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

NucPred

Fetching Q3T8J9 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MLPCKKRRTTVTESLQHKGNQEENNVDLESAVKPESDQVKDLSSVSLSWD    50
  51  PSHGRVAGFEVQSLQDAGNQLGMEDTSLSSGMLTQNTNVPILEGVDVAIS   100
 101  QGITLPSLESFHPLNIHIGKGKLHATGSKRGKKMTLRPGPVTQEDRCDHL   150
 151  TLKEPFSGEPSEEVKEEGGKPQMNSEGEIPSLPSGSQSAKPVSQPRKSTQ   200
 201  PDVCASPQEKPLRTLFHQPEEEIEDGGLFIPMEEQDNEESEKRRKKKKGT   250
 251  KRKRDGRGQEGTLAYDLKLDDMLDRTLEDGAKQHNLTAVNVRNILHEVIT   300
 301  NEHVVAMMKAAISETEDMPMFEPKMTRSKLKEVVEKGVVIPTWNISPIKK   350
 351  ANEIKPPQFVDIHLEEDDSSDEEYQPDDEEEDETAEESLLESDVESTASS   400
 401  PRGAKKSRLRQSSEMTETDEESGILSEAEKVTTPAIRHISAEVVPMGPPP   450
 451  PPKPKQTRDSTFMEKLHAVDEELASSPVCMDSFQPMDDSLIAFRTRSKMP   500
 501  LKDVPLGQLEAELQAPDITPDMYDPNTADDEDWKMWLGGLMNDDVGNEDE   550
 551  ADDDDDPEYNFLEDLDEPDTEDFRTDRAVRITKKEVNELMEELFETFQDE   600
 601  MGFSNMEDDGPEEEECVAEPRPNFNTPQALRFEEPLANLLNEQHRTVKEL   650
 651  FEQLKMKKSSAKQLQEVEKVKPQSEKVHQTLILDPAQRKRLQQQMQQHVQ   700
 701  LLTQIHLLATCNPNLNPEATTTRIFLKELGTFAQSSIALHHQYNPKFQTL   750
 751  FQPCNLMGAMQLIEDFSTHVSIDCSPHKTVKKTANEFPCLPKQVAWILAT   800
 801  SKVFMYPELLPVCSLKAKNPQDKIVFTKAEDNLLALGLKHFEGTEFPNPL   850
 851  ISKYLLTCKTAHQLTVRIKNLNMNRAPDNIIKFYKKTKQLPVLGKCCEEI   900
 901  QPHQWKPPIEREEHRLPFWLKASLPSIQEELRHMADGAREVGNMTGTTEI   950
 951  NSDRSLEKDNLELGSESRYPLLLPKGVVLKLKPVATRFPRKAWRQKRSSV  1000
1001  LKPLLIQPSPSLQPSFNPGKTPARSTHSEAPPSKMVLRIPHPIQPATVLQ  1050
1051  TVPGVPPLGVSGGESFESPAALPAVPPEARTSFPLSESQTLLSSAPVPKV  1100
1101  MLPSLAPSKFRKPYVRRRPSKRRGVKASPCMKPAPVIHHPASVIFTVPAT  1150
1151  TVKIVSLGGGCNMIQPVNAAVAQSPQTIPITTLLVNPTSFPCPLNQSLVA  1200
1201  SSVSPLIVSGNSVNLPIPSTPEDKAHVNVDIACAVADGENAFQGLEPKLE  1250
1251  PQELSPLSATVFPKVEHSPGPPLADAECQEGLSENSACRWTVVKTEEGRQ  1300
1301  ALEPLPQGIQESLNNPTPGDLEEIVKMEPEEAREEISGSPERDICDDIKV  1350
1351  EHAVELDTGAPSEELSSAGEVTKQTVLQKEEERSQPTKTPSSSQEPPDEG  1400
1401  TSGTDVNKGSSKNALSSMDPEVRLSSPPGKPEDSSSVDGQSVGTPVGPET  1450
1451  GGEKNGPEEEEEEDFDDLTQDEEDEMSSASEESVLSVPELQETMEKLTWL  1500
1501  ASERRMSQEGESEEENSQEENSEPEEEEEEEAEGMESLQKEDEMTDEAVG  1550
1551  DSAEKPPTFASPETAPEVETSRTPPGESIKAAGKGRNNHRARNKRGSRAR  1600
1601  ASKDTSKLLLLYDEDILERDPLREQKDLAFAQAYLTRVREALQHIPGKYE  1650
1651  DFLQVIYEFESSTQRRTAVDLYKSLQILLQDWPQLLKDFAAFLLPEQALA  1700
1701  CGLFEEQQAFEKSRKFLRQLEICFAENPSHHQKIIKVLQGCADCLPQEIT  1750
1751  ELKTQMWQLLKGHDHLQDEFSIFFDHLRPAASRMGDFEEINWTEEKEYEF  1800
1801  DGFEEVALPDVEEEEEPPKIPTASKNKRKKEIGVQNHDKETEWPDGAKDC  1850
1851  ACSCHEGGPDSKLKKSKRRSCSHCSSKVCDSKSYKSKEPHELVGSSPHRE  1900
1901  ASPMPGAKEAGQGKDMMEEEAPEERESTEATQSRTVRTTRKGEMPVSAGL  1950
1951  AVGSTLPSPREVTVTERLLLDGPPPHSPETPQFPPTTGAVLYTVKRNQVG  2000
2001  PEVRSCPKASPRLQKEREGQKAVSESEALMLVWDASETEKLPGTVEPPAS  2050
2051  FLSPVSSKTRDAGRRHVSGKPDTQERWLPSSRARVKTRDRTCPVHESPSG  2100
2101  IDTSETSPKAPRGGLAKDSGTQAKGPEGEQQPKAAEATVCANNSKVSSTG  2150
2151  EKVVLWTREADRVILTMCQEQGAQPQTFNIISQQLGNKTPAEVSHRFREL  2200
2201  MQLFHTACEASSEDEDDATSTSNADQLSDHGDLLSEEELDE           2241

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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