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

NucPred

Fetching Q6L3N7 from www.uniprot.org...

The NucPred score for your sequence is 0.38 (see score help below)

   1  MYFNNELSNLKDHLLVTLQNNSDVERDRINFILWDLKFLDCFLHLKRLPF    50
  51  ASECGMLEFSQKMIEIWKIQSHREPYDCPYWKEVIWKTKQEFRAEYSFPN   100
 101  TSLAANKVDDVSPKFVMEVIDVFVENLNVVVKINDPYSWLFVPEHKEQIE   150
 151  QVLKELKLLRFFVCFVSNKCIEPQYRHTTFYIHALIEASHIAMVVWLHLP   200
 201  VLNGIVNQYLAPSEVSRLRSDFMEMKIKSIQPDISRNNIYIDVLQALKST   250
 251  IPQAQNKHAVESGIVETPTQNLTVGLSDQMVNLQEMLCFLRDNLIHLPIL   300
 301  DLEFHLQDMDSVIVDAGLLIYSLYDIKGEKEDTVLDNMNRALGFDLPRNI   350
 351  EPIKAMVYLVMQKAFQSNLPRVHGLGYVDFLLKNLKDFQGRYSDSLAFLK   400
 401  NQLQVIQTKFESMQPFLKVVVEEPHNKLKTLNEDYATQIIRKAYEVEYVV   450
 451  DACINKEVPQWCIERWLLDIIEEITCIKAKIQEKNTVEDTMKSVIASSQL   500
 501  ARTPRMNEEIVGFEDVIETLRKKLLNGTKGQDVISMHGMPGLGKTTLANR   550
 551  LYSDRSVVSQFDICAQCCVSQVYSYKDLLLALLRDAIGEGSVRTELHANE   600
 601  LADMLRKTLLPRRYLILVDDVWENSVWDDLSGCFPDVNNRSRIILTTRHH   650
 651  EVAKYASVHSDPLHLRMFDEVESWKLLEKKVFGEESCSPLLRDIGQRIAK   700
 701  MCGQLPLSIVLVAGILSEMEKEVEYWEQVANNLGTHIHNDSRAVVDQSYH   750
 751  VLPCHLKSCFLYFGAFLEDRVIDISRLIRLWISESFVKSCEGRSLEDIAE   800
 801  GYLENLIGRNLVMVTQRDDSDGKVKACRLHDVLLDFCKERAAEENFLLWI   850
 851  NRDQITKPSSCVYSHNQHAHLAFTDMKNLVEWSASCSRVGSVLFKNYDPY   900
 901  FAGRPLSSHAFSISRILLNFKFLKVLDLEHQVVIDSIPTELFYLRYISAH   950
 951  IEQNSIPSSISNLWNLETLILNRTSAATGKTLLLPSTVWDMVKLRHLHIP  1000
1001  KFSPENKKALLKKSARLDDLETLFNPYFTRVEDAELMLRKTPNLRKLICE  1050
1051  VQCLEYPHQYHVLNFPIRLEMLKLHQSNIFNPISFCISAPNLKYLELSGF  1100
1101  YLDSQYLSETADHLKHLEVLKLYYVEFGDHREWKVSNGMFPQLKILKLKC  1150
1151  VSLLKWIVADDAFPNLEQLVLRGCRHLMEIPSCFMDILSLQYIEVENCNE  1200
1201  SVVKSAMNIQETQVEDNQNTNFKLILIEIHLFYLFDMKGIESISTDMKEK  1250
1251  KLTVTRDVDADEVQLVVEKLRNVAYADEVQLVVEKLRKRGML          1292

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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