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

NucPred

Fetching P43069 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MSSANYISDEVPPDMVSPHDHRPSKDEPLKHLDTVIALYDFPGTQSSHLP    50
  51  LNLGDTIHVLSKSATGWWDGVVMGNSGELQRGWFPHNYVRSVNYVQPVLK   100
 101  KLKDNKDLDSITAANTAANVVMPSLTNLIQKSLQESERNSPANSTRKNSV   150
 151  VSFASSETSMPSDSKYTQQQTNTNQNSPEYQSISLPSTRDHSTVEMQLPS   200
 201  QQSSISHTLTGFGIGDDEIIPMEVEEAEKLVEEYRLKYNKTVTWIPRTST   250
 251  KGDIIFYCEQLDVYCESLPLILFDGEASSPNLEYPGSDVIMDPTPISVQG   300
 301  SQSMENVLDTREGSAAGSFDSTKRDSNVSMSTQSSGSSYHRFSRPFFSVD   350
 351  NLFYKHSSDIGTWNELKEQCNYILDLMLKAIKDQNRQFFSTHFSRLNKLV   400
 401  VALCAAVRLNQEDYIDTKYENTTRRKLKRVCASFAQIYINGILHLSVLHY   450
 451  SLEGFNEGRLFGYDMGKLNRSSSSSAFQSPASSLSTIRQGSDDSTRFAQK   500
 501  LSQDRNSEGNGDMNYINQLVYEIDNLRENVNSIVKIFLKLSANKKIKNSD   550
 551  YDSSDASDDEGEDRFDILPQVYPRFLVDEFNGGNWCNPFFSTKNTVLNVS   600
 601  GDDLKNRYHTKIIIDHSAYDSLSQYVDKIVDACENILEALDPKVQNTFYY   650
 651  NEMLRNERNTQILRLTYKSLYHCSAMVDLIESFDFTVFCSVKRHTGNAID   700
 701  TEDESYENPSVWGDHYDSNLSFDYPVVLEFFRLKQELHDLVAKIIMATQS   750
 751  LTLEDPEVFKGLKEEDPLFYNREISKIPKEKAALLLSSILKEQLSFKDGG   800
 801  AISLNPDTLLSGYLVEIAKTTKTVLLITQQLIEERETIINYATRVMQDNF   850
 851  DVQLLLVERNNTSSSEKADDNSYYVGGHKKSTDVPWYLEGDDEYELLLDV   900
 901  KGNIKGGSKEALVSHLTHHLSLDSNFNAVFLLMFSSMMSLGELISLLIAR   950
 951  FNIEPPEGLSYEEYNLWVSKKRNPIRLRVINIMKLLLEKNWSMSYYNEPV  1000
1001  LRRWLTFAHSDQVQTYSLGNLLVNYLERLLRGERIYVERDPVIPNTKPPA  1050
1051  PLTKGSSLSKKPRVMDIDYVELARQLTLREFKLYCKITKFACLAKVWGKK  1100
1101  SGLSESIDSITQFIKASNQLTNFVGYMILRKADPKKRVQIIRYFIQVADK  1150
1151  CRQYNNFSSMTAIISALYSSPIHRLKKTWEYMNADALSNLKNMNKLMNSS  1200
1201  RNFNEYRDVLKFIGSEPCVPFFGVYLSDLTFVYHGNPDYLYNRTRQVNFA  1250
1251  KRAKTSEIVSGIDRFKTTGYNFQEVPEIQKFLDAWFEKCPTIDEQYQISL  1300
1301  NLEPREQAVGASNSNSTTNATTNIKSFKPFSLK                   1333

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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