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

NucPred

Fetching Q96JM2 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MEVLQCDGCDFRAPSYEDLKAHIQDVHTAFLQPTDVAEDNVNELRCGSVN    50
  51  ASNQTEVEFSSIKDEFAIAEDLSGQNATSLGTGGYYGHSPGYYGQHIAAN   100
 101  PKPTNKFFQCKFCVRYFRSKNLLIEHTRKVHGAQAEGSSSGPPVPGSLNY   150
 151  NIMMHEGFGKVFSCQFCTYKSPRRARIIKHQKMYHKNNLKETTAPPPAPA   200
 201  PMPDPVVPPVSLQDPCKELPAEVVERSILESMVKPLTKSRGNFCCEWCSY   250
 251  QTPRRERWCDHMMKKHRSMVKILSSLRQQQEGTNLPDVPNKSAPSPTSNS   300
 301  TYLTMNAASREIPNTTVSNFRGSMGNSIMRPNSSASKFSPMSYPQMKPKS   350
 351  PHNSGLVNLTERSRYGMTDMTNSSADLETNSMLNDSSSDEELNEIDSENG   400
 401  LSAMDHQTSGLSAEQLMGSDGNKLLETKGIPFRRFMNRFQCPFCPFLTMH   450
 451  RRSISRHIENIHLSGKTAVYKCDECPFTCKSSLKLGAHKQCHTGTTSDWD   500
 501  AVNSQSESISSSLNEGVVSYESSSINGRKSGVMLDPLQQQQPPQPPPPPP   550
 551  PPPPSQPQPLQQPQPPQLQPPHQVPPQPQTQPPPTQQPQPPTQAAPLHPY   600
 601  KCTMCNYSTTTLKGLRVHQQHKHSFCDNLPKFEGQPSSLPLENETDSHPS   650
 651  SSNTVKKSQTSILGLSSKNNFVAKASRKLANDFPLDLSPVKKRTRIDEIA   700
 701  SNLQSKINQTKQQEDAVINVEDDEEEEEDNEVEIEVELDREEEPTEPIIE   750
 751  VPTSFSAQQIWVRDTSEPQKEPNFRNITHDYNATNGAEIELTLSEDEEDY   800
 801  YGSSTNLKDHQVSNTALLNTQTPIYGTEHNSENTDFGDSGRLYYCKHCDF   850
 851  NNKSARSVSTHYQRMHPYIKFSFRYILDPNDHSAVYRCLECYIDYTNFED   900
 901  LQQHYGEHHPEAMNVLNFDHSDLIYRCRFCSYTSPNVRSLMPHYQRMHPT   950
 951  VKINNAMIFSSYVVEQQEGLNTESQTLREILNSAPKNMATSTPVARGGGL  1000
1001  PATFNKNTPKTFTPECENQKDPLVNTVVVYDCDVCSFASPNMHSVLVHYQ  1050
1051  KKHPEEKASYFRIQKTMRMVSVDRGSALSQLSFEVGAPMSPKMSNMGSPP  1100
1101  PPQPPPPDLSTELYYCKHCSYSNRSVVGVLVHYQKRHPEIKVTAKYIRQA  1150
1151  PPTAAMMRGVEGPQGSPRPPAPIQQLNRSSSERDGPPVENEMFFCQHCDY  1200
1201  GNRTVKGVLIHYQKKHRDFKANADVIRQHTATIRSLCDRNQKKPASCVLV  1250
1251  SPSNLERDKTKLRALKCRQCSYTSPYFYALRKHIKKDHPALKATVTSIMR  1300
1301  WAFLDGLIEAGYHCEWCIYSHTEPNGLLLHYQRRHPEHYVDYTYMATKLW  1350
1351  AGPDPSPPSLTMPAEAKTYRCRDCVFEAVSIWDITNHYQAFHPWAMNGDE  1400
1401  SVLLDIIKEKDAVEKPILSSEELAGPVNCENSIPTPFPEQEAECPEDARL  1450
1451  SPEKSLQLASANPAISSTPYQCTVCQSEYNNLHGLLTHYGKKHPGMKVKA  1500
1501  ADFAQDIDINPGAVYKCRHCPYINTRIHGVLTHYQKRHPSIKVTAEDFVH  1550
1551  DVEQSADISQNDVEETSRIFKQGYGAYRCKLCPYTHGTLEKLKIHYEKYH  1600
1601  NQPEFDVFSQSPPKLPVPLEPEMTTEVSPSQVSITEEEVGEEPVSTSHFS  1650
1651  TSHLVSHTVFRCQLCKYFCSTRKGIARHYRIKHNNVRAQPEGKNNLFKCA  1700
1701  LCAYTNPIRKGLAAHYQKRHDIDAYYTHCLAASRTISDKPNKVIIPSPPK  1750
1751  DDSPQLSEELRRAVEKKKCSLCSFQSFSKKGIVSHYMKRHPGVFPKKQHA  1800
1801  SKLGGYFTAVYADEHEKPTLMEEEERGNFEKAEVEGEAQEIEWLPFRCIK  1850
1851  CFKLSFSTAELLCMHYTDHHSRDLKRDFIILGNGPRLQNSTYQCKHCDSK  1900
1901  LQSTAELTSHLNIHNEEFQKRAKRQERRKQLLSKQKYADGAFADFKQERP  1950
1951  FGHLEEVPKIKERKVVGYKCKFCVEVHPTLRAICNHLRKHVQYGNVPAVS  2000
2001  AAVKGLRSHERSHLALAMFTREDKYSCQYCSFVSAFRHNLDRHMQTHHGH  2050
2051  HKPFRCKLCSFKSSYNSRLKTHILKAHAGEHAYKCSWCSFSTMTISQLKE  2100
2101  HSLKVHGKALTLPRPRIVSLLSSHSHHSSQKATPAEEVEDSNDSSYSEPP  2150
2151  DVQQQLNHYQSAALARNNSRVSPVPLSGAAAGTEQKTEAVLHCEFCEFSS  2200
2201  GYIQSIRRHYRDKHGGKKLFKCKDCSFYTGFKSAFTMHVEAGHSAVPEEG  2250
2251  PKDLRCPLCLYHTKYKRNMIDHIVLHREERVVPIEVCRSKLSKYLQGVVF  2300
2301  RCDKCTFTCSSDESLQQHIEKHNELKPYKCQLCYYETKHTEELDSHLRDE  2350
2351  HKVSRNFELVGRVNLDQLEQMKEKMESSSSDDEDKEEEMNSKAEDRELMR  2400
2401  FSDHGAALNTEKRFPCEFCGRAFSQGSEWERHVLRHGMALNDTKQVSREE  2450
2451  IHPKEIMENSVKMPSIEEKEDDEAIGIDFSLKNETVAICVVTADKSLLEN  2500
2501  AEAKKE                                              2506

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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