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

NucPred

Fetching P08566 from www.uniprot.org...

The NucPred score for your sequence is 0.08 (see score help below)

   1  MVQLAKVPILGNDIIHVGYNIHDHLVETIIKHCPSSTYVICNDTNLSKVP    50
  51  YYQQLVLEFKASLPEGSRLLTYVVKPGETSKSRETKAQLEDYLLVEGCTR   100
 101  DTVMVAIGGGVIGDMIGFVASTFMRGVRVVQVPTSLLAMVDSSIGGKTAI   150
 151  DTPLGKNFIGAFWQPKFVLVDIKWLETLAKREFINGMAEVIKTACIWNAD   200
 201  EFTRLESNASLFLNVVNGAKNVKVTNQLTNEIDEISNTDIEAMLDHTYKL   250
 251  VLESIKVKAEVVSSDERESSLRNLLNFGHSIGHAYEAILTPQALHGECVS   300
 301  IGMVKEAELSRYFGILSPTQVARLSKILVAYGLPVSPDEKWFKELTLHKK   350
 351  TPLDILLKKMSIDKKNEGSKKKVVILESIGKCYGDSAQFVSDEDLRFILT   400
 401  DETLVYPFKDIPADQQKVVIPPGSKSISNRALILAALGEGQCKIKNLLHS   450
 451  DDTKHMLTAVHELKGATISWEDNGETVVVEGHGGSTLSACADPLYLGNAG   500
 501  TASRFLTSLAALVNSTSSQKYIVLTGNARMQQRPIAPLVDSLRANGTKIE   550
 551  YLNNEGSLPIKVYTDSVFKGGRIELAATVSSQYVSSILMCAPYAEEPVTL   600
 601  ALVGGKPISKLYVDMTIKMMEKFGINVETSTTEPYTYYIPKGHYINPSEY   650
 651  VIESDASSATYPLAFAAMTGTTVTVPNIGFESLQGDARFARDVLKPMGCK   700
 701  ITQTATSTTVSGPPVGTLKPLKHVDMEPMTDAFLTACVVAAISHDSDPNS   750
 751  ANTTTIEGIANQRVKECNRILAMATELAKFGVKTTELPDGIQVHGLNSIK   800
 801  DLKVPSDSSGPVGVCTYDDHRVAMSFSLLAGMVNSQNERDEVANPVRILE   850
 851  RHCTGKTWPGWWDVLHSELGAKLDGAEPLECTSKKNSKKSVVIIGMRAAG   900
 901  KTTISKWCASALGYKLVDLDELFEQQHNNQSVKQFVVENGWEKFREEETR   950
 951  IFKEVIQNYGDDGYVFSTGGGIVESAESRKALKDFASSGGYVLHLHRDIE  1000
1001  ETIVFLQSDPSRPAYVEEIREVWNRREGWYKECSNFSFFAPHCSAEAEFQ  1050
1051  ALRRSFSKYIATITGVREIEIPSGRSAFVCLTFDDLTEQTENLTPICYGC  1100
1101  EAVEVRVDHLANYSADFVSKQLSILRKATDSIPIIFTVRTMKQGGNFPDE  1150
1151  EFKTLRELYDIALKNGVEFLDLELTLPTDIQYEVINKRGNTKIIGSHHDF  1200
1201  QGLYSWDDAEWENRFNQALTLDVDVVKFVGTAVNFEDNLRLEHFRDTHKN  1250
1251  KPLIAVNMTSKGSISRVLNNVLTPVTSDLLPNSAAPGQLTVAQINKMYTS  1300
1301  MGGIEPKELFVVGKPIGHSRSPILHNTGYEILGLPHKFDKFETESAQLVK  1350
1351  EKLLDGNKNFGGAAVTIPLKLDIMQYMDELTDAAKVIGAVNTVIPLGNKK  1400
1401  FKGDNTDWLGIRNALINNGVPEYVGHTAGLVIGAGGTSRAALYALHSLGC  1450
1451  KKIFIINRTTSKLKPLIESLPSEFNIIGIESTKSIEEIKEHVGVAVSCVP  1500
1501  ADKPLDDELLSKLERFLVKGAHAAFVPTLLEAAYKPSVTPVMTISQDKYQ  1550
1551  WHVVPGSQMLVHQGVAQFEKWTGFKGPFKAIFDAVTKE              1588

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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