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

NucPred

Fetching Q14674 from www.uniprot.org...

The NucPred score for your sequence is 0.85 (see score help below)

   1  MRSFKRVNFGTLLSSQKEAEELLPALKEFLSNPPAGFPSSRSDAERRQAC    50
  51  DAILRACNQQLTAKLACPRHLGSLLELAELACDGYLVSTPQRPPLYLERI   100
 101  LFVLLRNAAAQGSPEATLRLAQPLHACLVQCSREAAPQDYEAVARGSFSL   150
 151  LWKGAEALLERRAAFAARLKALSFLVLLEDESTPCEVPHFASPTACRAVA   200
 201  AHQLFDASGHGLNEADADFLDDLLSRHVIRALVGERGSSSGLLSPQRALC   250
 251  LLELTLEHCRRFCWSRHHDKAISAVEKAHSYLRNTNLAPSLQLCQLGVKL   300
 301  LQVGEEGPQAVAKLLIKASAVLSKSMEAPSPPLRALYESCQFFLSGLERG   350
 351  TKRRYRLDAILSLFAFLGGYCSLLQQLRDDGVYGGSSKQQQSFLQMYFQG   400
 401  LHLYTVVVYDFAQGCQIVDLADLTQLVDSCKSTVVWMLEALEGLSGQELT   450
 451  DHMGMTASYTSNLAYSFYSHKLYAEACAISEPLCQHLGLVKPGTYPEVPP   500
 501  EKLHRCFRLQVESLKKLGKQAQGCKMVILWLAALQPCSPEHMAEPVTFWV   550
 551  RVKMDAARAGDKELQLKTLRDSLSGWDPETLALLLREELQAYKAVRADTG   600
 601  QERFNIICDLLELSPEETPAGAWARATHLVELAQVLCYHDFTQQTNCSAL   650
 651  DAIREALQLLDSVRPEAQARDQLLDDKAQALLWLYICTLEAKMQEGIERD   700
 701  RRAQAPGNLEEFEVNDLNYEDKLQEDRFLYSNIAFNLAADAAQSKCLDQA   750
 751  LALWKELLTKGQAPAVRCLQQTAASLQILAALYQLVAKPMQALEVLLLLR   800
 801  IVSERLKDHSKAAGSSCHITQLLLTLGCPSYAQLHLEEAASSLKHLDQTT   850
 851  DTYLLLSLTCDLLRSQLYWTHQKVTKGVSLLLSVLRDPALQKSSKAWYLL   900
 901  RVQVLQLVAAYLSLPSNNLSHSLWEQLCAQGWQTPEIALIDSHKLLRSII   950
 951  LLLMGSDILSTQKAAVETSFLDYGENLVQKWQVLSEVLSCSEKLVCHLGR  1000
1001  LGSVSEAKAFCLEALKLTTKLQIPRQCALFLVLKGELELARNDIDLCQSD  1050
1051  LQQVLFLLESCTEFGGVTQHLDSVKKVHLQKGKQQAQVPCPPQLPEEELF  1100
1101  LRGPALELVATVAKEPGPIAPSTNSSPVLKTKPQPIPNFLSHSPTCDCSL  1150
1151  CASPVLTAVCLRWVLVTAGVRLAMGHQAQGLDLLQVVLKGCPEAAERLTQ  1200
1201  ALQASLNHKTPPSLVPSLLDEILAQAYTLLALEGLNQPSNESLQKVLQSG  1250
1251  LKFVAARIPHLEPWRASLLLIWALTKLGGLSCCTTQLFASSWGWQPPLIK  1300
1301  SVPGSEPSKTQGQKRSGRGRQKLASAPLRLNNTSQKGLEGRGLPCTPKPP  1350
1351  DRIRQAGPHVPFTVFEEVCPTESKPEVPQAPRVQQRVQTRLKVNFSDDSD  1400
1401  LEDPVSAEAWLAEEPKRRGTASRGRGRARKGLSLKTDAVVAPGSAPGNPG  1450
1451  LNGRSRRAKKVASRHCEERRPQRASDQARPGPEIMRTIPEEELTDNWRKM  1500
1501  SFEILRGSDGEDSASGGKTPAPGPEAASGEWELLRLDSSKKKLPSPCPDK  1550
1551  ESDKDLGPRLRLPSAPVATGLSTLDSICDSLSVAFRGISHCPPSGLYAHL  1600
1601  CRFLALCLGHRDPYATAFLVTESVSITCRHQLLTHLHRQLSKAQKHRGSL  1650
1651  EIADQLQGLSLQEMPGDVPLARIQRLFSFRALESGHFPQPEKESFQERLA  1700
1701  LIPSGVTVCVLALATLQPGTVGNTLLLTRLEKDSPPVSVQIPTGQNKLHL  1750
1751  RSVLNEFDAIQKAQKENSSCTDKREWWTGRLALDHRMEVLIASLEKSVLG  1800
1801  CWKGLLLPSSEEPGPAQEASRLQELLQDCGWKYPDRTLLKIMLSGAGALT  1850
1851  PQDIQALAYGLCPTQPERAQELLNEAVGRLQGLTVPSNSHLVLVLDKDLQ  1900
1901  KLPWESMPSLQALPVTRLPSFRFLLSYSIIKEYGASPVLSQGVDPRSTFY  1950
1951  VLNPHNNLSSTEEQFRANFSSEAGWRGVVGEVPRPEQVQEALTKHDLYIY  2000
2001  AGHGAGARFLDGQAVLRLSCRAVALLFGCSSAALAVRGNLEGAGIVLKYI  2050
2051  MAGCPLFLGNLWDVTDRDIDRYTEALLQGWLGAGPGAPLLYYVNQARQAP  2100
2101  RLKYLIGAAPIAYGLPVSLR                                2120

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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