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

NucPred

Fetching Q6DD51 from www.uniprot.org...

The NucPred score for your sequence is 0.86 (see score help below)

   1  MGRENELIQAVKSGDVGAVQKFLAKFRTPKSKLLGSTKRLNVNHQDADGF    50
  51  SALHHAALSGNSELLLLLLEMQASVDIKDGNGMRPLHYAAWQGQPEPVRL   100
 101  LLRASASVNAASHDGQIPLHLAAQYGHYEVSETLLQHQSNPCHVNKGKKT   150
 151  PLDLACEFGRVKVVQLLLNSHLCVSLLEGTSKDPTDPNFTTPLHLAAKNG   200
 201  HLEVIRLLLKLGIEINKVTKMGTALHEAALCGKTEVVKLLIENGVDVNIR   250
 251  NTYNQTALDIVNQFTTTHASIDIKQLLREASGILKVRALKDFWNAHDPTA   300
 301  LNIRAGDLITVLEQHPDGRWKGHIHDPQKGTDRVGFFPPSIVEVISKRLG   350
 351  STLSRNITVPSHQHLAKTVLTLPIQHSPGSQLGINPDTSVAGDRHSVGSE   400
 401  SSVRSAGSGQSCEGQQINTALLIENAQTMDFGSENLQNCQTFPGPVSGHH   450
 451  LSTILPVEKNPGDYLQGKDAEQIFCWLRGFQMETYVGNFISAGYDLPTIM   500
 501  RVTPEDLTAIGVTKPGHRKMISTEIGKLIVADGLPQQIPVDLWDWLSQLG   550
 551  LPEYHKQLSENGYESLSTVTELTWEGLQEIGIHRLGHQKKLLLGVKRLLD   600
 601  LQKGYPIGGTLRRRILGSQDTVAVVEPPENGDLPVTPKLLTFQGAELSQE   650
 651  LQSALTRGNEQLCTGRRSFSQESISSRSQGSGHSQESASSYPVLPVHLQG   700
 701  VDLNLPERNHPEGTDQILQNHWVPNGCLIQPEPPAPPPKPALKKRSLSAC   750
 751  RYALSDGEPEEEEEKKIATAGTGTLSTYATLTRRPGRSCLTNGKPEKKVQ   800
 801  RSQSFAVRARRKGPPPPPPKRLSSMSSAEGQSPEGQSSVKTIAAQLKDIG   850
 851  RGTGFSASTSKATDTEVLEGSGTRRRTVSESAAGLGGRLSLPLTTKKDEE   900
 901  EERKEEPISSQHSSSESIPFAEEGNLTIKQRPKPPGAKLEQDATSELSPT   950
 951  QESQLQSAEAQRHLESSAVLAKPVTVVLAQARPQIAAKPQIGPKPDTGAR  1000
1001  APPATSIPKNEEHDFNLTESDTVKRRPKVKEKEEESPKAPLANNSPSLIP  1050
1051  SQEPLTQDTLIAKIADIDKRLLSLGEVEDSVKKTGIDTRSTGVSISQTHL  1100
1101  VISGPQQVLQKPSRAVTGPLFPAGSILWDEESEASSREQTCIPQQSISNS  1150
1151  DKGPPVFTSSLQNTEELQDTRGKSCRETVQLTKNILDDISTMFDDLAEQL  1200
1201  EAMLD                                               1205

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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