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

NucPred

Fetching Q9CS84 from www.uniprot.org...

The NucPred score for your sequence is 0.34 (see score help below)

   1  MGTALVQRGGCCLLCLSLLLLGCWAELGSGLEFPGAEGQWTRFPKWNACC    50
  51  ESEMSFQLKTRSARGLVLYFDDEGFCDFLELILTRGGRLQLSFSIFCAEP   100
 101  ATLLADTPVNDGAWHSVRIRRQFRNTTLYIDRAEAKWVEVKSKRRDMTVF   150
 151  SGLFVGGLPPELRAAALKLTLASVREREPFKGWIRDVRVNSSQALPVDGG   200
 201  EVKLDDEPPNSGGGSPCEAGEEGEGGVCLNGGVCSVVDDQAVCDCSRTGF   250
 251  RGKDCSQEDNNVEGLAHLMMGDQGKSKGKEEYIATFKGSEYFCYDLSQNP   300
 301  IQSSSDEITLSFKTLQRNGLMLHTGKSADYVNLALKNGAVSLVINLGSGA   350
 351  FEALVEPVNGKFNDNAWHDVKVTRNLRQHSGIGHAMVNKLHCSVTISVDG   400
 401  ILTTTGYTQEDYTMLGSDDFFYVGGSPSTADLPGSPVSNNFMGCLKEVVY   450
 451  KNNDVRLELSRLAKQGDPKMKIHGVVAFKCENVATLDPITFETPESFISL   500
 501  PKWNAKKTGSISFDFRTTEPNGLILFSHGKPRHQKDAKHPQMIKVDFFAI   550
 551  EMLDGHLYLLLDMGSGTIKIKALQKKVNDGEWYHVDFQRDGRSGTISVNT   600
 601  LRTPYTAPGESEILDLDDELYLGGLPENKAGLVFPTEVWTALLNYGYVGC   650
 651  IRDLFIDGQSKDIRQMAEIQSTAGVKPSCSKETAKPCLSNPCKNNGMCRD   700
 701  GWNRYVCDCSGTGYLGRSCEREATVLSYDGSMFMKIQLPVVMHTEAEDVS   750
 751  LRFRSQRAYGILMATTSRDSADTLRLELDAGRVKLTVNLDCIRINCNSSK   800
 801  GPETLFAGYNLNDNEWHTVRVVRRGKSLKLTVDDQQAMTGQMAGDHTRLE   850
 851  FHNIETGIITERRYLSSVPSNFIGHLQSLTFNGMAYIDLCKNGDIDYCEL   900
 901  NARFGFRNIIADPVTFKTKSSYVALATLQAYTSMHLFFQFKTTSLDGLIL   950
 951  YNSGDGNDFIVVELVKGYLHYVFDLGNGANLIKGSSNKPLNDNQWHNVMI  1000
1001  SRDTSNLHTVKIDTKITTQITAGARNLDLKSDLYIGGVAKETYKSLPKLV  1050
1051  HAKEGFQGCLASVDLNGRLPDLISDALFCNGQIERGCEGPSTTCQEDSCS  1100
1101  NQGVCLQQWDGFSCDCSMTSFSGPLCNDPGTTYIFSKGGGQITYKWPPND  1150
1151  RPSTRADRLAIGFSTVQKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNV  1200
1201  GTDDIAIEESNAIINDGKYHVVRFTRSGGNATLQVDSWPVIERYPAGNND  1250
1251  NERLAIARQRIPYRLGRVVDEWLLDKGRQLTIFNSQATIIIGGKEQGQPF  1300
1301  QGQLSGLYYNGLKVLNMAAENDANIAIVGNVRLVGEVPSSMTTESTATAM  1350
1351  QSEMSTSIMETTTTLATSTARRGKPPTKEPISQTTDDILVASAECPSDDE  1400
1401  DIDPCEPSSGGLANPTRVGGREPYPGSAEVIRESSSTTGMVVGIVAAAAL  1450
1451  CILILLYAMYKYRNRDEGSYHVDESRNYISNSAQSNGAVVKEKQPSSAKS  1500
1501  ANKNKKNKDKEYYV                                      1514

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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