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

NucPred

Fetching Q6TFL3 from www.uniprot.org...

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

   1  MNLNTSSNTGDTQRLKIASLDVKQILKNETELDITDNLRKKLHWAKKEKL    50
  51  EITTKHNAELASYESQIAKLRSEVEKGEALRQSLEYDLAVARKEAGLGRR   100
 101  AAEERLAEAHRIQEKLCAQNSELQAKTNETEKAFQTSQQKWKEECRRFEH   150
 151  DLEERDNMIQNCNREYDLLMKEKSRLEKTLQEALEKHQREKNEMESHIRE   200
 201  TALEEFRLQEEQWEAERRELQFIVQEQDTAVQNMHKKVEKLETEHMDCSD   250
 251  LLRRQTSELEFSTQREERLRKEFEATTLRVRKLEENIEAERAAHLESKFN   300
 301  SEIIQLRIRDLEGALQVEKASQAEAVADLEIIKNEFKEVESAYEREKHNA   350
 351  QESFAKLNLLEKEYFSKNKKLNEDIEEQKKVIIDLSKRLQYNEKSCSELQ   400
 401  EELVMAKKHQAFLVETCENNVKELESILDSFTVSGQWTSGIHKDKDKPPS   450
 451  FSVVLERLRRTLTDYQNKLEDASNEEKACNELDSTKQKIDSHTKNIKELQ   500
 501  DKLADVNKELSHLHTKCADREALISTLKVELQNVLHCWEKEKAQAAQSES   550
 551  ELQKLSQAFHKDAEEKLTFLHTLYQHLVAGCVLIKQPEGMLDKFSWSELC   600
 601  AVLQENVDALIADLNRANEKIRHLEYICKNKSDTMRELQQTQEDTFTKVA   650
 651  EQIKAQESCWHRQKKELELQYSELFLEVQKRAQKFQEIAEKNMEKLNHIE   700
 701  KSHEQLVLENSHFKKLLSQTQREQMSLLAACALMAGALYPLYSRSCALST   750
 751  QRDFLQEQVNTFELFKLEIRTLAQALSTVEEKKQEEAKMKKKTFKGLIRI   800
 801  FRKGVIAVLAANRLKILGQSCASLFTWMESFKEGIGMLVCTGEPQDKHKF   850
 851  PKHQKEQLRCLQALSWLTSSDLLAAIISSMAELQDVIGKADPNSRICGHL   900
 901  LIGAAKNSFAKLMDKISLVMECIPLHSSRSITYVEKDSLVQRLAHGLHKV   950
 951  NTLALKYGLRGHVPITKSTASLQKQILGFTQRLHAAEVERRSLRLEVTEF  1000
1001  KRSVNEMKKELDKAQGLQMQLNEFKQSKLITHEKFESACEELNNALLREE  1050
1051  QAQMLLNEQAQQLQELNYKLELHSSEEADKNQTLGEAVKSLSEAKMELRR  1100
1101  KDQSLRQLNRHLTQLEQDKRRLEENIHDAESALRMAAKDKECVANHMRAV  1150
1151  ENTLHKVRDQISLSWSAASRNDFTLQLPKLHLETFAMEGLKGGPEVVACQ  1200
1201  AMIKSFMDVYQLASTRIMTLEKEMTSHRSHIAALKSELHTACLRENASLQ  1250
1251  SIGSRDHSNLSIPSRAPLPADTTGIGDFLPLKAELDTTYTFLKETFINTV  1300
1301  PHALTSSHSSPVTMSANANRPTQIGL                          1326

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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