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

NucPred

Fetching Q00748 from www.uniprot.org...

The NucPred score for your sequence is 0.12 (see score help below)

   1  MERDEVSTSSSEGKSQEEAPMAEGLEPTEPIAFLKLFRFSTYGEIGWLFF    50
  51  GFIMCCIKALTLPAVVIIYSEFTSMLVDRAMQFGTSSNVHALPLFGGGKT   100
 101  LTNASREENNEALYDDSISYGILLTIASVVMFISGIFSVDVFNMVALRQV   150
 151  TRMRIKLFSSVIRQDIGWHDLASKQNFTQSMVDDVEKIRDGISEKVGHFV   200
 201  YLVVGFIITVAISFSYGWKLTLAVSSYIPLVILLNYYVAKFQGKLTAREQ   250
 251  ESYAGAGNLAEEILSSIRTVVSFGGEKSEVQRYENFLVPARKASQWKGAF   300
 301  SGLSDAVLKSMLYLSCAGAFWYGVNLIIDDRNVENKEYTPAILMIAFFGI   350
 351  IVGADNIARTAPFLESFATARGCATNLFKVIDLTSKIDPLSTDGKLLNYG   400
 401  LRGDVEFQDVFFRYPSRPEVIVHRGLNIRIRAGQTVALVGSSGCGKSTCV   450
 451  QLLQRFYDPVFGSVLLDDLDIRKYNIQWLRSNIAVVGQEPVLFLGTIAQN   500
 501  ISYGKPGATQKEIEAAATQAGAHEFITNLPESYRSMIGERGSQLSGGQKQ   550
 551  RIAIARALIQNPKILLLDEATSALDYQSEKQVQQALDLASKGRTTIVVSH   600
 601  RLSAIRGADKIVFIHDGKVLEEGSHDDLMALEGAYYNMVRAGDINMPDEV   650
 651  EKEDSIEDTKQKSLALFEKSFETSPLNFEKGQKNSVQFEEPIIKALIKDT   700
 701  NAQSAEAPPEKPNFFRTFSRILQLAKQEWCYLILGTISAVAVGFLYPAFA   750
 751  VIFGEFYAALAEKDPEDALRRTAVLSWACLGLAFLTGLVCFLQTYLFNYA   800
 801  GIWLTTRMRAMTFNAMVNQEVGWFDDENNSVGALSARLSGEAVDIQGAIG   850
 851  YPLSGMIQALSNFISSVSVAMYYNWKLALLCLANCPIIVGSVILEAKMMS   900
 901  NAVVREKQVIEEACRIATESITNIRTVAGLRREADVIREYTEEIQRVEVL   950
 951  IRQKLRWRGVLNSTMQASAFFAYAVALCYGGVLVSEGQLPFQDIIKVSET  1000
1001  LLYGSMMLAQSLAFTPAFSAALIAGHRLFQILDRKPKIQSPMGTIKNTLA  1050
1051  KQLNLFEGVRYRGIQFRYPTRPDAKILNGLDLEVLKGQTVALVGHSGCGK  1100
1101  STCVQLLQRYYDPDEGTIHIDHDDIQHDLTLDGVRTKLGIVSQEPTLFER  1150
1151  SIAENIAYGDNRRSVSMVEIIAAAKSANAHSFIISLPNGYDTRMGARGTQ  1200
1201  LSGGQKQRIAIARALVRNPKILLLDEATSALDLQSEQLVQQALDTACSGR  1250
1251  TCIVIAHRLSTVQNADVICVIQNGQVVEQGNHMQLISQGGIYAKLHKTQK  1300
1301  DH                                                  1302

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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