<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 MDP05987

Description Mediator of RNA polymerase II transcription subunit 1 (Fragment)
SequenceLDIMSKDQQLLMEHLRQKSQHCMSWKDILKSAKMNLMEKRSPLDAEDRVEVAKSYERLLQGLRVASAYELFGRLEDIATKMNLTFVRTPGTANNQSCFITADCFFLEISAEETGSVFLVNVTHEKQTSESVLLRDIINDKRWTELQRHLWGLCSAYIPCKDIDTKNQAFKFMQNLENILHIQSLQRINDNTLPVVEYLRTSDMYFFRRREVGDPPRLYFFCTPLSFWDSETGDFKQLFQNDIDNVMDVSKFKSTIYAELAMENVQGEQFLSISMQSVNALGQFHDIPMSMQIAAVFTLTFPEKLIISMDSVTKIEALTGFKPAFSNQSKILDLILGEILSSGFSVLRSFVLLEDQLHCYTVDLEGCLTEGVVLEKIYWTNLDVLHKILPILRTEALFKHIFTSFIRNITTTQKQFAQKIFRRDIHVIPSPDLSILECQVKLPREREFFYIVFRLAPINEISVKVGGVVDNADVNLNDVAYEVFSRVWSIPVTIRALVKQLLCLSERNVVVAAAGDGNSGNGDHQNDVVLMQIDCDRSLHLSTDSNCAAHSSVSIPDGNYNMSEYSVCNDDANGVAVADDADDDADAVISVSGIAQSLIIEQQMQKLIVNVDKVLEELLLVCSGRLAGGPNLLDLFKKPKVWRELIPPRRCAGRRGQRSRQQMAPPLAQQCCASAAGQLPAPVAAVAAAAPFGKVGPNLKSRHFSSTSETLTELDELCQLSSSCAEGNGHQSEHASACGDSAVADGGEQKSSIQDTIDSVLGSVRFPGSMAESLINISSCCINNNNNTNNSNPNSNNSNANTSNNNNTNSNNNNNNSNNSMNALASIRKIELGYGQSSAGVAAPMSSSSSPALAAPMSRSSDSTGDVFDYETRSTTTAGMSIDQGGRSLSSSVCCADDLSIAAASASAPTLDVGFWPPAGGVERLDVRGALLNRGMRRRRRCRKAFANTGDRALDMVLKEMRKAERLVRGASSTRRPRRSRLATATASFTADMREVASKVTLKIRSSSAAALPGVQTAQESSSLAVASSSLSSADQGSSSGGKDEQKKSLKLAANANASGGAGAATLNTWTQPSSSVFRSLSDATGESCSSRSSSPPPQLVKPASKRKNSLDVVIGKLMDKVGTSPTKLDPSSDVPDSAGDKQRHLYGFCFSPTASQQQKSGTTAASVSASEFTIHKRGECSTTTTAMATSTGELSDAPEGGIKLVIKKGVIKLKSARHGRGAGAGRFVETGAPSARPRVSSPASAGDRLAASKFELLKQKMQARKIKRQSSTEKSRQRGPRSGALAAASKTAANRSKLSTVGSSSSGVAELPSVFPGAEGLLFSKSLKGFKIPKIDDNSSKTTTATTAATVTAAPASTSDSANTTTTVTVSTTTTATVVPAAASAAATMTTTTTTTNIVSATAAAAVVTSASTVATGTTTSANATTTASVAVTPLTVVEKRMADGPPMALVVNDGRASPAGVVSGGGGGILRMKPPLLAVQQVPPPCVGGSSKPLIRRSRPVPLPLPPRSLVATGPHFAGPPAVELALPTGPAVPRYVRRTLLPNPPLQTASSPRPPPPQPLLELNKHHQQQMLVHSTTQQRPTKQELLNPMTNQMSPKSASPDPTGLVIDDNLNTTAAISSPQKNAEEVDVLSPGLRIAVDEGDETKGPTTHSSSTT
Length1658
PositionMiddle
OrganismTrichinella sp. T9
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Enoplea> Dorylaimia> Trichinellida> Trichinellidae> Trichinella> unclassified Trichinella.
Aromaticity0.05
Grand average of hydropathy-0.256
Instability index49.02
Isoelectric point8.73
Molecular weight177046.20
Publications









Function






Annotated function

Component of the Mediator complex, a coactivator involved in
the 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

>MDP05987
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     103.10|      24|      24|    1372|    1395|       1
---------------------------------------------------------------------------
 1346- 1370 (29.43/14.57)	.TTAATVTaaPASTSDSANTTTTVTV
 1372- 1395 (42.81/25.11)	TTTTATVV..PAAASAAATMTTTTTT
 1401- 1420 (30.86/15.70)	ATAAAAVV......TSASTVATGTTT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      74.83|      20|      24|     775|     798|       2
---------------------------------------------------------------------------
  775-  797 (34.86/28.26)	NISScciNNNNNTNNSNPNSNNS
  800-  819 (39.97/18.12)	NTSN...NNNTNSNNNNNNSNNS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     140.59|      24|      24|    1463|    1486|       3
---------------------------------------------------------------------------
 1463- 1486 (43.26/26.16)	VSGGGGGILRMKPPL.LAVQQVP.P..P
 1488- 1508 (29.29/14.80)	VGGSSKPLIRRSRPV.....PLPlP..P
 1509- 1532 (30.24/15.57)	RSLVATGPHFAGPP...AVELAL.PtgP
 1534- 1558 (37.81/21.72)	VPRYVRRTLLPNPPLqTASSPRP.P..P
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      88.99|      24|      24|    1003|    1026|       4
---------------------------------------------------------------------------
 1003- 1026 (36.04/18.03)	IRSSSAAALPGVQT.AQESSSLAVA
 1030- 1052 (32.78/15.68)	LSSADQGSSSGGKD.EQK.KSLKLA
 1055- 1075 (20.17/ 6.62)	ANASGGAGAATLNTwTQPSSS....
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      46.42|      13|      20|     646|     664|       6
---------------------------------------------------------------------------
  648-  664 (20.16/22.91)	RRCAGRRGQRSrqqmAP
  669-  681 (26.26/ 9.30)	QCCASAAGQLP....AP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     105.94|      28|      28|    1122|    1149|       7
---------------------------------------------------------------------------
 1122- 1149 (53.27/37.19)	GTSPTKLDPS....SDVPDSAGDKQRHLYGFC
 1161- 1180 (33.53/19.99)	GTTAASV............SASEFTIHKRGEC
 1181- 1203 (19.13/ 7.44)	STTTTAMATStgelSDAPE.GGIK........
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      41.44|      12|      24|       2|      13|       8
---------------------------------------------------------------------------
    2-   13 (21.10/15.99)	DIMSKDQQLLME
   27-   38 (20.34/15.11)	DILKSAKMNLME
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      65.05|      18|      22|     197|     218|       9
---------------------------------------------------------------------------
  200-  218 (30.05/29.30)	TSDMYFFrRREVGDPPRLY
  221-  238 (35.00/18.21)	CTPLSFW.DSETGDFKQLF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      65.22|      20|      22|     535|     556|      10
---------------------------------------------------------------------------
  537-  556 (34.45/27.35)	SLHLSTDSNCAAHSS.VSIPD
  558-  578 (30.77/15.73)	NYNMSEYSVCNDDANgVAVAD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      58.44|      12|      24|     933|     944|      11
---------------------------------------------------------------------------
  933-  944 (23.17/13.59)	RGMRRRRR.CRKA
  958-  970 (15.06/ 6.21)	KEMRKAERlVRGA
  971-  982 (20.21/10.90)	SSTRRPRR.SRLA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      50.69|      17|      22|    1270|    1286|      12
---------------------------------------------------------------------------
 1270- 1286 (28.92/17.71)	SSTEKSRQR....GPRSGALA
 1289- 1309 (21.77/11.10)	SKTAANRSKlstvGSSSSGVA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      34.65|      11|      27|    1215|    1227|      14
---------------------------------------------------------------------------
 1215- 1227 (15.61/16.03)	SArhGRGAGAGRF
 1244- 1254 (19.04/10.41)	SA..GDRLAASKF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      31.28|       9|      22|     717|     726|      15
---------------------------------------------------------------------------
  717-  726 (13.94/12.87)	CQlSSSCAEG
  737-  745 (17.33/10.08)	CG.DSAVADG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      32.37|      13|      22|     300|     320|      16
---------------------------------------------------------------------------
  300-  320 (16.49/27.33)	FPEKliismdsvTKIEAL.......TGF
  324-  343 (15.88/ 6.87)	FSNQ........SKILDLilgeilsSGF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      83.63|      26|     217|     682|     714|      17
---------------------------------------------------------------------------
  682-  714 (36.37/35.30)	VAAVAAAAPFGKVGpnlksrhFSSTSETLTELD
  900-  925 (47.26/27.99)	IAAASASAPTLDVG.......FWPPAGGVERLD
---------------------------------------------------------------------------




































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 MDP05987 with Med1 domain of Kingdom Metazoa
Unable to open file!