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

NucPred

Fetching P14284 from www.uniprot.org...

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

   1  MSRESNDTIQSDTVRSSSKSDYFRIQLNNQDYYMSKPTFLDPSHGESLPL    50
  51  NQFSQVPNIRVFGALPTGHQVLCHVHGILPYMFIKYDGQITDTSTLRHQR   100
 101  CAQVHKTLEVKIRASFKRKKDDKHDLAGDKLGNLNFVADVSVVKGIPFYG   150
 151  YHVGWNLFYKISLLNPSCLSRISELIRDGKIFGKKFEIYESHIPYLLQWT   200
 201  ADFNLFGCSWINVDRCYFRSPVLNSILDIDKLTINDDLQLLLDRFCDFKC   250
 251  NVLSRRDFPRVGNGLIEIDILPQFIKNREKLQHRDIHHDFLEKLGDISDI   300
 301  PVKPYVSSARDMINELTMQREELSLKEYKEPPETKRHVSGHQWQSSGEFE   350
 351  AFYKKAQHKTSTFDGQIPNFENFIDKNQKFSAINTPYEALPQLWPRLPQI   400
 401  EINNNSMQDKKNDDQVNASFTEYEICGVDNENEGVKGSNIKSRSYSWLPE   450
 451  SIASPKDSTILLDHQTKYHNTINFSMDCAMTQNMASKRKLRSSVSANKTS   500
 501  LLSRKRKKVMAAGLRYGKRAFVYGEPPFGYQDILNKLEDEGFPKIDYKDP   550
 551  FFSNPVDLENKPYAYAGKRFEISSTHVSTRIPVQFGGETVSVYNKPTFDM   600
 601  FSSWKYALKPPTYDAVQKWYNKVPSMGNKKTESQISMHTPHSKFLYKFAS   650
 651  DVSGKQKRKKSSVHDSLTHLTLEIHANTRSDKIPDPAIDEVSMIIWCLEE   700
 701  ETFPLDLDIAYEGIMIVHKASEDSTFPTKIQHCINEIPVMFYESEFEMFE   750
 751  ALTDLVLLLDPDILSGFEIHNFSWGYIIERCQKIHQFDIVRELARVKCQI   800
 801  KTKLSDTWGYAHSSGIMITGRHMINIWRALRSDVNLTQYTIESAAFNILH   850
 851  KRLPHFSFESLTNMWNAKKSTTELKTVLNYWLSRAQINIQLLRKQDYIAR   900
 901  NIEQARLIGIDFHSVYYRGSQFKVESFLIRICKSESFILLSPGKKDVRKQ   950
 951  KALECVPLVMEPESAFYKSPLIVLDFQSLYPSIMIGYNYCYSTMIGRVRE  1000
1001  INLTENNLGVSKFSLPRNILALLKNDVTIAPNGVVYAKTSVRKSTLSKML  1050
1051  TDILDVRVMIKKTMNEIGDDNTTLKRLLNNKQLALKLLANVTYGYTSASF  1100
1101  SGRMPCSDLADSIVQTGRETLEKAIDIIEKDETWNAKVVYGDTDSLFVYL  1150
1151  PGKTAIEAFSIGHAMAERVTQNNPKPIFLKFEKVYHPSILISKKRYVGFS  1200
1201  YESPSQTLPIFDAKGIETVRRDGIPAQQKIIEKCIRLLFQTKDLSKIKKY  1250
1251  LQNEFFKIQIGKVSAQDFCFAKEVKLGAYKSEKTAPAGAVVVKRRINEDH  1300
1301  RAEPQYKERIPYLVVKGKQGQLLRERCVSPEEFLEGENLELDSEYYINKI  1350
1351  LIPPLDRLFNLIGINVGNWAQEIVKSKRASTTTTKVENITRVGTSATCCN  1400
1401  CGEELTKICSLQLCDDCLEKRSTTTLSFLIKKLKRQKEYQTLKTVCRTCS  1450
1451  YRYTSDAGIENDHIASKCNSYDCPVFYSRVKAERYLRDNQSVQREEALIS  1500
1501  LNDW                                                1504

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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