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

NucPred

Fetching Q811D2 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MKKIFGFRSKGPSPLGPSARPRSNCVGFGRESASGSHVPRYHIHDKDMGK    50
  51  IHKAASVGDVAKVQHILILGKSGVNDRDKKDRTALHLACAYGHPEVVTLL   100
 101  VERKCEIDARDSESSTALIKAVQCQEEECAAILLDHGADPNVMDSSGNTA   150
 151  LHYAVYSENTSMAAKLLAHNANIEAKNKDDLTPMLLAVKENKQHIVEFLV   200
 201  KKKASIHAVDQLGSNRQMFEYDGKRLQRSENSNPVDNGSEDGSLTRSYNT   250
 251  PGPADSWPTSDEEDYNFDNKNVPKINLTELWTAAQQSRKNQTKCGFEELD   300
 301  NGARFDDSDSPSESEDAIEVEPAPSVRVQTLSPSRQSPDPVEGATELAIE   350
 351  GEENGTDVIESASQEQPNHDNLTRADGWHKSNKSEMMSALGLGEDEDEDS   400
 401  PWDSESISESVSLKDVGHFSGTADQTGKRRAHGQIEDVTYIPSCMSGSRN   450
 451  FKMAKLEESRNVGLPVAHMEAPRKYVIMEPTIERRAPVLNKTETVGMTDA   500
 501  QTFKSEPESVSREEQTRLSGSEDSQQKVEEKRKYKNNEAEPSGNLYSGAA   550
 551  DGGADVKPQSGDTENQQSPREGSEGRGSGPALLMKEAKKMENEKWVSREP   600
 601  ARTAMSERTGLPTGGWPQMQDGSCWSDTDQSEARPTKKTSSKHNKDSGQT   650
 651  AAVDNLDDFTESSETASEDHELQGPDSESILCAIEHLRLECKDTASLLKI   700
 701  RDAVYSYKRLIELKRSHCELLTGKLKRMENKYKGLQKEMSETEEVKSRLE   750
 751  HEKVGWEQELCRLRFALKQEEEKRRSADQLSEKTMEQLRRKGEQCQSEVE   800
 801  ARQQLEASLRTLEMELKTVKSHLNQVLEERNETQRQLSREQNARMLQDGI   850
 851  LASHLCKQKEIEMTQKKMTSEVSVSHEKEKDLLHKNQRLQDEVAVLRLEM   900
 901  DTIKSHNQEKEKRYLEDIKIANEKNDNLQRMVKLNMLSSKLDNEKQNKER   950
 951  LETDVESFRSRLASALHDHAEIQTAKRDLEIAFQRARDEWFRVKDKMNFD  1000
1001  MSNLRDNNEVLSQQLSKTERKLNSLEIEFHHTKDELREKTLALKHAQRDL  1050
1051  SQTQCQMKEVEHMFQDEQGKVSKFMGKQESIEERLAQLQSENTLLRQQLD  1100
1101  DAANKAESKDKTIVNIQDQFQDVLTRFQAESQRHSLRLEDRNQELVSECS  1150
1151  HLRERLCQYENEKAEREVVVRQLQQELADTLKKQSMSEASLEVSSRYRSN  1200
1201  LEEEARDLKKKLGQLRSQLQEARDQHREAVHHAEKMEDHLQKLELEKSKF  1250
1251  EITIKKQSEEIDQLQENLSRVNLSEEDKEKLQKLTELKESLECTVDQEQK  1300
1301  RSSALEKELMRTIQKKCGKLEKNKKQLEQEVVNLRSHMEKNMVEHSQAQQ  1350
1351  YAREVEERARQDLVEKLKQVNLFLQAQAASQESLEQLRENSNASVRSQME  1400
1401  LRIKDLESQLYRMKAQEDFDKIELEKYKQLYQEEFRARKSLSSKLNKTSE  1450
1451  KLEEASSKLLLEEQQNRSLLSTLSTRPVVECPCVGSLHNSLVFNRTLIPR  1500
1501  ENIVVPTSGLQPSNKRVEIYLTKMHQELEKSINRELKEATAELESEFCRV  1550
1551  SPLGSATKASQDQLSDASQEFIDILKKKYMI                     1581

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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