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

NucPred

Fetching Q6NXI6 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MAAGGGGGSSKASSSSASSAGALESSLDRKFQSVTNTMESIQGLSSWCIE    50
  51  NKKHHSTIVYHWMKWLRRSTYPHRLNLFYLANDVIQNCKRKNAIIFRESF   100
 101  ADVLPEAAALVKDPSVSKSIERIFKIWEDRNVYPEDMIVALREALMDRAA   150
 151  SHNARLQKLQCFPGTTFKTQKQLKENLNKQPNKQWKKSQTSTNPKAALKS   200
 201  KIVAEFRSQALIEELLMYKRSEDQIELKEKQLSTMRVDVCSTETLKCLKD   250
 251  KTGGKKFSKEFEEASSKLEEFVNGLDKQVKNGPSLTEALENAGIFYEAQY   300
 301  KEVKVVANAYKTFANRVNNLKKKLDQLKSTLPDPEESPVPSPSMDAPSPT   350
 351  GSESPFQGMGGEEPQSPAMESDKSATPEPVTDNRDVEDMELSDVEDDGSK   400
 401  IIVEDRKEKPVEKPAVSTGVPTKSTESVSKASPCAPPSVPTTAAPPLPKP   450
 451  LSTALLSPSPTLVLPNLANVDLAKISSILSSLTSVMKNTGVSSASRPSPG   500
 501  IPTSPSNLSSGLKTPAPATTPSHNPLANILSKVEITPESILSALSKTQTQ   550
 551  SAPALQGLSSLLQSVTANPVPASEVTSQSTTASPASTTGSAVKGRNLLSS   600
 601  TQSFIPKSFNYSPSSSTSEVSSTSASKASVGQSPVLPSTTFKLPSSSLGF   650
 651  TGTHNPSPAAPPTEVAVCQSSEVSKPKPESESTSPSLEMKIHNFLKGNPG   700
 701  FSGLNLNIPILSSLGSSAPSEGHASDFQRGPTSTSVDSIDGTPVRDERSG   750
 751  TPTQDEMMDKPTSSSVDTMSLLSKIISPGSSTPSSTRSPPPGRDESYPQE   800
 801  LPNSVSTYRPFGLGSDSPYKQPSGGVERPSSLMDSSQEKLFPDTSFQEDE   850
 851  DYRDFEYSGPPPSAMMNLEKKPAKSILKSSKLSDATEYQPILSSYNHRAQ   900
 901  EFGVKSAFPPSVRALLDSSENCDRLSSPPGLFGAFNIRGNEPGSERSPSP   950
 951  SKNDAFFTPDSNHSGLSQSTAGHLTLPQTQYPDSPHSVPHRSIFSSQSTL  1000
1001  AAPAGHPPTSGVEKVLASTISTTSTIEFKNMLKNASRKPSDDKHFGQTPN  1050
1051  KGTSSDGVSLSNLTQPSLPTTDQQQEEHYRIETRVSSSCLDLPDSTEEKG  1100
1101  APIETLGYHNAANRRMSGEPIKTVESIRVPGKGNRGHGREVSRVGWFDLS  1150
1151  TPGSSFDNGPSSASELASLGGGGSGGLTGFKTTPYKERAPQFQESVTSFR  1200
1201  SNSFNSTFEHHLPPSPLEHGAPFQREPVGPSSAPPAPPKDHGGIFSREAP  1250
1251  THLPSVDLSNPFTKEASLAHAGPPPPPGEHSGVPFPPPPPPPPPGELSSG  1300
1301  GTGVPFATPAPPPPPVDHSGVVPFPTPPLPEHGVTGAVSVFPKDHSSLLQ  1350
1351  GTMAEHFGVLTGPRDLNGPGLNRSRESLSLPSHPLEHLGPALGGGGGGNT  1400
1401  SSSGLPLSPAHRDAIGRSGMILRSPRPDFRPREAFLGRDPFHSLKRPRPP  1450
1451  FVRGPPFFAPKRPFFPPRY                                 1469

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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