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

NucPred

Fetching P22467 from www.uniprot.org...

The NucPred score for your sequence is 0.78 (see score help below)

   1  MATFKRDLTKNVGVEDLIMLTEVSESSLHENLKIRYKEGLIYTSIGPVLV    50
  51  SMNPYKQLGIYGNDQINLYKGKHEFEIPPHIYSIADKAYRALRSEGENQC   100
 101  IIISGESGAGKTEASKYIMQYIASITGSSTEVERVKKTILESNPLLEAFG   150
 151  NAKTLRNNNSSRFGKYMEIQFNLGGDPEGGKITNYLLEKSRVINQTQGER   200
 201  NFHIFYQLLKGSSEEEKKTYNLLSPDQYHYLTRNASNGCFTADGIDDQIG   250
 251  FKQTKNAMKVVGIDEPLQKEIFATLSAILLLGNLSFNKSASGNGSVISDK   300
 301  KLANTIASLMGVDAIVLESSLVSRQISTGQGARISTYSVPQTVEQAMYAR   350
 351  DAFAKATYSKLFDFIVRKINQSIEVKTIGKVIGVLDIYGFEIFENNSFEQ   400
 401  FCINYVNETLQQIFIDLTLKTEQEEYVQEGITWIPVQYINNKACVDLIEK   450
 451  KPIGILSLLDEECLFPEGNDQTMIDKLNKHFSNHTHYSKVERQKNSQFII   500
 501  NHYAGKVFYNIDGFLDKNRDTLFNDLVTLATSSSCSLLVEIFKYVPPLEV   550
 551  DPEQEKKNRDKFSKNGFANNAAKTFIPTDKKRPITAGFQFKNQVTSLLKS   600
 601  LYSCSPHYVRCIKPNSNMRALEWDQSKCAEQVAYLGLFENLLVRRAGYCY   650
 651  RQTFSKFMRRYYMIGKSTWPKWSGDAEKGVNLLMGELTQEINIKEEVQYG   700
 701  KTKIFIRNPQPLFLLEDKRNKRLNDLATKIGSVWKMYKQRKWYLRTLAAI   750
 751  KIQRTYRGWLLVRECVKLKNQSISIFQNNKERNRQSIKLSKAAFIGDFLS   800
 801  LTRDNYTTATLKREEGPNAVLQLSLNVSKVSRHHKIQKRSLLVTNETIFT   850
 851  ITPHKPKKDGSWFAIKRKVPFSAIEKISFSKLSDDFFVIHIINEHDLCLE   900
 901  TNKKTVLITLLSNLYSKHLNGKELVFEFKDSIQYRNQKGPSELKFVKVDS   950
 951  IHEKSSNSPQANSPSFTAKAEKNYLKVCVLPGLSSESKSILIEK         994

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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