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

NucPred

Fetching P13382 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MSSKSEKLEKLRKLQAARNGTSIDDYEGDESDGDRIYDEIDEKEYRARKR    50
  51  QELLHDDFVVDDDGVGYVDRGVEEDWREVDNSSSDEDTGNLASKDSKRKK   100
 101  NIKREKDHQITDMLRTQHSKSTLLAHAKKSQKKSIPIDNFDDILGEFESG   150
 151  EVEKPNILLPSKLRENLNSSPTSEFKSSIKRVNGNDESSHDAGISKKVKI   200
 201  DPDSSTDKYLEIESSPLKLQSRKLRYANDVQDLLDDVENSPVVATKRQNV   250
 251  LQDTLLANPPSAQSLADEEDDEDSDEDIILKRRTMRSVTTTRRVNIDSRS   300
 301  NPSTSPFVTAPGTPIGIKGLTPSKSLQSNTDVATLAVNVKKEDVVDPETD   350
 351  TFQMFWLDYCEVNNTLILFGKVKLKDDNCVSAMVQINGLCRELFFLPREG   400
 401  KTPTDIHEEIIPLLMDKYGLDNIRAKPQKMKYSFELPDIPSESDYLKVLL   450
 451  PYQTPKSSRDTIPSDLSSDTFYHVFGGNSNIFESFVIQNRIMGPCWLDIK   500
 501  GADFNSIRNASHCAVEVSVDKPQNITPTTTKTMPNLRCLSLSIQTLMNPK   550
 551  ENKQEIVSITLSAYRNISLDSPIPENIKPDDLCTLVRPPQSTSFPLGLAA   600
 601  LAKQKLPGRVRLFNNEKAMLSCFCAMLKVEDPDVIIGHRLQNVYLDVLAH   650
 651  RMHDLNIPTFSSIGRRLRRTWPEKFGRGNSNMNHFFISDICSGRLICDIA   700
 701  NEMGQSLTPKCQSWDLSEMYQVTCEKEHKPLDIDYQNPQYQNDVNSMTMA   750
 751  LQENITNCMISAEVSYRIQLLTLTKQLTNLAGNAWAQTLGGTRAGRNEYI   800
 801  LLHEFSRNGFIVPDKEGNRSRAQKQRQNEENADAPVNSKKAKYQGGLVFE   850
 851  PEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRNKEDIDELPSVPPSE   900
 901  VDQGVLPRLLANLVDRRREVKKVMKTETDPHKRVQCDIRQQALKLTANSM   950
 951  YGCLGYVNSRFYAKPLAMLVTNKGREILMNTRQLAESMNLLVVYGDTDSV  1000
1001  MIDTGCDNYADAIKIGLGFKRLVNERYRLLEIDIDNVFKKLLLHAKKKYA  1050
1051  ALTVNLDKNGNGTTVLEVKGLDMKRREFCPLSRDVSIHVLNTILSDKDPE  1100
1101  EALQEVYDYLEDIRIKVETNNIRIDKYKINMKLSKDPKAYPGGKNMPAVQ  1150
1151  VALRMRKAGRVVKAGSVITFVITKQDEIDNAADTPALSVAERAHALNEVM  1200
1201  IKSNNLIPDPQYYLEKQIFAPVERLLERIDSFNVVRLSEALGLDSKKYFR  1250
1251  REGGNNNGEDINNLQPLETTITDVERFKDTVTLELSCPSCDKRFPFGGIV  1300
1301  SSNYYRVSYNGLQCKHCEQLFTPLQLTSQIEHSIRAHISLYYAGWLQCDD  1350
1351  STCGIVTRQVSVFGKRCLNDGCTGVMRYKYSDKQLYNQLLYFDSLFDCEK  1400
1401  NKKQELKPIYLPDDLDYPKEQLTESSIKALTEQNRELMETGRSVVQKYLN  1450
1451  DCGRRYVDMTSIFDFMLN                                  1468

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.)

Go back to the NucPred Home Page.