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

NucPred

Fetching Q6PFE3 from www.uniprot.org...

The NucPred score for your sequence is 0.67 (see score help below)

   1  MRRSAAPSQVQGKSFKKTRFIPPGRSNADVSKEITKMSPDPKLFQGAEQS    50
  51  QNDPGVCSSNPCPSEGIPREVGDGTRVDPLPPVHSASKEITESKAQEEEA   100
 101  SSLLKYFSVVWCKASKKKHKKWEGDAILIVRGRSFTLKDLEGKDIGRGIG   150
 151  YKFKDLENVEEGQTLIIGGKEIEILGTISSDDFNSGKCFQHGSGSPAVPS   200
 201  SQAARKCFSNPFKSVCQSTQAQGKRWNDCRPRHNPCTPNALVMPRPDENH   250
 251  QRMFNRHCSPIVDVVIDPHLVHHLRPHQKDGIIFLYECVMGMRAVGKCGA   300
 301  ILADEMGLGKTLQCISLIWTLQCQGPYGGKPVIKKTLIVTPGSLVNNWRK   350
 351  EFQKWLGSERIKIFTVDQDHKVEEFINSTFHSVLIISYEMLLRSLDQIKT   400
 401  IPFGLLICDEGHRLKNSSIKTTTALSSLSCEKTVILTGTPVQNDLQEFFA   450
 451  LVDFVNPGILGSLSSYRKIYEEPIIISREPSSSKEERELGERRATELTRL   500
 501  TGRFILRRTQEVINKYLPPKIENVVFCRPGALQIELYRKLLRSQSVRFCL   550
 551  QGLLENSAHLICIGALKKLCNHPCLLFSSVKGKEFSSSCEENEERNLCQG   600
 601  LLSVFPAGYNPLQFSEEESGKLQVLVKLLAVIHELRPTEKVILVSNYRQT   650
 651  LNVLEEVCKRHGYACARLDGQTPVSQRQHIVDSFNSKYSTDFIFLLSSKA   700
 701  GGVGLNLIGGSHLILYDIDWNPATDIQAMSRVWRDGQKHPVHIYRLLTTG   750
 751  TIEEKIYQRQISKQGLSGAVVDLTRSSEHIQFSVEELKNLFTLHESSHCV   800
 801  THDLLDCECTGEKGHTEDASEGPVASRQCQFGPQKSDALRPLSMSQLKQW   850
 851  KHFSGDHLNLPDPFLERIRENVSFFFQNITNQAPAV                 886

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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