<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 MDP31742

Description Mediator of RNA polymerase II transcription subunit 5
SequenceMSETVSLHKLVKKAVHSKLSFKTFLGLFSQLNTKQVVQDGEYQTEILEIVQNPRNLNDKKITEYKVVLAIQLSLSSSEELKRFWGNLSKISLVGQVDYLIRLNKILKYEYSKYDKDIVRLLIKVQYCDYIVEVLDSFGDKKLSTEQKSLANHIVFFASSVIEHVVVKDEALVNDLVFQLATRLEGLRLSNLLDFLLLKSKNILSEDQIRLTDSSGSGEDKSSDLPTITTSLYKNLSVGSLSSAKQETYNETIKFLWLNKIMKSWKFADNESIFNNFVHNFIPSSDKNKNPYLTSFELIKATFKGFGYAVINNDDCYVLFNWKNFIITRIPVILSTLKFANVNDEETLERAVLNAFNSLPDSIVKVLTNLASGSTKVYDLRQIFIKSLIFNRLLPPVAFQKFFPMESKITQQVILSELAQYNHDLNLRRKFNDKLINVNSEFTSLEESGLLELCNSLPASLEYSYSRQIELSNAINDIIDEMKISREHEKLNRLLLSVMSNVQLTNILVFNSNPYVVLGKMIDYIDSENFRIDDDDENFQDVYSYCGVLILSIISIIEKFKIDLSTFNIKNSFALDYINNFYYRLCDDLTNQIPVNSDEEDNTIATNYNNLLIDWINALFDDSNDGLSDDLIKSISIKQIYKLIPLVYQQAITATSIGKIDFSILTNGIDYLSQVFLIPTTVSIINWLLSEISNKKTDAESLPVKVLSEIVKSNISSESGSQELSSLVFKIVVNICGSNILIALKKIKDWENSQRIRDVVSIVTANLDSNYVEKDLSLPESKSDININEQIKSHLVNFQQQADSPTPIHAFIHRFISDSKDQVLRVLLQEVTSYQKQNNEATKIFINLASYLVVSSSIDSVEDKKYWHGYLSNVSSSATEHKILKNSDKEFNSSMDYHYSSIFNDASSGASNDDDLFNDKSSKQLSSGKLLEQLRTKVNRYNNLLAKFNVIFAENQDPSSPWHKTVNTLADKLLDDINDLYI
Length981
PositionTail
OrganismScheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) (Yeast) (Pichia stipitis)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Saccharomycotina> Saccharomycetes> Saccharomycetales> Debaryomycetaceae> Scheffersomyces.
Aromaticity0.10
Grand average of hydropathy-0.175
Instability index35.21
Isoelectric point5.30
Molecular weight111845.79
Publications
PubMed=17334359

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 (By similarity). 
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

>MDP31742
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     128.44|      23|      50|     521|     543|       1
---------------------------------------------------------------------------
  521-  543 (40.99/23.44)	IDYIDS..ENFRIDDDDENFQDVYS
  549-  573 (26.82/12.66)	ILSIISiiEKFKIDLSTFNIKNSFA
  574-  596 (36.34/19.90)	LDYINN..FYYRLCDDLTNQIPVNS
  609-  628 (24.29/10.73)	NLLIDW..INALFDDSNDGLSD...
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     158.33|      33|      78|     317|     349|       2
---------------------------------------------------------------------------
  271-  296 (43.99/26.80)	SIFN..NFV....HNFIP...SSD...............K..NKNPYLTSFE
  317-  349 (58.15/38.00)	VLFNWKNFI....ITRIPVILSTL...............KFANVNDEETLER
  370-  395 (36.00/20.47)	ASGSTKVYD....LRQI..FIKSL...............IFNRL.....LPP
  396-  440 (20.18/ 7.95)	VAFQ.KFFPmeskITQ.QVILSELaqynhdlnlrrkfndKLINVNSE.....
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      41.78|      13|      15|     688|     700|       3
---------------------------------------------------------------------------
  688-  700 (21.12/12.56)	LSEISNKKTDAES
  706-  718 (20.66/12.12)	LSEIVKSNISSES
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      41.75|      13|      15|      99|     113|       5
---------------------------------------------------------------------------
   99-  113 (17.90/15.28)	LIRLnkILKYEYSKY
  117-  129 (23.85/13.28)	IVRL..LIKVQYCDY
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      43.35|      14|      15|     443|     456|       7
---------------------------------------------------------------------------
  443-  456 (24.25/14.20)	SLE..ESGLLELCNSL
  459-  474 (19.10/ 9.71)	SLEysYSRQIELSNAI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     147.68|      50|     535|     201|     253|       8
---------------------------------------------------------------------------
  201-  253 (77.47/59.63)	NIL.SEDQIRLTDSSGSGEDKSSDLPTITTSLY..KNLsvgSLSSAKQE.TYNETIK
  738-  791 (70.21/45.88)	NILiALKKIKDWENSQRIRDVVSIVTANLDSNYveKDL...SLPESKSDiNINEQIK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      94.95|      33|     330|     483|     516|       9
---------------------------------------------------------------------------
  483-  516 (51.33/36.85)	ISREHEKLNRLLL.SVMS....NVQLTNILVfNSNPYVV
  815-  852 (43.62/25.79)	ISDSKDQVLRVLLqEVTSyqkqNNEATKIFI.NLASYLV
---------------------------------------------------------------------------




































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 MDP31742 with Med5 domain of Kingdom Fungi
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