<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 MDP00503

Description Pre-mRNA-processing protein 40C
SequenceMNASSTPNFAPVTSWMPTTQSFPMSTESSGTSGTAGHPGLVPSVQMITASAAVDSPSSAVPRPSAPVSSNQAVQQQIYPTYTPLPSMASSPQGFWMQHPPMGGFPRPPFVPYPTIYPGPFPSASSGMPHPAPSSDSQPPGVSPLATSPFAPSIAIPANQSSVASGIQTGFPPQGIDNRNVGTRVEAAVNEQSDIWTAHKTDTGIVYYYNALTGESTYEKPAGFKGEPDKVPVQPTPVSVEQLAGTEWALVTTSDGKKYYYNSKTKISSWQIPSEVAELRKKQDNDVSKEHAVPVPNIDVVAEKGSTPISLSAPAVSTGGRDAMPLRTSVVPGSSSALDLIKKKLQDSGVPSSSSSSVPVMPVTAAQELNGSRAVDVKGLQSENSKDKLKDANGDGNISDSSSDSEDTDSGPSKEECIMQFKEMLKERGVAPFSKWEKELPKIVFDPRFKAIPSHSARRTLFEHYVKTRAEEERREKRAALKAAIEGFKQLLDEASEDIDHNTNYQTFKRKWGSDLRFEALDRKDRELLLTERVLPLKRAAEEKAQAIRAAAASSLKSMLKEKGDITVNSRWSRVKDSIRDDPRYKCVKHEDREVLFNEYISELKAVEEKAERKERVKKEEEEKLKERERELRKRKEREEQEMERVRLKVRRKEAVASFQALLVETIKDPQASWTESKPKLEKDPQGRAANPDLDPSDTEKLFREHIKMLFERCTHDFRALLAEVITQDAAAQETEGGKTVFNSWSTAKRLLKPDPRYSKMPRKEREALWRRYAEDMLRKQKSALDQEEEKRTDAKVRSSGDLGRFSSGSRKVHERR
Length816
PositionUnknown
OrganismTheobroma cacao (Cacao) (Cocoa)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> rosids> malvids> Malvales> Malvaceae> Byttnerioideae> Theobroma.
Aromaticity0.06
Grand average of hydropathy-0.790
Instability index56.90
Isoelectric point8.78
Molecular weight90672.81
Publications
PubMed=23731509

Function

Annotated function 
GO - Cellular Component
nucleus	GO:0005634	IBA:GO_Central

GO - Biological Function
RNA polymerase binding	GO:0070063	IBA:GO_Central
transcription coregulator activity	GO:0003712	IBA:GO_Central

GO - Biological Process








Interaction





Binary Interactions











Repeat regions





Repeats

>MDP00503
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     142.31|      45|      64|      42|     105|       1
---------------------------------------------------------------------------
    7-   72 (63.93/26.82)	PNFAPVTS........WM..PTTQSFPmstessgtsgtaghpglvPSVQMItaSAAVDSPSSAVPRPsAPVSSNQA
   79-  138 (78.38/49.50)	PTYTPLPSmasspqgfWMqhPPMGGFP.............rppfvPYPTIY..PGPFPSASSGMPHP.APSSDSQP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             6|     406.46|      64|      64|     497|     560|       2
---------------------------------------------------------------------------
  434-  492 (48.33/23.83)	.............KWEKELpkivfdpRFKA....IPSHSARRT...LFEHY.VK.TRAEEERreK.RAALKAAIEGFKQLLD
  497-  560 (98.99/56.46)	DIDHNTNYQTFKRKWGSDL.......RFEA....LDRKDRELL...LTERV.LPLKRAAEEK..A.QAIRAAAASSLKSMLK
  564-  625 (82.98/46.15)	DITVNSRWSRVKDSIRDDP.......RYKC....VKHEDREVL...FNEYI.SELK.AVEEK..AeRKERVKKEEEEK..LK
  630-  662 (36.47/16.20)	E.................L.......R........KRKEREEQ...EMERVrLKVR.............RKEAVASFQALL.
  668-  733 (74.41/40.63)	..DPQASWTESKPKLEKDP.......QGRAanpdLDPSDTEKL...FREHI.KMLFERCTHD..F.RALLAEVITQDAAAQE
  737-  794 (65.28/34.75)	GKTVFNSWSTAKRLLKPDP.......RYSK....MPRKEREALwrrYAEDM.LRKQKSALDQ..E.EEKRTDA.........
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     230.51|      57|      60|     230|     286|       3
---------------------------------------------------------------------------
  195-  223 (39.36/19.29)	..........................WTAHKTDTGIVYYYNALTGESTYEKP..A.............GF
  230-  286 (100.85/61.11)	VPVQ.........PTPVSVEQLAGTEWALVTTSDGKKYYYNSKTKISSWQIP..SEVAELRKK..QDNDV
  292-  349 (55.28/30.12)	VPVPnidvvaekgSTPISLSAPA........VSTGGRDAMPLRTSV....VPgsSSALDLIKKklQDSGV
  357-  388 (35.03/16.35)	VPVM.........PV.TAAQELNGSRAVDVKGLQSE....NSKDKL........................
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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 MDP00503 with Med35 domain of Kingdom Viridiplantae
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