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

NucPred

Fetching Q10669 from www.uniprot.org...

The NucPred score for your sequence is 0.65 (see score help below)

   1  MTDKPGSAEDTIEMDDTCSPQFVQEVNRIKSQIKSLVEENHTRKFFRPLT    50
  51  SNIGDETAILRIQFNNMMSKMEEKEKQSLVKELIKMVHHVAEKNSPDRVF   100
 101  VGTNYERVVDQLLRYAHQKGAISTNLCAEGLIMTSDFRLCSRICQEKWKF   150
 151  INDCIPKIDYKGIRNILRYILESQLRRLPYSLSPEQVNEIRIVENVILHI   200
 201  VDRDSNLMPPLITLSEIMRGMPKQALMLPRLTEKLASLSVHFRPIADLSH   250
 251  VCGRGFVYPIPLHPSFYPLTSCWEEHGLNASNTIVQPHHTLPYRPEHTST   300
 301  YLYTLYMILRQPLGKDSLHPPSKTKTKTNWEMLISVMICESMAEAESLPE   350
 351  TEPIPRYQWDNIVNIVIYGITQHLLVPKTFFNVLKNLIKRCKYTRARDEV   400
 401  MWIVFQVVGSLSNLTRLDDAVTEIVELYNELFDGDVVWMGASDHPALFAR   450
 451  FLAAAGTWMILEKDFADKMPPANETIKSHIKFIQDGVDNFDSSNTAMLAV   500
 501  LSNIYRTDTKMGKLIVPTLQQMLESIDDTKSLFELSYKRMAVNCFSAFPV   550
 551  EFMEALTFRSKKTLLIQCFQPLRSFSTVRLPSPAVFETVAKICESEDYEM   600
 601  AVKDMEHLAQRSLHVATAADRSSGEHQNVQAKDQCYFLFDFLVYRLPHLH   650
 651  AYSKYSSTVNALSYFTQHIPNNPQNHQIYRLMEQFLMRRWCWAGFHGCIT   700
 701  AHTQMFGTSYKDNTMMRHMAYPKTFSVPDQYPFAINPEIFKMAIYSFLRA   750
 751  VKITAQDIAIEKTMFPTIINGFGWPEKSTSYFPKWALDAIKASDTSNAVN   800
 801  TEEILSDVRNTARMHTSLTPNQFVIRYGEDRDPATSHCMLAVLFHFAYNS   850
 851  VDSTYNITSEFYEVMEKKTPKEIVVMGNYLVDYIIADAKTQDCNEKTFKN   900
 901  IAKAAALLVFQFQVLRADRLLLSLIMHPATDEDALICIQIANEFILTPEF   950
 951  QERIRWYHQNVPKKDHFPTEYIKAIVKYHDAFPEFEACELVRSYDSSSNV  1000
1001  HMPTYYGCLIERLLPIMDQYLHVALEQQGYKLNPQILQSVSMLYKFHAMP  1050
1051  IHFMYSVLFTSHGLMSGPDAKSFVLAFATQIEECHLTEAFEKFNHQKSSR  1100
1101  EQLIMELIDRMSASLDFILTPPPFVAKDWKIAELSPGAQTLYLACIELMA  1150
1151  SPHSPETLVAAMINVMQMKPHARPFNIVNLTALLLTALPAAYSNALHDEF  1200
1201  VAVFVNGETANLKFEEIVFDNYEESLLLNLPNRARTINVISQQYWLHCSL  1250
1251  SLLNFFSHEYVPRILEHVKTEKDLWYTLRLVMPYLRRYYENWDTAKQMRS  1300
1301  QRENFGPLHIVKLVFQKLGSMAEEGVEIVYEQHLCDLFYNCKYFFAGDFL  1350
1351  RNTAITEFAKLPEKMRDRLKFYVSQSEPTAEQETPPEKEKSPEKEKEQEQ  1400
1401  EQHVKAHQPLESTPSVSSLPQMQHHLQQAPLLPSHQMMPPPQQHSSSLQH  1450
1451  HLQHHTSTHQMMDTSQHQTIQQQSNHPTQQQLQHQIPNMSMHQQMGPQYP  1500
1501  GAVFHHPSGPVGHVPMQYGMGHHMQQHPHLPHHQQMPAPMHTMNPMMQNM  1550
1551  TPQQQYLYMQQLQQHQQHQQYMQQQQQHHHQHQQQPH               1587

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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