SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching Q9JIS1 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MSAPLGPRGRPAPTPAASQPPPQPEMPDLSHLTEEERKIIQAVMDRQKKE    50
  51  EEKEQSVLKKLHQQFEMYKEQVKKMGEESQQQQEQKGDAPTCGICHKTKF   100
 101  ADGCGHNCSYCQTKFCARCGGRVSLRSNKVMWVCNLCRKQQEILTKSGAW   150
 151  FYNSGSNTPQQPDQKALRGLRSEEAPQEKKAKLHEQTQFQGPPGDSSVPA   200
 201  VERGRAHGLTRQDSIKNGSGMKHQIASDMPSDRKRSPSVSRDQNRRYDQS   250
 251  EEREEYSQYVPSDSTMPRSPSDYADRRSQREPQFYEEPDHLNYRDSNRRG   300
 301  HRHSKEYIVDDEDVESRDEYERQRREEEYQARYRSDPNLARYPVKPQPYE   350
 351  EQMRIHAEVSRARHERRHSDVSLANAELEDSRISLLRMDRPSRQRSVSER   400
 401  RAAMENQRSYSMERTREAQGQSSYPQRTTNHSPPTPRRSPIPLDRPELRR   450
 451  ADSLRKQHHLDPSSAVRKTKREKMETMLRNDSLSSDQSESVRPPPPRPHK   500
 501  SKKGGKMRQVSLSSSEEELASTPEYTSCDDVEIESESVGEKGDMEYSWLE   550
 551  HASWHSSEASPMSLHPVTWQPSKDGDRLIGRILLNKRLKDGSVPRDSGAM   600
 601  LGLKVVGGKMTESGRLCAFITKVKKGSLADTVGHLRPGDEVLEWNGRLLQ   650
 651  GATFEEVYNIILESKPEPQVELVVSRPIGDMPRIPDSTHAQLESSSSSFE   700
 701  SQKMDRPSISVTSPMSPGMLRDVPQFLSGQLSSQSLSRRTTPFVPRVQIK   750
 751  LWFDKVGHQLIVTILGAKDLPSREDGRPRNPYVKIYFLPDRSDKNKRRTK   800
 801  TVKKTLEPKWNQTFIYSPVHRREFRERMLEITLWDQARVREEESEFLGEI   850
 851  LIELETALLDDEPHWYKLQTHDVSSLPLPHPSPYMPRRQLHGESPTRRLQ   900
 901  RSKRISDSEVSDYDCEDGVGVVSDYRHDGRDLQSSTLSVPEQVMSSNHCS   950
 951  PSGSPHRVDVIGRTRSWSPSVPPPQRNVEQGLRGTRATGHYNTISRMDRH  1000
1001  RVMDDHYSSERDSHFLTLPRSRHRQTSEHHHRDGRDCEAADRQPYHRSRS  1050
1051  TEQRPLLERTTTRSRSSERADTNLMRSMPSLMTGRSAPPSPALSRSHPRT  1100
1101  GSVQTSPSSTPVTGRRGRQLPQLPPKGTLERMITEDMDSTRKRNSGAMDI  1150
1151  EERNRQMKLNKYKQVAGSDPRLEQDYHSKYRSGWDPHRGADTVSTKSSDS  1200
1201  DVSDVSAVSRTSSASRFSSTSYMSVQSERPRGNRKISVFTSKMQSRQMGV  1250
1251  SGKSMAKSTSISGDMCSLEKNDGSQSDTAVGALGTSGKKRRSSIGAKMVA  1300
1301  IVGLSRKSRSASQLSQTEGGGKKLRSTVQRSTETGLAVEMRNWMTRQASR  1350
1351  ESTDGSMNSYSSEGNLIFPGVRLASDSQFSDFLDGLGPAQLVGRQTLATP  1400
1401  AMGDIQVGMMDKKGQLEVEIIRARGLVVKPGSKTLPAPYVKVYLLDNGVC  1450
1451  IAKKKTKVARKTLEPLYQQLLSFEESPQGKVLQIIVWGDYGRMDHKSFMG  1500
1501  VAQILLDELELSNMVIGWFKLFPPSSLVDPTLAPLTRRASQSSLESSTGP  1550
1551  SYSRS                                               1555

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold Specificity Sensitivity
see above fraction of proteins predicted to be nuclear that actually are nuclear fraction of true nuclear proteins that are predicted (coverage)
0.10 0.45 0.88
0.20 0.52 0.83
0.30 0.57 0.77
0.40 0.63 0.69
0.50 0.70 0.62
0.60 0.71 0.53
0.70 0.81 0.44
0.80 0.84 0.32
0.90 0.88 0.21
1.00 1.00 0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

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