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

NucPred

Fetching Q80ZF8 from www.uniprot.org...

The NucPred score for your sequence is 0.89 (see score help below)

   1  MKAVRNLLIYIFSTYLLVMFGFNAAQDFWCSTLVKGVIYGSYSVSEMFPK    50
  51  NFTNCTWTLENPDPTKYSIYLKFSKKDLSCSNFSLLAYQFDHFSHEKIKD   100
 101  LLRKNHSIMQLCSSKNAFVFLQYDKNFIQIRRVFPTDFPGLQKKVEEDQK   150
 151  SFFEFLVLNKVSPSQFGCHVLCTWLESCLKSENGRTESCGIMYTKCTCPQ   200
 201  HLGEWGIDDQSLVLLNNVVLPLNEQTEGCLTQELQTTQVCNLTREAKRPP   250
 251  KEEFGMMGDHTIKSQRPRSVHEKRVPQEQADAAKFMAQTGESGVEEWSQW   300
 301  SACSVTCGQGSQVRTRTCVSPYGTHCSGPLRESRVCNNTALCPVHGVWEE   350
 351  WSPWSLCSFTCGRGQRTRTRSCTPPQYGGRPCEGPETHHKPCNIALCPVD   400
 401  GQWQEWSSWSHCSVTCSNGTQQRSRQCTAAAHGGSECRGPWAESRECYNP   450
 451  ECTANGQWNQWGHWSGCSKSCDGGWERRMRTCQGAAVTGQQCEGTGEEVR   500
 501  RCSEQRCPAPYEICPEDYLISMVWKRTPAGDLAFNQCPLNATGTTSRRCS   550
 551  LSLHGVASWEQPSFARCISNEYRHLQHSIKEHLAKGQRMLAGDGMSQVTK   600
 601  TLLDLTQRKNFYAGDLLVSVEILRNVTDTFKRASYIPASDGVQNFFQIVS   650
 651  NLLDEENKEKWEDAQQIYPGSIELMQVIEDFIHIVGMGMMDFQNSYLMTG   700
 701  NVVASIQKLPAASVLTDINFPMKGRKGMVDWARNSEDRVVIPKSIFTPVS   750
 751  SKELDESSVFVLGAVLYKNLDLILPTLRNYTVVNSKVIVVTIRPEPKTTD   800
 801  SFLEIELAHLANGTLNPYCVLWDDSKSNESLGTWSTQGCKTVLTDASHTK   850
 851  CLCDRLSTFAILAQQPREIVMESSGTPSVTLIVGSGLSCLALITLAVVYA   900
 901  ALWRYIRSERSIILINFCLSIISSNILILVGQTQTHNKSICTTTTAFLHF   950
 951  FFLASFCWVLTEAWQSYMAVTGKIRTRLIRKRFLCLGWGLPALVVATSVG  1000
1001  FTRTKGYGTDHYCWLSLEGGLLYAFVGPAAAVVLVNMVIGILVFNKLVSR  1050
1051  DGILDKKLKHRAGQMSEPHSGLTLKCAKCGVVSTTALSATTASNAMASLW  1100
1101  SSCVVLPLLALTWMSAVLAMTDKRSILFQILFAVFDSLQGFVIVMVHCIL  1150
1151  RREVQDAFRCRLRNCQDPINADSSSSFPNGHAQIMTDFEKDVDIACRSVL  1200
1201  HKDIGPCRAATITGTLSRISLNDDEEEKGTNPEGLSYSTLPGNVISKVII  1250
1251  QQPTGLHMPMSMNELSNPCLKKENTELRRTVYLCTDDNLRGADMDIVHPQ  1300
1301  ERMMESDYIVMPRSSVSTQPSMKEESKMNIGMETLPHERLLHYKVNPEFN  1350
1351  MNPPVMDQFNMNLDQHLAPQEHMQNLPFEPRTAVKNFMASELDDNVGLSR  1400
1401  SETGSTISMSSLERRKSRYSDLDFEKVMHTRKRHMELFQELNQKFQTLDR  1450
1451  FRDIPNTSSMENPAPNKNPWDTFKPPSEYQHYTTINVLDTEAKDTLELRP  1500
1501  AEWEKCLNLPLDVQEGDFQTEV                              1522

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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