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

NucPred

Fetching Q6BNG2 from www.uniprot.org...

The NucPred score for your sequence is 0.85 (see score help below)

   1  MPSKYGNGSGTGRFVKNSTIKSEFRNNGYNRAEVIDPSIANNPMLNDSIQ    50
  51  KRELVNRIDQLDSIMGFDRIEHGEMDGAKPRRGWLVNMHATTIPTDEYLA   100
 101  GYSGVDYYFLDEEGGSFKATIRYDPYFYLVVIPGHESEVEEMLRKVLEPC   150
 151  SLKGLLRVAKEDLSLPNHLVGLKKTLVKLSFHNVVDLLSARRLLNPIIKD   200
 201  NKMKRDTRDIYQVMNFNNVNNANGTEIQTNFNDKSTEQIADPATLIDDIR   250
 251  EYDVPYHVRVSIDEKIRVGKWYNVFVKHSEVRLEEDKEKIAFADPVILAF   300
 301  DIETTKAPLKFPDAKTDQIMMISYMIDGEGFLITNREIISEDIEDFEYTP   350
 351  KPEYPGLFTIFNEPDEKMVLVRFFEHIRDSRPTVIATFNGDFFDWPFVEK   400
 401  RTTFHDMDMFEEIGFAKDNEGEYKSKYCVHMDCYRWVKRDSYLPQGSQGL   450
 451  KAVTTAKLGYNPTELDPELMTPYAYEKPQLLSEYSVSDAVATYYLYYKYV   500
 501  HPFIFSLCTIIPLNPDEVLRKGTGTLCEMLLMVQAYENGIVLPNKHTEPI   550
 551  ERFYDGHLLESETYVGGHVESLEAGVFRSDLPNDFKVDPTAVDEILGDLH   600
 601  NALKFCIEVENNKKVEDVENYDEVYNQIKDSLVNLRETPIRHENPLIFHV   650
 651  DVASMYPNIMTSNRLQPDSMKSEEDCAACDFNRPGKNCDRRLPWSWRGEY   700
 701  YPAEMNEYGMIKRTLQNETFPPAKPWLPAKTFDELSYSEQASLIKKRLSD   750
 751  YSRKVYHRIKQSKTVSREAIVCQRENPFYVDTVRSFRDRRYEFKTLVKVW   800
 801  KGKTAKIDKHDTIAKDEAKKMVVLYDSLQLAHKVILNSFYGYVMRKGSRW   850
 851  YSMEMAGITCLTGATIIQMARSLVERLGRPLELDTDGIWCILPKSFPENY   900
 901  YFKCKDGKNIFLEYPCSMLNYLVHDKFTNHQYQDLVDPNTFKYKTRSENS   950
 951  IFFEVDGPYKAMVLPTSKEEGKGLKKRYAVFNDDGSLAELKGFELKRRGE  1000
1001  LQLIKNFQSDIFKLFLDGDSLENCYKSVATVANNWLDVLDTKGGMLEDED  1050
1051  LIELICENRSMSKSLAEYGNQKSTSITTAKRLGEFLGEEMIKDAGLACKY  1100
1101  IISSKPIGSPVTERAVPVSIFSSEKKEFFLKKWLKDPSLENFDPRSVIDW  1150
1151  NYYYERLASVVQKIISIPAALQDIKNPVPRVPHPEWLQKKINSKEDSKQQ  1200
1201  SSISSFFGQATKKEVLQKSIKSIQDIEDFGELDASIPKGRVSKVTSRKRR  1250
1251  NGKANNVSDSEEEERNNAILNGECPSMTEDYAGFLQYQKAKWKVQEKNRE  1300
1301  RRKKLFGSNAESSHRSSVGGIIRRQAENIAGSDWEILEYKADPSKPGDIK  1350
1351  VYVSASNKVHSFTFHVPKKVYASFKTELSPKKAIRNCEIEKSTAVLPNGH  1400
1401  DGSNLYKLTMPEETYLEESTKVESLLQDSNILGLYETQVGAVERAIIDLG  1450
1451  NNIRFDDTKVGALGKGLKNGFNVKDLMKVERDSYLKRFGMDIIYFLHLVT  1500
1501  NSYEFFTIFKSWENTASIFVLKPSANAQELPSNMDKIYREIFEAKKDRLG  1550
1551  KMYSIIEYPDEMKFETTYFHDTAKIFKKMDNCISKIYESRSNRALLAVQS  1600
1601  PYTTKVLNLLKSTSSFPTIKMNVSELSLPAVGWQSLIIKRVVNHYFVLAS  1650
1651  WIKKLISLAKYGNVPLCNLQIENMGYLIDIEYARRLSQSNIVLWLSSRPL  1700
1701  PDHGGFEMDKAQDFENLEFPTINNPEIYETACLEVEIGTLTINTILTSAL  1750
1751  INEAEGTDLADDAVQFDNNNGASTIAEDSFSTPALSILRGMVKDWWDDAL  1800
1801  KNNDNADSMMNNLVTWVQRSDSLLYDYSLHYHVHNLTTKALLQLIGEFKR  1850
1851  MNAQVIFANRNKMLIQTTKVSIENSYAYGQYILKAARSKPLFNFLDLRIV  1900
1901  KYWDLLVWMDEYNFGGRCCTEITNDEVQNLIPVNKWQITKFLPVIFQNEF  1950
1951  EDWLIIFLDSLTKFKNDTLIPGTQTGTPRVTQIAHILKGQKKLDSNETEE  2000
2001  ESISNGVMELFRKPLQKRIEKLARRQNESILNPELRQEYEFPKLPGSYTS  2050
2051  MKNPSLELVKFLCAVFGLSRKRNIEVRLLRRELLSIFDIKEFSDEAAFKN  2100
2101  PSSSLKIPHVICDYCNYIRDIDFCRDEQKNIWNCSNCNKTYNRVAIEEEL  2150
2151  VAQYNKLLTKFYIQDLKCSKCHQIKSDNMSEYCKCSGKWTETLKYTEVDK  2200
2201  RLQIFSNVGGFFNLQLLKGIIEELAL                          2226

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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