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

NucPred

Fetching P31424 from www.uniprot.org...

The NucPred score for your sequence is 0.41 (see score help below)

   1  MVLLLILSVLLLKEDVRGSAQSSERRVVAHMPGDIIIGALFSVHHQPTVD    50
  51  KVHERKCGAVREQYGIQRVEAMLHTLERINSDPTLLPNITLGCEIRDSCW   100
 101  HSAVALEQSIEFIRDSLISSEEEEGLVRCVDGSSSFRSKKPIVGVIGPGS   150
 151  SSVAIQVQNLLQLFNIPQIAYSATSMDLSDKTLFKYFMRVVPSDAQQARA   200
 201  MVDIVKRYNWTYVSAVHTEGNYGESGMEAFKDMSAKEGICIAHSYKIYSN   250
 251  AGEQSFDKLLKKLRSHLPKARVVACFCEGMTVRGLLMAMRRLGLAGEFLL   300
 301  LGSDGWADRYDVTDGYQREAVGGITIKLQSPDVKWFDDYYLKLRPETNLR   350
 351  NPWFQEFWQHRFQCRLEGFAQENSKYNKTCNSSLTLRTHHVQDSKMGFVI   400
 401  NAIYSMAYGLHNMQMSLCPGYAGLCDAMKPIDGRKLLDSLMKTNFTGVSG   450
 451  DMILFDENGDSPGRYEIMNFKEMGKDYFDYINVGSWDNGELKMDDDEVWS   500
 501  KKNNIIRSVCSEPCEKGQIKVIRKGEVSCCWTCTPCKENEYVFDEYTCKA   550
 551  CQLGSWPTDDLTGCDLIPVQYLRWGDPEPIAAVVFACLGLLATLFVTVIF   600
 601  IIYRDTPVVKSSSRELCYIILAGICLGYLCTFCLIAKPKQIYCYLQRIGI   650
 651  GLSPAMSYSALVTKTNRIARILAGSKKKICTKKPRFMSACAQLVIAFILI   700
 701  CIQLGIIVALFIMEPPDIMHDYPSIREVYLICNTTNLGVVTPLGYNGLLI   750
 751  LSCTFYAFKTRNVPANFNEAKYIAFTMYTTCIIWLAFVPIYFGSNYKIIT   800
 801  MCFSVSLSATVALGCMFVPKVYIILAKPERNVRSAFTTSTVVRMHVGDGK   850
 851  SSSAASRSSSLVNLWKRRGSSGETLRYKDRRLAQHKSEIECFTPKGSMGN   900
 901  GGRATMSSSNGKSVTWAQNEKSTRGQHLWQRLSVHINKKENPNQTAVIKP   950
 951  FPKSTENRGPGAAAGGGSGPGVAGAGNAGCTATGGPEPPDAGPKALYDVA  1000
1001  EAEESFPAAARPRSPSPISTLSHLAGSAGRTDDDAPSLHSETAARSSSSQ  1050
1051  GSLMEQISSVVTRFTANISELNSMMLSTAATPGPPGTPICSSYLIPKEIQ  1100
1101  LPTTMTTFAEIQPLPAIEVTGGAQGATGVSPAQETPTGAESAPGKPDLEE  1150
1151  LVALTPPSPFRDSVDSGSTTPNSPVSESALCIPSSPKYDTLIIRDYTQSS  1200
1201  SSL                                                 1203

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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