIRVEVDGKQRMWWPTQYVLVTLEETRRIVRDRFPVADLLKCVPEKVSMFSRNRFAHLTNSDGSVVDDSNFNMIENGKKIEMGLPKPDADIVSVYLTKRRLSDRKKKRKTQLTFEDRRRRKLENGMGAQRMVRVSSVSTDEGEDEGKEPNMKKEYKRMMVPNRFNCRSKNGRKNSKKETALRSMGLSSSDDDEEAEKKEVIEEKPEREWKYDNEKAIKIPRDISSMQPMQSIRALHKSTSKYRRKESNEIADESRLSKSKFTPVRALTPSSPQSEAAESEKFRSDASMSMGFQNEYTSYYDKKAAEMVPDIKYKPYHSRRNGPREHKERTRNKTDGRSRIDEVCSSDDDLLGEIHSCKRIREASPDVKPPRSHVIPDFEMEEVGGVNIPPPLDIPPDTVIREKKTSLFHPLRRSSIQFPELEGGDDFIELHYLKNLENRGYDIGSDEEPSDDRYSIGSDLQPPISTAVIDDAGEGTSSGAENWPRDEDEDMQDEYHHMDSSHDLMDTEGPSHSDSVLSPPASNERADSNNSMYPRLPGGPHSVGDTALNRIYPTPPSLLQVDICSPANMGGPHSQARKDDRDDASSTHDDEDDMQFLGDIELKDEDDSRGDHQIMNLNYKLHSRQFFDNAPKSDVPLSTRFGTHKHRSRVPEKRALPVYNKKDGERKEQLTPRIEEALAGADNFTTLSKISTSATAVGGQGWPSHAHQMSHPSMISHQQMQHQQQLHGSQSGPSMGTPPQSLHPMHPGYMGGTGQMGSFPGQPAGMRQSYTPQGYGVALHQQMQQQQQQYPMGGAQMMMGGQPGQSGYHPGAVRPPGYPGYPAQTGVPMGGNHPMQTPGMPMGYQQGMQNQMMYRPGMPTGSYPPQYGSPMGGMMSGGNGMGGMQMGGQYPGGGPMQQGGMMMQQMPHGQPMIAGAPHPMGMPGMTGHPSFPITSSAPGVIPPTSSAMIMMQRAAEPLKKNRPLALIDEEQTLIASRRGEDPYVKSLSIAPKGLFYKGNRQLKNEFDLYTTELILAKEGRKERRPFGPPTGGSEGLSIVAAVMLQDTILNLHFDWVFDSCPICACTTSIRSKELGVYITPPPILEETVEVQNVWIGTWHGMHLESTDSNICICGFSVIRHRLLSMRSGLFIEDSHEATGDLDSRTNPSKGKETKYLWFNPSSAADHALVETLRSMALTTDIGRLVGAIRNISTMGMKNAKRRGRRRNRNKKIPSIGPIGSSSEYVISQMDKMEVLLMGNSALTSAHVSGNKPTPSVGETPYFHPWGLQIASDVADPTEMEIKNLLEDVKPLIEGAVREARKLTTSTSASSVIEGPLTWRSLAAKNVKCSGNGDDDSHIAEPIPLLEMATEKDAIRIAPTVMKNWEQHNLGPIDVPKDVLYLAVTPDDDKVYDMTVVYVRRISKMYEQNLRLGRHTGYLARDEPNKTNVREGIVRAGVARSQHDSLDSPSLLFVREVEKEAEKHGCSKEFIHKLVTYVQSVEEILVEHLQKNCRIFERDVFRNEVDRDDASPMQIDESRKAESIMFNGPLAEALGMTGGSSSNSKAKKKVKRPFGHCSPYGMVGERLFKIPDEEPAALPHIVVIYLSIWPCFGSEGRNGDAARVAMIAIVKAFNSVMRKLPGKHRGQCQLELIPIQLVEESVGSAADLDRLDRSNNLNTWQIGNMHRSAEIYPNDRPKIEDVLKEIAFGIYRKPRFLHCDALKNALPKSMTKFGPASAILDWIDKKDGKKMTMYKFSQLCMDEISLYISYCLVSVDFIVVTVTDNLGARSDSAVLNLKPNIDQIGSTFRSQNKSSVVDGLHKLWKYIEGVMLHESKPLRLVIGKLGKMGHGEFKAWCHVLSRSNLKKYSTRVRESCSPCNANAGAPILLSACLVSTEPEAHLQVLPSYSISPDPNGSQKKIRPLHSPGDNTITHIMVFPISPAIQLNQSKENGGAEDEDDFSALDDIPDMEGNDMNDIMNDILMNKEEEGEGRAAARNHHMNSFFDAPLESGVQNQPLAAGWMISTAPGGDLPDWFWSSCPSLKRRLPVHLRSSLHINESQLSKSDDIGMKKEKEQEISHALDSQKTDEVLRMKSLSLHSEE
Length2383
PositionMiddle
OrganismPristionchus pacificus (Parasitic nematode)
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Chromadorea> Rhabditida> Rhabditina> Diplogasteromorpha> Diplogasteroidea> Neodiplogasteridae> Pristionchus.
Aromaticity0.06
Grand average of hydropathy-0.663
Instability index53.72
Isoelectric point6.47
Molecular weight266883.49
Publications
PubMed=18806794

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

>MDP29208
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             7|     402.52|      44|      45|    1107|    1151|       1
---------------------------------------------------------------------------
  998- 1023 (42.01/12.26)	.......AV...GGQGWPSHA.......HQMSHPSM.ISH....QQ.MQ
 1024- 1056 (60.14/20.35)	HQQQLHGS......QSGPS.MGTPPQSLHPMH.PGY.MG.......GTG
 1057- 1086 (43.62/12.98)	QMG.........SFPGQPA......G....MRQSYTPQGYgvalHQQMQ
 1089- 1105 (35.20/ 9.23)	QQQY...................PMGGAQ......MMMG.......GQP
 1107- 1151 (95.04/38.60)	QSGYHPGAVrPPGYPGYPAQTGVPMGGNHPMQTPGMPMGY....QQGMQ
 1153- 1187 (75.09/27.02)	QMMYRPG.M.PTG..SYPPQYGSPMGG...MMSGGNGMG.......GMQ
 1206- 1228 (51.43/16.47)	QQMPH..........GQPMIAGAP....HPM...GMP.........GMT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     123.34|      37|      51|    1330|    1380|       2
---------------------------------------------------------------------------
 1330- 1370 (50.58/50.29)	PPTGGSEGLSiVAAVMLqDTILNLHFDwVFDScPICACTTS
 1382- 1418 (72.76/62.82)	PPPILEETVE.VQNVWI.GTWHGMHLE.STDS.NICICGFS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     229.40|      84|      91|     513|     603|       3
---------------------------------------------------------------------------
  513-  573 (68.50/50.43)	.........................................................YDN.ekaiKIPR.DIsSMQPMQSIRA...LHKSTSKYRRKESNEI.....ADESRLSK.SKFTPVRALTP..SS
  574-  671 (112.23/74.69)	PQSEAAESEkfRSDASMS......MGFQN..EYTSYYD......................kkaaeMVP..DI.KYKPYHSRRNgprEHKERTRNKTDGRSRIdevcsSDDDLLGEiHSCKRIREASPdvKP
  874-  951 (48.66/25.00)	PHSQARKDD..RDDASSThddeddMQFLGdiELKDEDDsrgdhqimnlnyklhsrqfFDN......APKsDV....PLSTRFG...THKHRSR......................................
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      53.30|      13|      46|    1193|    1205|       4
---------------------------------------------------------------------------
 1193- 1205 (28.15/13.71)	PGGGPMQQGGMMM
 1240- 1252 (25.15/11.41)	PGVIPPTSSAMIM
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     166.34|      54|     525|    1526|    1687|       5
---------------------------------------------------------------------------
 1630- 1687 (87.47/195.47)	CSGNgddDSHIAEPIpLLE...MATEKDA.IRIAPTVM....KNWEQHNLGPIDVPKD..VLYLAVTP
 2157- 2220 (78.86/14.06)	CSPC...NANAGAPI.LLSaclVSTEPEAhLQVLPSYSispdPNGSQKKIRPLHSPGDntITHIMVFP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      41.95|      11|     525|    1319|    1329|       7
---------------------------------------------------------------------------
 1319- 1329 (21.59/12.23)	KEGRKERRPFG
 1846- 1856 (20.36/11.08)	KAKKKVKRPFG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      45.16|      13|      48|     438|     450|       8
---------------------------------------------------------------------------
  438-  450 (22.88/13.18)	SVSTDEGEDEGKE
  489-  501 (22.28/12.61)	SSSDDDEEAEKKE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     227.91|      73|     149|      32|     112|       9
---------------------------------------------------------------------------
   32-  112 (123.62/104.43)	CPSWNI.DSNPRTL...LQNEPILVAYSKLQsdgilsVWRRvvKKSPPTVVNLL..P.TLDGTAPKELWVFWYGATEPEEIEKHC...KDL
  184-  266 (104.29/70.73)	CHSFNIvGGNSMCMaikTQLQPNLVHIAPFH......IERN..KKNKDSRINVLlaPwSLNAHVSLRYSITPITKKEEEEVEKQLtqwKEL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     157.45|      33|      46|     695|     728|      10
---------------------------------------------------------------------------
  695-  726 (43.07/28.29)	.................DIPPDTVIREKKTSLFHPLrRSSIQFPELEGG
  727-  769 (33.25/16.10)	DDfielhylknlenrgyDIGSDEEPSDDRYSI.....GSDLQ.PPISTA
  772-  812 (47.34/26.77)	DD.....agegtssgaeNWPRDE..DEDMQDEYHHM.DSSHDLMDTEGP
  813-  841 (33.79/16.50)	SH...........sdsvLSPPASNERADSNNSM.........YPRLPGG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      83.55|      24|     525|    1526|    1596|      11
---------------------------------------------------------------------------
 1498- 1521 (44.03/35.03)	MKNAKRRGRRRNRNKKIPSIG......PIG
 1539- 1568 (39.52/61.33)	MGNSALTSAHVSGNKPTPSVGetpyfhPWG
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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 MDP29208 with Med13 domain of Kingdom Metazoa
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