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

NucPred

Fetching Q80XK6 from www.uniprot.org...

The NucPred score for your sequence is 0.84 (see score help below)

   1  MPWPFSESIKKRACRYLLQRYLGHFLQEKLSLEQLSLDLYQGTGSLAQVP    50
  51  LDKWCLNEILESADAPLEVTEGFIQSISLSVPWGSLLQDNCALEVRGLEM   100
 101  VFRPRPRVATGSEPMYWSSFMTSSMQLAKECLSQKLTDEQGEASQPFEGL   150
 151  EKFAETIETVLRRVKVTFIDTVLRIEHVPENSKTGAALEIRVDRTVYCDE   200
 201  TADESSGVNVHQPTAFAHKLLQLSGVSLFWDEFSASAKSSPVCSTAPVET   250
 251  EPKLSPSWNPKIVYEPHPQLTRTLPEIAPSDPVQIGRLLGRLELSLTLKQ   300
 301  NEVLPGAKLDVDGQIDSFHLFLSPRQVHLLLDMLAAIAGPENSSKIGLAN   350
 351  KDRKNRPMQQEDEYRIQMELNRYYLRKDSLSMGVSSEKSFYETETARTPS   400
 401  SREEEVFFSMADMDMSHSLSSLPPLGDPPHMDLELSLTSTYTNTPAGSPL   450
 451  SATVLQPTWGEFADHKEQPVRGPAFQSDVVHPASLQKAALSSRSASVDES   500
 501  RPEFICRLALGIFSVSVLHIDPLSPAETSLNVNPLTRMATDFFSCVEKMD   550
 551  PAIFSTGDFKSFRAVFAEACSHDHLRFIGTGIKVSYEQRQRSASRHFSTD   600
 601  MSVGQMEFLECLFPTDCHSVPSHYTELLTFHSKEGTDAHLPVCLQLHYKH   650
 651  SETRGPQGNQARLSSVPQKAELQIKLNPVCCELDISIVDRLNSLLQPQKL   700
 701  TTVEMMASHMYASYNKHISLHKAFTEVFLDDSHSPANRRVSVQVATPALH   750
 751  LSVRFPIPDLRSDQERGPWFKKSLQKETLHLEFTDLESKTEFVGGSTPEQ   800
 801  TKLELTFRELSGSFQEEKGGPSVKFFHVSGGVDGDTASSDDFDWPRMVLK   850
 851  INPPAMHSILERIAAEEEEENDGHYQEEEDGGAHSLKDVCDLRRPAPSPF   900
 901  SSRRVMFENEQMVMPGDPVEMTEFQDKAISNSHYVLELLLPNIHLTLPNK   950
 951  GFYEKLYNRIFNDLLLWEPTAPSPVETLENVSYGIGLSVASQLINTFSKD  1000
1001  SFSPFKSAVHYDEDSGSEEETLQYFSAVDPNYRSRRKKKLDSQNKNSQSF  1050
1051  LSVLLSINHGLMAVFTDVKQENGDPMESKHGEFWLEFNSGSFFCVTKYEG  1100
1101  FEDKHYICLHSSSLRLYHKGIVDGAILPTETRLPCSTRPHWLEPTIYSSE  1150
1151  EDGLSRTASDGVGGDNLNMLSVAVKILSDKSESNTKEFLVAVGLKGATLQ  1200
1201  HRVLPAGLSWHEQILNFLNIADEPVLGYNPPTSFTTFHVHLWSCALDYRP  1250
1251  LHLPLRSLLTVETFSISSSVALDKSSSTLRIIMDEAALHLSDKCNTVTVN  1300
1301  LNRDYVRVMDMGLLELTITAVKSDSDGEQTAPRFELHCSSDVVHIRTCSD  1350
1351  SCAALMNLIQYVASYGDLHGPHKAEMKPGVPQRKPKVDSSARSSSHGPVL  1400
1401  PEADQQILRDLMSDAMEEIDLQQASAPVGPQANGVLDEKSHTQEPCCSDL  1450
1451  FLFPDESGNVSQESSPAYPSLTHHLISDAVTGVTAENDDFCILFAPKTVV  1500
1501  QEKEEEPVIKIMVDDAIVIKDDYFSLPITRTDSSKAPLHFPIPAVRYVVK  1550
1551  EVSLVWHLYGGKDFATAPPTSPAKSYIPHSSPSQTPTRHGRHTVCGGKGR  1600
1601  NHDFLMEIQLSKVKFQHEVYPPCKPECESSLLEHPVSRQVFIVQDLEIRD  1650
1651  RLATSQMNKFLYLYCSKDMPRKAHSNMLTIKALHVRPESGRSPQECCLRV  1700
1701  SLMPLRLNIDQDALFFLKDFFTSLSTEVELLLTPDPEVTKSPGADVTCSL  1750
1751  PRHLSTSKEPNLVVSFPGPKQASPNHRANSAEGGNGLEEDVSAEETSFSD  1800
1801  QPVFFREFRFTAEVPIRLDYHGKHVSMDQGTLAGILIGLAQLNCSELKLK  1850
1851  RLFYRHGLLGIDKLFSYAISEWLSDIKKNQLPGILGGVGPMHSLVQLVQG  1900
1901  LKDLVWLPIEQYRKDGRIVRGFQRGAASFGTSTAMAALELTNRMVQTIQA  1950
1951  AAETAYDMVSPSTLSIEPKKAKRFPHHRLAHQPVDLREGVAKAYSVVKEG  2000
2001  ITDTAQTIYETAAREHESRGVTGAVGEVLRQIPPAVVRPLIVATEATSNV  2050
2051  LGGMRNQIRPDVRQDESQKWRHGED                           2075

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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