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

NucPred

Fetching P11276 from www.uniprot.org...

The NucPred score for your sequence is 0.40 (see score help below)

   1  MLRGPGPGRLLLLAVLCLGTSVRCTEAGKSKRQAQQIVQPQSPVAVSQSK    50
  51  PGCFDNGKHYQINQQWERTYLGNALVCTCYGGSRGFNCESKPEPEETCFD   100
 101  KYTGNTYKVGDTYERPKDSMIWDCTCIGAGRGRISCTIANRCHEGGQSYK   150
 151  IGDKWRRPHETGGYMLECLCLGNGKGEWTCKPIAEKCFDHAAGTSYVVGE   200
 201  TWEKPYQGWMMVDCTCLGEGNGRITCTSRNRCNDQDTRTSYRIGDTWSKK   250
 251  DNRGNLLQCVCTGNGRGEWKCERHALQSASAGSGSFTDVRTAIYQPQTHP   300
 301  QPAPYGHCVTDSGVVYSVGMQWLKSQGNKQMLCTCLGNGVSCQETAVTQT   350
 351  YGGNSNGEPCVLPFTYNGRTFYSCTTEGRQDGHLWCSTTSNYEQDQKYSF   400
 401  CTDHAVLVQTRGGNSNGALCHFPFLYNNRNYTDCTSEGRRDNMKWCGTTQ   450
 451  NYDADQKFGFCPMAAHEEICTTNEGVMYRIGDQWDKQHDLGHMMRCTCVG   500
 501  NGRGEWACIPYSQLRDQCIVDDITYNVNDTFHKRHEEGHMLNCTCFGQGR   550
 551  GRWKCDPIDQCQDSETRTFYQIGDSWEKFVHGVRYQCYCYGRGIGEWHCQ   600
 601  PLQTYPGTTGPVQVIITETPSQPNSHPIQWNAPEPSHITKYILRWRPKTS   650
 651  TGRWKEATIPGHLNSYTIKGLTPGVIYEGQLISIQQYGHREVTRFDFTTS   700
 701  ASTPVTSNTVTGETAPYSPVVATSESVTEITASSFVVSWVSASDTVSGFR   750
 751  VEYELSEEGDEPQYLDLPSTATSVNIPDLLPGRKYIVNVYQISEEGKQSL   800
 801  ILSTSQTTAPDAPPDPTVDQVDDTSIVVRWSRPQAPITGYRIVYSPSVEG   850
 851  SSTELNLPETANSVTLSDLQPGVQYNITIYAVEENQESTPVFIQQETTGT   900
 901  PRSDNVPPPTDLQFVELTDVKVTIMWTPPDSVVSGYRVEVLPVSLPGEHG   950
 951  QRLPVNRNTFAEITGLSPGVTYLFKVFAVHQGRESNPLTAQQTTKLDAPT  1000
1001  NLQFVNETDRTVLVTWTPPRARIAGYRLTAGLTRGGQPKQYNVGPLASKY  1050
1051  PLRNLQPGSEYTVTLVAVKGNQQSPKATGVFTTLQPLRSIPPYNTEVTET  1100
1101  TIVITWTPAPRIGFKLGVRPSQGGEAPREVTSDSGSIVVSGLTPGVEYTY  1150
1151  TIQVLRDGQERDAPIVNRVVTPLSPPTNLHLEANPDTGVLTVSWERSTTP  1200
1201  DITGYRITTTPTNGQQGTSLEEVVHADQSSCTFENLNPGLEYNVSVYTVK  1250
1251  DDKESAPISDTVVPEVPQLTDLSFVDITDSSIGLRWTPLNSSTIIGYRIT  1300
1301  VVAAGEGIPIFEDFVDSSVGYYTVTGLEPGIDYDISVITLINGGESAPTT  1350
1351  LTQQTAVPPPTDLRFTNIGPDTMRVTWAPPPSIELTNLLVRYSPVKNEED  1400
1401  VAELSISPSDNAVVLTNLLPGTEYLVSVSSVYEQHESIPLRGRQKTGLDS  1450
1451  PTGFDSSDITANSFTVHWVAPRAPITGYIIRHHAEHSVGRPRQDRVPPSR  1500
1501  NSITLTNLNPGTEYVVSIIAVNGREESPPLIGQQATVSDIPRDLEVIAST  1550
1551  PTSLLISWEPPAVSVRYYRITYGETGGNSPVQEFTVPGSKSTATINNIKP  1600
1601  GADYTITLYAVTGRGDSPASSKPVSINYKTEIDKPSQMQVTDVQDNSISV  1650
1651  RWLPSTSPVTGYRVTTTPKNGLGPSKTKTASPDQTEMTIEGLQPTVEYVV  1700
1701  SVYAQNRNGESQPLVQTAVTNIDRPKGLAFTDVDVDSIKIAWESPQGQVS  1750
1751  RYRVTYSSPEDGIRELFPAPDGEDDTAELQGLRPGSEYTVSVVALHDDME  1800
1801  SQPLIGIQSTAIPAPTNLKFSQVTPTSFTAQWIAPSVQLTGYRVRVNPKE  1850
1851  KTGPMKEINLSPDSSSVIVSGLMVATKYEVSVYALKDTLTSRPAQGVITT  1900
1901  LENVSPPRRARVTDATETTITISWRTKTETITGFQVDAIPANGQTPVQRS  1950
1951  ISPDVRSYTITGLQPGTDYKIHLYTLNDNARSSPVIIDASTAIDAPSNLR  2000
2001  FLTTTPNSLLVSWQAPRARITGYIIKYEKPGSPPREVVPRPRPGVTEATI  2050
2051  TGLEPGTEYTIYVIALKNNQKSEPLIGRKKTDELPQLVTLPHPNLHGPEI  2100
2101  LDVPSTVQKTPFITNPGYDTENGIQLPGTTHQQPSVGQQMIFEEHGFRRT  2150
2151  TPPTAATPVRLRPRPYLPNVDEEVQIGHVPRGDVDYHLYPHVPGLNPNAS  2200
2201  TGQEALSQTTISWTPFQESSEYIISCQPVGTDEEPLQFQVPGTSTSATLT  2250
2251  GLTRGVTYNIIVEALQNQRRHKVREEVVTVGNAVSEGLNQPTDDSCFDPY  2300
2301  TVSHYAIGEEWERLSDAGFKLTCQCLGFGSGHFRCDSSKWCHDNGVNYKI  2350
2351  GEKWDRQGENGQRMSCTCLGNGKGEFKCDPHEATCYDDGKTYHVGEQWQK  2400
2401  EYLGAICSCTCFGGQRGWRCDNCRRPGAAEPSPDGTTGHTYNQYTQRYNQ  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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