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

NucPred

Fetching Q2PCF1 from www.uniprot.org...

The NucPred score for your sequence is 0.33 (see score help below)

   1  MEESFLGDELTRLRSNSRMSSWRSSQSIREVFGGSSDVFMKNYSTRWREM    50
  51  AEEEEKELKWAAIDRLPTYNRLRKGMMKEVMSNGRVVHHEVDMTKLGNQD   100
 101  KKVLMESILKVVEDDNEQFLRRLRNRTDRVGIEIPKIEVRFQNLSVGGDA   150
 151  YVGTRALPTLLNSTLNTIEAVLGLIHLSPSKKRVVKILEDVSGIIRPSRM   200
 201  TLLLGPPGSGKTTFLKALAGKSEKDLRVNGKITYCGHEFHEFVPQRTSAY   250
 251  ISQHDLHHGEMTVRETLDFAGRCLGVGTRYDLLVELSRREKEAGIMPDPQ   300
 301  IDAFMKATAIDGQETSLITDYVLKILGLDICADIMVGDDMRRGISGGQKK   350
 351  RVTTGEMLVGPAKAFFMDEISKGLDSSTTYQIVKFMRQMVHINDITMVIS   400
 401  LLQPAPETFDLFDDVIVLSEGQIVYQGPRENVLEFFEYMGFRCPERKAIA   450
 451  DFLLEVTSKKDQEQYWFRKSRPYVYISVPEFSESFNSFQIGEQIIEELTI   500
 501  PYDKYSVHRAALVKNKYGISSWELFKSCFTREWLLMKRSSFLYIFKTTQI   550
 551  TIMATIALTVFLRTQMKAGTVKDSAKFWGALFFSLINVMFNGMQELAMTV   600
 601  FRLPVFFKQRNSLFYPAWAFALPIWVLKIPISLVESAIWIILTYYTIGFA   650
 651  PAASRFFKQLLAFIGVHQMALSLFRFIAAAGRTQVVANTLGTFTLLMVFI   700
 701  LGGFIVSKDDIQDWMIWGYYLSPMMYGQNAIAINEFLDDRWSAPTNGSQP   750
 751  TVGKTLLHARGLFTTESWYWISIGALFGFSLLFNVLFIAALTFLNPIGDT   800
 801  KAVKVENGDKNNRRPQETAIVGDIQMAPTRSQANTSSVIPFPNNESRKGM   850
 851  ILPFQPLSLAFNHVNYYVDMPAEMKTQGVEEERLQLLRDASGAFRPGILT   900
 901  ALVGVSGAGKTTLMDVLAGRKTGGYIEGSINISGYPKNQTTFARVSGYCE   950
 951  QNDIHSPYVTVYESLLYSAWLRLASDVKTETRKMFVEEVMELVELKLLRN  1000
1001  ALVGLPGVDGLSTEQRKRLTTAVELVANPSIIFMDEPTSGLDARAAAIVM  1050
1051  RTVRKTVDTGRTVVCTIHQPSIDIFEAFDELLLMKIGGQVIYAGPLGHRS  1100
1101  HKLVEYFETIPGVPKIRESDNPATWMLDVSSSSMEAQLVVDFAEVYANSN  1150
1151  LYQRNQLLIKELSTPATCSKDLYFPTQYSQSFITQCKACFWKQHWSYWRN  1200
1201  SQYNAIRFFMTVIIGILFGVIFWNKGNQIHRQQDLLNLLGATYAAVMFLG  1250
1251  ATNASAVQSVVAIERTVFYRERAAGMYSELPYAFAQVAIETIYVAIQTFV  1300
1301  YSLLLFSMIGYQWTAVKFFYFYYFIFMCFTYFSMYGMMVVALTPGYQIAA  1350
1351  IVMSFFLSFWNLFSGFLIPRPLIPVWWRWYYWASPVAWTIYGIFASQVGD  1400
1401  RTDELELTGETEKIQVNEFLKEYLGYDHDFLLVVVFAHVGWVLLFFFVFA  1450
1451  YGIKFLNYQKR                                         1461

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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