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

NucPred

Fetching Q5RAY1 from www.uniprot.org...

The NucPred score for your sequence is 0.95 (see score help below)

   1  MAQISSNSGFKECPSSHPEPTRAKDVDKEEALQMEAEALAKLQKDRQVTD    50
  51  NQRGFELSSSTRKKAQVYNKQDYDLMVFPESDSQKRALDIDVEKLTQAEL   100
 101  EKLLLDDSLETRKTPVLPVTPILSPSFSAQLYFRPTIQRGQWPPGLSGPS   150
 151  TYALPSIYPSTYSKQAAFQNGFNPRMPTFPSTEPIYLSLPGQSPYFSYPL   200
 201  TPATPFHPQGSLPIYRPVVSPDMAKLFDKIASTSEFLKNGKARADLEITD   250
 251  SKVSNLQVSPKSEDISKFDWLDLDPLSKPKVDNVEVLDHEEEKNVSSLLA   300
 301  KDPWDAVLLEERSTANCHLERKMNGKSLSVATVTRSQSLNIRTTQLAKAH   350
 351  ISQKDPNGTSSLPTGSSLLQEVEVQNEEMAAFSRSITKLKTKFPYTNHHT   400
 401  NPGYLLSPVTAQRNICGENASVKVSIDIEGFQLPVTFTCDVSSTVEIIIM   450
 451  QALCWVHDDLNQVDVGSYVLKVCGQEEVLQNNHCLGSHEHIQNCRKWDTE   500
 501  IRLQLLTFSAMCQNLARTAEDDETPVDLNKHLYQIEKPYKEAMTRHPVEE   550
 551  LLDSYHNQVELALQIENQHRAVDQVIKAVRKICSALDGVETLAITESVKK   600
 601  LKRAVNLPRSKTADVASLFGGEDTSKSSTRGSLNPENPVQVSINQLTAAI   650
 651  YDLLRLHANSGRSPTDCAQSSKSVKEAWTTTEQLQFTIFAAHGISSNWVS   700
 701  NYEKYYLICSLSHNGKDLFKPIQSKKVGTYKNFFYLIKWDELIIFPIQIS   750
 751  QLPLESLLHLTLFGILNQSSGSSPDSNKQRKGPEALGKVSLPLFDFKRFL   800
 801  TCGTKLLYLWTSSHTNSVPGAVTKKGYVMERIVLQVDFPSPAFDIIYTTP   850
 851  QVDRSIIQQHNLETLENDVKGKLLDILHKDSSLGLSKEDKAFLWEKRYYC   900
 901  FKHPNCLPKILASAPNWKWVNLAKTYSLLHQWPALYPLIALELLDSKFAD   950
 951  QEVRSLAVTWIEAISDDELTDLLPQFVQALKYEIYLNSSLVQFLLSRALG  1000
1001  NIQIAHNLYWLLKDALHDVQFSTRYEHVLGALLSVGGKRLREELRKQTKL  1050
1051  VQLLGGVAEKVRQASGSARQVVLQRSMERVQSFFQKNKCRLPLKPSLVAK  1100
1101  ELSIKSCSFFSSNAVPLKVTMVNADPMGEEINVMFKVGEDLRQDMLALQM  1150
1151  IKIMDKIWLKEGLDLRMVIFKCLSTGRDRGMVELVPASDTLRKIQVEYGV  1200
1201  TGSFKDKPLAEWLRKYNPSEEEYEKASENFIYSCAGCCVATYVLGICDRH  1250
1251  NDNIMLRSTGHMFHIDFGKFLGHAQMFGTFKRDRAPFVLTSDMAYVINGG  1300
1301  EKPTIRFQLFVDLCCQAYNLIRKQTNLFLNLLSLMIPSGLPELTSIQDLK  1350
1351  YVRDALQPQTTDAEATIFFTRLIESSLGSIATKFNFLIHNLAQLRFSGLP  1400
1401  SNDEPILSFSPKTYSFKQDGRIKEVSVFTYHKKYNPDKHYIYVVRILREG  1450
1451  QIEPSFVFRTFDEFQELHNKLSIIFPLWKLPGFPNRMVLGRTHIKDVAAK  1500
1501  RKIELNSYLQSLMNASTDVAECDLVCTFFHPLLRDEKAEGIARSADAGSF  1550
1551  SPPTPGQIGGAVKLSISYRNGTLFIMVMHTKDLVTEDGADPNPYVKTYLL  1600
1601  PDNHKTSKRKTKISRKTRNPTFNEMLVYSGYSKETLRQRELQLSVLSAES  1650
1651  LRENFFLGGVTLPLKDFNLSKETVKWYQLTAATYL                 1685

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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