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

NucPred

Fetching Q7Z406 from www.uniprot.org...

The NucPred score for your sequence is 0.87 (see score help below)

   1  MAAVTMSVPGRKAPPRPGPVPEAAQPFLFTPRGPSAGGGPGSGTSPQVEW    50
  51  TARRLVWVPSELHGFEAAALRDEGEEEAEVELAESGRRLRLPRDQIQRMN   100
 101  PPKFSKAEDMAELTCLNEASVLHNLRERYYSGLIYTYSGLFCVVINPYKQ   150
 151  LPIYTEAIVEMYRGKKRHEVPPHVYAVTEGAYRSMLQDREDQSILCTGES   200
 201  GAGKTENTKKVIQYLAHVASSPKGRKEPGVPGELERQLLQANPILEAFGN   250
 251  AKTVKNDNSSRFGKFIRINFDVAGYIVGANIETYLLEKSRAIRQAKDECS   300
 301  FHIFYQLLGGAGEQLKADLLLEPCSHYRFLTNGPSSSPGQERELFQETLE   350
 351  SLRVLGFSHEEIISMLRMVSAVLQFGNIALKRERNTDQATMPDNTAAQKL   400
 401  CRLLGLGVTDFSRALLTPRIKVGRDYVQKAQTKEQADFALEALAKATYER   450
 451  LFRWLVLRLNRALDRSPRQGASFLGILDIAGFEIFQLNSFEQLCINYTNE   500
 501  KLQQLFNHTMFVLEQEEYQREGIPWTFLDFGLDLQPCIDLIERPANPPGL   550
 551  LALLDEECWFPKATDKSFVEKVAQEQGGHPKFQRPRHLRDQADFSVLHYA   600
 601  GKVDYKANEWLMKNMDPLNDNVAALLHQSTDRLTAEIWKDVEGIVGLEQV   650
 651  SSLGDGPPGGRPRRGMFRTVGQLYKESLSRLMATLSNTNPSFVRCIVPNH   700
 701  EKRAGKLEPRLVLDQLRCNGVLEGIRICRQGFPNRILFQEFRQRYEILTP   750
 751  NAIPKGFMDGKQACEKMIQALELDPNLYRVGQSKIFFRAGVLAQLEEERD   800
 801  LKVTDIIVSFQAAARGYLARRAFQKRQQQQSALRVMQRNCAAYLKLRHWQ   850
 851  WWRLFTKVKPLLQVTRQDEVLQARAQELQKVQELQQQSAREVGELQGRVA   900
 901  QLEEERARLAEQLRAEAELCAEAEETRGRLAARKQELELVVSELEARVGE   950
 951  EEECSRQMQTEKKRLQQHIQELEAHLEAEEGARQKLQLEKVTTEAKMKKF  1000
1001  EEDLLLLEDQNSKLSKERKLLEDRLAEFSSQAAEEEEKVKSLNKLRLKYE  1050
1051  ATIADMEDRLRKEEKGRQELEKLKRRLDGESSELQEQMVEQQQRAEELRA  1100
1101  QLGRKEEELQAALARAEDEGGARAQLLKSLREAQAALAEAQEDLESERVA  1150
1151  RTKAEKQRRDLGEELEALRGELEDTLDSTNAQQELRSKREQEVTELKKTL  1200
1201  EEETRIHEAAVQELRQRHGQALGELAEQLEQARRGKGAWEKTRLALEAEV  1250
1251  SELRAELSSLQTARQEGEQRRRRLELQLQEVQGRAGDGERARAEAAEKLQ  1300
1301  RAQAELENVSGALNEAESKTIRLSKELSSTEAQLHDAQELLQEETRAKLA  1350
1351  LGSRVRAMEAEAAGLREQLEEEAAARERAGRELQTAQAQLSEWRRRQEEE  1400
1401  AGALEAGEEARRRAAREAEALTQRLAEKTETVDRLERGRRRLQQELDDAT  1450
1451  MDLEQQRQLVSTLEKKQRKFDQLLAEEKAAVLRAVEERERAEAEGREREA  1500
1501  RALSLTRALEEEQEAREELERQNRALRAELEALLSSKDDVGKSVHELERA  1550
1551  CRVAEQAANDLRAQVTELEDELTAAEDAKLRLEVTVQALKTQHERDLQGR  1600
1601  DEAGEERRRQLAKQLRDAEVERDEERKQRTLAVAARKKLEGELEELKAQM  1650
1651  ASAGQGKEEAVKQLRKMQAQMKELWREVEETRTSREEIFSQNRESEKRLK  1700
1701  GLEAEVLRLQEELAASDRARRQAQQDRDEMADEVANGNLSKAAILEEKRQ  1750
1751  LEGRLGQLEEELEEEQSNSELLNDRYRKLLLQVESLTTELSAERSFSAKA  1800
1801  ESGRQQLERQIQELRGRLGEEDAGARARHKMTIAALESKLAQAEEQLEQE  1850
1851  TRERILSGKLVRRAEKRLKEVVLQVEEERRVADQLRDQLEKGNLRVKQLK  1900
1901  RQLEEAEEEASRAQAGRRRLQRELEDVTESAESMNREVTTLRNRLRRGPL  1950
1951  TFTTRTVRQVFRLEEGVASDEEAEEAQPGSGPSPEPEGSPPAHPQ       1995

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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