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

NucPred

Fetching Q12659 from www.uniprot.org...

The NucPred score for your sequence is 0.71 (see score help below)

   1  MKEIIKLSILGKDSIHIGLHLWPHITNELFTCIFSPTYVIITDSNIETLY    50
  51  IPSFKTYFISMAKQRSINSRLLFFTIPPGEKSKSRKTKALIEDWLLSEKC   100
 101  TRDTVIIAIGGGVIGDLVGYVSATFMRGVRFIQIPTTLLAMVDSSIGGKN   150
 151  SINTSYGKNAIGTIWQPERIFIDFTFLETLTEKEFINGIAELIKTIIIWD   200
 201  ESEFASLENISEKIAKTVRSMSLTSNKHSKFNEIIKDLKRYIISSIKIKA   250
 251  HIVSIDEKEKDLRTLLNFGHSIGHAIETVLAPYILHGESISIGMVKEAEL   300
 301  SRHLGILNPNVVSRLIKCLNTWGLPTSFKDRRFKEVILGKKHLIEDILEI   350
 351  MSIDKKNDSNNKKIVLLSAIGKTYEKKASSVSDDDIRTILSQNILLYGIP   400
 401  LNAFQKHTTITLPGSKSISNRALILASLSNGICYLKNFLHSDDTYYMLSA   450
 451  LEKLNAAEFKWEQDGDVLVVKGKSGYLENPQMELYLGNSGTTARFLTSIC   500
 501  TLVQPNSRENHLILTGSNRMKQRPIGPLVDALKNNGCCIEYLELENCLPL   550
 551  LIKPKEIGLYGGNINLSATVSSQYVSSILMCSPYAKTQVTLSLIGGKPIS   600
 601  QPYIDMTISMMSSFGIKVTRSHSKENTYYIPKGCYTCPSEYIIEGDATSA   650
 651  TYPLAIAAITGGSCTISNVGSASLQGDSKFSEYILKPMGCEVVQSPTTTY   700
 701  IKGPPKGKLKSLGSINMESMTDTFLTAAVLASVAYEESKPYVTKITGISN   750
 751  QRIKECNRINAMVCELKKFGIEAGELPDGIYVKALNTSNLPYSVEGINCY   800
 801  NDHRIAMSFSVLACISSKPTTILDKACVNKTWPYWWDILNSTFKVQMKGI   850
 851  EFDLNPTINSSILHHPSECTIFLIGMRGAGKTTLGQLAANFLGREFIDLD   900
 901  SIIEEDIKTTILEFIQKYSWDVFRRKELHFLKTLLTEKKENYIISCGGGI   950
 951  IETEEARDLLISYIEANGIVIHIHRNIQDIIKYLNTDKTRAPYQDNIMHV  1000
1001  WERRKRWYNLCSSHQFHMTSTDPTEFKKNIPLNLKSSFNNFLRTITGKNN  1050
1051  IFSLILKKKRSYFLSLAFSDLENIFSLLDIITAGCDAIEIRIDLFQKPEE  1100
1101  IDKYPSLEYIAEKIFLLRQKTSLPLIYTLRTTNHGGSFLSSEKKLAKEYI  1150
1151  LHGAKWGFEFLDIELDIASELFKTINNSWPYTKIIASYHNIEKPISCDDF  1200
1201  EWIQKYKEAQHYGHIIKLVGTSSSIEDNFFLEEFKSKFINKKVPSIIINT  1250
1251  GIKGQLSRIMNTFMTPVTHPSLPSKIAPGQLSIKEINTALHIMGLLPEKK  1300
1301  YFLFGKPIKHSQSPNIHNLGFEILGLPYKYQLFETDSISELKEILHLEEF  1350
1351  GGASVTIPLKTNISILLDEISDHAALIGSVNTITRTYNNGQYILKGENTD  1400
1401  WQGIIKAIKNFNKFEKSFENFSGFIIGAGGASRAAIYALLSLGISPIYLI  1450
1451  NRSKDKLNKLYHFFNTNHIIPITEYHELNNINFDIRIGISTIPTDNPIDP  1500
1501  SVLEIAKIFFNLKRKSSEGIFLDMAYGSNTTDLTIIAKACNWKIIHGLEI  1550
1551  LLEQGSEQFLLWTETYIPYNQVKYAILGPNK                     1581

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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