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

NucPred

Fetching P46674 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MNTSFGSVVPSTNFNFFKGHGNNDNTSANSTVNNSNFFLNSNETKPSKNV    50
  51  FMVHSTSQKKSQQPLQNLSHSPSYTENKPDKKKKYMINDAKTIQLVGPLI   100
 101  SSPDNLGFQKRSHKARELPRFLINQEPQLEKRAFVQDPWDKANQEKMISL   150
 151  EESIDDLNELYETLKKMRNTERSIMEEKGLVDKADSAKDLYDAIVFQGTC   200
 201  LDMCPTFERSRRNVEYTVYSYEKNQPNDKKASRTKALKVFARPAAAAAPP   250
 251  LPSDVRPPHILVKTLDYIVDNLLTTLPESEGFLWDRMRSIRQDFTYQNYS   300
 301  GPEAVDCNERIVRIHLLILHIMVKSNVEFSLQQELEQLHKSLITLSEIYD   350
 351  DVRSSGGTCPNEAEFRAYALLSKIRDPQYDENIQRLPKHIFQDKLVQMAL   400
 401  CFRRVISNSAYTERGFVKTENCLNFYARFFQLMQSPSLPLLMGFFLQMHL   450
 451  TDIRFYALRALSHTLNKKHKPIPFIYLENMLLFNNRQEIIEFCNYYSIEI   500
 501  INGDAADLKTLQHYSHKLSETQPLKKTYLTCLERRLQKTTYKGLINGGED   550
 551  NLASSVYVKDPKKDRIPSIADQSFLMENFQNNYNEKLNQNSSVKPQINTS   600
 601  PKRVATRPNHFPFSQESKQLPQISQSHTLSTNPLLTPQVHGDLSEQKQQQ   650
 651  IKTVTDGGSPFVFDQSAQNSTVEASKAHMISTTSNGAYDEKLSSEQEEMR   700
 701  KKEEQRIEEEKTQLKKKQENADKQVITEQIANDLVKEVVNSSVISIVKRE   750
 751  FSEANYRKDFIDTMTRELYDAFLHERLYLIYMDSRAELKRNSTLKKKFFE   800
 801  KWQASYSQAKKNRILEEKKREEIKLVSHQLGVPGFKKSTCLFRTPYKGNV   850
 851  NSSFMLSSSDKNLIFSPVNDEFNKFATHLTKISKLWRPLEMQSIYYDNLT   900
 901  KKFPSNSLTPANLFIYAKDWTSLSNRWILSKFNLQTAQDSKKFSNNIISS   950
 951  RIICIDDEYEPSDFSDLQLLIFNTGVTNPDIFDLEMKLKDDGEELIKLIT  1000
1001  GISLNTNICFSLLIIYWESAENTLSESTIKHLLKLNRISKNYSSVIERID  1050
1051  LMNLTEESPHKCLEDKLSEISHSYVYKLTERGKYDKTLRQKRSLAGIHSR  1100
1101  STQLQTTKDIDQKMKKMLEKEKNKYQQQIGERNTYAHLESHIDASPRSKK  1150
1151  RKLPILLSTSHSSQFKTPLASRLNTSGSSTSPPLPSHLAMKFRKNSRVTS  1200
1201  LHTVLPVSTPSHSNNIPAASFSGNNTTDIQSQQLIENQKSTSVYLNNVSE  1250
1251  RILGNQEICQTPINPVTPVLDGADQGKEDIPDSILELKILIDSVKKKVNN  1300
1301  D                                                   1301

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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