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

NucPred

Fetching P87154 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MPLKTARGASKYQFRKFNGNYNGKSKSNGRTFAKSTEEVGFNDPMKIVYK    50
  51  KNEIDRMMGFDSYEGGQPREAWLLNVHPTVIESTKGNSTLSAVDFYFIQD   100
 101  DGDTFRCTIPYSPYFYIAAREGKEALVDDYLKKKFVGLIKSTTRIFKEDL   150
 151  QLKNHIVGYQKLYIKLVFDNLNDLQAVRKSLMSAVKANSSQQDAVDAYTN   200
 201  LSSENLNGIIENAFEDPLNHVLDIREYDVPYHSRTLIDLNIRVGQWYTVS   250
 251  YHEGHVQISLLASRIERAEPTIMAFDIETTKLPLKFPDSSFDKIMMISYM   300
 301  IDGQGFLITNREIISQNIEDFHYTPREEFEGPFIIFNEPDEVGLLHRFFK   350
 351  HIRSAKPSVIVTYNGDFFDWPFVDARAAFHGLNLTEETGFFRDAEDEYKS   400
 401  SYCSHMDAFRWVKRDSYLPQGSQGLKAVTVSKLGYNPIELDPELMTPYAS   450
 451  EKPQVLAQYSVSDAVATYFLYMKYVHPFIFSLCNIIPLNPDEVLRKGTGT   500
 501  LCETLLTVEACTKNIILPNKHVDASQKFFDGHLLASETYVGGHVESLESG   550
 551  VFRSDLPTNFNMDPKVYEELILQLDKALDFSLTVENNVNVDEIENYEEVR   600
 601  DSILKKLSDLRDRPKRSEKPRIYHLDVASMYPNIMITNRLQPDSVKDESF   650
 651  CATCDLNVPNKTCDRRMVWAWRGEYYPAKKGEYHMIYSALQSERFPGPTP   700
 701  FSPFRSFQELSPSEQAAMVQKRIADYSRKVYHRLYDNTVIERETIICQKE   750
 751  NSFYIDTVKSFRDRRYDFKGLQKKWVKQLAAIKEKGGLAEIEEAKKMVVL   800
 801  YDSLQLAHKVILNSFYGYVMRKGSRWYSIEMAGITCLTGATIIQMARQIV   850
 851  ERAGRPLELDTDGIWCILPESFPENFEFKKKSGGKVFISYPCVMLNHLVH   900
 901  EKFTNHQYSALKDPEKLVYETTSENSIFFEVDGPYRAMILPASTEEGKNL   950
 951  KKRYAVFNFDGSLAELKGFEVKRRGELKLIKDFQSQIFKVFLKGDSLEEC  1000
1001  YQEVAYVADTWLEILFTKGSNLTDDELIELISENRSMSKALSEYGSQKST  1050
1051  SITTARRLADFLGDQMTKDKGLACRFIISASPKGRPVAERAVPVAIFFAE  1100
1101  ESVKRHFLRLWLKDNGLYDVDIRDIIDWDYYLKRLGSVVQKLISIPAALQ  1150
1151  RISNPVTRFPLPDWLQKRVAVLNSKYQQKKIDSIFSLAPTNPSTINNTKV  1200
1201  TDIEDLGSVTHKDKRIVARVTKRKLLQQSGNSEAPVSFEVKPVSFMDGYS  1250
1251  NWLKYAKKKWKYQKQVKLRRRHLIGFQSRQFTNVLQSSAEVMFENLWHIL  1300
1301  QIRETDVPGILHAWVIIRNRLTSIRFIVNRKFFVCFKDETLPNVEIEGCL  1350
1351  IEKSNAILPHGSTSDKLFLLEIPEKSYLTEKVSISMIFAHPSVSGIYETR  1400
1401  IEPIERLILEMGSRKRFNNSVPGALGKGFEFGFESKMFTDPSDNDVSYLD  1450
1451  GVEMNYLYAFHFSISNRFVFSLFMPHLKKVEAIIYDKLPGSDMSFPSISK  1500
1501  IYEELRSKFDNLIKESSIEYPDTLSCNVIFSGNERKAYKLIDEKLLQYFS  1550
1551  TKTKNSLLIIESSLPHILKANVKQIEELPYIMIPRLESNIQSLSWKQHIA  1600
1601  TKMIQHFLAIGSWLFHRIQLSRFSDIPLCNFESDDIQYSIDVVYSRKLKE  1650
1651  HNIILWWNKGPTPDLGGIEKDSILQIASPKDPLEVNNPGAYSNACVDISL  1700
1701  SNLALCSILNSALINDIEGIGDMAALNDNYMTAINDDLEEKLGIHDNIGL  1750
1751  THSLPVLKALVKTWWNEAASGNNLADLIIQHLARWISSSKSYLYSPLLSS  1800
1801  HVEVIMRKTFLQLLSEIKRLGAHIIHASANKILIKTSKLIVQNAVTYSNY  1850
1851  LLKSIKTLPLFHFLDLNVTEYWDYLLWMDSVNYGGKMVAANFSATNEEPQ  1900
1901  TVVSWHIKSHLPPIIQPEFQSWIVEFIEEVYKQKLEKSNTKVGFVRVKNN  1950
1951  NADEDSEIVGSGILKSKLIHPLKRKVAQVRRCFQELQLDENTREDLKFPK  2000
2001  LPGSFLNYTDGALELVKSICAVFELSHDLNLEVRFLKKSLLSLLQIQEFS  2050
2051  TQAVFRYPSRRLSLDQIPCKQCGVHQDFDLCLHEHLWPTRDDMGTLVFSD  2100
2101  GWSCSSCNLVYDRWVFEETLVDNLYHQLTLYQLQDLICSKCKTVKQWSLK  2150
2151  ERCSCSGEWVLQLSPTKFREMLNVYQSVADFYEFSILQNSVQSILSVLN   2199

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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