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

NucPred

Fetching Q9ULB1 from www.uniprot.org...

The NucPred score for your sequence is 0.33 (see score help below)

   1  MGTALLQRGGCFLLCLSLLLLGCWAELGSGLEFPGAEGQWTRFPKWNACC    50
  51  ESEMSFQLKTRSARGLVLYFDDEGFCDFLELILTRGGRLQLSFSIFCAEP   100
 101  ATLLADTPVNDGAWHSVRIRRQFRNTTLFIDQVEAKWVEVKSKRRDMTVF   150
 151  SGLFVGGLPPELRAAALKLTLASVREREPFKGWIRDVRVNSSQVLPVDSG   200
 201  EVKLDDEPPNSGGGSPCEAGEEGEGGVCLNGGVCSVVDDQAVCDCSRTGF   250
 251  RGKDCSQEDNNVEGLAHLMMGDQGKSKGKEEYIATFKGSEYFCYDLSQNP   300
 301  IQSSSDEITLSFKTLQRNGLMLHTGKSADYVNLALKNGAVSLVINLGSGA   350
 351  FEALVEPVNGKFNDNAWHDVKVTRNLRQHSGIGHAMVTISVDGILTTTGY   400
 401  TQEDYTMLGSDDFFYVGGSPSTADLPGSPVSNNFMGCLKEVVYKNNDVRL   450
 451  ELSRLAKQGDPKMKIHGVVAFKCENVATLDPITFETPESFISLPKWNAKK   500
 501  TGSISFDFRTTEPNGLILFSHGKPRHQKDAKHPQMIKVDFFAIEMLDGHL   550
 551  YLLLDMGSGTIKIKALLKKVNDGEWYHVDFQRDGRSGTISVNTLRTPYTA   600
 601  PGESEILDLDDELYLGGLPENKAGLVFPTEVWTALLNYGYVGCIRDLFID   650
 651  GQSKDIRQMAEVQSTAGVKPSCSKETAKPCLSNPCKNNGMCRDGWNRYVC   700
 701  DCSGTGYLGRSCEREATVLSYDGSMFMKIQLPVVMHTEAEDVSLRFRSQR   750
 751  AYGILMATTSRDSADTLRLELDAGRVKLTVNLDCIRINCNSSKGPETLFA   800
 801  GYNLNDNEWHTVRVVRRGKSLKLTVDDQQAMTGQMAGDHTRLEFHNIETG   850
 851  IITERRYLSSVPSNFIGHLQSLTFNGMAYIDLCKNGDIDYCELNARFGFR   900
 901  NIIADPVTFKTKSSYVALATLQAYTSMHLFFQFKTTSLDGLILYNSGDGN   950
 951  DFIVVELVKGYLHYVFDLGNGANLIKGSSNKPLNDNQWHNVMISRDTSNL  1000
1001  HTVKIDTKITTQITAGARNLDLKSDLYIGGVAKETYKSLPKLVHAKEGFQ  1050
1051  GCLASVDLNGRLPDLISDALFCNGQIERGCEGPSTTCQEDSCSNQGVCLQ  1100
1101  QWDGFSCDCSMTSFSGPLCNDPGTTYIFSKGGGQITYKWPPNDRPSTRAD  1150
1151  RLAIGFSTVQKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTDDIAI  1200
1201  EESNAIINDGKYHVVRFTRSGGNATLQVDSWPVIERYPAGRQLTIFNSQA  1250
1251  TIIIGGKEQGQPFQGQLSGLYYNGLKVLNMAAENDANIAIVGNVRLVGEV  1300
1301  PSSMTTESTATAMQSEMSTSIMETTTTLATSTARRGKPPTKEPISQTTDD  1350
1351  ILVASAECPSDDEDIDPCEPSSGGLANPTRAGGREPYPGSAEVIRESSST  1400
1401  TGMVVGIVAAAALCILILLYAMYKYRNRDEGSYHVDESRNYISNSAQSNG  1450
1451  AVVKEKQPSSAKSSNKNKKNKDKEYYV                         1477

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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