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

NucPred

Fetching Q8VZZ4 from www.uniprot.org...

The NucPred score for your sequence is 0.28 (see score help below)

   1  MENPIDSLLLQPIYLSVLSFFLNLVLLLILFGSWLFKKRVACEDTDAIMN    50
  51  EEFKHISFSYNKLVLICCVSLSVFYSVLSLLSCLHWHTNGWPFLDLLLAA   100
 101  LTWGSISVYLFGRYTNSCEQKVLFLLRVWWVFFFVVSCYHLVVDFVLYKK   150
 151  QEMVSVHFVISDLVGVCAGLFLCCSCLWKKGEGERIDLLKEPLLSSAESS   200
 201  DNEEVTAPFSKAGILSRMSFSWMSPLITLGNEKIIDIKDVPQLDRSDTTE   250
 251  SLFWIFRSKLEWDDGERRITTFKLIKALFLSVWRDIVLSALLAFVYTVSC   300
 301  YVAPYLMDNFVQYLNGNRQYKNQGYVLVTTFFVAKLVECQTQRQWFFRGQ   350
 351  KAGLGMRSVLVSMIYEKGLTLPCHSKQGHTSGEIINLMAVDADRISAFSW   400
 401  FMHDPWILVLQVSLALWILYKSLGLGSIAAFPATILVMLANYPFAKLEEK   450
 451  FQSSLMKSKDNRMKKTSEVLLNMKILKLQGWEMKFLSKILELRHIEAGWL   500
 501  KKFVYNSSAINSVLWAAPSFISATAFGACLLLKIPLESGKILAALATFRI   550
 551  LQGPIYKLPETISMIVQTKVSLNRIASFLCLDDLQQDVVGRLPSGSSEMA   600
 601  VEISNGTFSWDDSSPIPTLRDMNFKVSQGMNVAICGTVGSGKSSLLSSIL   650
 651  GEVPKISGNLKVCGRKAYIAQSPWIQSGKVEENILFGKPMEREWYDRVLE   700
 701  ACSLNKDLEILPFHDQTVIGERGINLSGGQKQRIQIARALYQDADIYLFD   750
 751  DPFSAVDAHTGSHLFKEVLLGLLRHKTVIYVTHQVEFLPEADLILVMKDG   800
 801  KITQAGKYHEILDSGTDFMELVGAHTEALATIDSCETGYASEKSTTDKEN   850
 851  EVLHHKEKQENGSDNKPSGQLVQEEEREKGKVGFTVYKKYMALAYGGAVI   900
 901  PLILVVQVLFQLLSIGSNYWMTWVTPVSKDVEPPVSGFTLILVYVLLAVA   950
 951  SSFCILIRALLVAMTGFKMATELFTQMHLRIFRASMSFFDATPMGRILNR  1000
1001  ASTDQSVADLRLPGQFAYVAIAAINILGIIGVIVQVAWQVLIVFIPVVAA  1050
1051  CAWYRQYYISAARELARLAGISRSPVVHHFSETLSGITTIRSFDQEPRFR  1100
1101  GDIMRLSDCYSRLKFHSTGAMEWLCFRLELLSTFAFASSLVILVSAPEGV  1150
1151  INPSLAGLAITYALNLNTLQATLIWTLCDLENKMISVERMLQYTNIPSEP  1200
1201  PLVIETTRPEKSWPSRGEITICNLQVRYGPHLPMVLHGLTCTFPGGLKTG  1250
1251  IVGRTGCGKSTLIQTLFRIVEPAAGEIRIDGINILSIGLHDLRSRLSIIP  1300
1301  QDPTMFEGTIRSNLDPLEEYTDDQIWEALDNCQLGDEVRKKELKLDSPVS  1350
1351  ENGQNWSVGQRQLVCLGRVLLKRSKLLVLDEATASIDTATDNLIQETLRH  1400
1401  HFADCTVITIAHRISSVIDSDMVLLLDQGLIKEHDSPARLLEDRSSLFSK  1450
1451  LVAEYTTSSESKSKRS                                    1466

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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