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

NucPred

Fetching Q28749 from www.uniprot.org...

The NucPred score for your sequence is 0.35 (see score help below)

   1  GCYDNGKHYQINQQWERTYLGNALVCTCYGGSRGFNCESKPEPEETCFDK    50
  51  YTGNTYRVGDTYERPKDSMIWDCTCIGAGRGRISCTIANRCHEGGQSYKI   100
 101  GDTWRRPHETGGYMLECVCLGNGKGEWTCKPIAEKCFDHAAGTSYVVGET   150
 151  WEKPYQGWMMVDCTCLGEGSGRITCTSRNRCNDQDTRTSYRIGDTWSKKD   200
 201  NRGNLLQCICTGNGRGEWKCERHASLQTTSTGSGPFSDVRAAVYQPQPHP   250
 251  QPAPYGHCVTDSGVVYSEGMQWLKTQGNKQMLCTCLGNGVSCQETAVTQT   300
 301  YGGNSNGEPCVLPFTYNGRTFYSCTTEGRQDGHLWCSTTSNYEQDQKYSF   350
 351  CTDHTVLVQTRGGNSNGALCHFPFLYNNHNYTDCTSEGRRDNMKWCGTTQ   400
 401  NYDADQKFGFCPMAAHEEICTTNEGVMYRIGDQWDKQHDMGHMMRCTCVG   450
 451  NGRGEWTCVAYSQLRDQCIVDDITYNVNDTFHKRHEEGHMLNCTCFGQGR   500
 501  GRWKCDPVDQCQDSETRTFYQIGDSWEKYVHGVRYQCYCYGRGIGEWHCQ   550
 551  PLQTYPGTSGPVQVIITETPSQPNSHPIQWNAPEPSHISKYILRWRPKNS   600
 601  VGRWKEATIPGHLNSYTIKGLRPGVMYEGQLISIQQYGHREVTRFDFTTT   650
 651  STSTPVTSNTVTGETTPLSPVVATSESVTEITASSFVVSWVSASDTVSGF   700
 701  LVEYELSEEGDEPKYLDLPSTVTSVNIPDLLPGRKYIVNVYQISEEGKQS   750
 751  LILSTSQTTAPDAPPDPTVDQVDDTSIVVRWSRPQAPITGYRVVYSPSVE   800
 801  GSSTELNLPETANSVTLSDLQPGVQYNITIYAVEENQESAPVFIQQETTG   850
 851  VPRSDEVPPPKDLQFVEVTDVKVTIMWTPPDSAVTGYRVDVLPVHLPGEN   900
 901  GQRLPVSRNTFAEITGLSPGVTYYFKVFAVNHGRESRPLTAQQATKLDAP   950
 951  TNLQFVNETDSSVLVIWTPPRARITGYQLTIGPTRGGQPKQHNVGPTVSK  1000
1001  YLLRNLQPGSEYTVTLIAVKGNNQSPKVTGVFTTLQPQSSIPPYSTEVTE  1050
1051  TSIVITWTPAPRIGFKLGVRPSQGGEAPREVTSESGSIVVSGLTPGVEYV  1100
1101  YSIQVLRDGKERDAPIVNTVVTPLSPPTNLHLEANPDTGVLTVSWEKSTT  1150
1151  PDITGYRITTTPTNGQQGYSLEEVVHADQNSCIFENLSPGLEYNVSVYTV  1200
1201  KDDKESVPVSDTIIPEVPQLTDLSFVDITDSSIGLRWTPLNSSTIIGYRI  1250
1251  TVVAAGEGIPIFEDFVDSSVGYYTVTGLEPGIDYDISVITLINGGESAPT  1300
1301  TLTQQTAVPSPTDLRFTNIGPDTMRVTWAPPPSIELTNFLVRYSPVKNEE  1350
1351  DVAELSISPSDNAVVLTNLLPGTEYLVSVSSVYEQHESTPVRGRQKTGLD  1400
1401  APTGIDFSDVTPNSFTVYWTPPRAPITGFWIRHHPEHGVGRPREDRVPPS  1450
1451  RNSITLTNLNPGTEYVVSIVALNGREQSPPLIGQQSTVSDVPRDLEVIAS  1500
1501  TPTSLLISWEAPAVTVRYYRITYGETGGNSPVQEFTVPGSKSTATISGLK  1550
1551  PGADYTITVYAVTGRGDSPASSKPISIDYHTEIDKPSQMQVTDVQDNSIS  1600
1601  VRWLPSSSPVTGYRVTTTPKNGAGPTKTKTAGPDQTEMTIEGLQPTVEYV  1650
1651  VSVYAQNRNGESQPLVQTAVTNIDRPKGLAFTDVDVDSIKIAWESPQGQV  1700
1701  SRYRVTYSSPEDGIHELFPAPDGEEDTAELQGLRPGSEYTVSVVALHDDM  1750
1751  ESQPLIGTQSTAIPAPTNLKFTQVTPTSLSAQWTPPNVQLTGYRVRVTPK  1800
1801  EKTGPMKEINLAPDSSSVVVSGLMVATKYEVSVYALKDTLTSRPVQGVIT  1850
1851  TLENVSPPRRARVTDATETTITISWRTKTETITGFRVDAIPANGQNPIQR  1900
1901  IIKPDVRSYTITGLQPGTDYKIHLYTLNDNAQSSPVIIDASTAIDAPSNL  1950
1951  HFLATTPNSLLVSWQPPRAKITGYIIKFEKPGSPPREVVPRPRPGVTEAT  2000
2001  ITGLEPGTEYTIYIIALKNNQKSDPLIGRKKTDELPQLVTLPHPNLHGPE  2050
2051  ILDVPSTVQKTPFITNPGYDTGNGIQLPGTSGQQPSVGQQMIFEEHGFRR  2100
2101  TTPPTTATPVKLRPRPYLPNVDEDIQIGHVPRGDVDYHLYPHVLGLNPNA  2150
2151  STGQEALSQTTISWTPFQESSEYIISCHPVGTDEQPLQFRVPGTSTSATL  2200
2201  TGLTRGATYNIIVEALKDQRRHKVREEVVTVGNSVNEGLNQPTDDSCFDP  2250
2251  YTVTHYAVGEEWERLSESGFKLSCQCLGFGSGHFKCDSSKWCHDNGVNYK  2300
2301  IGEKWDRQGENGQMMSCTCLGNGKGEFKCDPHEATCYDDGKTYHVGEQWQ  2350
2351  KEYLGAICSCTCFGGQRGWRCDNCRRPGVEPSPDSSTGHSYNQYTQRYHQ  2400
2401  RTNTNVNCPIECFMPLDVQADREDSRE                         2427

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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