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

NucPred

Fetching P35498 from www.uniprot.org...

The NucPred score for your sequence is 0.61 (see score help below)

   1  MEQTVLVPPGPDSFNFFTRESLAAIERRIAEEKAKNPKPDKKDDDENGPK    50
  51  PNSDLEAGKNLPFIYGDIPPEMVSEPLEDLDPYYINKKTFIVLNKGKAIF   100
 101  RFSATSALYILTPFNPLRKIAIKILVHSLFSMLIMCTILTNCVFMTMSNP   150
 151  PDWTKNVEYTFTGIYTFESLIKIIARGFCLEDFTFLRDPWNWLDFTVITF   200
 201  AYVTEFVDLGNVSALRTFRVLRALKTISVIPGLKTIVGALIQSVKKLSDV   250
 251  MILTVFCLSVFALIGLQLFMGNLRNKCIQWPPTNASLEEHSIEKNITVNY   300
 301  NGTLINETVFEFDWKSYIQDSRYHYFLEGFLDALLCGNSSDAGQCPEGYM   350
 351  CVKAGRNPNYGYTSFDTFSWAFLSLFRLMTQDFWENLYQLTLRAAGKTYM   400
 401  IFFVLVIFLGSFYLINLILAVVAMAYEEQNQATLEEAEQKEAEFQQMIEQ   450
 451  LKKQQEAAQQAATATASEHSREPSAAGRLSDSSSEASKLSSKSAKERRNR   500
 501  RKKRKQKEQSGGEEKDEDEFQKSESEDSIRRKGFRFSIEGNRLTYEKRYS   550
 551  SPHQSLLSIRGSLFSPRRNSRTSLFSFRGRAKDVGSENDFADDEHSTFED   600
 601  NESRRDSLFVPRRHGERRNSNLSQTSRSSRMLAVFPANGKMHSTVDCNGV   650
 651  VSLVGGPSVPTSPVGQLLPEVIIDKPATDDNGTTTETEMRKRRSSSFHVS   700
 701  MDFLEDPSQRQRAMSIASILTNTVEELEESRQKCPPCWYKFSNIFLIWDC   750
 751  SPYWLKVKHVVNLVVMDPFVDLAITICIVLNTLFMAMEHYPMTDHFNNVL   800
 801  TVGNLVFTGIFTAEMFLKIIAMDPYYYFQEGWNIFDGFIVTLSLVELGLA   850
 851  NVEGLSVLRSFRLLRVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAII   900
 901  VFIFAVVGMQLFGKSYKDCVCKIASDCQLPRWHMNDFFHSFLIVFRVLCG   950
 951  EWIETMWDCMEVAGQAMCLTVFMMVMVIGNLVVLNLFLALLLSSFSADNL  1000
1001  AATDDDNEMNNLQIAVDRMHKGVAYVKRKIYEFIQQSFIRKQKILDEIKP  1050
1051  LDDLNNKKDSCMSNHTAEIGKDLDYLKDVNGTTSGIGTGSSVEKYIIDES  1100
1101  DYMSFINNPSLTVTVPIAVGESDFENLNTEDFSSESDLEESKEKLNESSS  1150
1151  SSEGSTVDIGAPVEEQPVVEPEETLEPEACFTEGCVQRFKCCQINVEEGR  1200
1201  GKQWWNLRRTCFRIVEHNWFETFIVFMILLSSGALAFEDIYIDQRKTIKT  1250
1251  MLEYADKVFTYIFILEMLLKWVAYGYQTYFTNAWCWLDFLIVDVSLVSLT  1300
1301  ANALGYSELGAIKSLRTLRALRPLRALSRFEGMRVVVNALLGAIPSIMNV  1350
1351  LLVCLIFWLIFSIMGVNLFAGKFYHCINTTTGDRFDIEDVNNHTDCLKLI  1400
1401  ERNETARWKNVKVNFDNVGFGYLSLLQVATFKGWMDIMYAAVDSRNVELQ  1450
1451  PKYEESLYMYLYFVIFIIFGSFFTLNLFIGVIIDNFNQQKKKFGGQDIFM  1500
1501  TEEQKKYYNAMKKLGSKKPQKPIPRPGNKFQGMVFDFVTRQVFDISIMIL  1550
1551  ICLNMVTMMVETDDQSEYVTTILSRINLVFIVLFTGECVLKLISLRHYYF  1600
1601  TIGWNIFDFVVVILSIVGMFLAELIEKYFVSPTLFRVIRLARIGRILRLI  1650
1651  KGAKGIRTLLFALMMSLPALFNIGLLLFLVMFIYAIFGMSNFAYVKREVG  1700
1701  IDDMFNFETFGNSMICLFQITTSAGWDGLLAPILNSKPPDCDPNKVNPGS  1750
1751  SVKGDCGNPSVGIFFFVSYIIISFLVVVNMYIAVILENFSVATEESAEPL  1800
1801  SEDDFEMFYEVWEKFDPDATQFMEFEKLSQFAAALEPPLNLPQPNKLQLI  1850
1851  AMDLPMVSGDRIHCLDILFAFTKRVLGESGEMDALRIQMEERFMASNPSK  1900
1901  VSYQPITTTLKRKQEEVSAVIIQRAYRRHLLKRTVKQASFTYNKNKIKGG  1950
1951  ANLLIKEDMIIDRINENSITEKTDLTMSTAACPPSYDRVTKPIVEKHEQE  2000
2001  GKDEKAKGK                                           2009

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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