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

NucPred

Fetching Q9VC45 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MSAFEITVTPSRLKQKKRAEGREPAVVVMAPFSAKAIVQFEDVPITKTAR    50
  51  RQVRVLNPSDDDIEVKVMKAIREEHNLSLEWMEHTVPARDEVSMELVWSP   100
 101  VLEVACKETLQLIDNRNFRKEVMIILKSKSNQPVKNPRKFPTVGKTLQLK   150
 151  SPTGAGKTMKSVVSAAVQQKKRMSAAAAPPSKQTWRVTAPSRPAAWAHPP   200
 201  PQAPLVEKNVYKTPQEEPVYISPQPRSLKENLSPMTPGNLLDVIDNLRFT   250
 251  PLTETRGKGQATIFPDNLAAWPTPTLKGNVKSCANDMRPRRITPDDLEDQ   300
 301  PATNKTFDVKHSETINISLDTLDCSRIDGQPHTPLNKTTTIVHATHTRAL   350
 351  ACIHEEEGPSPPRTPTKSAIHDLKRDIKLVGSPLRKYSESMKDLSLLSPQ   400
 401  TKYAIQGSMPNLNEMKIRSIEQNRYYQEQQIQIKAKDLNSSSSSEASLAG   450
 451  QQEFLFNHSEILAQSSRFNLHEVGRKSVKGSPVKNPHKRRSHELSFSDAP   500
 501  SNESLYRNETVAISPPKKQRVEDTTLPRSAAPANASARSSSAHAWPHAQS   550
 551  KKFKLAQTMSLMKKPATPRKVRDTSIQPSVKLYDSELYMQTCINPDPFAA   600
 601  TTTIDPFLASTMYLDEQAVDRHQADFKKWLNALVSIPADLDADLNNKIDV   650
 651  GKLFNEVRNKELVVAPTKEEQSMNYLTKYRLETLRKAAVELFFSEQMRLP   700
 701  CSKVAVYVNKQALRIRSDRNLHLDVVMQRTILELLLCFNPLWLRLGLEVV   750
 751  FGEKIQMQSNRDIVGLSTFILNRLFRNKCEEQRYSKAYTLTEEYAETIKK   800
 801  HSLQKILFLLLFLDQAKQKRIVKHNPCLFVKKSPHKETKDILLRFSSELL   850
 851  ANIGDITRELRRLGYVLQHRQTFLDEFDYAFNNLAVDLRDGVRLTRVMEV   900
 901  ILLRDDLTRQLRVPAISRLQRIFNVKLALGALGEANFQLGGDIAAQDIVD   950
 951  GHREKTLSLLWQLIYKFRSPKFHAAATVLQKWWRRHWLHVVIQRRIRHKE  1000
1001  LMRRHRAATVIQAVFRGHQMRKYVKLFKTERTQAAIILQKFTRRYLAQKQ  1050
1051  LYQSYHSIITIQRWWRAQQLGRQHRQRFVELREAAIFLQRIWRRRLFAKK  1100
1101  LLAAAETARLQRSQKQQAAASYIQMQWRSYQLGRIQRQQFLRQRDLIMFV  1150
1151  QRRMRSKWSMLEQRKEFQQLKRAAINIQQRWRAKLSMRKCNADYLALRSS  1200
1201  VLKVQAYRKATIQMRIDRNHYYSLRKNVICLQQRLRAIMKMREQRENYLR  1250
1251  LRNASILVQKRYRMRQQMIQDRNAYLRTRKCIINVQRRWRATLQMRRERK  1300
1301  NYLHLQTTTKRIQIKFRAKREMKKQRAEFLQLKKVTLVVQKRRRALLQMR  1350
1351  KERQEYLHLREVTIKLQRRFHAQKSMRFMRAKYRGTQAAVSCLQMHWRNH  1400
1401  LLRKRERNSFLQLRQAAITLQRRYRARLNMIKQLKSYAQLKQAAITIQTR  1450
1451  YRAKKAMQKQVVLYQKQREAIIKVQRRYRGNLEMRKQIEVYQKQRQAVIR  1500
1501  LQKWWRSIRDMRLCKAGYRRIRLSSLSIQRKWRATVQARRQREIFLSTIR  1550
1551  KVRLMQAFIRATLLMRQQRREFEMKRRAAVVIQRRFRARCAMLKARQDYQ  1600
1601  LIQSSVILVQRKFRANRSMKQARQEFVQLRTIAVHLQQKFRGKRLMIEQR  1650
1651  NCFQLLRCSMPGFQARARGFMARKRFQALMTPEMMDLIRQKRAAKVIQRY  1700
1701  WRGYLIRRRQKHQGLLDIRKRIAQLRQEAKAVNSVRCKVQEAVRFLRGRF  1750
1751  IASDALAVLSRLDRLSRTVPHLLMWCSEFMSTFCYGIMAQAIRSEVDKQL  1800
1801  IERCSRIILNLARYNSTTVNTFQEGGLVTIAQMLLRWCDKDSEIFNTLCT  1850
1851  LIWVFAHCPKKRKIIHDYMTNPEAIYMVRETKKLVARKEKMKQNARKPPP  1900
1901  MTSGRYKSQKINFTPCSLPSLEPDFGIIRYSPYTFISSVYAFDTILCKLQ  1950
1951  IDMF                                                1954

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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