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

NucPred

Fetching P12844 from www.uniprot.org...

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

   1  MSGNPDAFENDPGFPFLGISREARAATAARPFDSKKNCWIPDPEDGFVAA    50
  51  EIQSTTGEQVTVVTVKGNQITVKKDQCQEMNPPKFDKTEDMANLTFLNEA   100
 101  SVLGNLKDRYKDLMIYTYSGLFCVVINPYKRLPIYSESVIKHFMGKRRNE   150
 151  MPPHLFAVSDEAYRNMVQDKENQSMLITGESGAGKTENTKKVISYFAIVG   200
 201  ATQAASGKEAKDGKKGGTLEEQIVQTNPVLEAFGNAKTVRNNNSSRFGKF   250
 251  IRTHFSGSGKLAGGDIEHYLLEKSRVVRQAPGERCYHIFYQIMSGNDPSL   300
 301  RGKLKLSNDITYYHFCSQAELTIEGMDDKEEMRLTQEAFDIMGFEDNETM   350
 351  DLYRSTAGIMHMGEMKFKQRPREEQAEPDGEEDALNAAAMLGIQAEEFLK   400
 401  ALTKPRVRVGTEWVNKGQNLEQVNWAVSGLAKAIYARMFKWIITRCNKTL   450
 451  DAKEIERKHFIGVLDIAGFEIFDLNSFEQLWINFVNERLQQFFNHHMFVL   500
 501  EQEEYKREGIAWTFIDFGLDLQACIELIEKPLGIISILDEECIVPKATDM   550
 551  TYAQKLLDQHLGKHPNFQKPKPPKGKQGDAHFAIVHYAGTVRYNATNFLE   600
 601  KNKDPLNDTAVALLKHSTDNSLMLDIWQDYQTQEEAAEAAKAGQTAGGKR   650
 651  GKSSSFATVSMIYRESLNNLMNMLYQTHPHFIRCIIPNEKKASGVIDSAL   700
 701  VLNQLTCNGVLEGIRICRKGFPNRMLYPDFKHRYAILAADAAKESDPKKA   750
 751  SVGILDKISVDGNLTDEEFKVGETKIFFKAGVLAKLEDLRDEILSRIVTM   800
 801  FQSRIRSYLAKAEVRRRYEQQTGLLVVQRNVRAWCTLRTWEWFKLFGKVK   850
 851  PMLKAGKEQEAMGELAVKIQKLEEAVQRGEIARSQLESQVADLVEEKNAL   900
 901  FLSLETEKANLADAEERNEKLNQLKATLESKLSDITGQLEDMQERNEDLA   950
 951  RQKKKTDQELSDTKKHVQDLELSLRKAEQEKQSRDHNIRSLQDEMANQDE  1000
1001  AVAKLNKEKKHQEESNRKLNEDLQSEEDKVNHLEKIRNKLEQQMDELEEN  1050
1051  IDREKRSRGDIEKAKRKVEGDLKVAQENIDEITKQKHDVETTLKRKEEDL  1100
1101  HHTNAKLAENNSIIAKLQRLIKELTARNAELEEELEAERNSRQKSDRSRS  1150
1151  EAERELEELTERLEQQGGATAAQLEANKKREAEIAKLRREKEEDSLNHET  1200
1201  AISSLRKRHGDSVAELTEQLETLQKLKAKSEAEKSKLQRDLEESQHATDS  1250
1251  EVRSRQDLEKALKTIEVQYSELQTKADEQSRQLQDFAALKNRLNNENSDL  1300
1301  NRSLEEMDNQLNSLHRLKSTLQSQLDETRRNYDEESRERQALAATAKNLE  1350
1351  HENTILREHLDEEAESKADLTRQISKLNAEIQQWKARFDSEGLNKLEEIE  1400
1401  AAKKALQLKVQELTDTNEGLFAKIASQEKVRFKLMQDLDDAQSDVEKAAA  1450
1451  QVAFYEKHRRQFESIIAEWKKKTDDLSSELDAAQRDNRQLSTDLFKAKTA  1500
1501  NDELAEYLDSTRRENKSLAQEVKDLTDQLGEGGRSVAELQKIVRKLEVEK  1550
1551  EELQKALDEAEAALEAEEAKVLRAQIEVSQIRSEIEKRIQEKEEEFENTR  1600
1601  RNHQRALESMQATLEAETKQKEEALRIKKKLESDINDLEIALDHANRAYA  1650
1651  DAQKTIKKYMETVQELQFQIEEEQRQKDEIREQFLASEKRNAILQSEKDE  1700
1701  LAQQAEAAERARRNAEAECIELREQNNDLNAHVSALTGQRRKLEGELLAA  1750
1751  HAELEEIANELKNAVEQGQKASADAARLAEELRQEQEHSMHIERIRKGLE  1800
1801  LQIKEMQIRLDDAENAALKGGKKIIAQLEARIRAIEQELDGEQRRHQDTE  1850
1851  KNWRKAERRVKEVEFQVVEEKKNEERLTELVDKLQCKLKIFKRQVEEAEE  1900
1901  VAASNLNKYKVLTAQFEQAEERADIAENALSKMRNKIRASASMAPPDGFP  1950
1951  MVPSASSALIRSSSNARFL                                 1969

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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