<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 MDP27639

Description Mediator of RNA polymerase II transcription subunit 5
SequenceMVTVTDPLTARLEAAIKAWSDFFSDAEHERLDPAIFADQSQTLFANHPLAPVPLADLLLRPTPSNRECVDQRTLQYLQVLQKQGRITTAAVLRALYKYSTAHTRAQTPDGKPKHGAGDSSTNDADVGGSSKADLTSRMVRWRNSYMVEEDVLWRLARAVNHGTGIKTSHDVTEVAKVLARWTALFAEVSAAISRDAFNSMNGLQVKDESEDARNAFVLFYFAFCENQLVNETLSQPVCKDICRKLLDSLDAFLPTLMHLTADITGRLEHFRSEVLARYAPQEKKSMDMPSFMNDLSMSLESFQVPELPVVNTRAGLYIYLGAALVGRPMIDDEALFSYLHNRYQGDLQAMAVHLILASFDLLANAVFRNEGAKTGHLLKSFLINKVPLILVQLVAYAATTMYPFNAEMCITEALNQVDINMFPTLSGMFDMPNNNSFNDSVRQDFCFACQLHGLLSQAAIETLLGDITYQSLPPEGRYVKEQLVQACLQEPDRTLKLIGELDNMNGNVGAAAQAIVEICRDLASKPLSLDVLLLFDKPHKILHPLCELLDNWAGYEEDHGEYQPVYEEFGSVLLLLLAFVYRYNLSTADLGIRSSGSFVAKLLNGVDRCQPLEQLSEQEKSHLGGWIHGLFDTEAGGLGDELMSSCPPQDFYLLAPTLFHQIVNALSAGYLTDEMLKGGLEYLVDVLLLPALVPALLYLSNLLWADNQPIQNAVIKILQPILKPTSISNEASTMLSSVLNIVAKPLEHALKSYQRQDPECQKIEPLLLAIADNLAVSRRTGGADHTELESWCSAQITNPATGALIHGGLAAAVRTTIQQLVQWAQNPTLNSMNGMPAPYTHRQTLAAQQILGPHRLLGIILDELKSSPEPGIAYDVVTTMICAPDVRNSTISSPSTQSNNSSDHNDQAQNHQSQDAKHKHPHRLTLRDALRLEAHDFRAHLRADPVLAETVVRLYRRVEAQLTPLALPLPPAAAAAPAVGVNVGVDAATAAAAAAAAAMMPDALGLGVVGGVELGGMEGAIAAAVAAANGSGTGGAGGDGTQGGAGDAGMGLDGQQQGQGGSSAGDMGLGGGTADDIFSGLSGPDDFGADFGSWSMDLS
Length1099
PositionTail
OrganismChaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Pezizomycotina> Sordariomycetes> Sordariomycetidae> Sordariales> Chaetomiaceae> Chaetomium.
Aromaticity0.07
Grand average of hydropathy-0.047
Instability index38.29
Isoelectric point5.00
Molecular weight118675.43
Publications
PubMed=21784248

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

>MDP27639
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     125.59|      32|      34|     986|    1019|       1
---------------------------------------------------------------------------
  987- 1019 (38.57/24.61)	.AATAAAAAAAAAMMpDALGLGVVGGVeLGGMEG
 1024- 1043 (35.44/14.64)	AV......AAA.....NGSGTGGAGG...DGTQG
 1053- 1083 (51.57/24.49)	DGQQQGQGGSSAGDM..GLGGGTADDI.FSGLSG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      93.05|      29|      33|     635|     666|       2
---------------------------------------------------------------------------
  635-  666 (46.45/33.22)	AGGLGDELMSSCPPqdfYLLAPTLFHQIVNAL
  668-  696 (46.60/25.22)	AGYLTDEMLKGGLE...YLVDVLLLPALVPAL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      65.55|      23|      29|     791|     819|       3
---------------------------------------------------------------------------
  791-  819 (28.01/33.50)	WcsAQitNPATGALihGGLAAAV..RTTI..QQ
  823-  849 (37.55/20.70)	W..AQ..NPTLNSM..NGMPAPYthRQTLaaQQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      62.07|      19|      35|     248|     271|       4
---------------------------------------------------------------------------
  248-  271 (25.73/26.74)	SLDafLPTLMHltaDITGRLEHFR
  285-  303 (36.34/20.67)	SMD..MPSFMN...DLSMSLESFQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     103.57|      31|      35|     354|     387|       5
---------------------------------------------------------------------------
  352-  376 (27.80/20.16)	........VHLIL...asFDLLANAV.....FRNEGAKTGH
  378-  413 (44.48/28.37)	LKSFLINKVPLIL.....VQLVAYAAttmypFNAEMCITEA
  414-  442 (31.30/13.66)	LNQVDINMFP...tlsgmFDMPNNNS.....F.NDSVR...
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      40.73|      12|      29|     712|     723|       6
---------------------------------------------------------------------------
  712-  723 (20.09/14.72)	NAVIKILQPILK
  740-  751 (20.64/15.33)	NIVAKPLEHALK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      44.26|      13|      29|     570|     582|       7
---------------------------------------------------------------------------
  570-  582 (21.71/14.24)	GSVLLLLLAFVYR
  596-  608 (22.55/15.11)	GSFVAKLLNGVDR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      61.18|      18|      29|     931|     948|       9
---------------------------------------------------------------------------
  931-  948 (30.95/18.25)	RLEAHDFRAHLRADPVLA
  957-  974 (30.23/17.63)	RVEAQLTPLALPLPPAAA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     130.46|      37|      37|     151|     187|      10
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  114-  157 (38.13/26.89)	.....HGAGDSSTNDAdvggsskADLTSRMVRWRNSYmveEDVLWRLAR
  158-  194 (58.96/46.39)	AVN..HGTGIKTSHDV.......TEVAKVLARWTALF...AEVSAAISR
  196-  225 (33.37/22.43)	AFNsmNGLQVKDESED.......ARNAFVL..FYFAF...CE.......
---------------------------------------------------------------------------




































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 MDP27639 with Med5 domain of Kingdom Fungi
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