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

NucPred

Fetching Q6GYQ0 from www.uniprot.org...

The NucPred score for your sequence is 0.84 (see score help below)

   1  MFSKKPHGDVKKSTQKVLDTKKDALTRLKHLRIVIENAESIDLKQFFDQH    50
  51  FSHIYYVFFENFVTIEASLKQKGHKSQREELDAILFIFEKILQLLPERIH   100
 101  QRWQFHSIGLILKKLLHTGNSLKIRREGVRLFLLWLQALQNNCSKEQLWM   150
 151  FSCLIPGFSAPQSEHGPRTLDNLINPPLNLQETQVTIEEITPLVPPQSGD   200
 201  KGQEDLTSYFLEALLKYIVIQVKSLEWKNKENQERGFSFLFSHFKKYYLP   250
 251  YIFPNICKENSLYHPILDIPQMRPKPHYVVIKKDAETNEAIYCTKEPFIK   300
 301  ARVIVIRWLVSFWLEPKPHTGPHIPGMEGEVLPKNIQRAAASLVSREESK   350
 351  NDNADKTDRTTEPEQSHSNTSTLTEREPSSSSLCSIDEEHLTDIEIVRRV   400
 401  FSSKRSNVNFVTEIFRQAFLLPICEAAAMRKVVKVYQEWIQQEEKPLFMQ   450
 451  EPEEIVITSSDLPCIENVTDHDISMEEGEKREEENGTNTADHVRNSSWAK   500
 501  NGSYQGALHNASEEATEQNIRAGTQAVLQVFIINSSNIFLLEPANEIKNL   550
 551  LDEHTDMCKRILNIYRYMVVQVSMDKKTWEQMLLVLLRVTESVLKMPSQA   600
 601  FLQFQGKKNMTLAGRLAGPLFQTLIVAWIKANLNVYISRELWDDLLSVLS   650
 651  SLTYWEELATEWSLTMETLTKVLARNLYSLDLSDLPLDKLSEQKQKKHKG   700
 701  KGVGHEFQKVSVDKSFSRGWSRDQPGQAPMRQRSATTTGSPGTEKARSIV   750
 751  RQKTVDIDDAQILPRSTRVRHFSQSEETGNEVFGALNEEQPLPRSSSTSD   800
 801  ILEPFTVERAKVNKEDMSQKLPPLNSDIGGSSANVPDLMDEFIAERLRSG   850
 851  NASTMTRRGSSPGSLEIPKDLPDILNKQNQMRPIDDPGVPSEWTSPASAG   900
 901  SSDLISSDSHSDSFSAFQYDGRKFDNFGFGTDTGVTSSADVDSGSGHHQS   950
 951  AEEQEVASLTTLHIDSETSSLNQQAFSAEVATITGSESASPVHSPLGSRS  1000
1001  QTPSPSTLNIDHMEQKDLQLDEKLHHSVLQTPDDLEISEFPSECCSVMAG  1050
1051  GTLTGWHADVATVMWRRMLGILGDVNSIMDPEIHAQVFDYLCELWQNLAK  1100
1101  IRDNLGISTDNLTSPSPPVLIPPLRILTPWLFKATMLTDKYKQGKLHAYK  1150
1151  LICNTMKRRQDVSPNRDFLTHFYNIMHCGLLHIDQDIVNTIIKHCSPQFF  1200
1201  SLGLPGATMLIMDFIVAAGRVASSAFLNAPRVEAQVLLGSLVCFPNLYCE  1250
1251  LPSLHPNIPDVAVSQFTDVKELIIKTVLSSARDEPSGPARCVALCSLGIW  1300
1301  ICEELVHESHHPQIKEALNVICVSLKFTNKTVAHVACNMLHMLVHYVPRL  1350
1351  QIYQPDSPLKIIQILIATITHLLPSTEASSYEMDKRLVVSLLLCLLDWIM  1400
1401  ALPLKTLLQPFHATGAESDKTEKSVLNCIYKVLHGCVYGAQCFSNPRYFP  1450
1451  MSLSDLASVDYDPFMHLESLKEPEPLHSPDSERSSKLQPVTEVKTQMQHG  1500
1501  LISIAARTVITHLVNHLGHYPMSGGPAMLTSQVCENHDNHYSESTELSPE  1550
1551  LFESPNIQFFVLNNTTLVSCIQIRSEENMPGGGLSAGLASANSNVRIIVR  1600
1601  DLSGKYSWDSAILYGPPPVSGLSEPTSFMLSLSHQEKPEEPPTSNECLED  1650
1651  ITVKDGLSLQFKRFRETVPTWDTIRDEEDVLDELLQYLGVTSPECLQRTG  1700
1701  ISLNIPAPQPVCISEKQENDVINAILKQHTEEKEFVEKHFNDLNMKAVEQ  1750
1751  DEPIPQKPQSAFYYCRLLLSILGMNSWDKRRSFHLLKKNEKLLRELRNLD  1800
1801  SRQCRETHKIAVFYVAEGQEDKHSILTNTGGSQAYEDFVAGLGWEVNLTN  1850
1851  HCGFMGGLQKNKSTGLTTPYFATSTVEVIFHVSTRMPSDSDDSLTKKLRH  1900
1901  LGNDEVHIVWSEHTRDYRRGIIPTEFGDVLIVIYPMKNHMFSIQIMKKPE  1950
1951  VPFFGPLFDGAIVNGKVLPIMVRATAINASRALKSLIPLYQNFYEERARY  2000
2001  LQTIVQHHLEPTTFEDFAAQVFSPAPYHHLPSDADH                2036

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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