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

NucPred

Fetching Q9AU12 from www.uniprot.org...

The NucPred score for your sequence is 0.69 (see score help below)

   1  MANRNLEKMASIDAQLRQLAPSKVSEDDKLIEYDALLLDRFLDILQNLHG    50
  51  EDLKETVQEVYELSAEYEGKHDPKKLEELGNVITSLDAGDSIVVAKSFSH   100
 101  MLNLANLAEEVQISRRRRNKLKKGDFADENNATTESDIEETLKKLVFELK   150
 151  KSPQEVFDALKNQTVDLVLTAHPTQSVRRSLLQKHARIRNCLSKLYAKDI   200
 201  TPDDKQELDEALQREIQAAFRTDEIRRTPPTPQDEMRAGMSYFHETIWNG   250
 251  VPSFLRRVDTALNNIGIKERVPYNAPLIQFSSWMGGDRDGNPRVTPEVTR   300
 301  DVCLLARMMAANMYYSQIEDLMFELSMWRCNDELRVHADEVHRSSNKDEV   350
 351  AKHYIEFWKKVPTNEPYRVVLGEVRDRLYQTRERSRHLLSNGYSDIPEEN   400
 401  TFTSVEEFLQPLELCYRSLCACGDRAIADGSLLDFLRQVSTFGLSIVRLD   450
 451  IRQESDRHTDVLDAITKHLEIGSYQEWSEEKRQEWLLSELSGKRPLFGPD   500
 501  LPQTEEIRDVLDTFHVIAELPPDNFGAYIISMATAPSDVLAVELLQRECH   550
 551  VKHPLRVVPLFEKLADLEAAPAALARLFSVDWYKNRIDGKQEVMIGYSDS   600
 601  GKDAGRFSAAWQLYKAQEELVKVAKKFGIKLTMFHGRGGTVGRGGGPTHL   650
 651  AILSQPPDTIHGSLRVTVQGEVIEQCFGEQHLCFRTLQRFTAATLEHGMN   700
 701  PPISPKPEWRAMMDQMAVIATEEYRSIVFKEPRFVEYFRLATPELEYGRM   750
 751  NIGSRPAKRRPSGGIETLRAIPWIFAWTQTRFHLPVWLGFGAAFKQVLDK   800
 801  NAKKNLSMLQEMYNQWPFFRVTLDLVEMVFAKGDPKIGALNDRLLVSKDL   850
 851  WPFGDQLRNKYEETKKLLLQVAGHKEILEGDPYLKQRLRLRHSPITTLNV   900
 901  FQAYTLKRIRDPNYKVKARPRISKESAEASKSADELIKLNPTSEYAPGLE   950
 951  DTLILTMKGIAAGMQNTG                                   968

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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