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

NucPred

Fetching Q6GYP7 from www.uniprot.org...

The NucPred score for your sequence is 0.86 (see score help below)

   1  MFSKKPHGDVKKSTQKVLDTKKDALTRLKHLRIVIENAESIDLKQFFDQH    50
  51  FSHIYYVFFENFVTIEASLKQKGHKSQREELDAILFIFEKILQLLPERIH   100
 101  QRWQFHSIGLILKKLLHTGNSLKIRREGVRLFLLWLQALQDNCSKEQLWM   150
 151  FSCLIPGFSAPQSEYGPRTLDNLINPPLSLQETQVTIEEVTPLVPPQSGD   200
 201  KGQEDLTSYFLEALLKYIVIQVKSLEWKNKENQERGFSFLFSHFKKFYLP   250
 251  YIFPNICKENSLYHPVLDIPQIRPKPHYVMIKKDAETNETIYCTKEPFIQ   300
 301  ARVIVIRWLVSFWLEPKPHSGPNIPGMEGEVLPKNIQRAAASLVSREESK   350
 351  NDTVDKVDKSAEPEQSHSNTSTLTEREPSSSSLCSIDEEHLTDIEIVRRV   400
 401  FSSKRSNVNFVTEIFRQAFLLPICEAAAMRKVVKVYQEWIQQEEKPLFMQ   450
 451  EPEDTAITCSDIPCSETVADHDSAIEDGEKREEENGTSTSEHVRNSSWTK   500
 501  NGSYQEAFHVCEEATEQNIQAGTQAVLQVFIINSSNIFLLEPANEIKNLL   550
 551  DEHTDMCKRILNIYRYMVVQVSMDKKTWEQMLLVLLRVTESVLKMSSQAF   600
 601  LQFQGKKSMTLAGRLAGPLFQTLIVAWIKANLNVYISRELWDDLLSVLSS   650
 651  LTYWEELATEWSLTMETLTKVLARNLYSLDLSDLPLDKLSEQKQKKHKGK   700
 701  GVGHEFQKVSVDKSFSRGWSRDQPGQAPMRQRSATTTGSPGTEKARSIVR   750
 751  QKTVDIDDAQILPRSTRVRHFSQSEDTGNEVFGALHEEQPLPRSSSTSDI   800
 801  LEPFTVERAKVNKEDTSPKLPPLNSETGGNSANVPDLMDEFIAERLRSGN   850
 851  ASTMTRRGSSPGSLEIPKDLPDILNKQNQMRPVDDPGVPSEWTSPASAGS   900
 901  SDLMSSDSHSDSFSAFQCEGRKFDNFGFGTDIGIPSSADVDLGSGHHQST   950
 951  EEQEVASLTTLHLDSETSSLNQQAFSAEVATVTGSESASPVHSALGSRSQ  1000
1001  TPSPSTLSRAHIEQKDLQLDEKLHHSVLQTPDDLEISEFPSECCSVMAGG  1050
1051  TLTGWHADVATVMWRRMLGILGDVNAIMDPEIHAQVFDYLCELWQNLAKI  1100
1101  RDNLGISADNLTSPSPPVLIPPLRILTPWLFKATMLTDKYKQGKLHAYKL  1150
1151  ICNTMKRRQDVSPNRDFLTHFYNIMHCGLLHIDQDIVNTIIKHCSPQFFS  1200
1201  LGLPGATMLIMDFIIAAGRVASSAFLNAPRVEAQVLLGSLVCFPNLYCEL  1250
1251  PALHPNIPDIAVSQFTDVKELIIKTVLSSARDEPSGPARCVALCSLGIWI  1300
1301  CEELVHESHHPQIKEALNVICVSLKFTNKTVAHVACNMLHMLVHYVPRLQ  1350
1351  IHQPQSPLKIIQILIATITHLLPSTEASSYEMDKRLVVSLLLCLLDWIMA  1400
1401  LPLKTLLQPVHATGAENDKTEKSVLNCIYKVLHGCVYGAQSFSNPKYFPI  1450
1451  SLSDLASVDYDPFMHLESLKEPEPLHSPDSERSSKLQPVTEVKTQMQQGL  1500
1501  ISIAARTVITHLVNHLGHYPMSGGPAMLTSQVCENHDNHYSESTELSPEL  1550
1551  FESPNIQFFVLNNTTLVSCIQIRSEESMPGGGLAAGLVSANSNVRIIVRD  1600
1601  LSGKYSWDSAILYGPPIVSGLPEPTSFILSMSDQEKPEEPPTSNECLEDI  1650
1651  AVKDGLSLQLRRFRETVPTWSTIREEEDVLDELLQYLGTTSPECLQRTGI  1700
1701  SLNVPAPQPLCISEKQENDVINAILKQYTEEKEFVEKHFNDLNMKASEQD  1750
1751  EPTPQKPQSAFYYCRLLLSILGMNSWDKRRSFHLLKKNEKLLRELRNLDS  1800
1801  RQCRETHKIAVFYVAEGQEDKYSILTNIGGSQAYEDFVAGLGWEVNLTNH  1850
1851  CGFMGGLQKNRSTGLTTPYFATSTVEVIFHVSTRMPSDSDDSLTKKLRHL  1900
1901  GNDEVHIVWSEHTRDYRRGIIPTEFGDVLIVIYPMKNHMFSIQIMKKPEV  1950
1951  PFFGPLFDGAIVNGKVLPIMVRSTAINASRALKSLIPLYQNFYEERARYL  2000
2001  QTIVQHHLEPTTFEDFAAQVFSPAPYHHFPADADH                 2035

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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