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

NucPred

Fetching Q91VL9 from www.uniprot.org...

The NucPred score for your sequence is 0.80 (see score help below)

   1  MAKPSHSSYVLQQLNNQREWGFLCDCCIAIDDIYFQAHKAVLAACSSYFR    50
  51  MFFMNHQHSTAQLNLSNMKISAECFDLILQFMYLGKIMTAPSSFEQFKVA   100
 101  MNYLQLYNVPDCLEDIQDADCSSSKCSSSASSRQSSKMIFGVRMYEDTVA   150
 151  RNGNEANRWCAEPSSTVNTPHHREPEEESLQLANFPEPLFDVCKKSSVSK   200
 201  LSTPKERVSRRFGRSFTCDSCGFGFSCEKLLDEHVLTCTNRHSYQNTTRA   250
 251  YHRIVDIRDGKDSNIKAELAEKDSSKTFSAQPDKYREDANQAPDDSASTT   300
 301  GSRKSTVEAGIAGEEKSRATETKRIIIKMEPEDIPADDMKDFNIIKVTEK   350
 351  DCNESTDNDELEDEPEEPFYRYYVEEDVGIKKSGRKTLKPRMSISVDERG   400
 401  GLENMRPPNNTSPIQEDAENASCELCGLTITEEDLSSHYLAKHIENICAC   450
 451  GKCGQILVKGRQLQEHAQRCGEPQDLTMNGLGNADEKMDMEENPDEQSEI   500
 501  RDMFVEMLDDFRDNHYQINSIQKKQLFKHSACPFRCPNCGQRFETENLVV   550
 551  EHMSSCLDQDMFKGAIMEENERDHRRKHFCNLCGKGFYQRCHLREHYTVH   600
 601  TKEKQFVCQTCGKQFLRERQLRLHNDMHKGMARYVCSICDQGNFRKHDHV   650
 651  RHMISHLSGGETICQVCFQIFPNNEQLEQHMDVHLYTCGICGAKFNLRKD   700
 701  MRSHYNAKHLKRT                                        713

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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