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

NucPred

Fetching Q96QZ7 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MSKVIQKKNHWTSRVHECTVKRGPQGELGVTVLGGAEHGEFPYVGAVAAV    50
  51  EAAGLPGGGEGPRLGEGELLLEVQGVRVSGLPRYDVLGVIDSCKEAVTFK   100
 101  AVRQGGRLNKDLRHFLNQRFQKGSPDHELQQTIRDNLYRHAVPCTTRSPR   150
 151  EGEVPGVDYNFLTVKEFLDLEQSGTLLEVGTYEGNYYGTPKPPSQPVSGK   200
 201  VITTDALHSLQSGSKQSTPKRTKSYNDMQNAGIVHAENEEEDDVPEMNSS   250
 251  FTADSGEQEEHTLQETALPPVNSSIIAAPITDPSQKFPQYLPLSAEDNLG   300
 301  PLPENWEMAYTENGEVYFIDHNTKTTSWLDPRCLNKQQKPLEECEDDEGV   350
 351  HTEELDSELELPAGWEKIEDPVYGIYYVDHINRKTQYENPVLEAKRKKQL   400
 401  EQQQQQQQQQQQQQQQQQQQQTEEWTEDHSALVPPVIPNHPPSNPEPARE   450
 451  VPLQGKPFFTRNPSELKGKFIHTKLRKSSRGFGFTVVGGDEPDEFLQIKS   500
 501  LVLDGPAALDGKMETGDVIVSVNDTCVLGHTHAQVVKIFQSIPIGASVDL   550
 551  ELCRGYPLPFDPDDPNTSLVTSVAILDKEPIIVNGQETYDSPASHSSKTG   600
 601  KVNGMKDARPSSPADVASNSSHGYPNDTVSLASSIATQPELITVHIVKGP   650
 651  MGFGFTIADSPGGGGQRVKQIVDSPRCRGLKEGDLIVEVNKKNVQALTHN   700
 701  QVVDMLVECPKGSEVTLLVQRGGLPVPKKSPKSQPLERKDSQNSSQHSVS   750
 751  SHRSLHTASPSHSTQVLPEFPPAEAQAPDQTDSSGQKKPDPFKIWAQSRS   800
 801  MYENRPMSPSPASGLSKGEREREINSTNFGECPIPDYQEQDIFLWRKETG   850
 851  FGFRILGGNEPGEPIYIGHIVPLGAADTDGRLRSGDELICVDGTPVIGKS   900
 901  HQLVVQLMQQAAKQGHVNLTVRRKVVFAVPKTENEVPSPASSHHSSNQPA   950
 951  SLTEEKRTPQGSQNSLNTVSSGSGSTSGIGSGGGGGSGVVSTVVQPYDVE  1000
1001  IRRGENEGFGFVIVSSVSRPEAGTTFAGNACVAMPHKIGRIIEGSPADRC  1050
1051  GKLKVGDRILAVNGCSITNKSHSDIVNLIKEAGNTVTLRIIPGDESSNAT  1100
1101  LLTNAEKIATITTTHTPSQQGTQETRNTTKPKQESQFEFKAPQATQEQDF  1150
1151  YTVELERGAKGFGFSLRGGREYNMDLYVLRLAEDGPAERCGKMRIGDEIL  1200
1201  EINGETTKNMKHSRAIELIKNGGRRVRLFLKRGDGSVPEYDPSSDRHGPA  1250
1251  TGPQGVPEVRAGPDRRQHPSLESSYPPDLHKSSPHGEKRAHARDPKGSRE  1300
1301  YSRQPNEHHTWNGTSRKPDSGACRPKDRAPEGRRDAQAERAAAANGPKRR  1350
1351  SPEKRREGTRSADNTLERREKHEKRRDVSPERRRERSPTRRRDGSPSRRR  1400
1401  RSLERLLEQRRSPERRRGGSPERRAKSTDRRRARSPERRRERSLDKRNRE  1450
1451  DRASHREREEANLKQDAGRSSRHPPEQRRRPYKECSTDLSI           1491

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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