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

NucPred

Fetching Q8WWI1 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MKKIRICHIFTFYSWMSYDVLFQRTELGALEIWRQLICAHVCICVGWLYL    50
  51  RDRVCSKKDIILRTEQNSGRTILIKAVTEKNFETKDFRASLENGVLLCDL   100
 101  INKLKPGVIKKINRLSTPIAGLDNINVFLKACEQIGLKEAQLFHPGDLQD   150
 151  LSNRVTVKQEETDRRVKNVLITLYWLGRKAQSNPYYNGPHLNLKAFENLL   200
 201  GQALTKALEDSSFLKRSGRDSGYGDIWCPERGEFLAPPRHHKREDSFESL   250
 251  DSLGSRSLTSCSSDITLRGGREGFESDTDSEFTFKMQDYNKDDMSYRRIS   300
 301  AVEPKTALPFNRFLPNKSRQPSYVPAPLRKKKPDKHEDNRRSWASPVYTE   350
 351  ADGTFSSNQRRIWGTNVENWPTVQGTSKSSCYLEEEKAKTRSIPNIVKDD   400
 401  LYVRKLSPVMPNPGNAFDQFLPKCWTPEDVNWKRIKRETYKPWYKEFQGF   450
 451  SQFLLLQALQTYSDDILSSETHTKIDPTSGPRLITRRKNLSYAPGYRRDD   500
 501  LEMAALDPDLENDDFFVRKTGVFHANPYVLRAFEDFRKFSEQDDSVERDI   550
 551  ILQCREGELVLPDLEKDDMIVRRIPAQKKEVPLSGAPDRYHPVPFPEPWT   600
 601  LPPEIQAKFLCVFERTCPSKEKSNSCRILVPSYRQKKDDMLTRKIQSWKL   650
 651  GTTVPPISFTPGPCSEADLKRWEAIREASRLRHKKRLMVERLFQKIYGEN   700
 701  GSKSMSDVSAEDVQNLRQLRYEEMQKIKSQLKEQDQKWQDDLAKWKDRRK   750
 751  SYTSDLQKKKEEREEIEKQALEKSKRSSKTFKEMLQDRESQNQKSTVPSR   800
 801  RRMYSFDDVLEEGKRPPTMTVSEASYQSERVEEKGATYPSEIPKEDSTTF   850
 851  AKREDRVTTEIQLPSQSPVEEQSPASLSSLRSRSTQMESTRVSASLPRSY   900
 901  RKTDTVRLTSVVTPRPFGSQTRGISSLPRSYTMDDAWKYNGDVEDIKRTP   950
 951  NNVVSTPAPSPDASQLASSLSSQKEVAATEEDVTRLPSPTSPFSSLSQDQ  1000
1001  AATSKATLSSTSGLDLMSESGEGEISPQREVSRSQDQFSDMRISINQTPG  1050
1051  KSLDFGFTIKWDIPGIFVASVEAGSPAEFSQLQVDDEIIAINNTKFSYND  1100
1101  SKEWEEAMAKAQETGHLVMDVRRYGKAGSPETKWIDATSGIYNSEKSSNL  1150
1151  SVTTDFSESLQSSNIESKEINGIHDESNAFESKASESISLKNLKRRSQFF  1200
1201  EQGSSDSVVPDLPVPTISAPSRWVWDQEEERKRQERWQKEQDRLLQEKYQ  1250
1251  REQEKLREEWQRAKQEAERENSKYLDEELMVLSSNSMSLTTREPSLATWE  1300
1301  ATWSEGSKSSDREGTRAGEEERRQPQEEVVHEDQGKKPQDQLVIERERKW  1350
1351  EQQLQEEQEQKRLQAEAEEQKRPAEEQKRQAEIERETSVRIYQYRRPVDS  1400
1401  YDIPKTEEASSGFLPGDRNKSRSTTELDDYSTNKNGNNKYLDQIGNMTSS  1450
1451  QRRSKKEQVPSGAELERQQILQEMRKRTPLHNDNSWIRQRSASVNKEPVS  1500
1501  LPGIMRRGESLDNLDSPRSNSWRQPPWLNQPTGFYASSSVQDFSRPPPQL  1550
1551  VSTSNRAYMRNPSSSVPPPSAGSVKTSTTGVATTQSPTPRSHSPSASQSG  1600
1601  SQLRNRSVSGKRICSYCNNILGKGAAMIIESLGLCYHLHCFKCVACECDL  1650
1651  GGSSSGAEVRIRNHQLYCNDCYLRFKSGRPTAM                   1683

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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