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

NucPred

Fetching P60330 from www.uniprot.org...

The NucPred score for your sequence is 0.76 (see score help below)

   1  MRNFKGVNFATLLCSKEETQQLLPDLKEFLSRSRTDFPSSRTDAERRQIC    50
  51  DTILRACTQQLTAKLDCPGHLRSILDLAELACDGYLLSTPQRPPLYLERI   100
 101  LFILLRNGSTQGSPDTVLRLAQPLHACLVQNSGEAAPQDYEAVTRGSFSL   150
 151  FWKGAEALLERRAAFSTRLNALSFLVLLEDGSVPCEVPHFASPTACRLVA   200
 201  AYQLYDATGQGLDEADADFLYEVLSRHLIRVLVGEGGSSPGPLSPQRALC   250
 251  LLEITLEHCRRLCWNHHHRQAARAVERARNHLEKTSVAPSLQLCQMGVEL   300
 301  LEAVEERPGAVAQLLRKAAAVLINSIEAPSPPLRALYDSCQFFLSGLERG   350
 351  IRRHCGLDAILSLFAFLGGYSSLVRHLREVSEASSKQQQCLLQMHFQGFH   400
 401  LFTGIVYDFAQGCQATELAQLVDGCRSAAVWMLEALEGLSGGELADYLSM   450
 451  TASYTSNLAYSFFSQKLYEEACVISEPVCQHLGSATSGACPEVPPEKLHR   500
 501  CFRLHVESLKKLGKQAQGCKMVTLWLAALKPYSLEHMVEPVTFWVRVKMD   550
 551  ASRAGDKELQLQTLRDSLSCWDPETQSLLLREELRAYKSVRADTGQERFN   600
 601  IICDLLELSPEETAAGAWARATYLVELAQVLCYHNFTQQTNCSALDAVQE   650
 651  ALQLLESVSPEAQEQDRLLDDKAQALLWLYICTLEAKMQEGIERDRRAQA   700
 701  PSNLEEFEVNDLNYEDKLQEDRFLYSSIAFNLAADAAQSKCLDQALTLWK   750
 751  EVLTKGRAPAVRCLQQTAASLQILAAVYQLVAKPLQALETLLLLQIVSKR   800
 801  LQDHAKAASSSCQLTQLLLNLGCPSYAQLYLEEAESSLRSLDQTSDACQL   850
 851  LSLTCALLGSQLCWACQKVTAGVSLLLSVLRDPALQKSSKAWYLLRVQAL   900
 901  QVLAFYLSLSSNLLSSALREQLWDQGWQTPETALIDAHKLLRSIIILLMG   950
 951  SDVLSIQKAATESPFLDYGENLVQKWQVLTEVLTCSERLVGRLGRLGNVS  1000
1001  EAKAFCLEALKLTTKLQIPRQCALFLVLKGELELARGDIDLCQSDLQQVL  1050
1051  FLLESSTEFGVVTQHPDSVKKVHTQKGKHKAQGPCFPPLSEEEPFLKGPA  1100
1101  LELVDTVLNEPGPIQSSVNSSPVLKTKPPPNPGFLSHLPSCDCLLCASPA  1150
1151  LSAVCLRWVLVTAGVRLATGHKAQGLDLLQAVLTRCPAATKRFTQSLQAS  1200
1201  LNHRTTPSCVPSLFDEIMAQVYTHLALEFLNQTSEKSLGKVLASGLKFVA  1250
1251  TRIQSLEIWRAHLLLVQALAKLAHFSCCTSELFASSWGWHPPLVKSLPVL  1300
1301  EPAKIRRQKCSGRGRRRIASVPPPLHNSSQKGLEEEGPPCTPKPPGRARQ  1350
1351  AGPRVPFTIFEEVHPTKSKLQVPLAPRVHRRAQTRLKVIFSDDSDLEDLV  1400
1401  SADTQLVEEPKRRGTASRTRGQTRKGRSLKTDAVVAIESTPGHSSVSGRT  1450
1451  RRARKVASRNCEEESPKAPLCVWASQGPEIMRSIPEEEPVDNHLEKSFEI  1500
1501  LRGSDGEDSASGEKAAAADTGLPVGECEVLRRDSSKAERPVLYSDTEANS  1550
1551  DPSPWLPPFSVPAPIDLSTLDSISDSLSIAFRGVSHCPPSGLYAHLCRFL  1600
1601  ALCLGHRDPYATAFLVAESISITCRHQLLTHLHRQLSKAQKQQESPELAE  1650
1651  HLQRLDLKERPGGVPLARIQRLFSFKALGSGCFPQAEKESFQERLALIPS  1700
1701  GVTVCVLALATLQPGTLSNTLLLTRLEKDNPPITVKIPTAQNKLPLSAVL  1750
1751  KEFDAIQKDQKENSSCTEKRVWWTGRLALDQRMEALITALEEQVLGCWRG  1800
1801  LLLPCSADPSLAQEASKLQELLRECGWEYPDSTLLKVILSGARILTSQDV  1850
1851  QALACGLCPAQPDRAQVLLSEAVGQVQSQEAPRSQHLVLVLDKDLQKLPW  1900
1901  ESTPILQAQPVTRLPSFRFLLSYTVTKEAGASSVLSQGVDPQNTFYVLNP  1950
1951  HSNLSSTEERFRASFSSETGWKGVIGEVPSLDQVQAALTERDLYIYAGHG  2000
2001  AGARFLDGQAVLRLSCRAVALLFGCSSAALAVHGNLEGAGIVLKYIMAGC  2050
2051  PLFLGNLWDVTDRDIDRYTEALLQGWLGAGPGAPFLYYASQARQAPRLKY  2100
2101  LIGAAPVAYGLPISLQTP                                  2118

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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