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

NucPred

Fetching P59242 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MADPRGPVDHGVQIRFITEPEGATEMGTLRRSGRRPARDARASTYGVAVR    50
  51  VQGIAGQPFVVLNSGEKGTDSFGVQIKGGNNRGSPGALSSDSELPENPYS   100
 101  QVKGRPATSRSSTSDEEPKDHLNGKLIRSQSQASLTGLAFMSPSNRSTSL   150
 151  LELAPKPTSSINTIDTAPLSSVDSLINKFDSQKGGQVRGRTGRRTRTLPH   200
 201  EQRKRSQSLDSRLPRDTREEREHQSANHWTRGTKYDNHVDSSKNPSQKQS   250
 251  PFSSFSRSRQTQDWVLQSFEETRDPAMVQFKSTPDLLRDQRETAPPGSAD   300
 301  HVKATIYGILREGSSESEASVRRKVSLVLEQMQPLGMVSPASTKALAGQA   350
 351  ELTRKMEELQKKLDEEVKKRQKLEPSRVGLERQLEEKAEECHRLQELLER   400
 401  RKGEVQQSSKELQNMKLLLGQEEGLRHGLEAQVKELQLKLKHSQSPDSGK   450
 451  ESLLKDLLDTRELLEELLEGKQRVEEQLRLRERELTALKGALKEEVASHD   500
 501  QEVEHVRLQYQRDTEQLRRSMQDATQDHAALEAERQKMSSLVRELQRELE   550
 551  ETSEETGHWQSMFQKNKEELRATKQELLQLRMEKEEMEEELGEKMEVLQR   600
 601  DLEQARASTRDTHQVEELKKELRRTQGELKELQAEQQNQEVTGRHRNQVL   650
 651  EKQLAALREEADRGRELEQQNLQLQKTLQQLRQDCEEASKAKVASETEAM   700
 701  MLGQRRATVETTLRETQEENDEFRRRILGLEQQLKEARGLAEGGEAVEAR   750
 751  LRDKVHRLEVEKQQLEEALNAAQEEEGNLAAAKRALEVRLDEAQRGLARL   800
 801  GQEQQALNRALEEEGKQREALRRSKAELEEQKRLLNRTVDRLNKELEQIG   850
 851  DDSKLALQQLQAQMEDYKEKARKEVADAQRQAKDWASEAEKNSGGLSRLQ   900
 901  DELQRLRQALQTSQAERDTARLDKELLAQRLQGLEQEAENKKRFQDDKAR   950
 951  QLKSLEEKVSRLEAELDEEKNTVELLTDRVNRGRDQVDQLRTELMQERSA  1000
1001  RQDLECDKISLERQNKDLKTRLASSEGFQKPSASLSQLESQNQLLQERLQ  1050
1051  AEEREKTVLQSTNRKLERRVKELSIQIDDERQHVNDQKDQLTLRVKALKR  1100
1101  QVDEAEEEIERLDSLRKKAQRELEEQHEVNEQLQARIKSLEKDAWRKASR  1150
1151  SAAESALKQEGLSSDEEFDNVYDPSSIASLLTESNLQTSSC           1191

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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