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

NucPred

Fetching Q9M9E1 from www.uniprot.org...

The NucPred score for your sequence is 0.39 (see score help below)

   1  MEGTSFHQASNSMRRNSSVWKKDSGREIFSRSSREEDDEEALRWAALEKL    50
  51  PTFDRLRKGILTASHAGGPINEIDIQKLGFQDTKKLLERLIKVGDDEHEK   100
 101  LLWKLKKRIDRVGIDLPTIEVRFDHLKVEAEVHVGGRALPTFVNFISNFA   150
 151  DKFLNTLHLVPNRKKKFTILNDVSGIVKPGRMALLLGPPSSGKTTLLLAL   200
 201  AGKLDQELKQTGRVTYNGHGMNEFVPQRTAAYIGQNDVHIGEMTVRETFA   250
 251  YAARFQGVGSRYDMLTELARREKEANIKPDPDIDIFMKAMSTAGEKTNVM   300
 301  TDYILKILGLEVCADTMVGDDMLRGISGGQKKRVTTGEMLVGPSRALFMD   350
 351  EISTGLDSSTTYQIVNSLRNYVHIFNGTALISLLQPAPETFNLFDDIILI   400
 401  AEGEIIYEGPRDHVVEFFETMGFKCPPRKGVADFLQEVTSKKDQMQYWAR   450
 451  RDEPYRFIRVREFAEAFQSFHVGRRIGDELALPFDKTKSHPAALTTKKYG   500
 501  VGIKELVKTSFSREYLLMKRNSFVYYFKFGQLLVMAFLTMTLFFRTEMQK   550
 551  KTEVDGSLYTGALFFILMMLMFNGMSELSMTIAKLPVFYKQRDLLFYPAW   600
 601  VYSLPPWLLKIPISFMEAALTTFITYYVIGFDPNVGRLFKQYILLVLMNQ   650
 651  MASALFKMVAALGRNMIVANTFGAFAMLVFFALGGVVLSRDDIKKWWIWG   700
 701  YWISPIMYGQNAILANEFFGHSWSRAVENSSETLGVTFLKSRGFLPHAYW   750
 751  YWIGTGALLGFVVLFNFGFTLALTFLNSLGKPQAVIAEEPASDETELQSA   800
 801  RSEGVVEAGANKKRGMVLPFEPHSITFDNVVYSVDMPQEMIEQGTQEDRL   850
 851  VLLKGVNGAFRPGVLTALMGVSGAGKTTLMDVLAGRKTGGYIDGNITISG   900
 901  YPKNQQTFARISGYCEQTDIHSPHVTVYESLVYSAWLRLPKEVDKNKRKI   950
 951  FIEEVMELVELTPLRQALVGLPGESGLSTEQRKRLTIAVELVANPSIIFM  1000
1001  DEPTSGLDARAAAIVMRTVRNTVDTGRTVVCTIHQPSIDIFEAFDELFLL  1050
1051  KRGGEEIYVGPLGHESTHLINYFESIQGINKITEGYNPATWMLEVSTTSQ  1100
1101  EAALGVDFAQVYKNSELYKRNKELIKELSQPAPGSKDLYFPTQYSQSFLT  1150
1151  QCMASLWKQHWSYWRNPPYTAVRFLFTIGIALMFGTMFWDLGGKTKTRQD  1200
1201  LSNAMGSMYTAVLFLGLQNAASVQPVVNVERTVFYREQAAGMYSAMPYAF  1250
1251  AQVFIEIPYVLVQAIVYGLIVYAMIGFEWTAVKFFWYLFFMYGSFLTFTF  1300
1301  YGMMAVAMTPNHHIASVVSSAFYGIWNLFSGFLIPRPSMPVWWEWYYWLC  1350
1351  PVAWTLYGLIASQFGDITEPMADSNMSVKQFIREFYGYREGFLGVVAAMN  1400
1401  VIFPLLFAVIFAIGIKSFNFQKR                             1423

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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