<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 MDP06884

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMSSCFVPNGASLEDCHSNLFCLADLTGIKWKRYVWQGPTSAPILFPVTEEDPILSSFSRCLKADVLSVWRRDQRPGRRELWIFWWGDDPNFADLIHHDLAEEEDGVWENGLSYECRTLLFKAVHNLLERCLMNRNFVRIGKWFVKPYEKDEKPINKSEHLSCSFTFFLHGDSNVCTSVEISQHQPVYLLSEEHLTLAQQSNSPFQVILSPFGLNGTLTGQSFKLSDSSTKKLIGEWKQFYPITSNLKEGSEEKQEEMDWEDDSLAAVEVLVAGVRMVYPACFVLVPQTDIPAPSTVGASHCSTTCLGVHQVPATTRDPAMSSVTLTPPTSPEEVQTAVDAQSAQKWVKFSSVSDGFSSDSTSHHGGKIPRKLANQVVDRVWQECNMNRAQNKRKYSATSNGLCDEETADKVASWDFVEATQRTNCNCSRHKNLKPRNSGQQGQAPPASQQQQAAPKHKTNEKQDKGDKPQKRPLTPFHHRVSISDDVAMEAESASQRLVITAPDSQSQHFYQMPTPDPLVPSKAMEDRIDGLSQSFPAQFPEVIEPTIYIGTAVNLEEDEADNTWKYYKVPKKKDVEFLPPPLPCDKFRDDPVVPAGQENLTSVTELMVQCRKPLKVSDELVQQYQSKNQYLAAVVSETDQEPEIDPYAFVDGDVEFLFPDNKKERQNNERETGKKHKAEDGTPNVTVLSHEGKDAMSLFSPSVKPEQRTAAHARTASTSLIHETDLVVSYTDLDNLFNSDEDELTPGSKRTVNGSDDKPNCKESKTGNLDPLSCISTADLHKMYPTPPSLEQHIMGFSPMNMNNKEYGSMDTTLGGTVLEGNSSSIGAQFRIEVDEGFCSPKPSEIKDYSYVYKPENCQALVGCSMFAPLKTLPSQCLPSIKLPEECIYRQSWAVGKLELLPPGPAMPFIKEGDGSTMDQEYGPAYTPQTHTPFGMPPNSAPPSNSGAGILPSPSTPRFPTPRTPRTPRTPRGGGGPASAQGSVKYENSDLYSPASTPSTCRPLNSVEPATVPSIPEAHSLYVNLILSESVMNLFKDCNFDSCCICVCNMNIKGADVGVYIPDPTQEIQYRCTCGFSAVMNRKFGNNSGLFLEDELDILGRNTEGGKEAEKRFEALRATSVEHGGGGLKEPEKLPDELILLLQDQCTNLFSPFGAADQDPIPKVGAVSNLVRVEERDCCNDCYLALEHGRQFMDNMSGGKVDEALVKSTCLHHWSKRNVVDVSMQCSQDILRMLLSLQPVLQDAIQKKRTVRSWGVQGPLTWQQFHKMAGRGSYGTDESPEPLPIPTFLLGYDYDFLVLSPFALPYWERLMLEPYGSQRDVAYVVVCPENEALLNGAKSFFRDLTAIYESCRLGQHRPICKLLPDGIMRVGSTASKKLSEKLVAEWFSQAANANNEAFSKLKLYAQVCRYELGPYLASQPLDSSLLSQINLVPPTSQSVSTQPQAAATTTNSTLTTTAASSSSTNIGSGLSANKPSSFPPFSSMNSTTSASLPTQATTVQNGQPGGQQQQATLQAAGIPGEASSAPAQPHPEVSESTMDRDKVGVPTDGDSHAITYPPAIVIYIIDPFTYERKDENSSSSSVWTLGLLRCFMEMVQILPSSIRNIVSVQIVPCQYLLQPVKHEDRQIYTQHLKSLAFSAFTQCRRPLPTSTNVKTLTGFGPGLAMETALKSPDRPECIRLYTPPFILAPVKDKQTELGETFGEAGQKYNVLFVGYCLSHDQRWLLASCTDLYGELLETCIINIDVPNRARRKKGSARRLGLQKLWDWCLGLVQMSSLPWRVVIGRLGRIGHGELKDWSCLLSRRNLQSLSKRLKDMCRMCGISAADSPSFLSACLVAMEPQGSFIIMPDSVSTGSVFGRSTTLNMQTSQLNTPQDTSCTHILVFPTSASVQVASSTYTTENLDLAFNTNNDGADGMGIFDLLDTADELDPDIINILPASPTGSPVHSPGSHYPHGGDMGKGQSTDRLLSTESHDEVTNILQQPLALGYFVSTAKAGPLPDWFWSACPQAQNQCPLFLKASLHLHVPSVQSDELLHSKHSHPLDSNQTSDVLRFVLEQYNALSWLTCDPATQDRRSCLPVHFVVLNQLYNFIMNML
Length2096
PositionMiddle
OrganismAlligator mississippiensis (American alligator)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Archelosauria> Archosauria> Crocodylia> Alligatoridae> Alligatorinae> Alligator.
Aromaticity0.08
Grand average of hydropathy-0.405
Instability index50.40
Isoelectric point5.42
Molecular weight231343.51
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

>MDP06884
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     438.69|     124|     149|     760|     905|       1
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  760-  888 (210.76/134.74)	PNCKESKTGNLD....PLSC........ISTADLHKMYP..TPPSLEQH..IMGFSPMNMNNKEYGSMDTTLGGTVLEGNSSSIGAQFRIEVDEG.FCSP..KPSEIKDYSYVyKPENCQAL.VGCSMFAPLktLPSQCLpsIKLPEEC
  909- 1039 (187.18/86.28)	PFIKEGDGSTMDqeygPAYT........PQTHTPFGMPPnsAPPS..NS..GAGILP.SPSTPRFPTPRTPRTPRTPRGGGGPASAQGSVKYENSdLYSPasTPSTCRPLNSV.EPATVPSIpEAHSLYVNL..ILSESV..MNLFKDC
 1041- 1101 (40.75/ 9.26)	..........FD......SCcicvcnmnIKGADVGVYIP..DPTQEIQYrcTCGFSAV.MNRK.FGNN....SGLFLEDELDILG................................................................
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     330.19|     157|     515|    1313|    1540|       2
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  332-  453 (55.12/ 8.21)	EEVQTavDAQSAQKWVKFSSVSDGFSSDSTSHHGGkiprklanqvvdrvwqecnmnraqnkrkysatsnglcdeETADKVASW.DFVEATQRTncncsrHKNLKPRNSG.QQGQapPASQQQQA........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
 1343- 1437 (82.65/99.08)	............................................................................................................................apkhktnekqdkgdkpqkrpltpfhhrvsisddvameaesasqrlvitapdsqsqhfyqmptpdplvpskamedridglsqsfpaqfpevieptiyigtavnleedeadntwkyykvpkkkdveflppplpcdkfrddpvvpagqenltsvtelmvqcrkplkvsdelvqqyqsknqylaavvsetdqepeidpyafvdgdveflfpdnkkerqnneretgkkhkaedgtpnvtvlshegkdamslfspsvkpeqrtaahartastslihetdlvvsytdldnlfnsdedeltpgskrtvngsddkpnckesktgnldplscistadlhkmyptppsleqhimgfspmnmnnkeygsmdttlggtvlegnsssigaqfrievdegfcspkpseikdysyvykpencqalvgcsmfaplktlpsqclpsiklpeeciyrqswavgklellppgpampfikegdgstmdqeygpaytpqthtpfgmppnsappsnsgagilpspstprfptprtprtprtprggggpasaqgsvkyensdlyspastpstcrplnsvepatvpsipeahslyvnlilsesvmnlfkdcnfdsccicvcnmnikgadvgvyipdptqeiqyrctcgfsavmnrkfgnnsglfledeldilgrnteggkeaekrfealratsvehgggglkepeklpdelilllqdqctnlfspfgaadqdpipkvgavsnlvrveerdccndcylalehgrqfmdnmsggkvdealvkstclhhwskrnvvdvsmqcsqdilrmllslqpvlqdaiqkkrtvrswgvqgpltwqqfhkmagrgsygtdespeplpiptfllgydydflvlspfalpywerlmlepygsqrdvayvvvcpeneallngaksffRDLTAIyeSCRLgqhRPICKLLpdGIMRVGSTASkkLSEKLVAEWFSQAANANNEAFSKLKLYAQVCRYELGPYLASQPLDSSlLSQInLVPPTS
 1438- 1512 (77.80/68.48)	QSVST..QPQAAATTTNSTLTTTAASSSSTNIGSG.......................................LSANKPSSFpPFSSMNSTT......SASLPTQATTvQNGQ..PGGQQQQA........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
 1805- 1888 (114.63/46.33)	.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................tlqaagipgeassapaqphpevsestmdrdkvgvptdgdshaityppaiviyiidpftyerkdensssssvwtlgllrcfmemvqilpssirnivsvqivpcqyllqpvkhedrqiytqhlkslafsaftqcrrplptstnvktltgfgpglametalkspdrpecirlytppfilapvkdkqtelgetfgeagqkynvlfvgyclshdqrwllasctdlygelletciinidvpnrarrkkgsarrlglqklwdwclglvqmsslpwrvvigrlgrighgelkdwscllsrRNLQSL..SKRL...KDMCRMC..GISAADSPSF..LSACLVAMEPQGSFIIMPDSVSTGSVFGRSTTLNMQTSQLNTPQDTS.CTHI.LVFPTS
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     196.65|      73|     515|     612|     694|       3
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  563-  643 (114.99/63.40)	NTWKYYKVpkKKDVEFLPPplPCDKFRDDPVVPAGQ....ENLT.SVTEL....................................................................................................................................................................................................................................................................................................................................................................................................................................................mvqcRKPLKVSDELVQQYQSKNQYLAAVVSETDQEP
  644-  689 (46.29/39.11)	EIDPYAFV..DGDVEFLFP..DNKKERQNNERETGKkhkaEDGTpNVTVL........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
 1130- 1161 (35.37/11.82)	..................................................shegkdamslfspsvkpeqrtaahartastslihetdlvvsytdldnlfnsdedeltpgskrtvngsddkpnckesktgnldplscistadlhkmyptppsleqhimgfspmnmnnkeygsmdttlggtvlegnsssigaqfrievdegfcspkpseikdysyvykpencqalvgcsmfaplktlpsqclpsiklpeeciyrqswavgklellppgpampfikegdgstmdqeygpaytpqthtpfgmppnsappsnsgagilpspstprfptprtprtprtprggggpasaqgsvkyensdlyspastpstcrplnsvepatvpsipeahslyvnlilsesvmnlfkdcnfdsccicvcnmnikgadvgvyipdptqeiqyrctcgfsavmnrkfgnnsglfledeldilgrnteggkeaekrfealratsvehgggglKEPEKLPDELILLLQDQCTNLFSPFGAADQDP
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     265.06|      85|     270|     192|     290|       8
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  192-  290 (136.89/113.62)	EHLTLAQQ..SNSPFQVILSPFGLNGTLTGQSFKLSDSSTKKLI.....GEWKQFYPI.TSNLKEGSEEKQEEMDweddslaavevlvaGVRMVYPACF..VLVPQTDI
  456-  550 (128.17/82.82)	KHKTNEKQdkGDKPQKRPLTPFHHRVSISDDVAMEAESASQRLVitapdSQSQHFYQMpTPDPLVPSKAMEDRID..............GLSQSFPAQFpeVIEPTIYI
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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 MDP06884 with Med13 domain of Kingdom Metazoa
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