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

NucPred

Fetching Q9TL04 from www.uniprot.org...

The NucPred score for your sequence is 0.75 (see score help below)

   1  MNTQEKHQFEPVLPQAHDDPTLSKPPIFFNRTADKGMIKRLIAWFLVHYG    50
  51  LADTVSMIEDLKQVGFQYATRAGISLGIEDLRIPPTKPRLLQEAHREINR   100
 101  MEFRYQQGYVSLVERFQKVIDTWNGTSELLKDDVVENFLATDPLNPVYMM   150
 151  AFSGARGNLSQVRQLVGMRGLMSNPQGEIIDLPIRSNFREGLTVTEYIIS   200
 201  CYGARKGLVDTALRTANSGYLTRRLVDVAQDIVIRMTSCSPSAYPLISFT   250
 251  KSGKEVVYPLEERLLGRVLAIGAFNQEGELISGPDTAISQEIAVQLMDCD   300
 301  PKEILVRSVLLCKSKRGLCRLCYGWNLGTGTIVSIGEAVGIIAAQSIGEP   350
 351  GTQLTMRTFHTGGVFAGGVTNEIRAPHAGLVHYPRPIHPKWVRTRHGQFG   400
 401  ILISEKIEIIFEHESKKTIQVFDAGTVLTIHEGEKVHTNQLIGEIPAHGT   450
 451  LVTGWRSLKSGVDGEVRFDELELLKQRPRSDRTSPVRLDPRVCNKAHLWI   500
 501  LQGHVNTFEMPIQLVANIGDKVEKDSIVSTTKQVVSEEGRIIYRYDEKRG   550
 551  KEQTIITHAFGSVQFDGVDAWLPTKSQGIKQSIRTTGGKLSISSQGMTLS   600
 601  ATKIKQEGIGSFDWPALAEPSIEEDEELEEAYKKTKDPIIQPTPYPLQYC   650
 651  VLPEQKYVIQAQEGWIISVLGGQSVGASQSLATYVDSQWEVEQGQLSIRS   700
 701  IEYRVHDQSWIQVITPSLVEIESGRGSYHLMAKAGWIIPISTKIRCKDYR   750
 751  LISGSILLGKWSLPISRFAVEQAASYPAILIRPIHTYPVYPTTIWDETIN   800
 801  WQRGIASIGSNDWHPRCIAPTYQAPSYVESFKGRQTFTGEEKQEGNKPVE   850
 851  ITSKNRRKSAANSSHETRMTQNRTWPIVLADTRIQKGASPIQIEWTWPHA   900
 901  KNPWISPNHGAIAGHIRFVNMTILDSSSISTKQELDHREAQVIPTTQTVS   950
 951  GVHRLTPLLEKTVFSQDDGEIQRMLPFSRALVKPVRTNRSKTRRNASGKT  1000
1001  QVKAQARSQAKARSVRLKLKETVKTRSQEKFTNEMKKQLAKSSEGNKGFQ  1050
1051  IRQALFPKKLIRLMVVLRPVDIMTFATYGARVCIPLGAMIYQGEELFEGA  1100
1101  STPISGQLIEIRRDRVTLRIGQPYRVGWQSRLMVTRDQIVKAEKVLAHLL  1150
1151  YFKTKTGDIVQGLPKIEEILEARRKKGNEIIRSNLQDFVQQFYQDNLDEG  1200
1201  FSRKYASTRTMRAMQVLILRRVQLVYRSQGVQISDKHLEIISLRMTSRVL  1250
1251  VEKAYGTGILPGEIIEKRRADMLNQGRTRIRYCPIVLGITKASLTTKGFI  1300
1301  SSASFQETTRVLTQAVLQGKSDWLLGLKENVILGRLIPAGVGIYGHWVGP  1350
1351  HEFNIKQMLKLWVLPPIITGQSTMRAMFHSTTRYWQDLEAVMESPNKLYP  1400
1401  VTPYKCYPDTQHLAGLSIWMPEFEFRRFETFTEEEMVAAESLFTAHPNCH  1450
1451  ARRINNKQLNSLI                                       1463

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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