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

NucPred

Fetching Q9AWA5 from www.uniprot.org...

The NucPred score for your sequence is 0.56 (see score help below)

   1  MSNSLGNNLLYQGFLTSTVLEHKSRISPPCVGGNSLFQQQVISKSPLSTE    50
  51  FRGNRLKVQKKKIPMEKKRAFSSSPHAVLTTDTSSELAEKFSLGGNIELQ   100
 101  VDVRPPTSGDVSFVDFQVTNGSDKLFLHWGAVKFGKETWSLPNDRPDGTK   150
 151  VYKNKALRTPFVKSGSNSILRLEIRDTAIEAIEFLIYDEAHDKWIKNNGG   200
 201  NFRVKLSRKEIRGPDVSVPEELVQIQSYLRWERKGKQNYPPEKEKEEYEA   250
 251  ARTVLQEEIARGASIQDIRARLTKTNDKSQSKEEPLHVTKSDIPDDLAQA   300
 301  QAYIRWEKAGKPNYPPEKQIEELEEARRELQLELEKGITLDELRKTITKG   350
 351  EIKTKVEKHLKRSSFAVERIQRKKRDFGHLINKYTSSPAVQVQKVLEEPP   400
 401  ALSKIKLYAKEKEEQIDDPILNKKIFKVDDGELLVLVAKSSGKTKVHLAT   450
 451  DLNQPITLHWALSKSPGEWMVPPSSILPPGSIILDKAAETPFSASSSDGL   500
 501  TSKVQSLDIVIEDGNFVGMPFVLLSGEKWIKNQGSDFYVGFSAASKLALK   550
 551  AAGDGSGTAKSLLDKIADMESEAQKSFMHRFNIAADLIEDATSAGELGFA   600
 601  GILVWMRFMATRQLIWNKNYNVKPREISKAQDRLTDLLQNAFTSHPQYRE   650
 651  ILRMIMSTVGRGGEGDVGQRIRDEILVIQRNNDCKGGMMQEWHQKLHNNT   700
 701  SPDDVVICQALIDYIKSDFDLGVYWKTLNENGITKERLLSYDRAIHSEPN   750
 751  FRGDQKGGLLRDLGHYMRTLKAVHSGADLESAIANCMGYKTEGEGFMVGV   800
 801  QINPVSGLPSGFQDLLHFVLDHVEDKNVETLLERLLEAREELRPLLLKPN   850
 851  NRLKDLLFLDIALDSTVRTAVERGYEELNNANPEKIMYFISLVLENLALS   900
 901  VDDNEDLVYCLKGWNQALSMSNGGDNHWALFAKAVLDRTRLALASKAEWY   950
 951  HHLLQPSAEYLGSILGVDQWALNIFTEEIIRAGSAASLSSLLNRLDPVLR  1000
1001  KTANLGSWQIISPVEAVGYVVVVDELLSVQNEIYEKPTILVAKSVKGEEE  1050
1051  IPDGAVALITPDMPDVLSHVSVRARNGKVCFATCFDPNILADLQAKEGRI  1100
1101  LLLKPTPSDIIYSEVNEIELQSSSNLVEAETSATLRLVKKQFGGCYAISA  1150
1151  DEFTSEMVGAKSRNIAYLKGKVPSSVGIPTSVALPFGVFEKVLSDDINQG  1200
1201  VAKELQILMKKLSEGDFSALGEIRTTVLDLSAPAQLVKELKEKMQGSGMP  1250
1251  WPGDEGPKRWEQAWMAIKKVWASKWNERAYFSTRKVKLDHDYLCMAVLVQ  1300
1301  EIINADYAFVIHTTNPSSGDDSEIYAEVVRGLGETLVGAYPGRALSFICK  1350
1351  KKDLNSPQVLGYPSKPIGLFIKRSIIFRSDSNGEDLEGYAGAGLYDSVPM  1400
1401  DEEEKVVIDYSSDPLITDGNFRQTILSNIARAGHAIEELYGSPQDIEGVV  1450
1451  RDGKIYVVQTRPQM                                      1464

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.)

Go back to the NucPred Home Page.