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

NucPred

Fetching Q8GZ42 from www.uniprot.org...

The NucPred score for your sequence is 0.83 (see score help below)

   1  MIIKRKLKTLKRCNSTNEEDDIVRKKRKVNLNGGGSGGDYYYPLNLLGEI    50
  51  GAGIVPGKNGFSVSLCKQVSCSPKVEVVEEEEEEEEIKSTRLVSRPPLVK   100
 101  TSRGRVQVLPSRFNDSVIENWRKDNKSSGEEREEEIEEEACRKEKVKVSS   150
 151  NHSLKIKQQETKFTPRNYKYSSSSALCGEIDDEDKCEEIVRYGNSFEMKK   200
 201  QRYVDDEPRPKKEGVYGPEDFYSGDLVWGKSGRNEPFWPAIVIDPMTQAP   250
 251  ELVLRSCIPDAACVMFFGHSGTENERDYAWVRRGMIFPFVDYVERLQEQS   300
 301  ELRGCNPRDFQMALEEALLADQGFTEKLMQDIHMAAGNQTFDDSVYRWVE   350
 351  EAAGSSQYLDHVAPSQDMKKYRNPRACVGCGMVLSFKMAQKMKALIPGDQ   400
 401  LLCQPCSKLTKPKHVCGICKRIWNHLDSQSWVRCDGCKVWIHSACDQISH   450
 451  KHFKDLGETDYYCPTCRTKFDFELSDSEKPDSKSKLGKNNAPMVLPDKVI   500
 501  VVCSGVEGIYFPSLHLVVCKCGSCGPERKALSEWERHTGSKAKNWRTSVK   550
 551  VKSSKLPLEEWMMKLAEFHANATAAKPPKRPSIKQRKQRLLSFLREKYEP   600
 601  VNVKWTTERCAVCRWVEDWDYNKIIICNRCQIAVHQECYGTRNVRDFTSW   650
 651  VCKACETPEIKRECCLCPVKGGALKPTDVETLWVHVTCAWFQPEVCFASE   700
 701  EKMEPALGILSIPSSNFVKICVICKQIHGSCTQCCKCSTYYHAMCASRAG   750
 751  YRMELHCLEKNGRQITKMVSYCSYHRAPNPDTVLIIQTPSGVFSAKSLVQ   800
 801  NKKKSGTRLILANREEIEESAAEDTIPIDPFSSARCRLYKRTVNSKKRTK   850
 851  EEGIPHYTGGLRHHPSAAIQTLNAFRHVAEEPKSFSSFRERLHHLQRTEM   900
 901  ERVCFGRSGIHGWGLFARRNIQEGEMVLEYRGEQVRGIIADLREARYRRE   950
 951  GKDCYLFKISEEVVVDATEKGNIARLINHSCMPNCYARIMSVGDDESRIV  1000
1001  LIAKTTVASCEELTYDYLFDPDEPDEFKVPCLCKSPNCRKFMN         1043

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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