<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 MDP06885

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMSSCFVPNGASLEDCHSNLFCLADLTGIKWKRYVWQGPTSAPILFPVTEEDPILSSFSRCLKADVLSVWRRDQRPGRRELWIFWWGDDPNFADLIHHDLAEEEDGVWENGLSYECRTLLFKAVHNLLERCLMNRNFVRIGKWFVKPYEKDEKPINKSEHLSCSFTFFLHGDSNVCTSVEISQHQPVYLLSEEHLTLAQQSNSPFQVILSPFGLNGTLTGQSFKLSDSSTKKLIGEWKQFYPITSNLKEGSEEKQEEMDWEDDSLAAVEVLVAGVRMVYPACFVLVPQTDIPAPSTVGASHCSTTCLGVHQVPATTRDPAMSSVTLTPPTSPEEVQTVDAQSAQKWVKFSSVSDGFSSDSTSHHGGKIPRKLANQVVDRVWQECNMNRAQNKRKYSATSNGLCDEETADKVASWDFVEATQRTNCNCSRHKNLKPRNSGQQGQAPPASQQQQAAPKHKTNEKQDKGDKPQKRPLTPFHHRVSISDDVAMEAESASQRLVITAPDSQSQHFYQMPTPDPLVPSKAMEDRIDGLSQSFPAQFPEVIEPTIYIGTAVNLEEDEADNTWKYYKVPKKKDVEFLPPPLPCDKFRDDPVVPAGQENLTSVTELMVQCRKPLKVSDELVQQYQSKNQYLAAVVSETDQEPEIDPYAFVDGDVEFLFPDNKKERQNNERETGKKHKAEDGTPNVTVLSHEGKDAMSLFSPSVKPEQRTAAHARTASTSLIHETDLVVSYTDLDNLFNSDEDELTPGSKRTVNGSDDKPNCKESKTGNLDPLSCISTADLHKMYPTPPSLEQHIMGFSPMNMNNKEYGSMDTTLGGTVLEGNSSSIGAQFRIEVDEGFCSPKPSEIKDYSYVYKPENCQALVGCSMFAPLKTLPSQCLPSIKLPEECIYRQSWAVGKLELLPPGPAMPFIKEGDGSTMDQEYGPAYTPQTHTPFGMPPNSAPPSNSGAGILPSPSTPRFPTPRTPRTPRTPRGGGGPASAQGSVKYENSDLYSPASTPSTCRPLNSVEPATVPSIPEAHSLYVNLILSESVMNLFKDCNFDSCCICVCNMNIKGADVGVYIPDPTQEIQYRCTCGFSAVMNRKFGNNSGLFLEDELDILGRNTEGGKEAEKRFEALRATSVEHGGGGLKEPEKLPDELILLLQDQCTNLFSPFGAADQDPIPKVGAVSNLVRVEERDCCNDCYLALEHGRQFMDNMSGGKVDEALVKSTCLHHWSKRNVVDVSMQCSQDILRMLLSLQPVLQDAIQKKRTVRSWGVQGPLTWQQFHKMAGRGSYGTDESPEPLPIPTFLLGYDYDFLVLSPFALPYWERLMLEPYGSQRDVAYVVVCPENEALLNGAKSFFRDLTAIYESCRLGQHRPICKLLPDGIMRVGSTASKKLSEKLVAEWFSQAANANNEAFSKLKLYAQVCRYELGPYLASQPLDSSLLSQINLVPPTSQSVSTQPQAAATTTNSTLTTTAASSSSTNIGSGLSANKPSSFPPFSSMNSTTSASLPTQATTVQNGQPGGQQQQATLQAAGIPGEASSAPAQPHPEVSESTMDRDKVGVPTDGDSHAITYPPAIVIYIIDPFTYERKDENSSSSSVWTLGLLRCFMEMVQILPSSIRNIVSVQIVPCQYLLQPVKHEDRQIYTQHLKSLAFSAFTQCRRPLPTSTNVKTLTGFGPGLAMETALKSPDRPECIRLYTPPFILAPVKDKQTELGETFGEAGQKYNVLFVGYCLSHDQRWLLASCTDLYGELLETCIINIDVPNRARRKKGSARRLGLQKLWDWCLGLVQMSSLPWRVVIGRLGRIGHGELKDWSCLLSRRNLQSLSKRLKDMCRMCGISAADSPSFLSACLVAMEPQGSFIIMPDSVSTGSVFGRSTTLNMQTSQLNTPQDTSCTHILVFPTSASVQVASSTYTTENLDLAFNTNNDGADGMGIFDLLDTADELDPDIINILPASPTGSPVHSPGSHYPHGGDMGKGQSTDRLLSTESHDEVTNILQQPLALGYFVSTAKAGPLPDWFWSACPQAQNQCPLFLKASLHLHVPSVQSDELLHSKHSHPLDSNQTSDVLRFVLEQYNALSWLTCDPATQDRRSCLPVHFVVLNQLYNFIMNML
Length2095
PositionMiddle
OrganismAlligator mississippiensis (American alligator)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Archelosauria> Archosauria> Crocodylia> Alligatoridae> Alligatorinae> Alligator.
Aromaticity0.08
Grand average of hydropathy-0.406
Instability index50.42
Isoelectric point5.42
Molecular weight231272.44
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. 
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

>MDP06885
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     396.78|     183|     515|    1312|    1539|       1
---------------------------------------------------------------------------
  332-  483 (93.86/41.45)	EEVQTvDAQSAQKWVKFSSVSDGFSSDSTSHHGGkiprklanqvvdrvwqecnmnraqnkrkysatsnglcdeETADKVASWdfveaTQRTNCNCSRHKNLKPRNSG.QQGQapPASQQQQAapkhkTNEKQDKGDKPQKRPLTPfHHRVSIS.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
 1342- 1436 (72.25/109.18)	.........................................................................................................................................................ddvameaesasqrlvitapdsqsqhfyqmptpdplvpskamedridglsqsfpaqfpevieptiyigtavnleedeadntwkyykvpkkkdveflppplpcdkfrddpvvpagqenltsvtelmvqcrkplkvsdelvqqyqsknqylaavvsetdqepeidpyafvdgdveflfpdnkkerqnneretgkkhkaedgtpnvtvlshegkdamslfspsvkpeqrtaahartastslihetdlvvsytdldnlfnsdedeltpgskrtvngsddkpnckesktgnldplscistadlhkmyptppsleqhimgfspmnmnnkeygsmdttlggtvlegnsssigaqfrievdegfcspkpseikdysyvykpencqalvgcsmfaplktlpsqclpsiklpeeciyrqswavgklellppgpampfikegdgstmdqeygpaytpqthtpfgmppnsappsnsgagilpspstprfptprtprtprtprggggpasaqgsvkyensdlyspastpstcrplnsvepatvpsipeahslyvnlilsesvmnlfkdcnfdsccicvcnmnikgadvgvyipdptqeiqyrctcgfsavmnrkfgnnsglfledeldilgrnteggkeaekrfealratsvehgggglkepeklpdelilllqdqctnlfspfgaadqdpipkvgavsnlvrveerdccndcylalehgrqfmdnmsggkvdealvkstclhhwskrnvvdvsmqcsqdilrmllslqpvlqdaiqkkrtvrswgvqgpltwqqfhkmagrgsygtdespeplpiptfllgydydflvlspfalpywerlmlepygsqrdvayvvvcpeneallngaksffRDLTAIyeSCRLgqhRPICKLLpdGIMRVGSTASkkLSEKLVAEWFSQAANANNEAFSKLKLYAQVCRYELGPYLASQPLDSSlLSQInLVPPTS
 1437- 1536 (126.43/71.85)	QSVST.QPQAAATTTNSTLTTTAASSSSTNIGSG.......................................LSANKPSSF.....PPFSSMNSTTSASLPTQATTvQNGQ..PGGQQQQA.....TLQAAGIPGEASSAPAQP.HPEVSES.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
 1804- 1887 (104.23/51.02)	........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................tmdrdkvgvptdgdshaityppaiviyiidpftyerkdensssssvwtlgllrcfmemvqilpssirnivsvqivpcqyllqpvkhedrqiytqhlkslafsaftqcrrplptstnvktltgfgpglametalkspdrpecirlytppfilapvkdkqtelgetfgeagqkynvlfvgyclshdqrwllasctdlygelletciinidvpnrarrkkgsarrlglqklwdwclglvqmsslpwrvvigrlgrighgelkdwscllsrRNLQSL..SKRL...KDMCRMC..GISAADSPSF..LSACLVAMEPQGSFIIMPDSVSTGSVFGRSTTLNMQTSQLNTPQDTS.CTHI.LVFPTS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     431.87|     124|     150|     759|     904|       2
---------------------------------------------------------------------------
  759-  841 (130.22/65.78)	...................................................................PNCKESKTGN.LD....PLSC........ISTADLHKMYP..TPPSLEQH..IMGFSPMNMNNKEYGSMDTTLGGTVLEGNSSSIGAQFRIEVDEG.FCSP
  842-  994 (174.95/138.40)	KPSEIKDYSYVyKPENCQAL.VGCSMFAPLktLPSQCLpsIKLPEECiyrqswavgklellppgpamPFIKEGDGST.MDqeygPAYT........PQTHTPFGMPPnsAPPS..NS..GAGILP.SPSTPRFPTPRTPRTPRTPRGGGGPASAQGSVKYENSdLYSP
  997- 1100 (126.69/69.02)	TPSTCRPLNSV.EPATVPSIpEAHSLYVNL..ILSESV..MNLFKDC..............................nFD......SCcicvcnmnIKGADVGVYIP..DPTQEIQYrcTCGFSAV.MNRK.FGNN....SGLFLEDELDILG...............
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     150.56|      47|     515|     611|     693|       3
---------------------------------------------------------------------------
  556-  606 (76.16/63.53)	EEDEADNTWKYYKVpkKKDVEFLPPplPCDKFRDDPVVPAGQ....ENLT.SVTEL
  637-  688 (74.41/48.99)	ETDQEPEIDPYAFV..DGDVEFLFP..DNKKERQNNERETGKkhkaEDGTpNVTVL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     110.28|      33|     940|     176|     212|       5
---------------------------------------------------------------------------
  176-  212 (55.05/47.41)	TSVE...ISQHQPVYLLSEEHLTLAQQSNSPFqvilSPFG
 1119- 1154 (55.23/37.41)	TSVEhggGGLKEPEKLPDELILLLQDQCTNLF....SPFG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      41.91|      11|     271|      46|      56|       7
---------------------------------------------------------------------------
   46-   56 (20.49/12.50)	PVTEEDPILSS
  312-  322 (21.42/13.47)	PATTRDPAMSS
---------------------------------------------------------------------------




































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 MDP06885 with Med13 domain of Kingdom Metazoa
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