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

NucPred

Fetching Q5IS45 from www.uniprot.org...

The NucPred score for your sequence is 0.61 (see score help below)

   1  MGRVGYWTLLVLPALLVWRGPAPSAAAEKGPPALNIAVMLGHSHDVTERE    50
  51  LRTLWGPEQAAGLPLDVNVVALLMNRTDPKSLITHVCDLMSGARIHGLVF   100
 101  GDDTDQEAVAQMLDFISSHTFVPILGIHGGASMIMNDKDPTSTFFQFGAS   150
 151  IQQQATVMLKIMQDYDWHVFSLVTTIFPGYREFISFVKTTVDNSFVGWDM   200
 201  QNVITLDTSFEDAKTQVQLKKIHSSVILLYCSKDEAVLILSEARSLGLTG   250
 251  YDFFWIVPSLVSGNTELIPKEFPSGLISVSYDDWDYSLEARVRDGIGILT   300
 301  TAASSMLEKFSYIPEAKASCYGQMERPEVPMHTLHPFMVNVTWDGKDLSF   350
 351  TEEGYQVHPRLVVIVLNKDREWEKVGKWENHTLSLRHAVWPRYKSFSDCE   400
 401  PDDNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGM   450
 451  NVKKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEV   500
 501  VYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRSNGTVSPSAFL   550
 551  EPFSASVWVMMFVMLLIVSAIAVFVFEYFSPVGYNRNLAKGKAPHGPSFT   600
 601  IGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLA   650
 651  AFMIQEEFVDQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPY   700
 701  MHQYMTKFNQKGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTI   750
 751  GSGYIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGIC   800
 801  HNEKNEVMSSQLDIDNMAGVFYMLAAAMALSLITFIWEHLFYWKLRFCFT   850
 851  GVCSDRPGLLFSISRGIYSCIHGVHIEEKKKSPDFNLTGSQSNMLKLLRS   900
 901  AKNISNMSNMNSSRMDSPKRAADFIQRGSLIMDMVSDKGNLMYSDNRSFQ   950
 951  GKESIFGDNMNELQTFVANRQKDNLNNYVFQGQHPLTLNESNPNTVEVAV  1000
1001  STESKVNSRPRQLWKKSVDSIRQDSLSQNPVSQRDEATAENRTHSLKSPR  1050
1051  YLPEEMAHSDISETSNRATCHREPDNSKNPKTKDNFKRSVASKYPKDCSE  1100
1101  VERTYLKTKSSSPRDKIYTIDGEKEPGFHLDPPQFVENVTLPENVDFPDP  1150
1151  YQDPSENLRKGDSTLPMNRNPLQNEEGLSNNDQYKLYSKHFTLKDKGSPH  1200
1201  SETSERYRQNSTHCRSCLSNLPTYSGHFTMRSPFKCDACLRMGNLYDIDE  1250
1251  DQMLQETGNPATGEQVYQQDWAQNNALQLQKNKLRISRQHSYDNIVDKPR  1300
1301  ELDLSRPSRSISLKDRERLLEGNFYGSLFSVPSSKLSGKKSSLFPQGLED  1350
1351  SKRSKSLLPDHTSDNPFLHSHRDDQRLVIGRCPSDPYKHSLPSQAVNDSY  1400
1401  LRSSLRSTASYCSRDSRGHNDVYISEHVMPYAANKNNMYSTPRVLNSCSN  1450
1451  RRVYKKMPSIESDV                                      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.)

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