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

NucPred

Fetching Q9JKY5 from www.uniprot.org...

The NucPred score for your sequence is 0.66 (see score help below)

   1  MNSIKNVPARVLSRRPGHSLEAEREQFDKTQAISISKAINSQEAPVKEKH    50
  51  ARRIILGTHHEKGAFTFWSYAIGLPLSSSSILSWKFCHVLHKVLRDGHPN   100
 101  VLHDYQRYRSNIREIGDLWGHLRDQYGHLVNIYTKLLLTKISFHLKHPQF   150
 151  PAGLEVTDEVLEKAAGTDVNNIFQLTVEMFDYMDCELKLSESVFRQLNTA   200
 201  IAVSQMSSGQCRLAPLIQVIQDCSHLYHYTVKLMFKLHSCLPADTLQGHR   250
 251  DRFHEQFHSLKNFFRRASDMLYFKRLIQIPRLPEGPPNFLRASALAEHIK   300
 301  PVVVIPEEAPEEEEPENLIEISSAPPAGEPVVVADLFDQTFGPPNGSMKD   350
 351  DRDLQIENLKREVETLRAELEKIKMEAQRYISQLKGQVNGLEAELEEQRK   400
 401  QKQKALVDNEQLRHELAQLKALQLEGARNQGLREEAERKASATEARYSKL   450
 451  KEKHSELINTHAELLRKNADTAKQLTVTQQSQEEVARVKEQLAFQMEQAK   500
 501  RESEMKMEEQSDQLEKLKRELAARAGELARAQEALSRTEQSGSELSSRLD   550
 551  TLNAEKEALSGVVRQREAELLAAQSLVREKEEALSQEQQRSSQEKGELRG   600
 601  QLAEKESQEQGLRQKLLDEQLAVLRSAAAEAEAILQDAVSKLDDPLHLRC   650
 651  TSSPDYLVSRAQAALDSVSGLEQGHTQYLASSEDASALVAALTRFSHLAA   700
 701  DTIVNGAATSHLAPTDPADRLMDTCRECGARALELVGQLQDQTVLPRAQP   750
 751  SLMRAPLQGILQLGQDLKPKSLDVRQEELGAMVDKEMAATSAAIEDAVRR   800
 801  IEDMMSQARHESSGVKLEVNERILNSCTDLMKAIRLLVMTSTSLQKEIVE   850
 851  SGRGAATQQEFYAKNSRWTEGLISASKAVGWGATQLVESADKVVLHMGKY   900
 901  EELIVCSHEIAASTAQLVAASKVKANKNSPHLSRLQECSRTVNERAANVV   950
 951  ASTKSGQEQIEDRDTMDFSGLSLIKLKKQEMETQVRVLELEKTLEAERVR  1000
1001  LGELRKQHYVLAGGMGTPSEEEPSRPSPAPRSGATKKPPLAQKPSIAPRT  1050
1051  DNQLDKKDGVYPAQLVNY                                  1068

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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