<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 MDP31381

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMKATVEGEKDASRKVKVPKRPEVNNGGSLEDCISNVFSLLELPGIKWKCFRPKLNAPRGVPLTSDLVLKAYSRCLTDGILCTWRRKPSPPTGNNELLPPTHFFSNDSPKELWVFWYDAEPTALGKYCEGLDSDEELSSANQMNIVSYEVRTILFKALHVVLERDLTKDGFVRFGRWFTMPLVARDHYLHFMYPSHSPAIRFNFFVHGTSTICASIQAQRQPTLIKLARRHFECKTPKRFPVVIGPWSMRGYLIADQMTLLADQKIQEAAEKEWNQWKEYLQLEEKEPENVTEERQKTPEAEPPAPPQTTRVLLASSSDEDQEKNGGELKSEEVSQKIRWMFEPDLRQDKPKEETAAEKEKRMAAREVRRLRRQRREERRREMEKQRRADDNLEDYDSDVVTDQDEDEAGKEEIVNNDVPKMILIEIDNVRLLYPSKFVCITVEEDRQMLESMGFKCHPMPQELQVPGRRPRNKNVVNMSNPLLSTMAVYQYVQNEKRAEREHFYPRNKPVEIETDTNFEILSNPKARRVAPPKSPTFLSWESQRANHFDTTDIFVNRLFEKLFRLDADTFDENPRLIKFACLSSQFIRRKWKWLHKKQILFCGKARKRFGIGSPQNFALNMMKSREKRKEYQPYHRKRPAKSVKEKKKKAKRKVKKFVRYNSPEQFLASMSRTRKKFNAWKQKKKGPPPKKDLAKKEAAADKDKDKDKEKDKEKDKDNDDDPFVMDKVSQLDWANFSEDETNGNSFADIEEALVSEEHIKFSSLYNPAGGDIEEGDETSNESPDEKTPEGSPNGSPRPKEEIEPFFPITYLAAKPSNIESDLGPDVDDMTEEQFNTEYVPKEYDITQDPKKVKNGQIPISEFSKDNQFYHGEICRLGLRGYKKICAERDREEAARRTKWLQLYRLKVEKRSIKTARQCHRDYLRQIAKRCLRKALRRLRITAKKDALAPPPPKPKPVDPVLKKKEDAKKFEMSLKIMERDLGNLDMSAFCQVREKAGPHGVSFPEIILLTNPKWLKVRSTAGYMKPNYFNSPHGSFDHDSEPEFDEQRTGLGEGTSDQYQDGESVDMIDIERELANDPSSYLSNAEHIRTLGEHIGPDGMLSPPASNEMPKGGPLSVGPASIESQGLNQIYPTPPSVQMLQADASQAHSPSIGGKFRSTANDDIDRAAASGKTIVDIEIEDIETGNMQRWNKIANQSKLSKFLVASRDNPILKGRKTKYDTPATDKFEIRCQVERVTVPMAYESMVTRNFECAPPHTFAELIRQSRTGIKKYTRPLQIQSTLARPPPGATSPLPPPTPMFNPHTLPLHHTSPFSAGPMSHHSMGPPAYPPTPGPYPPTTPTYPGMTPRPGSSYGPGYPNHHQMMPPGYPNQMGQMGGMNGMGGMPGMGPIGMQRQFSNPQMYQHHQMMRMQQMRMQGGLPGYGAPGVPQYPQQSPVSGGPESIRNTDAPNDPTVSKLQSAVSRNGKSDDESDAATSIPTATDDATAATTTAAQLQLQRSQAHQIQHQPNQQTMQSLQLTPEQLQIQQSQQVQAVFQQLPDREKRKYQRRQIQLMNGLMPTSLQPASIKALKNPPDANIPYKRQDIIYNPPNPAHPRGDSLTIAIVLSDTLLDLHFDSVFDACPICSCSVSIRSRDLGMYIIPHAVLSSREIGETNKREYTTGTWSGFHVNSATSCTCGFSAIRHRYLSCCAGLFDEDADEATASEHANAPVIPPLFARNTTKTRDMMWFDPQSVHDLALTDQIRQMAFSNSLGKAVSQMATEKEHRRNITNAVDIGTDITVPTEYVLSHVDTLELMMLGMSALGPMQTPETTGNQFTPQSKYLSYFHPWGFQTANEIAELESSEWVDLLDIITPTLESSMKQARRPSVETPFVIEGPMTWKQVVTKAIRGKPPTDEDEDFSLAEPVPAVMRALEQEAVRAAPNIEQYYDQAELGPVDQPKDVMYITIIPDNDDIYERTVKFMHTMTETYERMRLGRHIPFPVSTGTASRFREVLKTYQHQFPYQEQNQQLVEFTNNRLEAVPQELSNNPDPLNTDPEKWSKRLKRKLELSEELKKADEHPAPPSTQSENSEGNAATPAAETLSSIFSDDAFVEERHINSTEEAPTTTERPPNSLPYRITNWHEKDDDTYEHPPEVHDTLPEGFYEREGILRVGKPLEPLRISHTVVSTREFDNMTQHLSDAQGFVSKLRIFLQQMEDLVFHTLSGSSEAFERRGYRYQMAVEGRLKRQKHKRDIEEERLRYEAAKVQDEADKREKMDEADLFPGAEVGEETPSPWVDDELEEKKRNKQKENEQYPAEESQAPSPVPAGMIHIPETLSEQERKVQPTLADMFADPSTVAPINAQNIPWKQRDTRVQNPFPYSNQPPVAFEAVGSNDTDAYSTLPHVIVLYVVNPFSYGAEGQSALHMRIALLSFIRAYNSIVGRLPFTKRTQLQLEIIGMESLDDMVKGIPDYLNDSQVPFDILHDYPVRNERPSESGQEAAARSLSVAVYTHPRVFTPEVYKAVSARCMTAFGPGSQLINTVNNIEKINQEAFYQMSKRSKTALNNMDGYMGMMGSHQVETKAHISYRVPSNIVCLAPPPAIYQMDEEGKPILNQLDEQTLFISYCLVGTEYLVATATDSQGKLIDNCIANMKPRRLHNQVYRYKNKTQILDGMGKLWSFILGVMSSDIKNWRLVVGRLGRIGHGEFRAWTHLLNKTSLLRYSSSLKDICGACRSMPSAIGTPAILSACLITLEPEPSIRIMPKFHDIDESIKKNLIFQTPGDLSCTHILTFPVGTEINLEVQDQTADTKGDENWEFGDLDIMEGLDDGDTEIMKDLGLETPSSAAIRQTGGVSMFFSEDSSSIEIQNQPLASGYYISTAPAPELPSWFWATCPSAKRHSPVHLKSSLHINISEVKNDDIAMESAKDKEKEKEEKDIHPLESRQTEEVLRHVLESYNALSWLNLNRQTGDRYSCLPIHVQHLLRLYHSVARLLV
Length2974
PositionMiddle
OrganismCaenorhabditis briggsae
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Chromadorea> Rhabditida> Rhabditina> Rhabditomorpha> Rhabditoidea> Rhabditidae> Peloderinae> Caenorhabditis.
Aromaticity0.08
Grand average of hydropathy-0.715
Instability index56.18
Isoelectric point6.10
Molecular weight337532.67
Publications
PubMed=14624247

Function

Annotated function Component of the Mediator complex, a coactivator involved in regulated gene 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 (By similarity). 
GO - Cellular Component
mediator complex	GO:0016592	IBA:GO_Central

GO - Biological Function
transcription coregulator activity	GO:0003712	IBA:GO_Central

GO - Biological Process
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP31381
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     179.79|      27|      28|    1324|    1350|       1
---------------------------------------------------------------------------
 1285- 1310 (31.98/10.63)	.PP..PGATSPLPPPTP.......MFnPHTLPlHHT
 1324- 1350 (60.11/27.35)	GPPAYPPTPGPYPPTTP.......TY.PGMTP.RPG
 1354- 1386 (43.54/17.50)	G.PGYPNHHQMMPPGYPnqmgqmgGM.NGMGG.MPG
 1412- 1438 (44.17/17.88)	QMRMQGGLPGYGAPGVP.......QY.PQQSP.VSG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      65.57|      20|      23|    2101|    2123|       2
---------------------------------------------------------------------------
 2061- 2080 (30.38/ 8.14)	APPSTQ.SENSEGNAATPAAE
 2103- 2123 (35.18/19.27)	APTTTErPPNSLPYRITNWHE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      86.86|      27|      32|    1490|    1518|       5
---------------------------------------------------------------------------
 1490- 1516 (49.54/34.62)	TAAQLQLQRSQAHQ..IQHQPNQ..........QTMQSL
 1519- 1557 (37.33/18.12)	TPEQLQIQQSQQVQavFQQLPDRekrkyqrrqiQLMNGL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      98.12|      29|      31|    2246|    2274|       6
---------------------------------------------------------------------------
 2246- 2274 (51.31/31.46)	VQDEAD..KREKMDEADLFPGAEVGEETPSP
 2276- 2306 (46.81/27.91)	VDDELEekKRNKQKENEQYPAEESQAPSPVP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      74.49|      22|      24|     681|     702|       7
---------------------------------------------------------------------------
  681-  702 (36.46/19.62)	KQKKKGPPPKKDLAKKEAAADK
  706-  727 (38.04/20.83)	KDKEKDKEKDKDNDDDPFVMDK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      53.23|      16|      24|     346|     361|       8
---------------------------------------------------------------------------
  346-  361 (25.92/18.66)	RQDKPKEETAAEKEKR
  372-  387 (27.31/20.24)	RQRREERRREMEKQRR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      70.17|      22|      29|    1886|    1907|       9
---------------------------------------------------------------------------
 1886- 1907 (39.50/22.72)	KAIRGKP............PTDEDEDFSLAEPVP
 1916- 1949 (30.67/15.70)	EAVRAAPnieqyydqaelgPVDQPKDVMYITIIP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     106.93|      28|      28|    2386|    2413|      10
---------------------------------------------------------------------------
 2365- 2389 (33.29/16.83)	...PVAFEAVGSNDTDAYSTLPHVIVLY
 2390- 2417 (45.58/25.77)	VVNPFSYGAEGQSALHMRIALLSFIRAY
 2420- 2442 (28.06/13.03)	IVGRLPFTKRTQLQLEI.IGMESL....
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      82.15|      24|     487|     282|     305|      12
---------------------------------------------------------------------------
  282-  305 (42.91/22.92)	LEEKEPENVTEERQKTPEAEP...PAP
  772-  798 (39.25/20.19)	IEEGDETSNESPDEKTPEGSPngsPRP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      71.54|      21|      32|     998|    1022|      13
---------------------------------------------------------------------------
  998- 1022 (31.14/29.71)	PHGvSFPEiilLTNPKWLKVRSTAG
 1032- 1052 (40.40/24.32)	PHG.SFDH...DSEPEFDEQRTGLG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      86.63|      27|      31|     867|     896|      14
---------------------------------------------------------------------------
  867-  896 (45.63/49.15)	QFYHGEI..........CRlglRGYKKICAERDREEAARR
  901-  937 (40.99/33.21)	QLYRLKVekrsiktarqCH...RDYLRQIAKRCLRKALRR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      62.72|      17|    1537|      52|      68|      15
---------------------------------------------------------------------------
   52-   68 (30.81/18.19)	PKLNAPRGVPLTSDLVL
 1590- 1606 (31.91/19.15)	PNPAHPRGDSLTIAIVL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      57.47|      18|      28|     489|     509|      16
---------------------------------------------------------------------------
  489-  509 (25.93/23.59)	YQYVQNEKrAERehFYPRNKP
  518-  535 (31.54/16.13)	FEILSNPK.ARR..VAPPKSP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      62.58|      19|    1538|     840|     858|      17
---------------------------------------------------------------------------
  840-  858 (36.44/20.36)	PKEYDITQDPKKVK..NGQ.IP
 2325- 2346 (26.15/12.47)	PTLADMFADPSTVApiNAQnIP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      81.99|      24|    1627|     947|     970|      21
---------------------------------------------------------------------------
  947-  970 (43.92/27.48)	LAPPPP...KPKPVDPVLKKKEDAKKF
 2576- 2602 (38.07/22.48)	LAPPPAiyqMDEEGKPILNQLDEQTLF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      74.47|      23|     875|    1254|    1277|      22
---------------------------------------------------------------------------
 1254- 1277 (39.25/33.18)	PP..H.TFAELIRQsRTGIKKYTRPLQ
 2132- 2157 (35.22/23.61)	PPevHdTLPEGFYE.REGILRVGKPLE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      53.91|      13|     871|     236|     248|      23
---------------------------------------------------------------------------
  236-  248 (28.35/12.95)	PKRFPVVIGPWSM
 1110- 1122 (25.56/10.98)	PKGGPLSVGPASI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      36.01|       9|     347|    1998|    2008|      25
---------------------------------------------------------------------------
 1998- 2008 (15.76/13.17)	QHQFPYqeQNQ
 2355- 2363 (20.25/ 9.83)	QNPFPY..SNQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      53.86|      15|      46|     613|     627|      28
---------------------------------------------------------------------------
  613-  627 (27.43/17.85)	SPQNFALNMMKSREK
  662-  676 (26.43/16.88)	SPEQFLASMSRTRKK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      46.04|      14|      15|     426|     439|      30
---------------------------------------------------------------------------
  426-  439 (25.26/18.26)	IDNVRLLYPS.KFVC
  442-  456 (20.77/13.33)	VEEDRQMLESmGFKC
---------------------------------------------------------------------------




































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 MDP31381 with Med13 domain of Kingdom Metazoa
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