<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 MDP16225

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMTSRPQFLVSIFLTPFFEHSFKRKQLFSRFEKRIFETENNSAKVSSQQSQPFYSEASKTPSGSGPVRDSTEDMASSKEGEKDASRKVKVPKRPEVNNGGSLEDCISNVFSLLELPGIKWKCFRPKLNAPRGVVPLTSDLVLKAYSRCLTDGILCTWRRKPSPPTGNNELLPPTHYFSNDSPKELWVFWYDAEPTALAKYCEGLDSDEELSSANQMNIVSYEVRTILFKALHVVLERDLTKDGFVRFGRWFTMPLVARDHYLHCMYPSHSPAIRFNFFVHGTSTICASIQAQRQPTLIKLARRHFECKTPKRFPVVVGPWSMRGYLIADQMTLLADPKIQEAAEKEWNQWKEYLQLEEKEPENVAEERQKTPEAEPSAPPQTTRVLLASSSDEDQEKSGGEEKNEEVSQKIRWMFEPDLRQDKPKEETAAEKEKRMAAREVRRLRRQRREERRREQEKQRRADDNQEDYDSDVVTDQEEDEAGKEEIVNNDVPKMILIEIDNVRLLYPSKFVCITVEEDRQMLESMGFKCHPMPQELQVPGRRPRNKNVVNMSNPLLSTMAVYQYVQNEKRAEREHFYPRNKPVEIEPLSNFEFLSNPEAARRVKPPKSPTFLSWKSQRANHFDTTDIFVNRLFENADTFDETPRPIKFACLSYQFIRRKWKWIRKKEIKFGGKAKKRFGIGSPQNFALNMMKFREKRKEYQPYHRKRPVKSVKEKKKKAKRKVKKFVKYANPNQFLASISRTKRKFNAWKQKMNGPPPKKGPAKKEAAADKDKDKDKEKDKEKDKEKDKEKDKEKDKEKEKDKEKDKENEDDPFVMDKVSQLDWANFSEDETNGNSFADPTEDLYNPAGGELEEGDEISNESPDEKTPEGSPNGSPRPKEDIEPFVPITHPAAKPSNIEWDLGREVDDMTEELEYVPKEDHITQDPKKVKNGHIPISEFAKDNQFYHGEICRLGLRGYKKICAERDREEAARRMKWLQLYREKAEKRNIKTARQCHRDYLRQIAKRCLRKALRRLRITAKKDALAPPPPKPKPVDPVLKKKEDAKKFEMSMKMMERDLGNLDMSAFCQIREKAGPHGVQSTAGYMKPNYTNSPHGSFDHDSESEIDEQRTGLGEGTSDQYQDGESVDMIDIERELANDPSSYLFNAGHIRTLGEHIGPDGMLSPPASNEMPKGGPLSVGPASIESQGLNQIYPTPPSVQMLQADASQAHSPSIGGKFRSTANDDIERAVAPGKTIVDVEIEDIETRNMQRWSKIANQSKLSKFLVASRDNPILKGRKKKYDTPATNKFDIQCQVERVTVPMAYKSMVTRNFECAPPHTFAELIRQSRTGIKKYTRPLQIQSTLARPPPGATSPVPPPTPMFNPHTLPLHHTSPFSAGPMSHHSMGPPAYPPTPGPYPPTTPTYPGMTPRPGSSYGPGYPNHHQMMPPGYPNQMGQMGGMNGMGGMPGMPGMGPMGMQRQFSNPQMYQHHQMMRMQQMRQMQAGQSGYGAPGVPQYPQQSPGGPGGFGVPSGPSSVQRLNNFVNQSQFGPSSGPQNPYGAQMIPQSPSFNQPYPGMGNQMMSPMQQHQFQQQQMMQQQQQQQQHQQQQQHQLQLQRSQAHQIQHQPNQQTIQQTPEQLQIQQSQQVQAVFQQLPDREKRKYQRRQIQLMNGLMPTSLQPASIKALKNPPDANIPYKRQDIIYNPPNPAHPRGDSLTIAIVLSDTLLDLHFDSVFDACPICSCSVSIRSRDLGMYITPHAVLSSREIGETNKREYTTGTWSGFHVNSATSCTCGFSAIRHRYLSCCAGLFDEDADEATASEHANASVIPPLFSRNTIKTRDMMWFDPQSVHDLALTYQIRQMAFSNSLGKAVSQMATEKEHRRNITNAVDIGTDITVPTEYVLSHVDTLELMMLGMSALGPMQTPETTGSQLPPQSKYLSYFHPWGFQTANEIAELESSEWVDLLDIVTPTLESSMKQARRPPAEIPFVIEGPMTWKQVVTKAIRGKPPTDEDEDFSLAEPVPAVMRALEQEAVRAAPNIEQYYDQAELGPVDQPKDVMYITIIPDNDDIYERTVKFMDTMTETYERMRLGRHIPFPVSTGTASRYREVLKDYQSRYPYQEQHQQCVDATNNHLRAVPKELASNPNPLNTDPEEWNKRLKRKLELSEELKKADEHPAPPSTQSENSEGNAAAPAATPAAETLSSIFAEDAFVEPENRNSEEAPTTTERPPNSFPYRVTNWHEKDDDTFEDPPEVHDILPEGFYEREGILRIGKPLEPSRISHTVVSTREFDNMTQHLSDAQGFVSKLRLFLQQMEDLVFHTLIESNEAFERKGYRYQMAVEGRLKRQKHRRDIEEERLRYEAAKVQDEADKREKIDEADLLLGAEVGEETPSPWVDDELEEKKRKKQKENEQYPAEEPQAPSPVPAGMIHIPETLSEQERKVQPTLADMFADPSTVAPINAQNIPWKQRDTRVANPFPYSNQPPVAFEAAGSNDTDAYSTLPHVIVLYVVNPFSYGAEGQSALHMRIALLSFIRAYNSIVGRLPFTKRTQLQLEIIGMESLDDMVKGIPDYLNDSQVPFDILHDYPVRNERPSESGQEAAARSLSVAVYTHPRVFTPEVYKAVSARCMTAFGPGSQLINTINNIEKMNQDAFYQMTKRSKTALNNMDGYMGMMGSHQVETKGHISYRIPSNIVCLAPPPAIYQMDEEGKPILNQLDEQTLFISYCLVGTEYLVATATDSQGKLIDNCIANMKPRRLHNQVYRYKNKTQILDGMGKLWSFILGVMSSDIKNWRLVVGRLGRIGHGEFRAWTHLLNKTSLLRYSSSLKDICGACRSMPSAIGTPAILSACLITLEPEPSIRIMPEFHDIDESIKKNLIFQTPGDLSCTHILTFPVGTEINLEVQDQAADTKGDENWEFGDLDIMEGLDDGDTEIMKDLGLETPSSAAIRQTGGVSMFFSEDSSSIEIQNQPLASGYYISTAPAPELPSWFWATCPSAKRHSPVHLKSSLHINISEVKNDDIAMESAKDKEKEKEEKDIHPLESRQTEEVLRHVLESYNALSWLNLNRQTGDRYSCLPIHVQHLLRLYHSVARLLV
Length3071
PositionMiddle
OrganismCaenorhabditis nigoni
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Chromadorea> Rhabditida> Rhabditina> Rhabditomorpha> Rhabditoidea> Rhabditidae> Peloderinae> Caenorhabditis.
Aromaticity0.08
Grand average of hydropathy-0.776
Instability index57.81
Isoelectric point6.33
Molecular weight349102.48
Publications









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

>MDP16225
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      63.97|      17|      17|    1387|    1403|       1
---------------------------------------------------------------------------
 1386- 1402 (35.59/13.54)	PPAYPPTPG.PYPPTTPT
 1403- 1420 (28.39/ 9.14)	YPGMTPRPGsSYGPGYPN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      85.23|      17|      17|    1569|    1585|       3
---------------------------------------------------------------------------
 1569- 1585 (35.22/18.32)	QQQQMMQ..QQQQQQ.QHQQ
 1588- 1605 (25.41/11.13)	QHQLQLQ..RSQAHQiQHQP
 1606- 1624 (24.59/10.53)	NQQTIQQtpEQLQIQ.QSQQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      59.91|      16|      17|     772|     788|       4
---------------------------------------------------------------------------
  772-  787 (30.39/18.07)	DKDKDKEKDKEKDKEK
  790-  805 (29.51/12.62)	EKDKEKDKEKEKDKEK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      59.82|      23|      28|    1424|    1451|       5
---------------------------------------------------------------------------
 1437- 1470 (30.11/20.42)	GGMNGMGGmPGMPGM.gpMgMqrqfsnPQMYQhHQ
 1501- 1567 (29.72/ 7.06)	GGPGGFGV.PSGPGMgnqM.M......SPMQQ.HQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      50.94|      13|      19|    1346|    1364|       6
---------------------------------------------------------------------------
 1347- 1360 (24.21/11.18)	PPGATSPVpPPTPM
 1367- 1379 (26.73/12.96)	PLHHTSPF.SAGPM
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      77.36|      17|      19|     833|     849|       7
---------------------------------------------------------------------------
  833-  849 (30.32/15.93)	NGNSFADPTEDLYNPAG
  854-  870 (27.14/13.29)	EGDEISNESPDEKTPEG
  871-  884 (19.90/ 7.28)	SPNGSPRPKEDI.EP..
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      97.65|      30|      33|    2369|    2401|       9
---------------------------------------------------------------------------
 2371- 2401 (50.29/29.54)	P....WVDDELEEKKRKKQKENEQYPAeEPQAPSP
 2403- 2436 (47.36/18.51)	PagmiHIPETLSEQERKVQPTLADMFA.DPSTVAP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      89.87|      24|      44|     248|     272|      10
---------------------------------------------------------------------------
  248-  272 (45.21/32.38)	RWFTMPLVARDHYlHCMYPSHSPAI
  292-  315 (44.66/27.20)	RQPTLIKLARRHF.ECKTPKRFPVV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     103.85|      33|      44|     689|     722|      11
---------------------------------------------------------------------------
  689-  722 (54.00/35.86)	NMMKF.....REKRKeYQPYHRK...RPVKSVKEKKKKAKRK
  731-  771 (49.86/28.48)	NPNQFlasisRTKRK.FNAWKQKmngPPPKKGPAKKEAAADK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      96.58|      26|      28|    2189|    2214|      13
---------------------------------------------------------------------------
 2189- 2214 (47.11/22.89)	FVEPENRNSEEAPTTTERPPNSFPYR
 2218- 2243 (49.47/24.44)	WHEKDDDTFEDPPEVHDILPEGFYER
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      53.76|      15|      15|     611|     625|      15
---------------------------------------------------------------------------
  611-  625 (28.82/17.47)	FLSWKSQRANHFDTT
  628-  642 (24.94/14.06)	FVNRLFENADTFDET
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      56.96|      20|      25|     413|     437|      16
---------------------------------------------------------------------------
  413-  437 (22.84/22.96)	MfepdLRQDKpKEETAAEKEKRMAA
  442-  461 (34.12/16.03)	R....LRRQR.REERRREQEKQRRA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      45.93|      17|      23|    2313|    2333|      17
---------------------------------------------------------------------------
 2313- 2333 (25.10/24.20)	RYQMA.VEGRL.KRQKhrrdIEE
 2337- 2355 (20.83/ 9.30)	RYEAAkVQDEAdKREK....IDE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      83.03|      24|      24|    1100|    1123|      18
---------------------------------------------------------------------------
 1098- 1121 (42.67/31.94)	DHDSESEIDEQRTGLGEGTSDQYQ
 1122- 1145 (40.35/29.67)	DGESVDMIDIERELANDPSSYLFN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      99.20|      23|      24|    1766|    1788|      19
---------------------------------------------------------------------------
 1719- 1741 (22.81/12.31)	...CSCSVS.IRSRdlgmYITPHAVLS
 1766- 1788 (46.51/34.30)	ATSCTCGFSAIRHR....YLSCCAGLF
 1792- 1810 (29.88/18.87)	ADEAT....ASEHA....NASVIPPLF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      69.88|      19|     767|    1671|    1689|      20
---------------------------------------------------------------------------
 1671- 1689 (39.49/23.85)	NIPYKRQDI.IYNP.PNPAHP
 2441- 2461 (30.39/16.19)	NIPWKQRDTrVANPfPYSNQP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      77.91|      24|      27|    1958|    1983|      22
---------------------------------------------------------------------------
 1283- 1312 (33.51/14.28)	PATnkfDIQCQVERvtvPMAYKSMVTRNFE
 1960- 1983 (44.39/29.66)	PPA...EIPFVIEG...PMTWKQVVTKAIR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      37.80|      14|      19|     969|     987|      23
---------------------------------------------------------------------------
  969-  987 (17.64/24.66)	EAARrmkwlQLYRE...KAEKR
  990- 1006 (20.15/10.69)	KTAR.....QCHRDylrQIAKR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      39.29|      10|      44|    1424|    1436|      26
---------------------------------------------------------------------------
 1424- 1436 (17.57/16.49)	MMPpgyPNQMGQM
 1471- 1480 (21.72/ 9.56)	MMR...MQQMRQM
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      53.63|      17|      19|    1208|    1226|      28
---------------------------------------------------------------------------
 1208- 1226 (25.76/20.66)	AHSPsiGGKFRSTANDDIE
 1228- 1244 (27.87/15.68)	AVAP..GKTIVDVEIEDIE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      64.10|      19|      27|     562|     582|      29
---------------------------------------------------------------------------
  562-  582 (30.36/24.34)	YQYVQNEKRAERehFYPRNKP
  591-  609 (33.74/19.61)	FEFLSNPEAARR..VKPPKSP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      62.83|      19|      23|    1814|    1832|      32
---------------------------------------------------------------------------
 1814- 1832 (35.48/27.66)	TIKTRDMMWFDP..QSVHDLA
 1834- 1854 (27.35/19.03)	TYQIRQMAFSNSlgKAVSQMA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      62.67|      20|      23|    2515|    2534|      33
---------------------------------------------------------------------------
 2515- 2534 (32.28/20.14)	NSIVGRLP.FTKRTQLQLEII
 2540- 2560 (30.39/18.47)	DDMVKGIPdYLNDSQVPFDIL
---------------------------------------------------------------------------




































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 MDP16225 with Med13 domain of Kingdom Metazoa
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