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

NucPred

Fetching Q8BL66 from www.uniprot.org...

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

   1  MFRRILQRTPGRVGSQGSDLDSSATPINTVDVNNESSSEGFICPQCMKSL    50
  51  GSADELFKHYQAVHDAGNDSGHGGEAGLALTRDDITLLRQEVQDLQASLK   100
 101  EEKWYSEELKKELEKYQGLQQQEAKSDGLVTDSSAELQALEQQLEEAQTE   150
 151  NFNIKQMKDLFEQKAAQLATEIADIKSKYDEEKSLRAAAEQKVTHLTEDL   200
 201  NKQTTVIQDLKTELLQRPGIEDVAVLKKELVQVQTLMDNMTLERERESEK   250
 251  LKDECKKLQSEHAHLEATINQLRSELAKGPQEVAVYVQEIQKLKGSINEL   300
 301  TQKNQNLTEKLQKKDLDYTHLEEKHNEESASRKTLQASLHQRDLDCQQLQ   350
 351  ARLTASESSLQRAQGELSEKAEAAQKLREELREVESTRQHLKVEVKQLQQ   400
 401  QREEKEQHGLQLQGEVSQLHCKLLETERQLGEAHGRLKEQRQLSSEKLME   450
 451  KEQQVADLQLKLSRLEEQLKEKVTNSTELQHQLEKSKQQHQEQQALQQSA   500
 501  TAKLREAQNDLEQVLRQIGDKDQKIQNLEALLQKGKESVSLLEKEREDLY   550
 551  AKIQAGEGETAVLNQLQEKNHALQQQLTQLTEKLKNQSESHKQAEENLHD   600
 601  QVQEQKAHLRAAQDRVLSLETSVSELSSQLNESKEKVSQLDIQIKAKTEL   650
 651  LLSAEAAKAAQRADLQNHLDTAQHALQDKQQELNKVSVQLDQLTAKFQEK   700
 701  QEHCIQLESHLKDHKEKHLSLEQKVEDLEGHIKKLEADALEVKASKEQAL   750
 751  QSLQQQRQLSTDLELRNAELSRELQEQEEVVSCTKLDLQNKSEILENIKQ   800
 801  TLTKKEEENVVLKQEFEKLSQDSKTQHKELGDRMQAAVTELTAVKAQKDA   850
 851  LLAELSTTKEKLSKVSDSLKNSKSEFEKENQKGKAAVLDLEKACKELKHQ   900
 901  LQVQAESALKEQEDLKKSLEKEKETSQQLKIELNSVKGEVSQAQNTLKQK   950
 951  EKDEQQLQGTINQLKQSAEQKKKQIEALQGEVKNAVSQKTVLENKLQQQS  1000
1001  SQAAQELAAEKGKLSALQSNYEKCQADLKQLQSDLYGKESELLATRQDLK  1050
1051  SVEEKLTLAQEDLISNRNQIGNQNKSIQELQAAKASLEQDSAKKEALLKE  1100
1101  QSKALEDAQREKSVKEKELVAEKSKLAEMEEIKCRQEKEITKLNEELKSH  1150
1151  KQESIKEITNLKDAKQLLIQQKLELQGRVDSLKAALEQEKESQQLMREQV  1200
1201  KKEEEKRKEEFSEKEAKLHSEIKEKEAGMKKHEENEAKLTMQVTTLNENL  1250
1251  GTVKKEWQSSQRRVSELEKQTDDLRGEIAVLEATVQNNQDERRALLERCL  1300
1301  KGEGEIEKLQTKALELQRKLDNTTAAVQELGRENQSLQIKHTQALNRKWA  1350
1351  EDNEVQNCMSCGKCFSVTVRRHHCRQCGNIFCAECSTKNALTPSSKKPVR  1400
1401  VCDACFNDLQG                                         1411

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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