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

NucPred

Fetching Q5RD64 from www.uniprot.org...

The NucPred score for your sequence is 0.51 (see score help below)

   1  MLAAPRAGCGAALLLWIVSSCLCRAWTAPSTSQKCDEPLVSGLPHGAFSS    50
  51  SSSISGSYSPGYAKINKRGGAGGWSPSDSDHYQWLQVDFGNRKQISAIAT   100
 101  QGRYSSSDWVTQYRMLYSDTGRNWKPYHQDGNIWAFPGNINSDGVVRHEL   150
 151  QHPVIARYVRVVPLDWNGEGRIGLRIEVYGCSYWADVINFDGHVVLPYRF   200
 201  RNKKMKTLKDVIALKFKTSESEGVILHGEGQQGDYITLELKKAKLVLSLN   250
 251  LGSNQLGPIYGHTSVMTGSLLDDHHWHSVIIERQGRSINLTLDRSMQHFR   300
 301  TNGEFDYLDLDYEITFGGIPFSGKPSSSSRKNFKGCMESINYNGINITVL   350
 351  ARRKKLEPSNVGNLSFSCVEPYTVPVFFNATSYLEVPGRLNQDLFSVSFQ   400
 401  FRTWNPNGLLVFSHFADNLGNVEIDLTESKVGVHINITQTKMSQIDISSG   450
 451  SGLNDGQWHEVRFLAKENFAILTIDGDEASAVRTNSPLQVKTGEKYFFGG   500
 501  FLNQMNNSSHSVLQPSFQGCMQLIQVDDQLVNLYEVAQRKPGSFANVSID   550
 551  MCAIIDRCVPNHCERGGKCSQTWDSFKCTCDETGYTGATCHNSIYEPSCE   600
 601  AYKHLGQTSNYYWIDPDGSGPLGPLKVYCNMTEDKVWTIVSHDLQMQTTV   650
 651  VSYNPEKHSVIQLVYSASMDQISAITDSAEYCEQYISYFCKMSRLLNTPD   700
 701  GSPYTWWVGKANEKHYYWGGSGPGIQKCACGIERNCTDPKYYCNCDADYK   750
 751  QWRKDAGFLSYKDHLPVSQVVVGDTDRQGSEAKLSVGPLRCQGDRNYWNA   800
 801  ASFPNPSSYLHFSTFQGETSADISFYFKTLTPWGVFLENMGKEDFIKLEL   850
 851  KSATEVSFSFDVGNGPVEIVVRSPTPLNDDQWHRITAERNVKQASLQVDR   900
 901  LPQQIRKAPTEGHTRLELYSQLFVGGAGGQQGFLGCIRSLRMNGVTLDLE   950
 951  ERAKVTSGFISGCSGHCTSYGTNCENGGKCLERYHGYSCDCSNTAYDGTF  1000
1001  CNKDVGAFFEEGMWLRYNFQAPATNARDSSSRVENAPDQQNSHPDLAQEE  1050
1051  IRFSFSTTKAPCILLYISSFTTDFLAVLVKPTGSLQIRYNLGGTREPYNI  1100
1101  DTDHRNMANGQPHSVNNTRHEKTIILKLDHYPSVSYHLPSSSDTLFNSPK  1150
1151  SLFLGKVIETGKIDQEIHKYNTPGFTGCLSRVQFNQIAPLKAALRQTNAS  1200
1201  AHVHIQGELVESNCGASPLTLSPMSSATDPWHLDHLDSASADFPYNPGQG  1250
1251  QAIRNGVNRNSAIIGGVIAVVIFTILCTLVFLIRYMFRHKGTYHTNEAKG  1300
1301  AESAESADAAIMNNDPNFTETIDESKKEWLI                     1331

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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