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

NucPred

Fetching Q94A18 from www.uniprot.org...

The NucPred score for your sequence is 0.34 (see score help below)

   1  METLSRSLSKSLGELLASNSNNHFSRRSGSTIDDHDEEALKWAALEKLPT    50
  51  FARLRTTIIHPHEDLVDVTKLGVDDRQKFIDSIFKVTEEDNEKFLKKFRN   100
 101  RIDRVRIKLPTVEVRFEKVTIEANCHIGKRALPTLPNAALNIAERGLRLL   150
 151  GFNFTKTTKVTILRDVSGIIKPSRMTLLLGPPSSGKTTLLLALAGKLDQS   200
 201  LKVTGRVTYNGHGLEEFVPQKTSAYISQNDVHVGVMTVQETLDFSARCQG   250
 251  VGTRYDLLSELVRREKDAGILPEPEVDLFMKSIAAGNVKSSLITDYTLRI   300
 301  LGLDICKDTVVGDEMIRGISGGQKKRVTTGEMIVGPTKTLFMDEISTGLD   350
 351  SSTTYQIVKCLQEIVRFTDATVLMSLLQPAPETFELFDDIILLSEGQIVY   400
 401  QGPRDHVLTFFETCGFKCPDRKGTADFLQEVTSRKDQEQYWADSKKPYSY   450
 451  ISVSEFSKRFRTFHVGANLEKDLSVPYDRFKSHPASLVFKKHSVPKSQLF   500
 501  KVCWDRELLLMKRNAFFYITKTVQIIIMALIASTVYLRTEMGTKNESDGA   550
 551  VYIGALMFSMIVNMFNGFAELALMIQRLPVFYKQRDLLFHPPWTFSLPTF   600
 601  LLGIPISIFESVVWVTITYYMIGFAPELSRFLKHLLVIFLTQQMAGGIFR   650
 651  FIAATCRSMILANTGGALVILLLFLLGGFIVPRGEIPKWWKWAYWVSPMA   700
 701  YTYDALTVNEMLAPRWINQPSSDNSTSLGLAVLEIFDIFTDPNWYWIGVG   750
 751  GILGFTVLFNILVTLALTFLNPLEKQQAVVSKENTEENRAENGSKSKSID   800
 801  VKRGMVLPFTPLTMSFDNVNYYVDMPKEMKEQGVSKDKLQLLKEVTGVFR   850
 851  PGVLTALMGVSGAGKTTLMDVLAGRKTGGYIEGDIRISGFPKRQETFARI   900
 901  SGYCEQNDIHSPQVTVKESLIYSAFLRLPKEVTKYEKMRFVDEVMELVEL   950
 951  ESLKDAVVGLPGITGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARA  1000
1001  AAIVMRTVRNTVDTGRTVVCTIHQPSIDIFEAFDELLLLKRGGQVIYAGP  1050
1051  LGQNSHKIIEYFQAIHGVPKIKEKYNPATWMLEVSSMAAEAKLEIDFAEH  1100
1101  YKTSSLYQQNKNLVKELSTPPQGASDLYFSTRFSQSLLGQFKSCLWKQWI  1150
1151  TYWRTPDYNLARFFFTLAAAVMLGSIFWKVGTKRENANDLTKVIGAMYAA  1200
1201  VLFVGVNNSSSVQPLIAVERSVFYRERAAEMYSALPYALAQVVCEIPYVL  1250
1251  IQTTYYTLIIYAMMCFEWTLAKFFWFYFVSFMSFLYFTYYGMMTVALTPN  1300
1301  QQVAAVFAGAFYGLFNLFSGFVIPRPRIPKWWIWYYWICPVAWTVYGLIV  1350
1351  SQYGDVEDTIKVPGMANDPTIKWYIENHYGYDADFMIPIATVLVGFTLFF  1400
1401  AFMFAFGIRTLNFQQR                                    1416

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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