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

NucPred

Fetching Q8CEL2 from www.uniprot.org...

The NucPred score for your sequence is 0.23 (see score help below)

   1  MSILTSPRGKVEVVHCRRTESQDIFCIKNLVRKFTQKLFGRLNIIYLLEK    50
  51  ANLAVTVCNDKEEIMAHSIFLDYPNWNVAKQDNWIPLFRELDKEIPCTPL   100
 101  NTLFMHFFVAVDEYATGCLKEIIRTVFKAVPELYFIFLIVPTYLSLGSTL   150
 151  ITVFDQVGNIPCLNYNEDFAVHICHRHNHYPQLHIRKARVEDHDDLMPIF   200
 201  MHYDNTLKEIYGEYFLAELIEAQDKDHHAVVCEVEGKAVGFMSVCTSVNL   250
 251  PLLHECFDLGPFHGFCTPHPDDILKPSREPSLEEGEEKHLKKCSTSLIIR   300
 301  EMQIKTTLRFHLTPVRMAKIKNSETETSASCEEALPTVLGLVSEERLKQD   350
 351  MEKNLSILSLVDEEDVASSLSSSLLLSVESSHFRPLYLGDPIAFCIQLFC   400
 401  IDERYEARQVLISNVSLSLDFMSFVFSLFPGKNFCLISVPHLTPEFVLIQ   450
 451  NFVKVVPFNNCTLDHDLYVFHRAGLLRSITIRLAKFLDTAGVEKLVSTLL   500
 501  LSTKILDDLAQYNEAGRDPDGTALQVFVAEVADQIVGIAVIRKEMDIEYI   550
 551  RSHYNIEDFIYFSHHQQEEHGRLNHFALNPIFRHYTKFFLKEILRLGYKS   600
 601  CLYYPVYPQTREGKLQSSYSHSLTSALHYLVPVRPRRQIVYPLEKLGINA   650
 651  PSKEVSKDQVSFALNHTNRKLTLEPKVTVNARIVVVGASSVGISFLETLV   700
 701  FCSHLKFNNLTLISTHGLPGKRLLHNEQRKFLASDHCFNDKDYALMSLCS   750
 751  WVNVVVGRMTAIDRAAKQVVVSKSEIVFYDHLILCTGLQYQVPCPTGADT   800
 801  EQHLTNREVLELSKQRYTGTVPSNLFILNDEEDCVRMLCWLRNSSILTEG   850
 851  KVIVYGNTLDAYTTVETLLNIGMKGSGIYFVHPPTESNITCINNNDVESA   900
 901  VEDALSAAGVTVFHDALLAQWNHGQHPDPIYNACFTTSTKPIRLECSAFF   950
 951  SFYKKNVDYETFKAFNDACLVYDGRLVIDTTFHTNDIAIRAAGSLTKFSN  1000
1001  RYYSNEWTHSNFSSKEIGFQLAAAMLSLFDPTLEPVTEPPADLDRLIPMY  1050
1051  KGAKIQGGILPGSYHYLHISKPAIPTPLNLQRSQPDFGSDVVTGNAKKGT  1100
1101  YFRLYINNYKLVEAITCFSKEPFPSSNYIRLFGQHEQVLNNLCTRFDDKL  1150
1151  IPDLYSYFTEPWCMALFHDRFIDLKKELRQILISKQEEDKPTMEEIAYRL  1200
1201  EEEEINLNEKPQKYLQRVFEDSIYKSLLEKSILDYLHYNQYHLPMYAWPG  1250
1251  II                                                  1252

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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