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

NucPred

Fetching Q04164 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MQTCRRRKASGGQSTIKWSRMCLATLCGLLLLGIQIERAASAPAGEDAAA    50
  51  TTMPPLDTTTDAPDAVAATTTPATTAAEQSSSISSITTEAADGSTTSTTT   100
 101  TTEAANKSNATETDFTTNVPVASSLPEETSVRSTSIEPITSTEPTTTPRQ   150
 151  ETEGPDQHMVFSNTEPDQSHIQHIPLRDEHAESSGADDATTEMQRQREQD   200
 201  QQQNELNQISNEQDDVVKDLNNFRHPATLITASNSNSEENVEIESDKQVE   250
 251  TTTTAVPAAATSTSTEATGTPPTGTPATSTSTVPNEREEDPYHVHILSEN   300
 301  HDRLAEHEDYQMLSTSTEESSTTSTTSTTNSTTESGIVAGIVVSQENKAT   350
 351  AEPSTATESTSISTSTTTAATAATSTTSRARAMHMNDPEDEAATTIMPDS   400
 401  ESVPVINIVEGQHMLQQEDQKDEEEEGVVKESESSSTTEASTTTTEPSPF   450
 451  VAFAGEGRSAGGGNDIELFLHHNGSTHEQLMDLSDVSMDGDQNEGSSKTE   500
 501  SSTTSTTTTTAQPETEMPKIVEITASGDTMQRECLANNKSYKHGELMERD   550
 551  CDERCTCNRGDWMCEPRCRGLSYPRGSQRSMANPNCLEKMVEEDECCRVM   600
 601  ECSEPQLEPTVVATEGAAPSTNGTGESAVTLPTTDDEATPKPRTDCHYNS   650
 651  GVYKFRERLEIGCEQICHCAEGGVMDCRPRCPERNHTRLDKCVYVKDPKD   700
 701  VCCQLELCDVTLDDHEQQPTPLQSNNNEDPEEIDPFRFQEQARDAGGAKP   750
 751  TCTFKGAEYDVGQQFRDGCDQLCICNEQGIHCAKLECPSNFGLDVQDPHC   800
 801  IRWEPVPADFKPSPPNCCPESMRCVDNGTCSYQGVQIENWSPVPANLTGC   850
 851  DQHCYCENGRVECRAACPPVPALPPADLPCHPALARLLPIPDDECCKHWM   900
 901  CAPQIPKIGGAGQDEETEATSTHSSIPANETTTTTATANKSTSIPSKVPQ   950
 951  IKKDEEKRPPASGAFYPTLDGKPPKSIGGLGIFEKPEKPEKAHKKVQHQQ  1000
1001  QQHQQQEQQEQQQHQNDVIFDGDRTEEQEEPLPPNGGFVPFQFGQQHPHQ  1050
1051  PHLGPYGFYNPVKPVYEDYNPYEPYDINPNGTPQGKPPPVPTSQSDLFNI  1100
1101  LGAEQPGHPVHPGHGGPPRIHPGQTQKDNHNLGPQVRIEQILQHLQQTVP  1150
1151  GGPPPPPPHQQHQSLTPQLHPQQQQISQQHPGHYVPIVHSGVPPPPPGHG  1200
1201  IAIVDGQTVAYESYPVIPGLGVPQHHPQQHQTTPQQHLQQTILPSSSTTS  1250
1251  GLSTQASEHSLHQNQGKLAKQQQSGANNLQPDIEVHTLEAIDPRSIRIVF  1300
1301  TVPQVYVNLHGRVELRYSNGPSNDTSTWEQQIFAPPEDLIATSQMEFDLP  1350
1351  SLEPNSLYKVKITLILRDLNSQPTSSIYTVKTPPERTITPPPPFPDYRPD  1400
1401  FQDIFKNVEDPELTVSETNASWLQLTWKKLGDDQMEYVDGVQLRYKELTG  1450
1451  MIYSSTPLIHRTLTSYTIQNLQPDTGYEIGLYYIPLAGHGAELRAGHMIK  1500
1501  VRTAQKVDVYGFDVTVNVTKVKTQSVEISWNGVPYPEDKFVHIYRAIYQS  1550
1551  DAGKEDSSVFKVAKRDSTTGTLIMDLKPGTKYRLWLEMYLTNGNTKKSNV  1600
1601  VNFITKPGGPATPGKTGKLLTAGTDQPVGDYYGPLVVVSVIAALAIMSTL  1650
1651  ALLLIITRRRVHQTASITPPRKSDAAYDNPSYKVEIQQETMNL         1693

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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