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

NucPred

Fetching P08104 from www.uniprot.org...

The NucPred score for your sequence is 0.53 (see score help below)

   1  MAQALLVPPGPESFRLFTRESLAAIEKRAAEEKAKKPKKEQDIDDENKPK    50
  51  PNSDLEAGKNLPFIYGDIPPEMVSEPLEDLDPYYVSKKTFVVLNKGKAIF   100
 101  RFSATSALYILTPLNPVRKIAIKILVHSLFSMLIMCTILTNCVFMTLSNP   150
 151  PDWTKNVEYTFTGIYTFESLIKILARGFCLEDFTFLRDPWNWLDFSVIVM   200
 201  AYVTEFVDLGNVSALRTFRVLRALKTISVIPGLKTIVGALIQSVKKLSDV   250
 251  MILTVFCLSVFALIGLQLFMGNLRNKCSQWPPSDSAFETNTTSYFNGTMD   300
 301  SNGTFVNVTMSTFNWKDYIADDSHFYVLDGQKDPLLCGNGSDAGQCPEGY   350
 351  ICVKAGRNPNYGYTSFDTFSWAFLSLFRLMTQDYWENLYQLTLRAAGKTY   400
 401  MIFFVLVIFLGSFYLVNLILAVVAMAYEEQNQATLEEAEQKEAEFQQMLE   450
 451  QLKKQQEEAQAVAAASAASRDFSGIGGLGELLESSSEASKLSSKSAKEWR   500
 501  NRRKKRRQREHLEGNHRADGDRFPKSESEDSVKRRSFLLSLDGNPLTGDK   550
 551  KLCSPHQSLLSIRGSLFSPRRNSKTSIFSFRGRAKDVGSENDFADDEHST   600
 601  FEDSESRRDSLFVPHRPGERRNSNGTTTETEVRKRRLSSYQISMEMLEDS   650
 651  SGRQRSMSIASILTNTMEELEESRQKCPPCWYRFANVFLIWDCCDAWLKV   700
 701  KHLVNLIVMDPFVDLAITICIVLNTLFMAMEHYPMTQQFSSVLTVGNLVF   750
 751  TGIFTAEMVLKIIAMDPYYYFQEGWNIFDGIIVSLSLMELGLANVEGLSV   800
 801  LRSFRLLRVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVV   850
 851  GMQLFGKSYKECVCKINVDCKLPRWHMNDFFHSFLIVFRVLCGEWIETMW   900
 901  DCMEVAGQTMCLIVFMLVMVIGNLVVLNLFLALLLSSFSSDNLAATDDDN   950
 951  EMNNLQIAVGRMQKGIDFVKNKIRECFRKAFFRKPKVIEIQEGNKIDSCM  1000
1001  SNNTGIEISKELNYLKDGNGTTSGVGTGSSVEKYVIDENDYMSFINNPSL  1050
1051  TVTVPIAVGESDFENLNTEEFSSESELEESKEKLNATSSSEGSTVDVAPP  1100
1101  REGEQAEIEPEEDLKPEACFTEGCIKKFPFCQVSTEEGKGKIWWNLRKTC  1150
1151  YSIVEHNWFETFIVFMILLSSGALAFEDIYIEQRKTIKTMLEYADKVFTY  1200
1201  IFILEMLLKWVAYGFQTYFTNAWCWLDFLIVDVSLVSLVANALGYSELGA  1250
1251  IKSLRTLRALRPLRALSRFEGMRVVVNALVGAIPSIMNVLLVCLIFWLIF  1300
1301  SIMGVNLFAGKFYHCVNTTTGNMFEIKEVNNFSDCQALGKQARWKNVKVN  1350
1351  FDNVGAGYLALLQVATFKGWMDIMYAAVDSRDVKLQPIYEENLYMYLYFV  1400
1401  IFIIFGSFFTLNLFIGVIIDNFNQQKKKFGGQDIFMTEEQKKYYNAMKKL  1450
1451  GSKKPQKPIPRPANKFQGMVFDFVTRQVFDISIMILICLNMVTMMVETDD  1500
1501  QSKYMTLVLSRINLVFIVLFTGEFLLKLISLRYYYFTIGWNIFDFVVVIL  1550
1551  SIVGMFLAELIEKYFVSPTLFRVIRLARIGRILRLIKGAKGIRTLLFALM  1600
1601  MSLPALFNIGLLLFLVMFIYAIFGMSNFAYVKKEAGIDDMFNFETFGNSM  1650
1651  ICLFQITTSAGWDGLLAPILNSAPPDCDPDAIHPGSSVKGDCGNPSVGIF  1700
1701  FFVSYIIISFLVVVNMYIAVILENFSVATEESAEPLSEDDFEMFYEVWEK  1750
1751  FDPDATQFIEFCKLSDFAAALDPPLLIAKPNKVQLIAMDLPMVSGDRIHC  1800
1801  LDILFAFTKRVLGESGEMDALRIQMEDRFMASNPSKVSYEPITTTLKRKQ  1850
1851  EEVSAAIIQRNYRCYLLKQRLKNISSKYDKETIKGRIDLPIKGDMVIDKL  1900
1901  NGNSTPEKTDGSSSTTSPPSYDSVTKPDKEKFEKDKPEKEIKGKEVRENQ  1950
1951  K                                                   1951

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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