<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 MDP20480

Description Mediator of RNA polymerase II transcription subunit 1
SequenceMKAQGETEESEKLSKMSSLLERLHAKFNQNRPWSETIKLVRQVMEKRVVMSSGGHQHLVSCLETLQKALKVTSLPAMTDRLESIARQNGLGSHLSASGTECYITSDMFYVEVQLDPAGQLCDVKVAHHGENPVSCPELVQQLREKNFDEFSKHLKGLVNLYNLPGDNKLKTKMYLALQSLEQDLSKMAVMYWKATNAGPLDKILHGSVGYLTPRSGGHLMNLKYYASPSDLLDDKTTSPIILHENNVPRSLGMNASVTIEGTSAMYKLPIAPLIMGSHPVDNKWTPSFSSITSANSVDLPACFFLKFPQPIPVSRAFVQKLQNCTGIPLFETQPTYVPLYELITQFELSKDPDPLPLNHNMRFYAALPGQQHCYFLNKDAPLPDGRSLQGTLVSKITFQHPGRVPLILSLIRHQVAYNTLIGSCVKRTILKEDSPGLLQFEVCPLSESRFSVSFQHPVNDSLVCVVMDVQDSTHVSCKLYKGLSDALICTDDFIAKVVQRCMSIPVTMRAIRRKAETIQADTPALSLIAETVEDMVKKNLPPASSPGYGMTTGNNPMSGTTTPTNTFPGGPITTLFNMSMSIKDRHESVGHGEDFSKVSQNPILTSLLQITGNGGSTIGSSPTPPHHTPPPVSSMAGNTKNHPMLMNLLKDNPAQDFSTLYGSSPLERQNSSSGSPRMEICPGSNKTKKKKSSRLPPDKPKHQTEDDFQRELFSMDVDSQNPIFDVNMTADTLDTPHITPAPSQCSTPPTTYPQPVPHPQPSIQRMVRLSSSDSIGPDVTDILSDIAEEASKLPSTSDDCPPIGTPVRDSSSSGHSQSALFDPDVFQTNNNENPYTDPADLIADAAGSPSSDSPTNHFFPDGVDFNPDLLNSQSQGGFGEEYFDESSQSGDNDDFKGFASQALNTLGVPMLGGDNGETKFKGNSQADTVDFSIISVAGKALGPADLMEHHSGSQSPLLTTGDLGKEKTQKRVKEGNGTSNSSLSGPGLDSKPGKRSRTPSNDGKSKDKPPKRKKADTEGKSPSHSSSNRPFTPPTSTGGSKSPGSSGRSQTPPGVATPPIPKITIQIPKGTVMVGKPSHSQYTSSGSVSSSGSKSHHSHSSSSSSSSSASNSGKMKSSKSEGSSSSKLSSSVYSSQGSSGSSQSKNSSQSGGKPGSSPITKHGLSSGSSSTKMKPQGKPSSLMNPSLSKPNISPSHSRPPAGSDKLASPMKAVPGTPPSSKAKSPISSGSGGSHMSGTSSSTGMKSSSGLGSSGSLSQKTPPSSNSCTASSSSFSSSGSSMSSSQNQHGSSKGKSPSRNKKPSLTAVIDKLKHGVVTSGPGGEDPMDGQMGVSTNSSSHPMSSKHNMSGGEFQGKREKSDKEKSKVSTSGGSVDSSKKTSESKNVGSTGVAKIIISKHDGGSPSIKAKVTLQKPGESSGEGLRPQMASSKNYGSPLISGSTPKHERGSPSHSKSPAYTPQNLDSESESGSSIAEKSYQNSPSSDDGIRPLPEYSTEKHKKHKKEKKKVKDKDRDRDRDKDRDKKKSHSIKPESWSKSPISSDQSLSLTSNTILSTDRPSRLSPDFMIGEEDDDLMDVALIGN
Length1582
PositionMiddle
OrganismOdobenus rosmarus divergens (Pacific walrus)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Mammalia> Eutheria> Laurasiatheria> Carnivora> Caniformia> Odobenidae> Odobenus.
Aromaticity0.04
Grand average of hydropathy-0.680
Instability index54.03
Isoelectric point8.88
Molecular weight168500.21
Publications









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

>MDP20480
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     219.29|      47|      50|     965|    1011|       1
---------------------------------------------------------------------------
  965- 1011 (77.32/19.37)	KEKTQKRVKEGNGTSNS.SLSGPGLDSKPG.KRSRTPSNDGKSKDKPPK
 1012- 1054 (54.92/11.70)	RKKADT...EGKSPSHS.SSNRPFTPPTST.GGSKSPGSSGRSQ.TPPG
 1219- 1262 (46.52/ 8.82)	SSKAKSPISSGSGGSH...MSGTS..SSTGmKSSSGLGSSGSLSQKTPP
 1263- 1297 (40.54/ 6.77)	SSNS......CTASSSSfSSSGSSMSSSQN.QH.......GSSKGKSPS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     134.77|      24|      24|    1084|    1107|       2
---------------------------------------------------------------------------
  615-  635 (29.79/ 6.31)	..GSTIGSSPTPPH.HTPPPVSSM
  798-  818 (31.58/ 7.16)	DDCPPIG...TPVRDSSSSGHSQS
 1084- 1107 (40.21/11.26)	SSGSVSSSGSKSHHSHSSSSSSSS
 1149- 1171 (33.19/ 7.93)	QSGGKPGSSPITKHG.LSSGSSST
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     305.34|      67|      68|    1364|    1430|       3
---------------------------------------------------------------------------
 1108- 1179 (37.02/ 6.51)	........................SASNSGKMKSSKSEGSSSSKLSSSVYSSQG.SSGSSqsknssqsggkpgsspitkhglssgssstkMKPQ.GKP
 1312- 1362 (80.88/22.56)	KHGVV.TSGPG..GEDPMDGQMGVSTNSSSHPMSSKHNMSG............GEFQGK................................REKSDKE
 1363- 1429 (102.42/30.44)	KSKVS.TSGGSVDSSKKTSESKNVGSTGVAKIIISKHDGGSPSIKAKVTLQKPGESSGEG..............................LRPQMASS
 1430- 1489 (85.01/24.07)	KNYGSpLISGSTPKHERGSPSHSKSPAYTPQNLDSESESGS.SIAEKSYQNSP..SSDDG..............................IRP.....
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      64.28|      13|      25|     300|     312|       4
---------------------------------------------------------------------------
  300-  312 (27.76/17.40)	PA...............CFFLKFPQPIP
  328-  338 (20.69/10.86)	P.................LFETQPTYVP
  356-  383 (15.83/ 6.37)	PLnhnmrfyaalpgqqhCYFLNKDAPLP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     486.08|     112|     340|     490|     605|       5
---------------------------------------------------------------------------
  392-  482 (95.70/34.98)	.....LVSKITfQHPGRVPLILSLIRHQ...VAYNT....LIG....SCVKRTILKED..SPGL.LQ.FEVCPLS.ESRF.SVSFQH.PVNdSLVCVVMDVQD.sTHVSckLYKG............................................
  490-  605 (184.42/79.28)	TD..DFIAKVV.QRCMSIPVTMRAIRRKAETIQADTPALSLIAetveDMVKKNLPPAS..SPGYGMT.TGNNPMSGTTTP.TNTFPGGPIT.TLFNMSMSIKD..RHES..VGHGE......DFS..................KV.......SQNPILT
  636-  722 (77.58/27.04)	................................AGNTKNHPMLM....NLLKDN..PAQdfSTLYGSS.PLERQNSSSGSPrMEICPGSNKT.KKKKSSRLPPDkpKHQT.....ED......DFQ..................RElfsmdvdSQNP...
  836-  959 (128.38/49.31)	TDpaDLIADAA.GSPSSDSPTNHFF...PDGVDFN....PDL...........LNSQS..QGGFGEEyFDESSQSGDNDD.FKGFASQALN.TL.GVPMLGGD..NGET..KFKGNsqadtvDFSiisvagkalgpadlmehhSG.......SQSPLLT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     132.64|      45|      48|     152|     199|       6
---------------------------------------------------------------------------
  165-  213 (68.11/43.34)	GDNKLKTKMYLALQSLEQDLSKMAVMYWKatNAGP......ldKILHGSVG.YLTP
  216-  269 (64.53/39.94)	GGHLMNLKYYASPSDLLDDKTTSPIILHE..NNVPrslgmnasVTIEGTSAmYKLP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      39.52|      12|      16|    1496|    1507|       8
---------------------------------------------------------------------------
 1496- 1507 (19.60/12.17)	EKHKKHKKEKKK
 1514- 1525 (19.91/12.49)	DRDRDKDRDKKK
---------------------------------------------------------------------------




































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 MDP20480 with Med1 domain of Kingdom Metazoa
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