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

NucPred

Fetching P25848 from www.uniprot.org...

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

   1  MSATKKTYSSTTSAKSKHSVRVAQTTADAALEAVYEMSGDSGDSFDYSKS    50
  51  VGQSAESVPAGAVTAYLQRMQREGLIQNFGCMVAVEEPNFCVIAYSENAS   100
 101  EFLDLIPQAVPSMGEMDVLGIGTDIRTLFTPSSSAALEKAAATQDISLLN   150
 151  PITVHCRRSGKPLYAIAHRIDIGIVIDFEAVKMIDVPVSAAAGALQSHKL   200
 201  AARAITRLQALPGGDIELLCDTIVEEVRELTGYDRVMAFKFHEDEHGEVV   250
 251  AEIRRMDLEPYMGLHYPATDIPQASRFLLMKNRVRLIADCYASPVKLIQD   300
 301  PDIRQPVSLAGSTLRAPHGCHAQYMGNMGSIASLVMAVIINDNEEYSRGA   350
 351  IQRGRKLWGLVVCQHTSPRTVPFPLRSVCEFLMQVFGMQLNLHVELAAQL   400
 401  REKHILRTQTLLCDMLLRDAPIGIVSQTPNIMDLVKCDGAALYYGKRVWL   450
 451  LGTTPTENQIKEIADWLLEHHNDSTGLSTDSLADANYPGAHLLGDAVCGM   500
 501  AAAKITAKDFLFWFRSHTATEVKWGGAKHDPDEKDDGRKMHPRSSFKAFL   550
 551  EVVNKRSPPWEDVEMDAIHSLQLILRGSFRDIADSDTKTMIHARLNDLKL   600
 601  QGVEERNALANEMSRVLETAAAPILAVDSRGMINAWNAKIAQVTGLPVEE   650
 651  AMHCSLTKDLVLDESVVVVERLLSLALQGEEEQNVEIKLKTFGTQTTERA   700
 701  VILIVNACCSRDASDFVVGVFFVGQDVTEQRMFMDRFTRIQGGEKTTVQD   750
 751  PHPLMRPSFDGDEFGRTFKRNSALGGLKDHATGSVERLDLYLRRAEECME   800
 801  VMETIPSPKFNNKQCQYLAGKLKAVLQSASLFLRISHHEHHELGASIDMG   850
 851  RHVEIFKLLLALAKEIESFIQGCCKDEWIKAAMTLTNVSEYVSSMGFNLE   900
 901  LCKIAFCKSCAASGSLTLDQIEVICKDEAEVVKRNASIDVDTLFAKVIYD   950
 951  LTEKTLSSDQNDLAIYLLQRLKRAKPILPSFSSRPSWWNFYDDWSFSEKF  1000
1001  FQWIQITGSLGSGSSATVEKAVWLGTPVAKKTFYGRNNEDFKREVEILAE  1050
1051  LCHPNITSMFCSPLYRRKCSIIMELMDGDLLALMQRRLDRNEDHDSPPFS  1100
1101  ILEVVDIILQTSEGMNYLHEKGIIHRDLKSMNILVKSVKVTKSEIGYVHV  1150
1151  KVADFGLSKTKDSSTRYSNQTWNRGTNRWMAPEVINLGYESTEGEISFDG  1200
1201  KVPKYPLKSDVYSFGMVCYEVLTGDVPFPEEKNPNNVKRMVLEGVRPDLP  1250
1251  AHCPIELKALITDCWNQDPLKRPSFAVICQKLKYLKYLLMTGFSSYQDSY  1300
1301  PSTEEPS                                             1307

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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