<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 MDP28426

Description Mediator of RNA polymerase II transcription subunit 1
SequenceMSSLLERLHVKFNQNRPWSETIKLVRQVMEKRVVMSSGGHQHLVSCLETLQKALKVTSLPAMTDRLESIARQNGLGSHLSASGTECYITSDMFYVEVQLDPAGQLCDVKVAHHGENPVSCPELVQQLREKNFDEFSKHLKGLVNLYNLPGDNKLKTKMYLALQSLEQDLSKMAIMYWKATNAGPLDKILHGSVGYLTPRSGGHLMNLKYYASPSDLLDDKTASPIILHENNVPRSLGMNASVTIEGTSAMYKLPIAPLIMGSHPADSKWTPSFSSITSANSVDLPACFFLKFPQPIPVSRAFVQKLQNCTGIPLFESQPTYVPLYELITQFELSKDPDPIPLNHNMRFYAALPGQQHCYFLNKDAPLPDGRSLQGTLISKITFQHPGRVPLILNMIRHQVAYNTLIGSCVKRTILKEDSPGLLQFEVCPLSESRFSVSFQHPVNDSLVCVVMDVQDSTHVSCKLYKGLSDALICTDDFIAKVVQRCMSIPVTMRAIRRKAETIQADTPALSLIAETVEDMVKKNLPPASSPGYGMTTGNNPMSGTTTPTNTFPGGPITTLFNMSMSIKDRHESVGHGEDFSKVSQNPILTSLLQITGNGGSTIGSSPTPPHHTPPPVSSMAGNTKNHPMLMNLLKDNPAQDFSTLYGSSPLERQNSSSGSPRMEMCSGSNKTKKKKSSRLPPDKPKHQTEDDFQRELFSMDVDSQNPIFDVNMTADALDTPHITPAPSQCSTPPTAYPQPVPHPQPSIQRMVRLSSSDSIGPDVTDILSDIAEEASKLPSTSDDCPPIGTPVRDSSSSGHSQSALFDSDVFQTNNNENPYTDPADLIADAAGSPSSDSPTNHFFPDGVDFNPDLLNSQSQSGFGEEYFDESSQSGDNDDFKGFASQALNTLGVPILGADNGETKFKSNSQADTVDFSIISVTGKALGPAELMEHHSGSQSPLLTTGDLGKXKTPKRVKEGNGTTNSSLSGPGLDSKPGKRSRTPSNDGKSKDKPPKRKKVDTEGKSPSHSSSNRPFTPPTSTGGSKSPGSSGRSQTPPGVATPPIPKITIQIPKGTVMVGKPSSHSQYTSSGSVSSSGSKSHHGHSSSSSSSSSASTSSKMKSSKSEGSSSSKLASSVYSSQGSSGSSQSKNSSQSGGKPGSSPITKHGLSSGSSSTKMKPQGKPSSLMNPLSKPNISPSHSRPPGSSDKLASPMKPVPGTPPSSKAKSPISSGSGGSHMSATSSSSGMKSSSGLGSSGSLSQKTPPSSNSCTASSSSFSSSGSSMSSSQNQHGSSKGKSPSRNKKPSLTAVIDKLKHGVVTSGPGSEDAVDGQMGVSTNSSHLMSSKHNMSGGEFQGKREKSDKDKSKVSTSGGSVDSSKKTSESKNVGSTGVAKIIISKHDGGSPSIKAKVTLQKPGESSGEGLRPQMTSSKNYGSPLISGSTPKHERGSPSHSKSPAYTPQNLDSESESGSSIAEKSYQNSPSSDDGIRPLPEYSTEKHKKHKKEKKKVKDRDRDRDKDRDKKKSHSIKPESWSKSPISSDQSLSVTSNAILSVDRPSRLSPDFMIGEEDDDLMDVALIGN
Length1564
PositionMiddle
OrganismHeterocephalus glaber (Naked mole rat)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Mammalia> Eutheria> Euarchontoglires> Glires> Rodentia> Hystricomorpha> Bathyergidae> Heterocephalus.
Aromaticity0.04
Grand average of hydropathy-0.646
Instability index54.24
Isoelectric point8.95
Molecular weight166386.00
Publications
PubMed=21993625

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. 
ECO:0000256	RuleBase:RU364059
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

>MDP28426
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             7|     365.25|      48|      48|    1063|    1110|       1
---------------------------------------------------------------------------
  966- 1009 (51.06/11.51)	S..........SLSGPGLD..S..........KPGKRSRTP.....SN....DGKSKdkP..PK..R.....KKVDTEGKS.....PSH
 1010- 1065 (45.79/ 9.45)	SSsnrpFTPPT..STGGSK..S...........PGSSGRSQ.....TP....PGVAT..PpiPK..ItiqipKGTVMVGKP.....SSH
 1066- 1113 (80.11/22.85)	SQ....YTSSGSVSSSGSK..S..........HHGHSSSSS.....SS....SSAST..S..SK..M.....KSSKSEGSS.....SSK
 1117- 1168 (47.00/ 9.93)	SV....YSSQGSSGSSQSKnsS..........QSGGKPGSSpitkhGL....SSGSS..S..TK..M.....KP...QGKP.....SSL
 1169- 1219 (56.50/13.63)	MN....PLSKPNISPSHSR..P..........P.GSSDKLA.....SPmkpvPGTPP..S..SK..A.....KSPISSGSG.....GSH
 1220- 1270 (43.61/ 8.61)	MS....ATS....SSSGMK..S..........SSGLGSSGS.....LS....QKTPP..S..SNscT.....ASSSSFSSSgssmsSSQ
 1271- 1323 (41.19/ 7.66)	NQ....HGSSKGKSPSRNK..KpsltavidklKHGVVTSGP.....GS....EDAVD..G..QM..G.....VS.....TN.....SSH
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     165.52|      44|      50|     309|     358|       2
---------------------------------------------------------------------------
  253-  307 (47.96/19.03)	...LPiaplIMGSHPAdskWTPSFSSITsansvdlpaCFFL.KFPQPIPVSRA..FVQKL...Q
  309-  356 (75.56/53.42)	CTGIP....LFESQPT...YVPLYELIT.........QFELSKDPDPIPLNHNMrFYAALpgqQ
  419-  447 (42.00/16.86)	SPGLL....QFE.......VCPLSE..S.........RFSVSFQH...PVNDSL..........
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      40.01|      14|      19|    1425|    1441|       3
---------------------------------------------------------------------------
 1425- 1438 (26.19/ 6.88)	TPKH.....ERGSPSHSKS
 1442- 1460 (13.83/ 6.36)	TPQNldsesESGSSIAEKS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      48.14|      18|      19|    1327|    1344|       4
---------------------------------------------------------------------------
 1336- 1356 (23.48/ 9.03)	FQGKREKSDkdkSKVSTSGGS
 1387- 1404 (24.66/ 9.91)	PSIKAKVTL...QKPGESSGE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      89.48|      18|      20|     526|     543|       5
---------------------------------------------------------------------------
  526-  543 (37.77/17.02)	PPASSPGYGMTTGNNPMS
  548-  564 (26.87/ 9.63)	PTNTFPGGPITTLFN.MS
  656-  673 (24.84/ 8.26)	SSSGSPRMEMCSGSNKTK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|      88.27|      18|      64|     714|     731|       6
---------------------------------------------------------------------------
  714-  728 (21.72/ 8.22)	......TADALD.TPHITPAPS
  729-  747 (23.40/ 9.60)	QCStppTAYPQP.VPH..PQPS
  753-  769 (22.20/ 8.62)	RLS...SSDSIG..PDVTDILS
  841-  859 (20.95/ 7.59)	NHF...FPDGVDfNPDLLNSQS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      97.98|      30|      64|     138|     182|       7
---------------------------------------------------------------------------
  138-  168 (47.97/48.63)	HLKGLVNlYNLP..GDNKLKTKMYLALQSLEQD
  188-  219 (50.02/20.70)	ILHGSVG.YLTPrsGGHLMNLKYYASPSDLLDD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      87.25|      26|     157|     618|     655|       9
---------------------------------------------------------------------------
  587-  612 (48.57/29.22)	PILTSLLQ.ITGNGGSTI.GSSPTPPHH
  628-  655 (38.68/18.83)	PMLMNLLKdNPAQDFSTLyGSSPLERQN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      55.43|      19|      21|     876|     896|      11
---------------------------------------------------------------------------
  876-  896 (25.86/21.86)	DNDD..FKGfASQAlNTLGVPIL
  899-  919 (29.57/15.22)	DNGEtkFKS.NSQA.DTVDFSII
---------------------------------------------------------------------------




































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 MDP28426 with Med1 domain of Kingdom Metazoa


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) FSIISVTGKALGPAELMEHHSGSQSPLLTTGDLGKXKTPKRVKEGNGTTNSSLSGPGLDSKPGKRSRTPSNDGKSKDKPPKRKKVDTEGKSPSHSSSNRPFTPPTSTGGSKSPGSSGRSQTPPGVATPPIPKITIQIPKGTVMVGKPSSHSQYTSSGSVSSSGSKSHHGHSSSSSSSSSASTSSKMKSSKSEGSSSSKLASSVYSSQGSSGSSQSKNSSQSGGKPGSSPITKHGLSSGSSSTKMKPQGKPSSLMNPLSKPNISPSHSRPPGSSDKLASPMKPVPGTPPSSKAKSPISSGSGGSHMSATSSSSGMKSSSGLGSSGSLSQKTPPSSNSCTASSSSFSSSGSSMSSSQNQHGSSKGKSPSRNKKPSLTAVIDKLKHGVVTSGPGSEDAVDGQMGVSTNSSHLMSSKHNMSGGEFQGKREKSDKDKSKVSTSGGSVDSSKKTSESKNVGSTGVAKIIISKHDGGSPSIKAKVTLQKPGESSGEGLRPQMTSSKNYGSPLISGSTPKHERGSPSHSKSPAYTPQNLDSESESGSSIAEKSYQNSPSSDDGIRPLPEYSTEKHKKHKKEKKKVKDRDRDRDKDRDKKKSHSIKPESWSKSPISSDQSLSVTSNAILSVDRPSRLSPDFMIGEEDDDLMDVALIGN
2) KNLPPASSPGYGMTTGNNPMSGTTTPTNTFPGGP
3) LFNMSMSIKDRHESVGHGEDFSKVSQNPILTSLLQITGNGGSTIGSSPTPPHHTPPPVSSMAGNTKNHPMLMNLLKDNPAQDFSTLYGSSPLERQNSSSGSPRMEMCSGSNKTKKKKSSRLPPDKPKHQTEDDFQRELFSMDVDSQNPIFDVNMTADALDTPHITPAPSQCSTPPTAYPQPVPHPQPSIQRMVRLSSSDSIGPDVTDILSDIAEEASKLPSTSDDCPPIGTPVRDSSSSGHSQSALFDSDVFQTNNNENPYTDPADLIADAAGSPSSDSPTNHFFPDGVDFN
4) LLNSQSQSGFGEEYFDESSQSGDNDDFKGFA
916
523
560
854
1564
556
851
884










Molecular Recognition Features






MoRF SequenceStartStop




1) DQTKKEAEPTPETIKS
2) KNVQQTLSTKGPPEKRIRLQ
3) RDDYGLL
4) VDALLVDLRQKFPPKFVQ
248
270
8
220
263
289
14
237