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

NucPred

Fetching P98999 from www.uniprot.org...

The NucPred score for your sequence is 0.55 (see score help below)

   1  MASPVNQQLLHHTEVRCDGSGDGSSVTVRINRQHHQAPSRRCKYSISSSC    50
  51  SSGESGVKKTGGSGGARRQKKLPQLFERSTSNWWNPKFDSNNLEEACVER   100
 101  CFPQTQRRFRYALMYLSVAGLLWSIYFSVHMKTKLVSHLVPTLCFLIVCL   150
 151  GFFFFTFTKSYARHCTAISLLVTLLVFTLTLASQFQVLNPGLGSDSLSNL   200
 201  TSFSATGSSSCLSQVGSFSICVEVLLLLYTVMHLPLYLSACLGVAYSILF   250
 251  ETFGYHFRDESCFVLLVGRMAHWELLSKALLHVCIHAIGVHLFIMSEVRS   300
 301  RSTFLKVGQSIMHGKDLEVEKALKERMIHSVMPRIIADDLMKQGDDESEN   350
 351  SVKRHSASSPKSRKKKSSIQKTPIIFRPFKMQRIEQVSILFADIVGFTKM   400
 401  SANKSAHALVGLLNDLFGRFDRLCEETKCEKISTLGDCYYCVAGCPEPRP   450
 451  DHAYCCIEMGLGMIEAIDQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFK   500
 501  FDVWSNDVNLANLMEQLGVAGKVHISEKTARYLDDRYLMEDSMVVERLGQ   550
 551  IVAADQLKGLKTFLISGGRTRVPSCSCSQTLIPVQEGTDLSSPSLAPHVQ   600
 601  AAISETSDSHTNCTQPETLKSCPSCGETAARDGPEEGVSAANGGGEEWKG   650
 651  GAPRPSAIGASLKDPERSPESSTGDTLTNSQASLYDMLQEKGRWCGVSMD   700
 701  QSALLPLRFKNIREKTDAHFVEVIKEDSLMKDYFFKPPINPLSLNFLDKE   750
 751  LETSYRASYQEEVIRMAPVKTFASATFSSLQDVLLNYFIFVLLSVACLLK   800
 801  PGTNTVSPPTLALVLLSVCGLLGFLSLLVSVRMAFYLEDMLLCTRRLLEI   850
 851  ISGWVPRHFIGTVLVCLPAAVIFSYLSSDFYTDIHYTMFLCSALLIPMVQ   900
 901  YCNFCQLSSSALLLATITGATMLILIYLPLCPQRPPLDPGTDIEANLSTS   950
 951  NSSYETLDNPRTELPFTRLGQEIAVAYFLLLLLVWFLNREFDVSYRLHYH  1000
1001  GDVEADLHRTKIQSMRDQADWLLRNIIPYHVAEQLKVSQSYSKNHDDAGV  1050
1051  IFASIVNFSEFYEENYEGGKECYRALNELIGDFDELLSKPHYSCIEKIKT  1100
1101  IGATYMAASGLNPSQCQDSSQPHRHLQTLFEFAKEMMSVVDEFNNNMLWF  1150
1151  NFKLRIGFNHGPLTAGVIGTTKLLYDIWGDTVNIASRMDTTGVECRIQAS  1200
1201  EESYRVLVKMGYDFDYRGTVNVKGKGQMKTYHFPKCTDNGGLVPHHQLCI  1250
1251  SPDIRVQVDGSIGRSPTDEISSLVTGGKGAVELGSGEAERKREKAEERGR  1300
1301  DGGAR                                               1305

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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