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

NucPred

Fetching Q8C3Y4 from www.uniprot.org...

The NucPred score for your sequence is 0.68 (see score help below)

   1  MWNNIELLTSDDTGSGCLSVGSRKENVTALYQADLLGKISSEKTSLSPKI    50
  51  QAFSLSHGFIIVADQSVILLDSICRSLQLFLIFDTDVDVVGLCQEGKFLF   100
 101  VGERSGNFHLIYVTSKQTLFTKAFVEKALDESQRTYRNLIIEKDGSNEGT   150
 151  YYMLLLTNNGFFYITNLQLSQIEQAIENTDLDSAKKLQGQFKCSFISTEN   200
 201  YHSCLSLVASQSGTFASKTSVIIGGTGSCAFSKWEPDSTKKEMSLKNFVG   250
 251  TDIIKGAKSFQLIDNLLFVLDTDNVLSLWDAYTLTPVWNWPSLPVEQFVL   300
 301  TTEADSPSSVTWQGITNLKLVTLTATAKEKMRSLIIYSLPSMETLYSLEV   350
 351  SSVSSLVQTGISTDTIYLLEGIHKNDPNLCEDSVSDLVLRYLTEVLPENR   400
 401  LSRLLHKHRFAEAESFAIQFGLDVELVYKVKSNDMLEKLALISSDKSEQS   450
 451  KWQQLVDEAKENLCKIQDDDFVVNFCLKAQWVTYETTQEMLSYAKTRLMK   500
 501  KEDRALPASSDAFMEVLKAHAKLTTFYGAFGPEKFSGSSWIEFLNNEDDL   550
 551  RDVFLQLSEGNFACAQYLWLRHRADFESKFDVKMLENLLNSISTQFPLEN   600
 601  LCSWFKNEVIPFVRRIVPEGQNILAKWLEQASRNLELTDKANWPENGLQL   650
 651  AEVFFTAEKTDRFGFASSWHWISLDYQNTEEVRQLRTLVSKLRELIILHR   700
 701  KYNCKLALSDFEKENATTVVFRMFDRVSAPELIPSVLEKSVRVYIREQNL   750
 751  QEEELLLLYIEDLLKRCSSKSMTLFDTAWEAKAMAVIRCLSDTDLIFDAV   800
 801  LKIMYKAVVPWSAAVEQLVKQHLEMDHPKVKLLQESYKLMEMKKLLRGYG   850
 851  IREVNLLNKEIMRVIRYILKQDIPSSLEDALKVAQGYRLSDDEIYSLRII   900
 901  DLIDREQGGDCLLLLKSLPAAEAEKTAERVIIWARLALQEEPDGSEEDKA   950
 951  WRISVAKTSVDILKILCDIRKDNLQKKDESEEFLKRFQMVASLQENFEVF  1000
1001  LPFEDYSNTALVAGLREQYIKAQEAAQAEHKHRGPPGPTPARGTHLSIKS  1050
1051  KLHRQALALQVSEQELEAELTLRALKDGKVVAALSKCRDLLKHYCNADTG  1100
1101  RLLFVVCQKLCQMLADDVPMVAPGGLSLPSEIHDLACHAVTICSPDYLLD  1150
1151  VLELSKYTLTAVELCRQCQMDDCGMLMKAALGTHKDPYEEWSFSDFFSED  1200
1201  GIVLESQVVLPVIYELISSVMPPAESKRHPLDSISLPYCSTSEGENRILP  1250
1251  LVSSISALLRSLQECSQWELALRFVVGSFGTCLQHSMSNVMSISLSKQLL  1300
1301  GKNTLANSRHIIMELKEKSITFIRENATTLLHKVFNCRVVDLDLALAYCT  1350
1351  LLPQKDVFDNLWKFIDKAWQNYDKILALSLVGSQLANLYQDIETGLWFHE  1400
1401  LSIDAKWGIRLGKLGISFQPAFRQNFLTKKDLIKALVNNIDMDTSLILEY  1450
1451  CSTFQLDSDAALRLFIETLLRNTSSQSQGDAAPESTKHQHSKLLAKATEL  1500
1501  VPLLKNTKDLVISLSEILYKLDPYDYEMIDVVLKVLEQANEKITSVNINQ  1550
1551  ALNLLRHLKSYRRISPPVDHEYQYALEHMITLPPAAHTRLPFHLILFGTA  1600
1601  QNFWKILSSELSEESLPTLLLIAKLMKFSLDTLYVSTAKHLFEKNLKPKL  1650
1651  LKSAQARSSTLMSKEVDKLMQTLESYLLSIVNPEWAVAIAISLTQEVPEG  1700
1701  PFKMSSLKFCLYLAERWLQNIPPQDETCEKAKALQKKLCLQVRLSGTEAV  1750
1751  LIAHKLNDQEYLRVIGKPAHLIVSLYEHPSISERLCTTSGKDYPDIHTAA  1800
1801  KEIAEVNEVNLEKIWDMLLEKWLCPSTVPSEKASEFFELEEDEVLHRVVY  1850
1851  LLQARPVDYCSRMLFVFATSATSTLGMRQLTFAHKARALQCLLYLADKET  1900
1901  IESLFKKPIKEMKSYLKCITFLASFETLNIPITYELFCNSPKEGMIKGLW  1950
1951  KNHSHEPMAVRLVAELCLEYKIYDLQLWNGLLQKLLGFNMIPYLRKVLSC  2000
2001  ISSIHSLWQVPYFSKAWQRVIQIPLLSASCPLRPSQLADCCDSLVAILEC  2050
2051  PVSDDLDMMGVAKQYVQLDLPAFALTCLTLMPHSEKRHQQIKNFLNSCDA  2100
2101  RIILQQIEEHMNTGQLAGFSHQIGSLVLNHVVNKKEFGILAKTKYFQLLK  2150
2151  CHVINTGNVTELVNYLANDFSVDEASALINEYSKHCGKPVPADAAPCEIL  2200
2201  QTFLGGS                                             2207

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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