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

NucPred

Fetching Q69ZA1 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MPSSSDTALGGGGGLSWAEKKLEERRKRRRFLSPQQPPLLLPLLQPQLLQ    50
51 PPPPPPPLLFLAAPGAAAAAAAAAAASSSCFSPGPPLEVKRLARGKRRPG 100
101 GRQKRRRGPRAGQEAEKRRVFSLPQPQQDGGGGASSGGGVTPLVEYEDVS 150
151 SQSEQGLLLGGASAATAATAAGGTGGNGGSPASSSGTQRRAEGSERRPRR 200
201 DRRSSSGRSKERHREHRRRDGTRSGSEASKARSRHGHSGEERAEAAKSGS 250
251 SSSSGGRRKSASATSSSSSSRKDRDLKAHRSRTKSSKEPPSAYKEPPKAY 300
301 REDKSEPKAYRRRQRSLSPLGGRDESPVSHRASQSLRSRKSPSPAGGGSS 350
351 PYSRRLPRSPSPYSRRRSPSYSRHSSYERGGDVSPSPYSSSSWRRSRSPY 400
401 SPVLRRSAKSRSRSPYSSRHSRSRSRHRLSRSRSRHSSISPSTLTLKSSL 450
451 AAELNKNKKARAAEAARAAEAAKAAEAAKAAEAAAKAAKASNASTPTKGN 500
501 TETGASVSQTNHVKEVKKLKTEHAPSPSSGGTVKSDKAKTKPPLQVTKVD 550
551 NNLTVEKATKKTVVGKESKPAATKEEPVSTKEKSKPLTPSTGAKEKEQHV 600
601 ALVTSTLPPLPLPPMLPEDKDADSLRGNISVKAVKKEVEKKLRCLLADLP 650
651 LPPELPGGDDLSKSPEEKKTAAQLHSKRRPKICGPRYGEIKEKDIDWGKR 700
701 CVDKFDIIGIIGEGTYGQVYKARDKDTGEMVALKKVRLDNEKEGFPITAI 750
751 REIKILRQLTHQSIINMKEIVTDKEDALDFKKDKGAFYLVFEYMDHDLMG 800
801 LLESGLVHFNENHIKSFMRQLMEGLDYCHKKNFLHRDIKCSNILLNNRGQ 850
851 IKLADFGLARLYSSEESRPYTNKVITLWYRPPELLLGEERYTPAIDVWSC 900
901 GCILGELFTKKPIFQANQELAQLELISRICGSPCPAVWPDVIKLPYFNTM 950
951 KPKKQYRRKLREEFVFIPAAALDLFDYMLALDPSKRCTAEQALQCEFLRD 1000
1001 VEPSKMPPPDLPLWQDCHELWSKKRRRQKQMGMTDDLSTIKAPRKDLSLG 1050
1051 LDDSRTNTPQGVLPPAQLKSQSNSNVAPVITGPGQPLNHSELAILLNLLQ 1100
1101 SKSSVNMADFVQVLNIKVNSETQQQLNKINLPAGILATGEKQTDPSTPQQ 1150
1151 ESSKSLGGVQPSQTIQPKVETDAAQAAVQSAFAVLLTQLIKAQQSKQKDA 1200
1201 MLEERENGSGHEAPLQLRPPLEPSTPGSGQDDLIQHQDRRILELTPEPDR 1250
1251 PRILPPDQRPPEPPEPPPVTEEDLDYRTENQHVPTTSSSLTDPHAGVKAA 1300
1301 LLQLLAQHQPQDDPKREGGIDYPTGDTYVPSSDYKDNFGSSFSAAPYVSS 1350
1351 DGLGSSSAAAPLEARSFIGNSDIQSLDNYSTASSHTGGPPQTSAFTESFA 1400
1401 SSVAGYGDIYLNAGPMLFSGDKDHRFEYSHGPITVLTNSNDPSTGPESTH 1450
1451 PLPAKMHNYNYGGNLQENPGGPSLMHGQTWTSPAQGPGYSQGYRGHISTS 1500
1501 AGRGRGRGLPY 1511

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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