<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 MDP06883

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMTAAANWVANGASLEDCHSNLFSLAELTGIKWRRYNFEGHGDCGPIISAPAQDDPILLSFIRCLQANLLCVWRRDVKPDCKELWIFWWGDEPNLVDVIHRELHMVEEGLWENGLSYECRTLLFKAIHNLLERCLMDKNFVRIGKWFIRPYEKDEKPVNKSEHLSCAFTFFLHGESNVCTSVEIAQHQPIYLINEEHIHMAQSSPTPFQVLVSPYGLNGTLTGQAYKMSDPATRKLMEEWQYFYPMVLKKKEGMKEEEELGYDDDFPVAVEVIVGGVRMVYPSAFVLISQSDIPMAQSAASCGGHINVGQPGLGSTKDPSSCGMPLTPPTSPEQAIISESGGTHNSVSLSAAQEGTVTVHSPKKSGKMPPKFHSHMVHRVWKECILNRAQSKRSQIATPNMEEEVPSNTVSWDFVDPVQRVSCSCSRHKLFKQRCATGTSRPPTISQPGFTVGSSSTSASLPPPASSKHKITERQEKGDKLQKRPMMPFHHRPSVTEELCMEQDAAGQKLGLAGMETSLEVPNSRKYEKQLSIPTGNPSKQMNLNPMDSPHSPTSPLPPTLSPQPRGQEAENLDPPSVPVNPALYGNGLELQPLPSLDDRTVLVGQRLPLMAEVSETALYCGIIHNNESSDKWRSYVLPSSEDPEFRLPDLPCERCDAKMEVNSDSTALKRLLAQPNKRFKILEDVKPGQTVNYLDPLPLIQQSGEGLGDASDPYTFEDGDIKYSFTGTKKCKLGTDKDPLKKNKSEDGIGTKEIPTPGHSTPVPDGKDAMSIFSSAPKADTRQDGAAGRVGSGSLTQVTDLAPSLHDLDNIFDNSDEDELGAVSPALRSSKMPAVGTEERPLGKDGRTAVPYPPTVADLQRMFPTPPSLEQHPAFSPVMNYKDGISSETVTALGMMESPMVNMVQTQLTEFKMEVEDGLGSPKPEEIKDFSYVHKVPSFQPFVGSSMFAPLKILPSQCLLPLKLPDACIFRPSWAVPPKIEQLPMPPAATFIRDGYNNVPSVGSLADQDYLQMNTPQMNTPVTLNSAAPASNSGAGVLPSPATPRFSVPTPRTPRTPRTPRGGGTASGQGSVKYDSTDQGSPASTPSTTRPLNSVEPATVQPIPEAHSLYVTLILSDSVLNIFKDRNFDSCCICACNMNIKGADVGLYIPDSSNEDQYRCTCGFSAIMNRKLGYNSGLFIEDELDIFGKTSDIGQAAERRLMMCQTTLLSQVGDGGRRTQEPPMSLLLLLQNQHTQPFTSLSCLDYMSSNNRQTLPCMNWSYDRLQAESNDSWIECFNALEQGRQYVDNPTGGKVDEALVRSATVHSWPHSNVLDISMLSSQDVVRMLLSLQPFLQDAIQKKRTGRTWENIQHVQGPLTWQQFHKMAGRGTYGSEESPEPLPIPTLLVGYDKDFLTISPFSLPFWERLLLDPYGGHRDVAYIVVCPENEALLDGAKTFFRDLSAVYEMCRLGQHKPICKVLRDGIMRVGKTVAQKLTDELVSEWFNQPWGTEECDNHSKLKLYAQVCRHHLAPYLATLQLDSSLLLPPKYQTPASASQGQTIPGNSGSVPPNSTSHSAPGAPPTGNSFNSTPSGGNTNLAAGSSSASGPPVPQLSASSSTPSINQMSATSSSGFSGSVGPGQNTSTGGNSADRPQGNTGSGGDTESGQNSSQQQSQQEGQEGVTERERIGIPTEPESADSNAYPPAVVIYMVDPFTYTADEESASANFWLLSLMRCYTEMLDNLPENMRNSFILQIVPCQYMLQTMKDEQVFYIQHLKSLAFSVYCQCRRPLPTQIHIKSLTGFGPAASIEMTLKNPERPSAIQLYSPPFILAPIKDKQTELGETFGEASQKYNVLFVGYCLSHDQRWLLASCTDLHGELLETCIVNIDLPNRSRRSKLSARKIGLQKLWEWCIGIVQMTSLPWRVVIGRLGRLGHGELKDWSILLGECSLQTISKQLKEVCRMCGISSADSPSILSACLVAMEPQGSFVVMPDAVTMGSVFGRSTALNLQSSQLNTPQDASCTHILVFPTSATIQVAPAHYPNEDGFSPNNDDMFDLPFPEDMDNDIGILITGNLHSSPNSSPVPSPGSPGIGVGSHFQHSRSQGERLLSREAPEELKQQPLALGYFVSTAKAENLPQWFWSSCPQAQNQCPLFLKASLHHHISVAQTDELLPARNSQRVPHPLDSKTTSDVLRFVLEQYNALSWLTCNPATQDRSSCLPVHFVVLTQLYNAIMNIL
Length2218
PositionMiddle
OrganismAlligator mississippiensis (American alligator)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Archelosauria> Archosauria> Crocodylia> Alligatoridae> Alligatorinae> Alligator.
Aromaticity0.07
Grand average of hydropathy-0.387
Instability index58.08
Isoelectric point5.55
Molecular weight243446.81
Publications
PubMed=22293439

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. 
ECO:0000256	RuleBase:RU364134
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

>MDP06883
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     195.72|      37|      39|    1557|    1593|       1
---------------------------------------------------------------------------
 1051- 1079 (44.27/18.11)	.....PRTPRT.PRTPRGGGTASGQGS..VKYDSTDQ
 1557- 1593 (67.12/31.79)	SAPGAPPTGNSFNSTPSGGNTNLAAGSSSASGPPVPQ
 1595- 1621 (44.00/17.95)	SASS.........STPS.INQMSATSSSGFSGSVGPG
 1624- 1651 (40.33/15.75)	TSTGGNSADRPQGNTGSGGDTESGQNSS.........
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             5|     145.20|      27|      27|     536|     562|       2
---------------------------------------------------------------------------
  441-  460 (31.76/12.13)	PPTISQ.....................P....GFTV.G...S.SSTSASL
  536-  556 (28.79/10.17)	..........................NPSKQMNLNPMD...SPHSPTSPL
  557-  578 (30.87/11.55)	PPTLSP....................QPRGQEAEN.LD...PPSVP....
  977- 1001 (29.09/10.37)	PPKIEQ....................LP.....MPPAAtfiRDGYNNVPS
 1002- 1048 (24.69/ 7.46)	VGSLADqdylqmntpqmntpvtlnsaAPASNSGAGVLP...SPATPRFSV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      88.43|      25|      28|    1127|    1151|       3
---------------------------------------------------------------------------
 1127- 1151 (51.81/32.72)	NFDSC.CICACN..MNIK.GADVGLYIPD
 1154- 1182 (36.63/20.85)	NEDQYrCTCGFSaiMNRKlGYNSGLFIED
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     108.51|      33|      38|      53|      86|       4
---------------------------------------------------------------------------
   53-   86 (55.95/38.98)	DDPILLSFI.RCLQANLLCVWRRDVKPDCKELwIF
   90-  123 (52.56/30.83)	DEPNLVDVIhRELHMVEEGLWENGLSYECRTL.LF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      64.79|      18|      18|    1242|    1259|       5
---------------------------------------------------------------------------
 1242- 1259 (33.58/22.17)	SCLDYMSSNNRQTLPCMN
 1261- 1278 (31.20/19.97)	SYDRLQAESNDSWIECFN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      57.82|      17|      22|    2039|    2058|       7
---------------------------------------------------------------------------
 2039- 2058 (28.76/22.31)	PFPEDMDNDIGIlitGN..LHS
 2064- 2082 (29.07/14.62)	PVPSPGSPGIGV...GShfQHS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      58.06|      16|      21|     287|     302|       8
---------------------------------------------------------------------------
  287-  302 (28.25/15.67)	ISQSDIPMAQSAASCG
  307-  322 (29.81/17.03)	VGQPGLGSTKDPSSCG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     118.80|      26|      38|     348|     383|       9
---------------------------------------------------------------------------
  348-  373 (44.92/16.37)	LSAAQEGTVTVHSPKKSGKMPPKFHS
  385-  410 (40.18/30.21)	LNRAQSKRSQIATPNMEEEVPSNTVS
 1535- 1555 (33.70/11.61)	.SASQGQTI....PGNSGSVPPNSTS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      49.40|      17|      21|    1700|    1720|      10
---------------------------------------------------------------------------
 1700- 1717 (25.94/23.63)	DE..ESASANFwLLSLMRC.Y
 1722- 1741 (23.45/ 7.00)	DNlpENMRNSF.ILQIVPCqY
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      50.51|      14|      21|    1377|    1390|      14
---------------------------------------------------------------------------
 1377- 1390 (27.59/13.99)	SPEPLPI..PTLLVGY
 1398- 1413 (22.92/10.25)	SPFSLPFweRLLLDPY
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      76.20|      23|      33|    2095|    2117|      16
---------------------------------------------------------------------------
 2095- 2117 (39.20/22.80)	PEELKQQPL....ALGYFVSTAKAENL
 2126- 2152 (37.00/21.09)	PQAQNQCPLflkaSLHHHISVAQTDEL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     127.54|      33|      33|     855|     887|      17
---------------------------------------------------------------------------
  855-  887 (59.31/37.53)	TVADLQRMFPTP.PSLEQ...HPAFSPVMNYKDGISS
  889-  921 (46.23/27.24)	TVTALG.MMESPmVNMVQ...TQLTEFKMEVEDGLGS
  926-  950 (21.99/ 8.17)	EIKDFSYVHKV..PSFQPfvgSSMFAP..........
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      96.02|      30|      37|    1296|    1327|      18
---------------------------------------------------------------------------
 1296- 1327 (44.62/28.95)	DEALVRSATVHSWphSNVLDI.SMLSSQDVVRM
 1336- 1366 (51.40/26.89)	QDAIQKKRTGRTW..ENIQHVqGPLTWQQFHKM
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      94.84|      23|      27|     463|     485|      19
---------------------------------------------------------------------------
  463-  485 (36.65/20.50)	PASSKHKITERQEKGDKLQKRPM
  492-  514 (38.06/21.57)	PSVTEELCMEQDAAGQKLGLAGM
  594-  609 (20.13/ 7.77)	PSLDDRTVL....VGQRLPL...
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      48.72|      13|      21|     727|     739|      20
---------------------------------------------------------------------------
  727-  739 (23.92/11.34)	GTKKCKLGTDKDP
  750-  762 (24.80/12.03)	GTKEIPTPGHSTP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     188.16|      58|    1267|     156|     215|      21
---------------------------------------------------------------------------
  156-  215 (98.97/75.01)	PVNKSeHLSCAFTFFlHGESNVCTSVEIAQHQPIYLINEEHI.HMAQSSPTPF.QVLVS.....PYG
 1426- 1490 (89.19/58.70)	PENEA.LLDGAKTFF.RDLSAVYEMCRLGQHKPICKVLRDGImRVGKTVAQKLtDELVSewfnqPWG
---------------------------------------------------------------------------




































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 MDP06883 with Med13 domain of Kingdom Metazoa


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) GHINVGQPGLGSTKDPSSCGMPLTPPTSPEQAIISESGGTHNSVSLSAAQEGTVTVHSPKKSGKMPPKFH
2) GSLADQDYLQMNTPQMNTPVTLNSAAPASNSGAGVLPSPATPRFSVPTPRTPRTPRTPRGGGTASGQGSVKYDSTDQGSPASTPSTTRPLNSVEPATV
3) GTDKDPLKKNKSEDGIGTKEIPTPGHSTPVPDGKDAMSIFSSAPKADTRQDGAAGRVGSGSLTQVTDLAPSLHDLDNIFDNSDEDELGAVSPALRSSKMPAVGTEERPLGKDGRTAVPYPPTVADLQRMFPTPPSLEQHPAFSPV
4) PPKYQTPASASQGQTIPGNSGSVPPNSTSHSAPGAPPTGNSFNSTPSGGNTNLAAGSSSASGPPVPQLSASSSTPSINQMSATSSSGFSGSVGPGQNTSTGGNSADRPQGNTGSGGDTESGQNSSQQQSQQEGQEGVTERERIGIPTEPESA
5) RCATGTSRPPTISQPGFTVGSSSTSASLPPPASSKHKITERQEKGDKLQKRPMMPFHHRPSVTEELCMEQDAAGQKLGLAGMETSLEVPNSRKYEKQLSIPTGNPSKQMNLNPMDSPHSPTSPLPPTLSPQPRGQEAENLDPPSVPVNPALYGNGLELQ
303
1003
734
1527
433
372
1100
878
1678
591










Molecular Recognition Features






MoRF SequenceStartStop




NANANA