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

NucPred

Fetching Q06434 from www.uniprot.org...

The NucPred score for your sequence is 0.33 (see score help below)

   1  MQVSKYFTHQLSQFSGYPSIVSERDACGVGFIANLNSKPSNKIVTEALNA    50
  51  LSCMEHRGGCGADNISGDGAGVTIQIPWDIFISEGINFLPKLQSNQSILN   100
 101  YGVRMILRSSDDLDKIKKIFSWALDEYQLDLISWRNVPVDKSILGEESKF   150
 151  NQPLVVQCIVRSNNLIDYKLDKHLYLVRKKIEKLVSKLDINTNKQFYICS   200
 201  FSSKTIVYKGMLRSEFLVKYYNDLSNSLYVSNFAMYHRRFSTNTMPKWSL   250
 251  AQPMRFMAHNGEINTLLGNLNWNKSKESLLKSSIWSDYYDILSPITNLEN   300
 301  SDSANLDSVLELFIHSGRTPQEALMILIPEAYKNQPALSLFPEITDFYEY   350
 351  YSILQEPWDGPALVVFTDGKFVGATLDRNGLRPARYTITDDGFISLSSET   400
 401  GVSNINSQNVVTKGRLGPGQMLCVDLSKNLVLDNWMIKQQISQKFPYKEW   450
 451  VNKYQSNLNLLEYLNDFTFDKVQMNRWHTAFGYTNEDVELVIEHMASSAK   500
 501  EPTFSMGDDTPLPILSEKPHLIYDYFKQRFAQVTNPAIDPLRESLVMSLI   550
 551  TYLGPKGNILEPTAIMAKSIKLESPIINENELAQLNSFNLSVVTVPTFID   600
 601  KHLSTQTFVDKILEICSQCDSYISQGIEILVLSDRIEILPVDKIFVSPLL   650
 651  IVGAVHHYLIKKQLRHKVSLVIDTGQCWTTHHFALLIGYGASAICPYLAF   700
 701  LTVRQWWHNSRTQKLMSTGKLSRLTIQESQDNYRSAIEKGLLKILSKMGI   750
 751  SLLSSYHGAQIFEILGLGQDVVDLAFSGTVSRLNGMTLNELYEDSLKSYN   800
 801  LAFITEIPKKLPNLGYVQYRPSAEYHVNNPEMSKTLHKAVRNNDNILYSK   850
 851  YKSLLNDRRPTNLRDLLELKTDRQPISIDQVEDVNSVLMRFCTGGMSLGA   900
 901  LSRETHETLAIRMNRIGGKSNSGEGGEDSTRFKSIQDLDTSGVSRTFSHL   950
 951  KGLKINDLASSAIKQIASGRFGVTPEYLVNAKQLEIKIAQGAKPGEGGQL  1000
1001  PGKKVSPYIAELRNCKPGVTLISPPPHHDIYSIEDLAQLIFDLHQINPDA  1050
1051  QVSVKLVASLGIGTIAAGVAKGNADIIQISGHDGGTGASPLSSIKHAGAP  1100
1101  WDVGLAEVHTTLVENSLREKVILRVDGGLRTGKDIIIAALMGAEEFGFGT  1150
1151  VAMIATGCVMARVCHTNNCPVGVATQRQDLRNRFPGIPSDVVNFFIFVAE  1200
1201  EVREILAELGYKSLEELIGLNDLFKVKDIELSKTKNLNLNILFNSINMNR  1250
1251  NLIPKLKHKTVHTNGNVLDDILLSKSNIINAINLQSNIVQDIEILNTDRC  1300
1301  VGARISGLITKMYGRDNFNGNLQLNFVGSAGQSFGAFISKGIHLYLKGEA  1350
1351  NDYVGKGMNGGEIIICPPIEQKTSSSNQVILGNTCLYGATGGYLFANGQA  1400
1401  GERFAVRNSNGYSVVEGVGDHACEYMTGGLIVVLGTFGRNIGAGMTGGIA  1450
1451  YFLDEDNTLKNKLNTEIVKAQRLLTKESEEQLKNIMELYEIKTKSEKAKL  1500
1501  ILDNWSQYLAKFYQIVPPSEQIQHLLMLIFFFSKYC                1536

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.)

Go back to the NucPred Home Page.