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

NucPred

Fetching Q9H0D2 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MDQYSLGDEGALPSEMHLPSFSESQGLNCSDTLNRDLGPNTRGFLYAGLS    50
  51  GLDPDPSLPTPDMSSEVLEDNLDTLSLYSGKDSDSVKLLEEYADSESQAS   100
 101  LQDLGLGVLKAKEADEGGRATSGSARKGKRQHSSPQNPLLDCSLCGKVFS   150
 151  SASSLSKHYLTHSQERKHVCKICSKAFKRQDHLTGHMLTHQKTKPFVCIE   200
 201  QGCSKSYCDYRSLRRHYEVHHGLCILKEAPPEEEACGDSPHAHESAGQPP   250
 251  PSSLRSLVPPEARSPGSLLPHRDLLRRIVSSIVHQKTPSPGPAPAGASDS   300
 301  EGRNTACPCPASSGSSSCTPAGPHAAPAALDTELPEEPCLPQKEPATDVF   350
 351  TAPNSRAAENGAPDPPEPEPDTALLQARSTAECWPEGGSVPACLPLFRGQ   400
 401  TVPASSQPSSHSFQWLRNLPGCPKSKGNNVFVVHKPSAVPSREGSESGPG   450
 451  PSSGSPSEESPPGPGGGLEDALPFPAALLRVPAEAPSDPRSASGEDDPCA   500
 501  PKKVKVDCDSFLCQNPGEPGLQEAQKAGGLPADASPLFRQLFLKSQEPLV   550
 551  SHEQMQVFQMITKSQRIFSHAQVAAVSSQLPAPEGKPAALRPLQGPWPQQ   600
 601  PPPLAPAVDSLHAGPGNPEAEGSPARRRKTTPGVPREASPGSTRRDAKGG   650
 651  LKVAAVPTPLAAPSLDPSRNPDISSLAKQLRSSKGTLDLEDIFPSTGQRQ   700
 701  TQLGGEEPPGASLPGKQAPAENGAASRITKGEKGPACSRGGGYRLLGNPR   750
 751  APRFSGFRKEKAKMDMCCAASPSQVAMASFSSAGPPADPSKSKLTIFSRI   800
 801  QGGNIYRLPHPVKEENVAGRGNQQNGSPTDWTKPRSTFVCKNCSQMFYTE   850
 851  KGLSSHMCFHSDQWPSPRGKQEPQVFGTEFCKPLRQVLRPEGDRHSPPGT   900
 901  KKPLDPTAAAPLVVPQSIPVVPVTRHIGSMAMGQEKDGEERDSKESSQQR   950
 951  KRKKRPPPSTAGEPGPAGCHQSRLRSPMFLVDCLLKGLFQCSPYTPPPML  1000
1001  SPIREGSGVYFNTLCSTSTQASPDQLISSMLDQVDGSFGICVVKDDTKIS  1050
1051  IEPHINIGSRFQAEIPELQERSLAGTDEHVASLVWKPWGDMMISSETQDR  1100
1101  VTELCNVACSSVMPGGGTNLELALHCLHEAQGNVQVALETLLLRGPHKPR  1150
1151  THLLADYRYTGSDVWTPIEKRLFKKAFYAHKKDFYLIHKMIQTKTVAQCV  1200
1201  EYYYIWKKMIKFDCGRAPGLEKRVKREPEEVERTEEKVPCSPRERPSHHP  1250
1251  TPKLKTKSYRRESILSSSPNAGSKRTPELLGSAESQGIFPCRECERVFDK  1300
1301  IKSRNAHMKRHRLQDHVEPIIRVKWPVKPFQLKEEELGADIGPLQW      1346

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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