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

NucPred

Fetching P33302 from www.uniprot.org...

The NucPred score for your sequence is 0.50 (see score help below)

   1  MPEAKLNNNVNDVTSYSSASSSTENAADLHNYNGFDEHTEARIQKLARTL    50
  51  TAQSMQNSTQSAPNKSDAQSIFSSGVEGVNPIFSDPEAPGYDPKLDPNSE   100
 101  NFSSAAWVKNMAHLSAADPDFYKPYSLGCAWKNLSASGASADVAYQSTVV   150
 151  NIPYKILKSGLRKFQRSKETNTFQILKPMDGCLNPGELLVVLGRPGSGCT   200
 201  TLLKSISSNTHGFDLGADTKISYSGYSGDDIKKHFRGEVVYNAEADVHLP   250
 251  HLTVFETLVTVARLKTPQNRIKGVDRESYANHLAEVAMATYGLSHTRNTK   300
 301  VGNDIVRGVSGGERKRVSIAEVSICGSKFQCWDNATRGLDSATALEFIRA   350
 351  LKTQADISNTSATVAIYQCSQDAYDLFNKVCVLDDGYQIYYGPADKAKKY   400
 401  FEDMGYVCPSRQTTADFLTSVTSPSERTLNKDMLKKGIHIPQTPKEMNDY   450
 451  WVKSPNYKELMKEVDQRLLNDDEASREAIKEAHIAKQSKRARPSSPYTVS   500
 501  YMMQVKYLLIRNMWRLRNNIGFTLFMILGNCSMALILGSMFFKIMKKGDT   550
 551  STFYFRGSAMFFAILFNAFSSLLEIFSLYEARPITEKHRTYSLYHPSADA   600
 601  FASVLSEIPSKLIIAVCFNIIFYFLVDFRRNGGVFFFYLLINIVAVFSMS   650
 651  HLFRCVGSLTKTLSEAMVPASMLLLALSMYTGFAIPKKKILRWSKWIWYI   700
 701  NPLAYLFESLLINEFHGIKFPCAEYVPRGPAYANISSTESVCTVVGAVPG   750
 751  QDYVLGDDFIRGTYQYYHKDKWRGFGIGMAYVVFFFFVYLFLCEYNEGAK   800
 801  QKGEILVFPRSIVKRMKKRGVLTEKNANDPENVGERSDLSSDRKMLQESS   850
 851  EEESDTYGEIGLSKSEAIFHWRNLCYEVQIKAETRRILNNVDGWVKPGTL   900
 901  TALMGASGAGKTTLLDCLAERVTMGVITGDILVNGIPRDKSFPRSIGYCQ   950
 951  QQDLHLKTATVRESLRFSAYLRQPAEVSIEEKNRYVEEVIKILEMEKYAD  1000
1001  AVVGVAGEGLNVEQRKRLTIGVELTAKPKLLVFLDEPTSGLDSQTAWSIC  1050
1051  QLMKKLANHGQAILCTIHQPSAILMQEFDRLLFMQRGGKTVYFGDLGEGC  1100
1101  KTMIDYFESHGAHKCPADANPAEWMLEVVGAAPGSHANQDYYEVWRNSEE  1150
1151  YRAVQSELDWMERELPKKGSITAAEDKHEFSQSIIYQTKLVSIRLFQQYW  1200
1201  RSPDYLWSKFILTIFNQLFIGFTFFKAGTSLQGLQNQMLAVFMFTVIFNP  1250
1251  ILQQYLPSFVQQRDLYEARERPSRTFSWISFIFAQIFVEVPWNILAGTIA  1300
1301  YFIYYYPIGFYSNASAAGQLHERGALFWLFSCAFYVYVGSMGLLVISFNQ  1350
1351  VAESAANLASLLFTMSLSFCGVMTTPSAMPRFWIFMYRVSPLTYFIQALL  1400
1401  AVGVANVDVKCADYELLEFTPPSGMTCGQYMEPYLQLAKTGYLTDENATD  1450
1451  TCSFCQISTTNDYLANVNSFYSERWRNYGIFICYIAFNYIAGVFFYWLAR  1500
1501  VPKKNGKLSKK                                         1511

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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