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

NucPred

Fetching Q8WW38 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MSRRKQSKPRQIKRPLEDAIEDEEEECPSEETDIISKGDFPLEESFSTEF    50
  51  GPENLSCEEVEYFCNKGDDEGIQETAESDGDTQSEKPGQPGVETDDWDGP   100
 101  GELEVFQKDGERKIQSRQQLPVGTTWGPFPGKMDLNNNSLKTKAQVPMVL   150
 151  TAGPKWLLDVTWQGVEDNKNNCIVYSKGGQLWCTTTKAISEGEELIAFVV   200
 201  DFDSRLQAASQMTLTEGMYPARLLDSIQLLPQQAAMASILPTAIVNKDIF   250
 251  PCKSCGIWYRSERNLQAHLMYYCSGRQREAAPVSEENEDSAHQISSLCPF   300
 301  PQCTKSFSNARALEMHLNSHSGVKMEEFLPPGASLKCTVCSYTADSVINF   350
 351  HQHLFSHLTQAAFRCNHCHFGFQTQRELLQHQELHVPSGKLPRESDMEHS   400
 401  PSATEDSLQPATDLLTRSELPQSQKAMQTKDASSDTELDKCEKKTQLFLT   450
 451  NQRPEIQPTTNKQSFSYTKIKSEPSSPRLASSPVQPNIGPSFPVGPFLSQ   500
 501  FSFPQDITMVPQASEILAKMSELVHRRLRHGSSSYPPVIYSPLMPKGATC   550
 551  FECNITFNNLDNYLVHKKHYCSSRWQQMAKSPEFPSVSEKMPEALSPNTG   600
 601  QTSINLLNPAAHSADPENPLLQTSCINSSTVLDLIGPNGKGHDKDFSTQT   650
 651  KKLSTSSNNDDKINGKPVDVKNPSVPLVDGESDPNKTTCEACNITFSRHE   700
 701  TYMVHKQYYCATRHDPPLKRSASNKVPAMQRTMRTRKRRKMYEMCLPEQE   750
 751  QRPPLVQQRFLDVANLNNPCTSTQEPTEGLGECYHPRCDIFPGIVSKHLE   800
 801  TSLTINKCVPVSKCDTTHSSVSCLEMDVPIDLSKKCLSQSERTTTSPKRL   850
 851  LDYHECTVCKISFNKVENYLAHKQNFCPVTAHQRNDLGQLDGKVFPNPES   900
 901  ERNSPDVSYERSIIKCEKNGNLKQPSPNGNLFSSHLATLQGLKVFSEAAQ   950
 951  LIATKEENRHLFLPQCLYPGAIKKAKGADQLSPYYGIKPSDYISGSLVIH  1000
1001  NTDIEQSRNAENESPKGQASSNGCAALKKDSLPLLPKNRGMVIVNGGLKQ  1050
1051  DERPAANPQQENISQNPQHEDDHKSPSWISENPLAANENVSPGIPSAEEQ  1100
1101  LSSIAKGVNGSSQAPTSGKYCRLCDIQFNNLSNFITHKKFYCSSHAAEHV  1150
1151  K                                                   1151

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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