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

NucPred

Fetching Q90ZS6 from www.uniprot.org...

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

   1  MVRKKNPPLRNIASEGEAQITESAASKREDTISSKEISTDPMQENSEQSG    50
  51  LVEHNSDDHSFHDQEPSSSINKDSASLSLSERAVVNYSHLKGRNVYFSPM   100
 101  EVTDRNMLALVTTDTRSACDPLKSPIKSEADDTQELASSASVDSLEAKEE   150
 151  NDMSPRATDFTVQCGKVDCQSSSPASVASDNLHVPSDGIAGLNKSQAVLL   200
 201  VNDNSDSAPLSPELQDFKCNICGYGYYGNDPTDLIKHFRKYHLGLHNRTR   250
 251  QDVELDTKILALHNMVQFSQSKDFQKMNRSVLSGVLQDFNSPRPVLLNGT   300
 301  YDVQVTFGETFIGIGRKTPDCQGNTKYFRCKFCNFTYLAKSATELEQHFL   350
 351  KTHPNKMKMSSDSGKPSEKSTNKSSPIPRSCEPGDLGKWQDKITVKAADD   400
 401  IPVGYSVPIKPVDSCRQNGTDDTNYYWCKFCSFSCESSSNSKLLEHHSKQ   450
 451  HGGGKSESPNSDLNDEIFRGSVINQNEITKSSDEQLPTKIDKGLAKKKDV   500
 501  SSVPTEDIIVTNYNCQFCDFRYSKSHGPEVILVGPLLRHYQQHHNIHKCT   550
 551  IKHCPFCPRGLCTPEKHLGEITYPFACKKSNCSHCALLLLHLSSGGTEST   600
 601  RVKHQCDQCSFSSPDVDVLLLHYENAHEAQACEIKQELNHQHGADGQPSI   650
 651  KEIKEHSCTKCDFIVQVEEDLPRHYRRVHNCYKCRQCNFTAADTQSLLDH   700
 701  FNSAHCQEFEITTSNGGEHHGTSSIKEEPKTDLKVYNLVTPDSKMGEAIF   750
 751  DSTVKKEKLEDKETLREKAWSDGSVDDLRGVAWRAPDILRTSPSYSQMGL   800
 801  GLLTTVSVNQDQQKSSRDSPNVEAAHLARPVYGLSIEPKGFQGVTAGASG   850
 851  EKSGQHTPQYPTAGDSKSKDESQSLLRRRRGSGVFCANCLTTKTSLWRKN   900
 901  ANGGYVCNACGLYQKLHSTPRPLNIIKQNNGEQIIRRRTRKRLNPEALQP   950
 951  EQLTKHQRASSEEQANGSPLDIRSEDHSMEGHQRENQQLSMNKYGSQASL  1000
1001  TKSHSAQQTMIVSQTMDIHKRMQPLHIQIKSPQESSGEPGNSSSVSDGKG  1050
1051  SSERGSPIEKYMRPIKHPNYSPPGSPIEKYQYPLFGLPFVHNDFQSEADW  1100
1101  LRFWSKYKLSVPGNPHYLSHVPGLPNPCPNYVPYPTFNLPAQYSSVGSDN  1150
1151  DIPLDLAMKHSRPGSGTNGDSKEKSKSPVSVKDDGPLNVTKIEKSDKSTQ  1200
1201  DELSTKCVHCGIVFLDEVMYALHMSCHGESGPFQCSICQHLCTDKYDFTT  1250
1251  HIQRGLHRNIAQAEKNGKNKD                               1271

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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