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

NucPred

Fetching Q9UPZ3 from www.uniprot.org...

The NucPred score for your sequence is 0.75 (see score help below)

   1  MAFVPVIPESYSHVLAEFESLDPLLSALRLDSSRLKCTSIAVSRKWLALG    50
  51  SSGGGLHLIQKEGWKHRLFLSHREGAISQVACCLHDDDYVAVATSQGLVV   100
 101  VWELNQERRGKPEQMYVSSEHKGRRVTALCWDTAILRVFVGDHAGKVSAI   150
 151  KLNTSKQAKAAAAFVMFPVQTITTVDSCVVQLDYLDGRLLISSLTRSFLC   200
 201  DTEREKFWKIGNKERDGEYGACFFPGRCSGGQQPLIYCARPGSRMWEVNF   250
 251  DGEVISTHQFKKLLSLPPLPVITLRSEPQYDHTAGSSQSLSFPKLLHLSE   300
 301  HCVLTWTERGIYIFIPQNVQVLLWSEVKDIQDVAVCRNELFCLHLNGKVS   350
 351  HLSLISVERCVERLLRRGLWNLAARTCCLFQNSVIASRARKTLTADKLEH   400
 401  LKSQLDHGTYNDLISQLEELILKFEPLDSACSSRRSSISSHESFSILDSG   450
 451  IYRIISSRRGSQSDEDSCSLHSQTLSEDERFKEFTSQQEEDLPDQCCGSH   500
 501  GNEDNVSHAPVMFETDKNETFLPFGIPLPFRSPSPLVSLQAVKESVSSFV   550
 551  RKTTEKIGTLHTSPDLKVRPELRGDEQSCEEDVSSDTCPKEEDTEEEKEV   600
 601  TSPPPEEDRFQELKVATAEAMTKLQDPLVLFESESLRMVLQEWLSHLEKT   650
 651  FAMKDFSGVSDTDNSSMKLNQDVLLVNESKKGILDEDNEKEKRDSLGNEE   700
 701  SVDKTACECVRSPRESLDDLFQICSPCAIASGLRNDLAELTTLCLELNVL   750
 751  NSKIKSTSGHVDHTLQQYSPEILACQFLKKYFFLLNLKRAKESIKLSYSN   800
 801  SPSVWDTFIEGLKEMASSNPVYMEMEKGDLPTRLKLLDDEVPFDSPLLVV   850
 851  YATRLYEKFGESALRSLIKFFPSILPSDIIQLCHHHPAEFLAYLDSLVKS   900
 901  RPEDQRSSFLESLLQPESLRLDWLLLAVSLDAPPSTSTMDDEGYPRPHSH   950
 951  LLSWGYSQLILHLIKLPADFITKEKMTDICRSCGFWPGYLILCLELERRR  1000
1001  EAFTNIVYLNDMSLMEGDNGWIPETVEEWKLLLHLIQSKSTRPAPQESLN  1050
1051  GSLSDGPSPINVENVALLLAKAMGPDRAWSLLQECGLALELSEKFTRTCD  1100
1101  ILRIAEKRQRALIQSMLEKCDRFLWSQQA                       1129

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.)

Go back to the NucPred Home Page.