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

NucPred

Fetching P08799 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MNPIHDRTSDYHKYLKVKQGDSDLFKLTVSDKRYIWYNPDPKERDSYECG    50
  51  EIVSETSDSFTFKTVDGQDRQVKKDDANQRNPIKFDGVEDMSELSYLNEP   100
 101  AVFHNLRVRYNQDLIYTYSGLFLVAVNPFKRIPIYTQEMVDIFKGRRRNE   150
 151  VAPHIFAISDVAYRSMLDDRQNQSLLITGESGAGKTENTKKVIQYLASVA   200
 201  GRNQANGSGVLEQQILQANPILEAFGNAKTTRNNNSSRFGKFIEIQFNSA   250
 251  GFISGASIQSYLLEKSRVVFQSETERNYHIFYQLLAGATAEEKKALHLAG   300
 301  PESFNYLNQSGCVDIKGVSDSEEFKITRQAMDIVGFSQEEQMSIFKIIAG   350
 351  ILHLGNIKFEKGAGEGAVLKDKTALNAASTVFGVNPSVLEKALMEPRILA   400
 401  GRDLVAQHLNVEKSSSSRDALVKALYGRLFLWLVKKINNVLCQERKAYFI   450
 451  GVLDISGFEIFKVNSFEQLCINYTNEKLQQFFNHHMFKLEQEEYLKEKIN   500
 501  WTFIDFGLDSQATIDLIDGRQPPGILALLDEQSVFPNATDNTLITKLHSH   550
 551  FSKKNAKYEEPRFSKTEFGVTHYAGQVMYEIQDWLEKNKDPLQQDLELCF   600
 601  KDSSDNVVTKLFNDPNIASRAKKGANFITVAAQYKEQLASLMATLETTNP   650
 651  HFVRCIIPNNKQLPAKLEDKVVLDQLRCNGVLEGIRITRKGFPNRIIYAD   700
 701  FVKRYYLLAPNVPRDAEDSQKATDAVLKHLNIDPEQYRFGITKIFFRAGQ   750
 751  LARIEEAREQRISEIIKAIQAATRGWIARKVYKQAREHTVAARIIQQNLR   800
 801  AYIDFKSWPWWKLFSKARPLLKRRNFEKEIKEKEREILELKSNLTDSTTQ   850
 851  KDKLEKSLKDTESNVLDLQRQLKAEKETLKAMYDSKDALEAQKRELEIRV   900
 901  EDMESELDEKKLALENLQNQKRSVEEKVRDLEEELQEEQKLRNTLEKLKK   950
 951  KYEEELEEMKRVNDGQSDTISRLEKIKDELQKEVEELTESFSEESKDKGV  1000
1001  LEKTRVRLQSELDDLTVRLDSETKDKSELLRQKKKLEEELKQVQEALAAE  1050
1051  TAAKLAQEAANKKLQGEYTELNEKFNSEVTARSNVEKSKKTLESQLVAVN  1100
1101  NELDEEKKNRDALEKKKKALDAMLEEMKDQLESTGGEKKSLYDLKVKQES  1150
1151  DMEALRNQISELQSTIAKLEKIKSTLEGEVARLQGELEAEQLAKSNVEKQ  1200
1201  KKKVELDLEDKSAQLAEETAAKQALDKLKKKLEQELSEVQTQLSEANNKN  1250
1251  VNSDSTNKHLETSFNNLKLELEAEQKAKQALEKKRLGLESELKHVNEQLE  1300
1301  EEKKQKESNEKRKVDLEKEVSELKDQIEEEVASKKAVTEAKNKKESELDE  1350
1351  IKRQYADVVSSRDKSVEQLKTLQAKNEELRNTAEEAEGQLDRAERSKKKA  1400
1401  EFDLEEAVKNLEEETAKKVKAEKAMKKAETDYRSTKSELDDAKNVSSEQY  1450
1451  VQIKRLNEELSELRSVLEEADERCNSAIKAKKTAESALESLKDEIDAANN  1500
1501  AKAKAERKSKELEVRVAELEESLEDKSGTVNVEFIRKKDAEIDDLRARLD  1550
1551  RETESRIKSDEDKKNTRKQFADLEAKVEEAQREVVTIDRLKKKLESDIID  1600
1601  LSTQLDTETKSRIKIEKSKKKLEQTLAERRAAEEGSSKAADEEIRKQVWQ  1650
1651  EVDELRAQLDSERAALNASEKKIKSLVAEVDEVKEQLEDEILAKDKLVKA  1700
1701  KRALEVELEEVRDQLEEEEDSRSELEDSKRRLTTEVEDIKKKYDAEVEQN  1750
1751  TKLDEAKKKLTDDVDTLKKQLEDEKKKLNESERAKKRLESENEDFLAKLD  1800
1801  AEVKNRSRAEKDRKKYEKDLKDTKYKLNDEAATKTQTEIGAAKLEDQIDE  1850
1851  LRSKLEQEQAKATQADKSKKTLEGEIDNLRAQIEDEGKIKMRLEKEKRAL  1900
1901  EGELEELRETVEEAEDSKSEAEQSKRLVELELEDARRNLQKEIDAKEIAE  1950
1951  DAKSNLQREIVEAKGRLEEESIARTNSDRSRKRLEAEIDALTAQVDAEQK  2000
2001  AKNQQIKENKKIETELKEYRKKFGESEKTKTKEFLVVEKLETDYKRAKKE  2050
2051  AADEQQQRLTVENDLRKHLSEISLLKDAIDKLQRDHDKTKRELETETASK  2100
2101  IEMQRKMADFFGGFKA                                    2116

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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