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

NucPred

Fetching Q6CAD2 from www.uniprot.org...

The NucPred score for your sequence is 0.83 (see score help below)

   1  MVIRGVCDSISRDIASSAVTGKRHTTQMSIFKTIARGHGRFKARSSRQFI    50
  51  VSTVCELLLARHKDRGSQLIVASNLRLVLSHKPHLEHLLWDHYRRSVACL   100
 101  CRELSALCVNSMEESGLEMLIQELLLCLDLLTKPKYVGMAELKHDLWNCI   150
 151  DSMLYKYKEVSEMHVLILSISVSLFQVVFGSDYEICHEMVPSIFAIGTKL   200
 201  FTSKSKAVREISLRFLLKMEIYLASIFGKTCPVPLDQDRLNQIEDHMVEL   250
 251  LQVLKNEYNSSSLQDNDVVFEDEIVLVNSKKTMQFLICKLIAMLEYVLSY   300
 301  TLTDGNVKQEEDLHGPRKKPRVSISPETPTLNAISAQIQAFQASKPISEV   350
 351  DKPLASLLSSISGSLDKTTRWKFFSAAKLLAQSPPLSPKNAHDVVFLTKW   400
 401  WTEGVAKLRTRSEDSACVLLTTILRQHSSALDPKLVVSLASNAESKGPLK   450
 451  YSNVSLEFVTCASQFLISHKACSQSQWSDWLFVVLASEQIGATSSKMMLD   500
 501  TAGLLLASVGCLIRMIETPQNTLETTTSSIMWKTDFKTTSSTSGDIELTE   550
 551  CMPSITIRDLKSGFQNYLNELGDWCESASIDVNVVLPSTVFALVVCAVLD   600
 601  RQGTPVGLNSRISDFLAVVTKRVEGGSCDSHVFFEAITLINRLRHYNLLG   650
 651  DSLCILWDSFINGIEKLLNVSQVTENEFDPDSPSGKNIMPDLRLSLLLRG   700
 701  PLKSEPFLLAIFPSDIKQYASCDPGKRLPELFRYVGQTLLSSYLWDCSPL   750
 751  AKQLVVDLLDVYFKSGMTESSDADDLQRWVSRDKFLVGPQLLYGLMQVST   800
 801  PSEYLNLYSSVAICAAERVSSQDSYHCMDATLTRMSSAKSKSRLVVEEMI   850
 851  VALLSVHRECLSLLPVVIERVKTDMLRQKLDTDSESLVRFCKQTGTDSIL   900
 901  DKILSVKVGSCVFEEEGHFSTQQLLCSEDSLQWNTQGPPLDILSRTWPDY   950
 951  SPCTLLMLVRGLLNLMLKPRVSFEVPLRLVQLKYVLCLFPKRDLCSPDNY  1000
1001  VLQQMVSCLISFLSHSTVGASVRHLLSELFEVIKLPHLEGYIADLGEQSF  1050
1051  FGADVSQLLYLLHPSEPHLCKYIEWVNSGFSDPEAFLSVFLHTEISDKLK  1100
1101  ATLLKSLDFGVTNMTLLGLMDIVCTKETVSFIKRASKLYSFDWEESRVLS  1150
1151  LLLGRGYLLFGESSNSAPKTNTETSFWNALTSEFLTLLRGSDFTAKFAVE  1200
1201  VCLSKIVTKVQVQVPAELQHVFDSGVLEYTHTDEPTTGWVQKTTLELLGL  1250
1251  LGGDFELLIPLVRTLSSTSPLLPFIFKWTCLEYCRQGEPSYLSQILSQNS  1300
1301  SLVVIETFFFVNSFTAHRTLNWQPEIVNSALTLHLYTEALYFLEADKACW  1350
1351  ASQEIQPSYYDIYQNIDDPDLFYGLKFTPCLESALKQLNHENQNLTCFEY  1400
1401  ESGLFDWSVETGGGESKTDILSHLSTSGMNGLAYTINSDDVYRWKLGLLE  1450
1451  DPILETGTDDQTVLSQLRSIVVDEKPVLKSTLSDKYLGMQYLLYQMQLDA  1500
1501  NSDYLDRIQPPDGVLDILQFCASAWRTIKTETASYNGILTLSKLGAVSRE  1550
1551  LNNAQISKNCAVSLQELSRTASHISGNVCAISIASCLWSEAAVSRTTPVE  1600
1601  MLKRMLGSINPGQSPVLASQFCQATVLLTDWSSQARMMSPEKIHRLYIAG  1650
1651  ASEYMALIPAGNPKTRMFHVFAKFCETQLHSQNYDEQIHNAVMDIERLEG  1700
1701  ELANLSRISMTREIKHAQRISRKSLDRAKESKLNYERLKAMFLDSAVQFY  1750
1751  LLSCAVRDSEYHEDVTRLISLWFGNSHVNFVNERMQDYALIPSFKLAPLI  1800
1801  NQLSSKLSYEPNNYFQTLLLDLVSATCKAHPFHCLYQISSLMRTDASPQT  1850
1851  ERRIQAAVKVWNTVKTQEKTICRAMEIFTDKCVELANAEWPGKGQKASIN  1900
1901  QFPNGSWWQNGLRKLNIPPPTAQIPLSLDYTDIPSMNKVLAQVIKAGGIS  1950
1951  HPKIMDFQLSDGSVSKALLKGGKDDMRQDAIMEQVFCRVNQYFLGDPETR  2000
2001  KRGLSIRTYNVVPMGPRAGMIEFVANTESLQAALVPLHEKDDWDYLTGRT  2050
2051  KMSAVAKESNSRRVEVLEEIYTHVTPVMSQYFFQNFRSSAQAWFKARTNY  2100
2101  VRSAAASSMLGYILGIGDRHCNNIMIDYKTGQLVHIDLGISFDQGKNLTV  2150
2151  PEKVPFRLTRDMVDAMGSVGVDGPFRRCCELSLGLFREQQDNILSILNVL  2200
2201  RYDPLYSWTMSPKKKQTRSSSGSDLSDIKLEESNVTADMCLSGVKGKLAV  2250
2251  RLSTEAVVRELIGEAVSVENLAVIFHGWTPFY                    2282

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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