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

NucPred

Fetching Q9QYC1 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MGSQTLQILRQGVWAALSGGWYYDPHQATFVNALHLYLWLFLLGLPFTLY    50
  51  MALPSSMIIVAVYCPVVAAVFIILKMVNYRLHRALDAGEIVDRSAKEFTD   100
 101  QRAKAEQGNCSTRRKDSNGPSDPGGGIEMSEFIREATPPVGCSSRNSYAG   150
 151  LDPSNQIGSGSSRLGTAATIKGDTDTAKTSDDISLSLGQSSSLCKEGSEE   200
 201  QDLATDRKLFRLVSNDSFISIQPSLSSCGQDLPRDFSDKVSLPSHSQHHR   250
 251  VDQSLCSACDTEVASLVPLHSHSYRKEHRPRGVPRTSSSAVAFPDASLSG   300
 301  LPLYQQQQRRGLDPVTELDSSKPHSGTRESSAGKSCPPAQSQPAADRRKS   350
 351  SSQPPTKCGKSRALNAEKSVDSLRSLSTRSSGSTESYCSGTDRDTNSTLS   400
 401  SYKSEQTSSTHIESILSEHEESPKVGDKSARKRECGADSVEERSHRADDR   450
 451  RTSSDKTAPEGNTPAGPPEAPDAQASEEMADQAAPSSSASEDANKNPHAN   500
 501  EFTVPGDRPPEQSAESKEEQSEKPSLATDSRVCKDDGGKQKEGDVRPKSS   550
 551  SLIHRTTSAHKPGRRRTGKKRASSFDSSRHRDYVSFRGVSGTKPHSAVFG   600
 601  HDEDSSDQSDLSRAPSIHSAHQFSSDSSSSATSHSCQSPEGKYGALKTKH   650
 651  GHRDRGTDSDHTHRAHPGPEGTTKKRASRRTSSTSSAKTRARVLSLDSGT   700
 701  VACLNDSNRLLAPDSMKPLTTSKSDLEAKEGEVLDELSLLGRASQLETVT   750
 751  RSRNSLPSQVAFPEGEEQDAATGAAQASEEAVAFRRERSTFRRQAVRRRH   800
 801  NAGSNPTPPTLLIGSPLSLQDGQQGQQSTAQVKVQSRPPSQAAVLSASAS   850
 851  LLVRKGSVHLEASHDHASAVGGSSLHDELGKFSSTLYETGGCDMSLVNFE   900
 901  PAARRASNICDTDSHVSSSTSVRFYPHDMLSLPQIRLNRLLTIDTDLLEQ   950
 951  QDIDLSPDLAATYGPTEEAAQKVKHYYRFWVLPQLWIGINFDRLTLLALF  1000
1001  DRNREILENILAVVLAILVAFLGSILLIQGFFRDIWVFQFCLVIASCQYS  1050
1051  LLKSVQPDSSSPRHGHNRIIAYSRPVYFCLCCGLIWLLDYGSRNLTTSKF  1100
1101  KLYGVTFTNPLVLLSARDLVIVFTLCFPIVFFIGLLPQVNTFVMYLCEQL  1150
1151  DIHIFGGNATTSLLAALYSFLCSIVAVALLYGLCYGALRDSWDGQHVPVL  1200
1201  FSVFCGLLVAVSYHLSRQSSDPSVLFSLMQSKIFPKADEKNPEDPLSEVK  1250
1251  DPLPEKLSNSVSERLQSDLVVCVIIGVLYFAIHVSTVFTALQPALKYVLY  1300
1301  ALVGVVGLVTHYVLPQVRKQLPWHCFSRPLLRTAEHSQYEVRNAATMMWF  1350
1351  EKLHVWLLFVEKNIIYPLIVLNELSSSAETIASPKKLDTELGALMITIAG  1400
1401  LKLLRSSFSSPTYQYITVIFTVLFFKFDYEAFSETMLLDLFFMSILFSKL  1450
1451  WELLYKLQFVYTYVAPWQITWGSAFHAFAQPFAVPHSAMLFVQAIVSAFF  1500
1501  STPLNPFLGSAIFITSYVRPVKFWERDYNTKRVDHSNTRLASQLDRNPGS  1550
1551  DDNNLNSIFYEHLTRSLQHSLCGDLLLGRWGNYSTGDCFILASDYLNALV  1600
1601  HLIEIGNGLVTFQLRGLEFRGTYCQQREVEAITEGVEEDEGFCCCEPGHV  1650
1651  PHVLSFNAAFGQRWLAWEVVVTKYILEGYSITDNSAASMLQVFDLRRVLT  1700
1701  TYYVKGIIYYVTTSSKLEEWLANETMQEGLRLCADRNYVDVDPTFNPNID  1750
1751  EDYDHRLAGISRESFCVIYLSWIEYCSSRRAKPLDVDKDSSLVTLCYGLC  1800
1801  VLGRRALGTASHHMSSNLESFLYGLHALFKGDFRISSVRDEWIFADMELL  1850
1851  RKVVVPGIRMSIKLHQDHFTSPDEYDDPTVLYEAIVSHEKNLVIAHEGDP  1900
1901  AWRSAVLANSPSLLALRHVMDDGTNEYKIIMLNRRYLSFRVIKVNKECVR  1950
1951  GLWAGQQQELVFLRNRNPERGSIQNAKQALRNMINSSCDQPIGYPIFVSP  2000
2001  LTTSYSDSHDQLKEILGGPISLGNIRNFIVSTWHRLRKGCGAGCNSGGNI  2050
2051  EDSDTGGGTSCPGNSAVTASDPHNNVSQGSTGHPGQGAGSGLHPPTTSYP  2100
2101  PTLGTSHSAHSVQSSLVRQSPARASMASQSSYCYSSRHSSLRMSTTGFVP  2150
2151  CRRSSTSQISLRNLPSSIQSRLSMVNQMEAASQGGMGCVQHGLPSSSSSS  2200
2201  QSIPACKHHTLVAFLGAEGGQGSATEAQPGNTSSPANISHARKGEVIYRV  2250
2251  QIVDLSQILEGINVSKRKELHWPDEGIRLKAGRNSWKDWSPQEGMEGHVV  2300
2301  HRWVPCSRDPSTRSHIDKTVLLVQIDDKYVTIIETGVLELGAEV        2344

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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