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

NucPred

Fetching Q9NTG1 from www.uniprot.org...

The NucPred score for your sequence is 0.76 (see score help below)

   1  MRPGPALLLLGVGLSLSVGRLPLPPVPRGAQAAVSGAPGGLLRGAPGLGV    50
  51  RGGRALLSLRPSAVRAGGAVLSGRGSLCFPHGGTGRRWYCLDLRVLLSAQ   100
 101  RLPWPAAPALALVDLQLSARGGRLSLTWSVRLPRSPGRLAWAFRLRLLGP   150
 151  GAARPASPAARVSPRSAAPGPRPQQGFVARTECPTDGPARVMLQAVNSSS   200
 201  HRAVESSVSCQINACVIQRVRINTDQKGAPVRLSMQAEATINASVQLDCP   250
 251  AARAIAQYWQVFSVPAVGQAPDWTQPLDLPQLEIRNSPLFIHIPNNSLQW   300
 301  GVYVFNFTVSITTGNPKMPEVKDSDAVYVWIVRSSLQAVMLGDANITANF   350
 351  TEQLILDGSTSSDPDADSPLQGLQFFWYCTTDPRNYGGDRIILGSKEVCH   400
 401  PEQANLKWPWASGPVLTLLPETLKGDHVYFFRMVIRKDSRTAFSDKRVHV   450
 451  LQGPKAIAHITCIENCERNFIVSDRFSLFLNCTNCASRDFYKWSILSSSG   500
 501  GEMLFDWMGETVTGRNGAYLSIKAFAFRHFLEAEFSISLYLACWSGVTSV   550
 551  FRHSFIINHGPQIGECKINPAKGIALITKFVVQCSNFRDKHVPLTYKIIV   600
 601  SDLHSVGEISSVKENTLGTILYLGPQSTVPPSFLPVGMLASQYGLKIYAQ   650
 651  VYDSLGAFSQVTLHATAQAPTDKNSSKTVLNQLLSFTVGPSSLLSTLIQK   700
 701  KDFLPAGYLLYIVASVLNNMKTELPLRDDRVNLRKHLIDQSFLLPVSTLV   750
 751  EIGQVVMTITKLTQKPSEFTWDAQKRATMRVWQANQALQEYQQKDKRFRS   800
 801  EQIEIVSTGILMSLSNILKMTSPHQVVKDPFYVIESLSDTILANKVPGNK   850
 851  TTSMRTPNFNMYVKKVEKWGINQLFRNEKHCRNCFYPTLNVSSVPGLSAN   900
 901  GPISTMFCDFTNDLFPWLNDQENTSVEVSGFRMTGVADNGSVLEITPDVA   950
 951  EVYLVRKNLTFAAFNLTVGPNSEVDGSLKKTTGGFSFQVDSTVLREVLVH  1000
1001  IVTEVMVLFTVLVYTGSQITPTALVATFLVPHDIPPFASQSALFDPACTV  1050
1051  KKARVVCLPVSLLQLIAQHSHSPHCTVSIVLQAPRFVMKLNDKLVRISIF  1100
1101  SVQCLDMYGIQSEWREGYCILGEKTSWYEVHCICKNVVRARRQLGTIGLT  1150
1151  GIHLHTHYVMAKVIVIPNPVDLRLNIIKSLHQNPVTLFTVLFIILLYVGL  1200
1201  AFWALYRDEMDQHLRGHVIVLPDNDPYDNLCYLVTIFTGSRWGSGTRANV  1250
1251  FVQLRGTVSTSDVHCLSHPHFTTLYRGSINTFLLTTKSDLGDIHSIRVWH  1300
1301  NNEGRSPSWYLSRIKVENLFSRHIWLFICQKWLSVDTTLDRTFHVTHPDE  1350
1351  RLTRKDFFFIDVSSNLRKNHMWFSIFASVVAKTFNRLQRLSCCLAMLLSS  1400
1401  LLCNIMFFNLNRQEQTESRERKYMRSMMIGIESVLITIPVQLLITFLFTC  1450
1451  SQRKPQADLKEVSPQKHPLMSEASEHWEEYLRKWHAYETAKVHPREVAKP  1500
1501  ASKGKPRLPKASPKATSKPKHRHRKAQIKTPETLGPNTNSNNNIEDDQDV  1550
1551  HSEQHPSQKDLQQLKKKPRIVLPWWCVYVAWFLVFATSSISSFFIVFYGL  1600
1601  TYGYDKSIEWLFASFCSFCQSVLLVQPSKIILLSGFRTNKPKYCKNLSWS  1650
1651  TKYKYTEIRLDGMRMHPEEMQRIHDQIVRIRGTRMYQPLTEDEIRIFKRK  1700
1701  KRIKRRALLFLSYILTHFIFLALLLILIVLLRHTDCFYYNQFIRDRFSMD  1750
1751  LATVTKLEDIYRWLNSVLLPLLHNDLNPTFLPESSSKILGLPLMRQVRAK  1800
1801  SSEKMCLPAEKFVQNSIRREIHCHPKYGIDPEDTKNYSGFWNEVDKQAID  1850
1851  ESTNGFTYKPQGTQWLYYSYGLLHTYGSGGYALYFFPEQQRFNSTLRLKE  1900
1901  LQESNWLDEKTWAVVLELTTFNPDINLFCSISVIFEVSQLGVVNTSISLH  1950
1951  SFSLADFDRKASAEIYLYVAILIFFLAYVVDEGCIIMQERASYVRSVYNL  2000
2001  LNFALKCIFTVLIVLFLRKHFLATGIIRFYLSNPEDFIPFHAVSQVDHIM  2050
2051  RIILGFLLFLTILKTLRYSRFFYDVRLAQRAIQAALPGICHMAFVVSVYF  2100
2101  FVYMAFGYLVFGQHEWNYSNLIHSTQTVFSYCVSAFQNTEFSNNRILGVL  2150
2151  FLSSFMLVMICVLINLFQAVILSAYEEMKQPVYEEPSDEVEAMTYLCRKL  2200
2201  RTMFSFLTSQSKAKDEPEFFIDMLYGQPEKNSHRYLGLKTRNINGKKMVY  2250
2251  LVV                                                 2253

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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