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

NucPred

Fetching Q4WAS9 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MQDGSLNGLSHHNDERVNHENEDKSLNTSALGDSPDSANRELIPSESKEN    50
  51  GVPTDSIEGPPSKRRKLAGPDNSRRSTPRPPSPPWKKAGVDGPTSFLQDG   100
 101  KRRSSRVNAIPLELQPPSDKRKTRAAQRSTVNKNLSGNGKVVASSPLSMS   150
 151  VSQSGINGKHTGGNLTTGSPRTATPRGASARRRRISRSPPRQTPSRTRSQ   200
 201  SSATSAPNDPTSHNARSKRSHSNVTSTPTIGIDELWNDIGGETDLGDEQG   250
 251  QRVPRLRIKVKKPVIGFQHPSHVIPPRKYNSFREWLESGEGRIEDGAVLT   300
 301  PEAALVEARKRCRVLEATEPGGLLSPEVCSAYLPEQQEEPPQQYSHQDHL   350
 351  VAHALYFKKLLDQEHRRHRNTARLLAQWCADAWRKRNKRPEDILREQQEE   400
 401  VRVKRKQLARDLQKMFDLARAEVDRMRLARWEEERKVEDQRALDRAIKQS   450
 451  TMLFEKRRLEILGETGSDFLDSTDAEESGTDATTSDAEEDESNMSSTDSE   500
 501  TEDEDEVDDDEGLTAEELRQKYADLPQSSLVSDRESVASDTSESSDGTRT   550
 551  SHILQNIEDINDSQGETPLEQIELDEVDPMLLDDSEDESTDMDDDMGDSD   600
 601  EDGDADGTDSDDESDDGPGLLGFFSSKDRVLNDAHRFDDEGDDPLAVSNH   650
 651  EGGSGFDDDGQSVSVDEDGDEELEDADEVSLVPNGPSNSVSISQSTAEVS   700
 701  PVTETPDEEPDEQAEVVDTDMAAAAPSEGPAPLEASAPLEDLVAIDKRGD   750
 751  AMGECHRQQCSPLVNNLDEQELRQNGGASSEASPGTLATKPSEPESISSF   800
 801  EAPGEKPPQPSESPAPGLKTPIPHLLRGTLREYQHYGLDWLAGLYNNHIN   850
 851  GILADEMGLGKTIQTIALLAHLAVEHEVWGPHLVVVPTSVILNWEMEFKK   900
 901  WCPGFKIMTYYGSIEERRQKRKGWTDDTSWNVLITSYQLVLQDQQVLKRR   950
 951  NWHYMVLDEAHNIKNFRSQKWQTLLTFRTRARLLLTGTPLQNNLTELWSL  1000
1001  LFFLMPSDGDGTGIEGFADLRNFSEWFRRPVEQILEHGRETMDDETKRVV  1050
1051  TKLHTILRPYILRRLKADVEKQMPAKYEHVVYCRLSKRQRFLYDGFMSMA  1100
1101  QTKETLASGNYLSIINCLMQLRKVCNHPDLFETRQISTSFVMHHSVATEY  1150
1151  ASKEQLVRRRLLYEHPLTKLDLDFLNLVPISREDISRRLADDSTRLMAYG  1200
1201  PFNILRERQYKRTNWQMMFDGSTVQSTLEALENDARKRRMAELERCLYFE  1250
1251  SKRHGRRPVYGTSLVEFLTADSKQKPTLGGRPQTQSLAEWLSNRSSILAS  1300
1301  MILSIEERSQAMDGYVRRFACVTPAAVASGITEAALTPIETRYLTEKERF  1350
1351  PPYDPFHEAQMRLSIAFPDKRLLQYDCGKLQRLDKLLRDLKAGGHRALIF  1400
1401  TQMTKMLDILEQFLNIHGHRYLRLDGTTKVEQRQILTDRFNNDDRILVFI  1450
1451  LSSRSGGLGINLTGADTVIFYDLDWNPAMDKQCQDRCHRIGQTRDVHIYR  1500
1501  FVSEHTIESNILRKANQKRMLDDVVIQEGEFTTDYFTKLDVRDMIGEEAE  1550
1551  AQDEASAAMDRVLSSRVATGGSRVFEQAEDKEDIDAAKNAQKEMEQADND  1600
1601  DFGDRSISHTPGQVGTPLATGPQEGETPGAQLITTPQIHGVDETVDVEPQ  1650
1651  PGHIDDYLLRFMEWNMKDEPLVLPPDKTKKKSKKGKEHRLSKRRR       1695

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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