<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 MDP13861

Description Mediator of RNA polymerase II transcription subunit 13 (Fragment)
SequenceMNRHSNIFVLLSPNGIPAYLYSSEIQNSYEIEFILTEWSKCYGIPKEKLYYQDKNCNMPLVITVYIPELDCYINYPTRCIFIIDSKNSFNIGRRLCYNPRIYHQFNKFIWRDQSIHNDTLIFANVNNSIKYENNDIINQIDKINNTIKSKNISVEKIILNELIKEDKIINEIDNESMSVKNNNINGKTSNSNPNTPTNINKANTPYTTIENNTQVEDNYDMPGIFNESNFDDFGDWGTTGIEITDKDFDFFDDKPSQSKTMSDDFGLNGFLSDPIFDNKDINKQSSMDSLSQNTLTDIKMEEKNESNNILPTTLGAQDIGTPSSINININQTINSIHNSPEQISMSPINNIMSPQSVMPTSSPLVNVHSQNSISSASNEVINNSTNDINNSTFINNVSYNTNNSLNNGNNVASPIINEESVNDGDSAIPREWELKSSNYNYFENIIEKYHKGKWSYEPKLSSYIAKNNDINANNKTILHTDTDITTENKISIDFASAWKMLNIPDYNSISNIIEKSLNDMSLRQDLLCNNMNVKIKDRNNDDVSVNVEQEHINLYSVLDRISQKIFIDQYTGSLSSWNKSVSSSLSTITFSEENQLYDEYLIPSLVSKALNQLQVIFEDLFGSDNESKYNMKNIYVEGPLTIKQLYDSEHLQHAKYGKYQVKKKTKKNLDYVLEKLSTPNIIVENNNEWIELSSTSLRFWDKIGVLPYSGKKNISWFALCPTMKEYNGEPNINSDLINIVREWIQSLSYIYESSNFGTHTPGTLKSIKGIIPCLLEDNNINTNSHNNILAIENILNSYEKSISYFASIMGENIHGIIEEGEETTMSEIDECLNNDQKYIVLYLLSPFSSSDKTFIDDNEAKSINYRLCQMFVNSFLYKLALNTRLSIEKLKAKIILQIIPLDLIANNHSFDGYITIGLKDLVFTIYSKCRKLLQKNINVNNSEFLIFNDLYQPSYILSQSAIPIPYFSFEKFSRKNQLKNRINIMEPDRILHIAYINVDNRAIACMTDNIGELFEIIIVDDINERLNSISPLDYNKYTKQQIRFIKIWEKAMKLILFGCNFYWRIAIVKIGHVLQDEVNDWEFISSIYLGKLQHLYNRPALNIINNLNEYIYSVSVLGIYKNSTLQLFKEKIKTNGTNTNPLSRRDSEKLSSSQNSSQSIFKNSSKMDINDLNEIIINLSNSCYTYIHSVQRSPSFPSNPEIIWPLLSSKNNNSLKESLALPLSVGWMIYTPSMESKQVGINTKNFEILLLSHQHCNPGKSSKTCFPTWNPVIPTTPISMPNSPSNNSVNNSKNVNGINPPTLIKSNSISMKDINSPLSMASSSSSLSLNTTTSVPYNVILSDLIKQYFSLSFLEIHWSNLINTANGYASDDIRLPIHISSANRISKILKGFNF
Length1394
PositionKinase
OrganismNeocallimastix californiae
KingdomFungi
LineageEukaryota> Fungi> Fungi incertae sedis> Chytridiomycota> Chytridiomycota incertae sedis> Neocallimastigomycetes> Neocallimastigales> Neocallimastigaceae> Neocallimastix.
Aromaticity0.09
Grand average of hydropathy-0.419
Instability index47.11
Isoelectric point5.44
Molecular weight159110.48
Publications









Function






Annotated function

Component of the SRB8-11 complex. The SRB8-11 complex is a
regulatory module of the Mediator complex which is itself involved in
regulation of basal and activated RNA polymerase II-dependent
transcription. The SRB8-11 complex may be involved in the
transcriptional repression of a subset of genes regulated by Mediator.
It may inhibit the association of the Mediator complex with RNA
polymerase II to form the holoenzyme complex.



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

>MDP13861
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     111.21|      26|      31|     126|     152|       1
---------------------------------------------------------------------------
   92-  120 (35.12/12.96)	GRRLCY.NPRIYHQFNKFiwrDQSIHNDTL
  126-  152 (40.68/19.61)	NNSIKYeNNDIINQIDKI...NNTIKSKNI
  160-  184 (35.41/13.14)	NELIK..EDKIINEIDNE...SMSVKNNNI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             5|     175.93|      30|      31|    1270|    1299|       2
---------------------------------------------------------------------------
  307-  336 (29.77/ 7.72)	NNILP.TTLGAQDiGTPSSINININQTINSI.
  338-  361 (28.21/ 6.93)	......NSPEQIS.MSPINN.IMSPQSVMPTS
  362-  389 (35.05/10.37)	SPLVNvHSQNSI..SSASNEVINNS..TNDIN
 1270- 1299 (52.28/19.02)	NPVIP.TTPISMP.NSPSNNSVNNSKNVNGIN
 1312- 1335 (30.62/ 8.14)	KDI...NSPLSMA.SSSSSLSLNTTTSV....
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     818.58|     264|     309|     421|     727|       3
---------------------------------------------------------------------------
  187-  297 (66.23/17.49)	.............................................KTSNSNPNTPTnINKANTPYTTiENNTQVednyDMPGIFNESNFDDFGDWGTTgIEITDKDFDFFDDKPSQSKTM......SDDFG.....LNgflsdpiFDNKDINKQSSMDSL..SQNTLTD..................................................................................................................................................................................
  421-  706 (411.80/271.77)	VNDGDSAIPREWeLKSSNYNYFENIIEKYHKGKWSYEPKLSSYIAKNNDINANNKT.ILHTDTDITT.ENKISI....DFASAWKMLNIPDYNSISNI.IEKSLNDMSLRQDLLCNNMNVKIKDRNNDDVS.....VN.......VEQEHINLYSVLDRI..SQKIFIDQYTGslsswnKSVSSSLSTI...TFseenqLYDEYL.....IPSLVSKALnqLQVIFEDLFgSDNES.....................KYNMKNIYVEGP..LTIKQLYDSEHL..QHA......KYGKYQVKKKTKKNLDyVLEklstPNIIVenNNEWIELSSTSLR.FWDKIGVL
  732- 1013 (340.56/162.76)	INSDLINIVREW.IQSLSYIYESSNFGTHTPGTLKSIKGIIPCLLEDNNINTN............................SHNNILAI...ENILNS.YEKSI...SYFASIMGENIHGIIEEGEETTMSeidecLN.......NDQKYIVLY.LLSPFssSDKTFIDDNEA......KSINYRLCQMfvnSF.....LYKLALntrlsIEKLKAKII..LQIIPLDLI.ANNHSfdgyitiglkdlvftiyskcrKLLQKNINVNNSefLIFNDLYQPSYIlsQSAipipyfSFEKFSRKNQLKNRIN.IME....PDRIL..HIAYINVDNRAIAcMTDNIGEL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      73.93|      23|      25|    1189|    1211|       4
---------------------------------------------------------------------------
 1189- 1211 (42.67/25.62)	SVQRSPSFP.SNPEIIW.PLLSSKN
 1214- 1238 (31.25/16.52)	SLKESLALPlSVGWMIYtPSMESKQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      72.68|      22|      31|    1121|    1142|       5
---------------------------------------------------------------------------
 1121- 1142 (36.29/21.15)	KNSTLQLFKEKIKTNGTNTNPL
 1154- 1175 (36.39/21.24)	QNSSQSIFKNSSKMDINDLNEI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      76.13|      25|      27|      16|      42|       6
---------------------------------------------------------------------------
   16-   42 (37.54/29.89)	IP.AYLYSSEiQNSyEIEFILTEW...SKCY
   44-   72 (38.58/20.94)	IPkEKLYYQD.KNC.NMPLVITVYipeLDCY
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      63.88|      19|      31|    1048|    1067|       7
---------------------------------------------------------------------------
 1048- 1067 (33.61/22.68)	WEkAMKLILFG..CNFYWRIAI
 1081- 1101 (30.27/15.69)	WE.FISSIYLGklQHLYNRPAL
---------------------------------------------------------------------------




































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 MDP13861 with Med13 domain of Kingdom Fungi
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