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

NucPred

Fetching Q28377 from www.uniprot.org...

The NucPred score for your sequence is 0.53 (see score help below)

   1  MLRGPGPGLLLLVVLSLGTAVPSSGASKRKRQDQQIIQPQSPVAVGQSKP    50
  51  GCYDNGKHYQINQQWERTYLGNALVCTCYGGSRGFNCESKPEPEETCFDK   100
 101  YTGNTYRVGDTYERPKDSMIWDCTCIGAGRGRISCTIANRCHEGGQSYKI   150
 151  GDTWRRPHETGGYMLECVCLGNGKGEWTCKPIAEKCFDHAAGTSYVVGET   200
 201  WEKPYQGWMMVDCTCLGEGNGRITCTSRNRCNDQDTRTSYRIGDTWSKKD   250
 251  NRGNLLQCICTGNGRGEWKCERHASLQTTSTGSGPFTDVRTAIYQPQPHP   300
 301  QPAPYGHCVTDSGVVYSVGMQWLKTQGNKQMLCTCLGNGVSCQETAVTQT   350
 351  YGGNSNGEPCVLPFTYNGRTFYSCTTEGRQDGHLWCSTTSNYEQDQKYSF   400
 401  CTDSAVLVQTRGGNSNGALCHFPFLYNNHNYTDCTSEGRRDNMKWCGTTQ   450
 451  NYDADQKFGFCPMAAHEEICTTNEGVMYRVGDQWDKQHDMGHMMRCTCVG   500
 501  NGRGEWTCVAYSQLRDQCIVDDITYNVNDTFHKRHEEGHMLNCTCFGQGR   550
 551  GRWKCDPIDQCQDSETRTFYQIGDSWEKYVHGVRYQCYCYGRGIGEWHCQ   600
 601  PLQTYPGTTGPVQVIITETPSQPNSHPIQWNAPEPSHISKYILRWKPKNA   650
 651  PGRWKEATIPGHLNSYTIKGLRPGVVYEGQLISVQHYGHKEVTRFDFTTT   700
 701  STSPAVTSNTVTGETTPFSPVVATSESVTEITASSFVVSWVSASDTVSGF   750
 751  RVEYELSEEGDEPQYLDLPSTATSVNIPDLLPGRKYIVNVYQISEEGEQS   800
 801  LILSTSQTTAPDAPPDPTVDQVDDTSIVVRWSRPQAPITGYRIVYSPSVE   850
 851  GSSTELTLPETANSVTLSDLQPGVQYNITIYAVEENQESTPVFIQQETTG   900
 901  VPRADKVPPPRDLQFVEVTDVKITIMWTPPESAVTGYRVDVLPVNLPGEH   950
 951  GQRLPISRNTFAEVTGLSPGVTYHFKIFAVNHGRESKPLTGEQTTKLDAP  1000
1001  TNLRFINETESTVIVTWTPPRARIAGYRLTVGLTRGGQPKQYNVGPSASQ  1050
1051  YPLRSLQPGSEYTVTLVAVKGNQQSPKATGVFTTLQSPGSIPPYNTEVTE  1100
1101  TTIVITWTPAPRIGFKLGVRPSQGGEAPREVTSDSGSIVVSGLTPGVEYV  1150
1151  YTISVLRDGQERDAPIVKKVVTPLSPPTNLHLEANPDTGVLTVSWERSTT  1200
1201  PDITGYRITTTPTSGQQGYSLEEVVHADQSSCTFENLSPGLEYNVSVYTV  1250
1251  KDDKESVPISDTIIPEVPQLTDLSFVDITDSSIGLRWTPLNSSTIIGYRI  1300
1301  TVVAAGEGIPIFEDFVDSSVGYYTVTGLEPGIDYDISVITLINGGESAPT  1350
1351  TLTQQTAVPPPTDLRFTNVGPDTMRVTWAPPPSIELTNLLVRYSPVKNEE  1400
1401  DVAELSISPSDNAVVLTNLLPGTEYLVSVSSVYEQHESTPLRGRQKTGLD  1450
1451  SPTGIDFSDITANSFTVHWIAPRATITGYRIRHHPEHTGGRPREDRVPPS  1500
1501  RNSITLTNLNPGTEYVVSIVALNGREESPPLVGQQSTVSDVPRDLEVIAT  1550
1551  TPTSILISWDAPAVTVRYYRITYGETGGNSPVQEFTVPGSKSTATISGLK  1600
1601  PGVDYTITVYAVTGRGDSPASSKPISIDYRTEIDKPSQMQVTDVQDNSIS  1650
1651  VRWLPSSSPVTGYRVTTTPKNGPGQSKTKTAGPDQTEMTIEGLQPTVEYV  1700
1701  VSVYAQNQNGESQPLVQTAVTNIDRPRGLAFTDVDVDSIKIAWESPQGQV  1750
1751  SRYRVTYSSPEDGIHELFPAPDGEEDTAELQGLRPGSEYTVSVVALHDDM  1800
1801  ESQPLIGTQSTAIPAPTELKFTQVTPTSLTAQWTAPNVQLTGYRVRVTPK  1850
1851  EKTGPMKEINLAPDSTSVVVSGLMVATKYEVSVYALKDTLTSRPAQGIVT  1900
1901  TLENVSPPRRARVTDATETTITISWRTKTETITGFQVDAVPANGQPPIQR  1950
1951  TIKPDVRSYTITGLQPGTDYKIYLYTLNDNARSSPVIIDASTAIDAPSNL  2000
2001  HFLATTPNSLLISWQPPRARITGYIIKYEKPGSPPREVVPRPHPGVTEAT  2050
2051  ITGLEPGTEYTIQVIAIKNNQKSEPLIGRRKTDELPQLVTLPHPNLHGPE  2100
2101  ILDVPSTVQKTPFITNPGYDNGNGIQLPGTSGQQPSVGQQMIFEEHGFRR  2150
2151  TTPPTTATPVRHRPRPYPPNVNEEIQIGHVPRGDVDQHLYPHVLGLNPNT  2200
2201  STGQEALSQTTISWTPFQESSEYIISCHPVGIDEEPLQFRVPGTSASATL  2250
2251  TGLTRGATYNIIVEALKDQKRHKVREEVVTVGNSVDQGLGQPTADSCFDP  2300
2301  YTVSHYAIGEEWERLSESGFKLSCQCLGFGSGHFRCDSSKWCHDNGVNYK  2350
2351  IGEKWDRQGENGQMMSCTCLGNGKGEFKCDPHEATCYDDGKTYHVGEQWQ  2400
2401  KEYLGAICSCTCFGGQRGWRCDNCRRPGAEPGHEGSTGHSYNQYSQRYQQ  2450
2451  RTNTNVNCPIECFMPLDVQADRDDSRE                         2477

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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