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

NucPred

Fetching Q95V25 from www.uniprot.org...

The NucPred score for your sequence is 0.38 (see score help below)

   1  MGEIYSPSQSKGFNQPYGYPMNCNLSRVFMEMTEEDRKCLEERKYWCFLL    50
  51  SSITTFCASMILVVIWRVVTHLCCQRREKEFVEPIPAPEAVQINMNGSKH   100
 101  APSETDPFLKQQEEKHLGWMTEAKDWAGELISGQSLTGRFLVLLVFILSI   150
 151  GSLIIYFYDASFQNFQVETCIPWQDSPSQQIDLGFNIFFLVYFFIRFIAA   200
 201  SDKVWFLLEMYSWIDFFTIPPSFVAIYLQRNWLGFRFLRALRLMTVPDIL   250
 251  QYLNILKTSSSIRLTQLVTIFVAVCLTGAGLVHLLENSGDFFKGFINPHR   300
 301  ITYADSVYFVLVTMSTVGYGDIYCTTLCGRLFMIFFILFGLAMFASYVPE   350
 351  IADLIGNRQKYGGEYKGEHGKKHIVVCGHITYDSVSHFLQDFLHEDRDDV   400
 401  DVEVVFLHRVVPDLELEGLFKRHFTKVEFFTGTVMDSLDLSRVKIGDADA   450
 451  CLVLANKYSTNPDAEDAANIMRVISIKNYSSDIRVIVQLMQYHNKAYLLN   500
 501  IPSWDWKRGDDVICLAELKLGFIAQSCLAPGFSTMMANLFAMRSFKTSQT   550
 551  TPDWLNLYLCGAGMEMYTDTLSHSFVGMTFPEAVDLLFNRLGLLLLAIEL   600
 601  KDEENKECNIAINPGPHIVIQPQTQGFFIAQSADEVKRAFFWCKQCHDDI   650
 651  KDVSLIKKCKCKNLALFRRNTKHSTAARARATDVLQQFQPQAPAGPMGHL   700
 701  GQQVQLRMINQQSSTSDTHLNTKSLRFAYEIKKLMPSSGGRRNSMSIPPD   750
 751  GRGVDFSKDFEQQFQDMKYDSTGMFHWCPSRNLEDCVLERHQAAMTVLNG   800
 801  HVVVCLFADQDSPLIGLRNFIMPLRSSNFHYHELKHVVIVGDLEYLRKEW   850
 851  KTLYNLPKISILNGSPLSRADLRAVNINLCDMCVIISARVPNTEDTTLAD   900
 901  KEAILASLNIKAMQFDDTLGFFPMRHQTGDRSPLGSPISMQKKGAKFGTN   950
 951  VPMITELVNDSNVQFLDQDDDDDPDTELYLTQPFACGTAFAISVLDSLMS  1000
1001  TTYFNDSALTLIRTLVTGGATPELELILAEGAGLRGGYSTPETLSNRDRC  1050
1051  RIAQISLQDNPYDGVVHNTTYGAMFTIALRRYGQLCIGLYRLHDQDNPDS  1100
1101  MKRYVITNPPAELRIKNTDYVYVLEQFDPGLEYEPGKRHF            1140

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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