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

NucPred

Fetching O46669 from www.uniprot.org...

The NucPred score for your sequence is 0.34 (see score help below)

   1  MEFPFGSLETTNFRRFTPESLVEIEKRIAAKQAAKKAKGKHREQKDQEEK    50
  51  PRPQLDLKACNQPPKFYGELPAELVGEPLEDLDPFYSTHRTFMVLDKGRT   100
 101  ISRFSATRALWLFSPFNLIRRTAIKVSVHSWFSLFITVTILVNCVGMTQT   150
 151  ELPDRIEYVFTVIYTFEALIKILARGFCLNEFAYLRDPWDWLDFSVITLA   200
 201  YIGEATALRGISGLRTFRVLRALKTVSVIPGLKVIVGALIHSVRKLADVT   250
 251  ILTVFCLSVFALVGLQLFKGNLKNKCVKNCAALNETGNYSSYGKQEWNFC   300
 301  HRDEDFYYNKPGTSDPLLCGNGSDAGHCPKGYLCLKTSDNPDFNYTSFDS   350
 351  FAWAFLSLFRLMTQDSWERLYQQTLRASGKMYMVFFVLVIFLGSFYLVNL   400
 401  ILAVVTMAYEEQNQATIDEIEAKEKTFQETLEMPRKEQEVLAALGIDTAS   450
 451  LHSCNGSPLPSKNASERMRRMKPRVSEGSTDDNKSPQSDPYNQRRMSFLG   500
 501  LTSGRRRASHGSVFHFRTPCLDTSFPDGVTDDGVFPGDRESHRGSLLLGG   550
 551  GTSQQGPLLRSPLPQPPNPGSGHGEDGHSTLPTGELAPGGIEVSAFDAGQ   600
 601  KKTFLSAEYLNEPFRAQRAMSVVSIMTSVLEELEESERRCPPCLTSFAQK   650
 651  YLIWECCPTWVKLKTVLFGIVTDPFAELTTTLCIVVNTVFMAMEHHGMSS   700
 701  AFEAMLQIGNIVFTVFFTAEMVFKIIAFDPYYYFQKRWNIFDCIIVTVSL   750
 751  IELGAARKGSLSVLRTFRLLRVFKLAKSWPTLNTLIKIIGNSVGALGNLT   800
 801  IILAIIVFVFALVGKQLLGENYRDNRRNISAPNEEWPRWHMHDFFHSFLI   850
 851  VFRILCGEWIENMWACMEVGQKSICLILFLTVMVLGNLVVLNLFTALLLN   900
 901  SFSADNLATPDEDGEVNNLQVALARIQAFGHRTKKAICNFFTRPCLLPWP   950
 951  KAEPQLVVKLPLSSSKAENHIAANAAVGSPGGLSVSRGLRDDHSDFITNP  1000
1001  NIWVSVPIAEGESDLDDLEEDGEEDSQSSQQEVILQGQEQLQVETCEGHT  1050
1051  APRSPGSGMSSEDLASYVDEKWKDEAVAQAPAEGGDDSSSSGGSTVDCLD  1100
1101  PEEILRKIPELADDLEEPDDCFTEGCLRRCPCCKVDISKFPWTVGWQVRK  1150
1151  TCYRIVEHSWFESFIIFMILLSSGSLAFEDYHLDQKPTVKALLEYTDRMF  1200
1201  TFIFVLEMLLKWVAYGFKKYFTNAWCWLDFLIVNISLISLIAKILQYSDV  1250
1251  ASIKALRTLRALRPLRALSRFEGMRVVVDALVGAIPSIMNVLLVCLIFWL  1300
1301  IFSTMGVNFFAGKFGRCINKTNEYFSLVPLSIVNNISDCKYQNHTGSFFW  1350
1351  VNVKVNFDNVAMGYLALLQVATFKGWMDIMYAAVDARDVNLQPKWEDNVY  1400
1401  MYLYFVIFIIFGGFFTLNLFVGVIIDNFNQQKKKLGGQDIFMTEEQKKYY  1450
1451  NAMKKLGSKKPQKPIPRPLNKYQGFVFDIVTKQAFDIVIMVLICLNMITM  1500
1501  MVETDEQSAEKTKILNKINQFFVAVFTGECVMKMFALRHYYFTNGWNVFD  1550
1551  FIVVVLSIGSLVFSVILTSLENYFSPTLFRVIRLARIGRILRLIRAAKGI  1600
1601  RTLLFALMMSLPALFNIGLLLFLVMFIYSIFGMASFPHVSWEAGIDDMFN  1650
1651  FQTFANSMLCLFQITTSAGWDGLLSPILNTGPPYCDPNLPNSNGSRGNCG  1700
1701  SPAVGILFFTTYIIISFLIVVNMYIAVILENFNVATQESSEPLSEDDFDM  1750
1751  FYETWEKFDPEATQFITFSALSDFADTLSGPLRIPKPNQNILIQMDLPLV  1800
1801  PGDKIHCLDILFAFTKNVLGESGELDSLKANIEEKFMATNVSKASYEPIA  1850
1851  TTLRWKQEDISATVIQKAYRSYVLHRSMTISNPPAVPRAEEAVPPPDEAF  1900
1901  VEFMVNENCALPDKSETASAASFPPSYDSVTRGLSDQINMSTSSSMQNED  1950
1951  EGTSKKVTAPGP                                        1962

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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