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

NucPred

Fetching P08045 from www.uniprot.org...

The NucPred score for your sequence is 0.79 (see score help below)

   1  MEEPKCLQREMYKSVMTENYQCVLSLGYPIRKPEIVSMMEVGEELWSKND    50
  51  SARPGQKEVEGETPKESDWAAENCKRAQMHKEVLDLDTLAAVKSEPVEEG   100
 101  SNSAKKSHICSHYGKLFSCYAAVVRHQRMHQLQKSHHCPHCKKSFVQRSD   150
 151  FIKHQRTHTGERPYQCVECQKKFTERSALVNHQRTHTGERPYTCLDCQKT   200
 201  FNQRSALTKHRRTHTGERPYRCSVCSKSFIQNSDLVKHLRTHTGEKPYEC   250
 251  PLCVKRFAESSALMKHKRTHSTHRPFRCSECSRSFTHNSDLTAHMRKHTE   300
 301  FRNVLNLDSVVGTDPLSSQNVASSPYSCSKCRKTFKRWKSFLNHQQTHSR   350
 351  EKPYLCSHCNKGFIQNSDLVKHFRTHTGERPYQCAECHKGFIQKSDLVKH   400
 401  LRTHTGEKPFKCSHCDKKFTERSALAKHQRTHTGEKPYKCSDCGKEFTQR   450
 451  SNLILHQRIHTGERPYKCTLCDRTFIQNSDLVKHQKVHANLPLSDPHTAN   500
 501  SPHKCSKCDLTFSHWSTFMKHSKLHSGEKKFQCAECKKGFTQKSDLVKHI   550
 551  RVHTGEKPFKCLLCKKSFSQNSDLHKHWRIHTGEKPFPCYTCDKSFTERS   600
 601  ALIKHHRTHTGERPHKCSVCQKGFIQKSALTKHSRTHTGEKPYPCTQCGK   650
 651  SFIQNSDLVKHQRIHTGEKPYHCTECNKRFTEGSSLVKHRRTHSGEKPYR   700
 701  CPQCEKTFIQSSDLVKHLVVHNGENPPAATAFHEILIRRENLTRSEPDPY   750
 751  PCTECGKVFHQRPALLKHLRTHKTEKRYPCNECDKSFFQTSDLVKHLRTH   800
 801  TGERPYHCPECNKGFIQNSDLVKHQRTHTGERPYTCSQCDKGFIQRSALT   850
 851  KHMRTHTGEKPYKCEQCQKCFIQNSDLVKHQRIHTGEKPYHCPDCDKRFT   900
 901  EGSSLIKHQRIHSRIKPYPCGVCGKSFSQSSNLLKHLKCHSEQNPPVALS   950
 951  SELGFVAETQTHPDPVDHIVYGDTASYISPEAAGERSFKCNDCGKCFAHR  1000
1001  SVLIKHVRIHTGERPYKCSQCTRSFIQKSDLVKHYRTHTGERPYKCGLCE  1050
1051  RSFVEKSALSRHQRVHKNESPVLNSAMEQQQVTYWGESKDDPNSLVPQLH  1100
1101  VIKEEESPHIVNAYSPLSILQSYFPPILEPKGTPRYSCSECGKCFTHRSV  1150
1151  FLKHWRMHTGEQPYTCKECGKSFSQSSALVKHVRIHTGEKPYPCSTCGKS  1200
1201  FIQKSDLAKHQRIHTGEKPYTCTVCGKKFIDRSSVVKHSRTHTGERPYKC  1250
1251  NECTKGFVQKSDLVKHMRTHTGEKPYGCNCCDRSFSTHSASVRHQRMCNT  1300
1301  GRPYQDEEYENSLFYSADITWKGDYAQLLQIPCGLEEPMKAIGWISEVAL  1350

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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