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

NucPred

Fetching P34229 from www.uniprot.org...

The NucPred score for your sequence is 0.30 (see score help below)

   1  MYPTTGVNTPQSAASLRPLVLSHGQTEHSLLVPTSLYINCTTLRDQFYAS    50
  51  LPPATEDKADDDEPSSSTELLAAFLGFTAKTVEEEPGPYDDVLSLVLNEF   100
 101  ETRYLRGNDIHAVASSLLQDEDVPTTVGKIKRVIRAYYAARIACNRPIKA   150
 151  HSSALFRAASEDSDNVSLYAIFGGQGNTEDYFEELREIYDIYQGLVGDFI   200
 201  RECGAQLLALSRDHIAAEKIYTKGFDIVKWLEHPETIPDFEYLISAPISV   250
 251  PIIGVIQLAHYAVTCRVLGLNPGQVRDNLKGATGHSQGLITAIAISASDS   300
 301  WDEFYNSASRILKIFFFIGVRVQQAYPSTFLPPSTLEDSVKQGEGKPTPM   350
 351  LSIRDLSLNQVQEFVDATNLHLPEDKQIVVSLINGPRNVVVTGPPQSLYG   400
 401  LCLVLRKQKAETGLDQSRVPHSQRKLKFTHRFLPITSPFHSYLLEKSTDL   450
 451  IINDLESSGVEFVSSELKVPVYDTFDGSVLSQLPKGIVSRLVNLITHLPV   500
 501  KWEKATQFQASHIVDFGPGGASGLGLLTHKNKDGTGVRTILAGVIDQPLE   550
 551  FGFKQELFDRQESSIVFAQNWAKEFSPKLVKISSTNEVYVDTKFSRLTGR   600
 601  APIMVAGMTPTTVNPKFVAATMNSGYHIELGGGGYFAPGMMTKALEHIEK   650
 651  NTPPGSGITINLIYVNPRLIQWGIPLIQELRQKGFPIEGLTIGAGVPSLE   700
 701  VANEWIQDLGVKHIAFKPGSIEAISSVIRIAKANPDFPIILQWTGGRGGG   750
 751  HHSFEDFHAPILQMYSKIRRCSNIVLIAGSGFGASTDSYPYLTGSWSRDF   800
 801  DYPPMPFDGILVGSRVMVAKEAFTSLGAKQLIVDSPGVEDSEWEKTYDKP   850
 851  TGGVITVLSEMGEPIHKLATRGVLFWHEMDKTVFSLPKKKRLEVLKSKRA   900
 901  YIIKRLNDDFQKTWFAKNAQGQVCDLEDLTYAEVIQRLVDLMYVKKESRW   950
 951  IDVTLRNLAGTFIRRVEERFSTETGASSVLQSFSELDSEPEKVVERVFEL  1000
1001  FPASTTQIINAQDKDHFLMLCLNPMQKPVPFIPVLDDNFEFFFKKDSLWQ  1050
1051  CEDLAAVVDEDVGRICILQGPVAVKHSKIVNEPVKEILDSMHEGHIKQLL  1100
1101  EDGEYAGNMANIPQVECFGGKPAQNFGDVALDSVMVLDDLNKTVFKIETG  1150
1151  TSALPSAADWFSLLAGDKNSWRQVFLSTDTIVQTTKMISNPLHRLLEPIA  1200
1201  GLQVEIEHPDEPENTVISAFEPINGKVTKVLELRKGAGDVISLQLIEARG  1250
1251  VDRVPVALPLEFKYQPQIGYAPIVEVMTDRNTRIKEFYWKLWFGQDSKFE  1300
1301  IDTDITEEIIGDDVTISGKAIADFVHAVGNKGEAFVGRSTSAGTVFAPMD  1350
1351  FAIVLGWKAIIKAIFPRAIDADILRLVHLSNGFKMMPGADPLQMGDVVSA  1400
1401  TAKIDTVKNSATGKTVAVRGLLTRDGKPVMEVVSEFFYRGEFSDFQNTFE  1450
1451  RREEVPMQLTLKDAKAVAILCSKEWFEYNGDDTKDLEGKTIVFRNSSFIK  1500
1501  YKNETVFSSVHTTGKVLMELPSKEVIEIATVNYQAGESHGNPVIDYLERN  1550
1551  GTTIEQPVEFEKPIPLSKADDLLSFKAPSSNEPYAGVSGDYNPIHVSRAF  1600
1601  ASYASLPGTITHGMYSSAAVRSLIEVWAAENNVSRVRAFSCQFQGMVLPN  1650
1651  DEIVTRLEHVGMINGRKIIKVTSTNRETEAVVLSGEAEVEQPISTFVFTG  1700
1701  QGSQEQGMGMDLYASSEVAKKVWDKADEHFLQNYGFSIIKIVVENPKELD  1750
1751  IHFGGPKGKKIRDNYISMMFETIDEKTGNLISEKIFKEIDETTDSFTFKS  1800
1801  PTGLLSATQFTQPALTLMEKASFEDMKAKGLVPVDATFAGHSLGEYSALA  1850
1851  SLGDVMPIESLVDVVFYRGMTMQVAVPRDAQGRSNYGMCAVNPSRISTTF  1900
1901  NDAALRFVVDHISEQTKWLLEIVNYNVENSQYVTAGDLRALDTLTNVLNV  1950
1951  LKLEKINIDKLLESLPLEKVKEHLSEIVTEVAKKSVAKPQPIELERGFAV  2000
2001  IPLKGISVPFHSSYLRNGVKPFQNFLVKKVPKNAVKPANLIGKYIPNLTA  2050
2051  KPFEITKEYFEEVYKLTGSEKVKSIINNWESYESKQ                2086

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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