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

NucPred

Fetching P11277 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MTSATEFENVGNQPPYSRINARWDAPDDELDNDNSSARLFERSRIKALAD    50
  51  EREVVQKKTFTKWVNSHLARVSCRITDLYKDLRDGRMLIKLLEVLSGEML   100
 101  PKPTKGKMRIHCLENVDKALQFLKEQRVHLENMGSHDIVDGNHRLVLGLI   150
 151  WTIILRFQIQDIVVQTQEGRETRSAKDALLLWCQMKTAGYPHVNVTNFTS   200
 201  SWKDGLAFNALIHKHRPDLIDFDKLKDSNARHNLEHAFNVAERQLGIIPL   250
 251  LDPEDVFTENPDEKSIITYVVAFYHYFSKMKVLAVEGKRVGKVIDHAIET   300
 301  EKMIEKYSGLASDLLTWIEQTITVLNSRKFANSLTGVQQQLQAFSTYRTV   350
 351  EKPPKFQEKGNLEVLLFTIQSRMRANNQKVYTPHDGKLVSDINRAWESLE   400
 401  EAEYRRELALRNELIRQEKLEQLARRFDRKAAMRETWLSENQRLVAQDNF   450
 451  GYDLAAVEAAKKKHEAIETDTAAYEERVRALEDLAQELEKENYHDQKRIT   500
 501  ARKDNILRLWSYLQELLQSRRQRLETTLALQKLFQDMLHSIDWMDEIKAH   550
 551  LLSAEFGKHLLEVEDLLQKHKLMEADIAIQGDKVKAITAATLKFTEGKGY   600
 601  QPCDPQVIQDRISHLEQCFEELSNMAAGRKAQLEQSKRLWKFFWEMDEAE   650
 651  SWIKEKEQIYSSLDYGKDLTSVLILQRKHKAFEDELRGLDAHLEQIFQEA   700
 701  HGMVARKQFGHPQIEARIKEVSAQWDQLKDLAAFCKKNLQDAENFFQFQG   750
 751  DADDLKAWLQDAHRLLSGEDVGQDEGATRALGKKHKDFLEELEESRGVME   800
 801  HLEQQAQGFPEEFRDSPDVTHRLQALRELYQQVVAQADLRQQRLQEALDL   850
 851  YTVFGETDACELWMGEKEKWLAEMEMPDTLEDLEVVQHRFDILDQEMKTL   900
 901  MTQIDGVNLAANSLVESGHPRSREVKQYQDHLNTRWQAFQTLVSERREAV   950
 951  DSALRVHNYCVDCEETSKWITDKTKVVESTKDLGRDLAGIIAIQRKLSGL  1000
1001  ERDVAAIQARVDALERESQQLMDSHPEQKEDIGQRQKHLEELWQGLQQSL  1050
1051  QGQEDLLGEVSQLQAFLQDLDDFQAWLSITQKAVASEDMPESLPEAEQLL  1100
1101  QQHAGIKDEIDGHQDSYQRVKESGEKVIQGQTDPEYLLLGQRLEGLDTGW  1150
1151  NALGRMWESRSHTLAQCLGFQEFQKDAKQAEAILSNQEYTLAHLEPPDSL  1200
1201  EAAEAGIRKFEDFLGSMENNRDKVLSPVDSGNKLVAEGNLYSDKIKEKVQ  1250
1251  LIEDRHRKNNEKAQEASVLLRDNLELQNFLQNCQELTLWINDKLLTSQDV  1300
1301  SYDEARNLHNKWLKHQAFVAELASHEGWLENIDAEGKQLMDEKPQFTALV  1350
1351  SQKLEALHRLWDELQATTKEKTQHLSAARSSDLRLQTHADLNKWISAMED  1400
1401  QLRSDDPGKDLTSVNRMLAKLKRVEDQVNVRKEELGELFAQVPSMGEEGG  1450
1451  DADLSIEKRFLDLLEPLGRRKKQLESSRAKLQISRDLEDETLWVEERLPL  1500
1501  AQSADYGTNLQTVQLFMKKNQTLQNEILGHTPRVEDVLQRGQQLVEAAEI  1550
1551  DCQDLEERLGHLQSSWDRLREAAAGRLQRLRDANEAQQYYLDADEAEAWI  1600
1601  GEQELYVISDEIPKDEEGAIVMLKRHLRQQRAVEDYGRNIKQLASRAQGL  1650
1651  LSAGHPEGEQIIRLQGQVDKHYAGLKDVAEERKRKLENMYHLFQLKRETD  1700
1701  DLEQWISEKELVASSPEMGQDFDHVTLLRDKFRDFARETGAIGQERVDNV  1750
1751  NAFIERLIDAGHSEAATIAEWKDGLNEMWADLLELIDTRMQLLAASYDLH  1800
1801  RYFYTGAEILGLIDEKHRELPEDVGLDASTAESFHRVHTAFERELHLLGV  1850
1851  QVQQFQDVATRLQTAYAGEKAEAIQNKEQEVSAAWQALLDACAGRRTQLV  1900
1901  DTADKFRFFSMARDLLSWMESIIRQIETQERPRDVSSVELLMKYHQGINA  1950
1951  EIETRSKNFSACLELGESLLQRQHQASEEIREKLQQVMSRRKEMNEKWEA  2000
2001  RWERLRMLLEVCQFSRDASVAEAWLIAQEPYLASGDFGHTVDSVEKLIKR  2050
2051  HEAFEKSTASWAERFAALEKPTTLELKERQIAERPAEETGPQEEEGETAG  2100
2101  EAPVSHHAATERTSPVSLWSRLSSSWESLQPEPSHPY               2137

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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