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

NucPred

Fetching P58283 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MAEGNNKEEVIHLNNFPCHRGKEWMAVREGPITISDSSDEEGIPMLVTPA    50
  51  TEQQEDDLDDDVILTEDDSEDEYGGFLDLESGKKEGEAKPGPSSKQTADD   100
 101  IVNPRLEQKVIILGENGLLFPESEPLEVQNQSSEDSETELLSNPGEPAAS   150
 151  VDDQLIGEEYWLDHPYFQAPNPQPQERTNQVVPQERHSESEMGPMFFRHD   200
 201  FPEPAFPRPEPQQEGIPGPASPQPAHPLGELEDQQLAIDEDPGPAFPLSG   250
 251  PQEANLANMWEQEAAEVDQDLIPLLVKETEARFPDVASGYVEEIIHLKNY   300
 301  YDLNVLCNFLLENPDYPKREDRLIIHPSSSLLASQDDAKLPKIDFFDYSK   350
 351  LTPLDQRCFIQAADLLMADFKMLSSQDIKWALHELKGHYAITRKAFSDAI   400
 401  KKWQELSPETSGKRKKRKEMNQYSFIDFKFEQGNIKIEKRMFFLENKRRH   450
 451  CRYYDHQALLPAVKQEQEFYEQKIKEMAEHEDFLLALQMNEEQYQKDGQL   500
 501  IECRCCYGEFPFEELTQCADAHLFCKECLIRYAQEAVFGSGKSELSCMEG   550
 551  SCTCSFPTSELEKVLPQTILYKYYERKAEEEVAAAYADELVRCPSCSFPA   600
 601  LLDSDVKRFSCPNPRCRKETCRKCQGLWKEHNGLTCEELAEKDDIKYRTS   650
 651  IEEKMTAARIRKCHKCGTGLIKSEGCNRMSCRCGAQMCYLCRVSINGYDH   700
 701  FCQHPRSPGAPCQECSRCSLWTDPTEDDEKLIEEIQKEAEEEQKRKNGEN   750
 751  TFKRIGPPLEKPAEKVQRVEALPRPVPQNLHPQMPPYAFVHPPFPLPPVR   800
 801  PVFNNFPINMGPVPAPYVPPLPNVRVNYDFGHMHVPLEHNLPMHFGPQPR   850
 851  HRF                                                  853

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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