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

NucPred

Fetching Q5D1Z7 from www.uniprot.org...

The NucPred score for your sequence is 0.67 (see score help below)

   1  MQRSPLEKANVFSKLFFSWTRPILKKGFRRRLELSDIYQIPSCNSADHLS    50
  51  EKLEREWDRELASKKKPKLINALRRCFFWRFVFHGIILYLGEVTKAVQPL   100
 101  LLGRIIASYDPDNKAERSIAIYLGIGLCLLFIVRTLLLHPAIFGLHHMGM   150
 151  QMRIALFSLIYKKTLKLSSRVLDKISTGQLISLLSNNLNKFDEGLALAHF   200
 201  VWIAPLQVVLLMGLLWDLLQASAFCGLAFLVVLALFQAWLGQMMMKYRER   250
 251  RAGKINERLVITSEMIDNIQSVKAYCWEEAMETMIENLRQTELKLTRKTA   300
 301  YVRYFNSSAFFFSGFFVVFLAVLPYALIKGIILRKIFTTISFCIVLRMAV   350
 351  TRQFPWAVQTWYDSLGAINKIQDFLQKEEYKTLEYNLTTTDVMMENITAF   400
 401  WDEGFGDLFIKVKQSNSDGKIPNGDHGLFFSNFSLLGTPVLKNISFKIEK   450
 451  GQLLAVAGSTGAGKTSLLMLIMGELEPSEGKIKHSGRISFCSQFSWIMPG   500
 501  TIKENIIFGVSYDEYRYRSVIKACQLEEEISKFAEKDNTILGEGGITLSG   550
 551  GQRARISLARAIYKDADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTR   600
 601  ILITSKMEHLKKADKILILHEGSCYFYGAFSELQSLRPDFSSKLMGFDSF   650
 651  DQFSADRRSSILTETLRRFSIEGDAAVSWNEGKMQSFKQTGDFGERRKNS   700
 701  VLSPLNSNRKFSVVQKGQQQMNGIEENDDEPLERRLSLVPDSEQGEAILP   750
 751  RSNMINTGPTFQGRNRRQSVLNLMTRPSVHQGQGMYRTGNAAVRKMSMVP   800
 801  QSQLSEIDIYSRRLSRDSGMDISDEINEEDLKEWFFDDVENIPAVTTWNT   850
 851  YLRYITVHKSLIFVLIWCLVIFLVEVGASLVGLWVLKETSLKDKANTTNN   900
 901  TYAVIITNTSKYYLFYIYVGVADTFFALGLLRGLPLVHTLISVSKILHHK   950
 951  MLCSVLKAPMSTFSTLKAGGILNRFSKDIAILDDLLPLTIFDFVQLILIV  1000
1001  VGALIVVSVLQPYIFLATVPVIIAFIMLRAYFLQTSQQLKQLESEARTPI  1050
1051  FTHLVTSLKGLWTLRAFGRQPYFETLFHKALNLHTANWFLYMSTLRWFQM  1100
1101  RIEIIFVTFFCIVTFISILTTGDGEGRVGILLTLAMNIMSTLQWAVNSSI  1150
1151  DVDSLMRSVSRVFKFIDMPSEEPLPPKPTKSKKNQLSQVLIIENEHVKKE  1200
1201  NWPSGGQMTVKDLTAKYIDGGNAVLENISFSISSGQRVGLLGRTGSGKST  1250
1251  LLAAFLRLLNTQGDIQIDGVSWDSVPLQQWRKAFGVIPQKVFIFSGTFRK  1300
1301  NLDPYGQWSDHELWKVADEVGLKSVIEQFPGKLDFVLVDAGCVLSHGHKQ  1350
1351  LICLARSVLSKAKILLLDEPSAHLDPITYQIIRRALKNAFADCTVILSEH  1400
1401  RIEAMLECQRFLVIEESKVRQYESIQKLVTEKRLYGQAISHSDRMKLFPH  1450
1451  RNSSRHKSRAKITALKEETEEEVQETRL                        1478

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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