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

NucPred

Fetching O64474 from www.uniprot.org...

The NucPred score for your sequence is 0.32 (see score help below)

   1  MALQNKEEEKKKVKKLQKSYFDVLGICCTSEVPIIENILKSLDGVKEYSV    50
  51  IVPSRTVIVVHDSLLISPFQIAKALNEARLEANVRVNGETSFKNKWPSPF   100
 101  AVVSGLLLLLSFLKFVYSPLRWLAVAAVAAGIYPILAKAFASIKRPRIDI   150
 151  NILVIITVIATLAMQDFMEAAAVVFLFTISDWLETRASYKATSVMQSLMS   200
 201  LAPQKAIIAETGEEVEVDEVKVDTVVAVKAGETIPIDGIVVDGNCEVDEK   250
 251  TLTGEAFPVPKQRDSTVWAGTINLNGYICVKTTSLAGDCVVAKMAKLVEE   300
 301  AQSSKTKSQRLIDKCSQYYTPAIILVSACVAIVPVIMKVHNLKHWFHLAL   350
 351  VVLVSGCPCGLILSTPVATFCALTKAATSGLLIKSADYLDTLSKIKIVAF   400
 401  DKTGTITRGEFIVIDFKSLSRDINLRSLLYWVSSVESKSSHPMAATIVDY   450
 451  AKSVSVEPRPEEVEDYQNFPGEGIYGKIDGNDIFIGNKKIASRAGCSTVP   500
 501  EIEVDTKGGKTVGYVYVGERLAGFFNLSDACRSGVSQAMAELKSLGIKTA   550
 551  MLTGDNQAAAMHAQEQLGNVLDVVHGDLLPEDKSRIIQEFKKEGPTAMVG   600
 601  DGVNDAPALATADIGISMGISGSALATQTGNIILMSNDIRRIPQAVKLAR   650
 651  RARRKVVENVCLSIILKAGILALAFAGHPLIWAAVLVDVGTCLLVIFNSM   700
 701  LLLREKKKIGNKKCYRASTSKLNGRKLEGDDDYVVDLEAGLLTKSGNGQC   750
 751  KSSCCGDKKNQENVVMMKPSSKTSSDHSHPGCCGDKKEEKVKPLVKDGCC   800
 801  SEKTRKSEGDMVSLSSCKKSSHVKHDLKMKGGSGCCASKNEKGKEVVAKS   850
 851  CCEKPKQQVESVGDCKSGHCEKKKQAEDIVVPVQIIGHALTHVEIELQTK   900
 901  ETCKTSCCDSKEKVKETGLLLSSENTPYLEKGVLIKDEGNCKSGSENMGT   950
 951  VKQSCHEKGCSDEKQTGEITLASEEETDDQDCSSGCCVNEGTVKQSFDEK  1000
1001  KHSVLVEKEGLDMETGFCCDAKLVCCGNTEGEVKEQCRLEIKKEEHCKSG  1050
1051  CCGEEIQTGEITLVSEEETESTNCSTGCCVDKEEVTQTCHEKPASLVVSG  1100
1101  LEVKKDEHCESSHRAVKVETCCKVKIPEACASKCRDRAKRHSGKSCCRSY  1150
1151  AKELCSHRHHHHHHHHHHHVSA                              1172

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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