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

NucPred

Fetching Q9Y6Y1 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MWRAEGKWLPKTSRKSVSQSVFCGTSTYCVLNTVPPIEDDHGNSNSSHVK    50
  51  IFLPKKLLECLPKCSSLPKERHRWNTNEEIAAYLITFEKHEEWLTTSPKT   100
 101  RPQNGSMILYNRKKVKYRKDGYCWKKRKDGKTTREDHMKLKVQGVECLYG   150
 151  CYVHSSIIPTFHRRCYWLLQNPDIVLVHYLNVPAIEDCGKPCGPILCSIN   200
 201  TDKKEWAKWTKEELIGQLKPMFHGIKWTCSNGNSSSGFSVEQLVQQILDS   250
 251  HQTKPQPRTHNCLCTGSLGAGGSVHHKCNSAKHRIISPKVEPRTGGYGSH   300
 301  SEVQHNDVSEGKHEHSHSKGSSREKRNGKVAKPVLLHQSSTEVSSTNQVE   350
 351  VPDTTQSSPVSISSGLNSDPDMVDSPVVTGVSGMAVASVMGSLSQSATVF   400
 401  MSEVTNEAVYTMSPTAGPNHHLLSPDASQGLVLAVSSDGHKFAFPTTGSS   450
 451  ESLSMLPTNVSEELVLSTTLDGGRKIPETTMNFDPDCFLNNPKQGQTYGG   500
 501  GGLKAEMVSSNIRHSPPGERSFSFTTVLTKEIKTEDTSFEQQMAKEAYSS   550
 551  SAAAVAASSLTLTAGSSLLPSGGGLSPSTTLEQMDFSAIDSNKDYTSSFS   600
 601  QTGHSPHIHQTPSPSFFLQDASKPLPVEQNTHSSLSDSGGTFVMPTVKTE   650
 651  ASSQTSSCSGHVETRIESTSSLHLMQFQANFQAMTAEGEVTMETSQAAEG   700
 701  SEVLLKSGELQACSSEHYLQPETNGVIRSAGGVPILPGNVVQGLYPVAQP   750
 751  SLGNASNMELSLDHFDISFSNQFSDLINDFISVEGGSSTIYGHQLVSGDS   800
 801  TALSQSEDGARAPFTQAEMCLPCCSPQQGSLQLSSSEGGASTMAYMHVAE   850
 851  VVSAASAQGTLGMLQQSGRVFMVTDYSPEWSYPEGGVKVLITGPWQEASN   900
 901  NYSCLFDQISVPASLIQPGVLRCYCPAHDTGLVTLQVAFNNQIISNSVVF   950
 951  EYKARALPTLPSSQHDWLSLDDNQFRMSILERLEQMERRMAEMTGSQQHK  1000
1001  QASGGGSSGGGSGSGNGGSQAQCASGTGALGSCFESRVVVVCEKMMSRAC  1050
1051  WAKSKHLIHSKTFRGMTLLHLAAAQGYATLIQTLIKWRTKHADSIDLELE  1100
1101  VDPLNVDHFSCTPLMWACALGHLEAAVVLYKWDRRAISIPDSLGRLPLGI  1150
1151  ARSRGHVKLAECLEHLQRDEQAQLGQNPRIHCPASEEPSTESWMAQWHSE  1200
1201  AISSPEIPKGVTVIASTNPELRRPRSEPSNYYSSESHKDYPAPKKHKLNP  1250
1251  EYFQTRQEKLLPTALSLEEPNIRKQSPSSKQSVPETLSPSEGVRDFSREL  1300
1301  SPPTPETAAFQASGSQPVGKWNSKDLYIGVSTVQVTGNPKGTSVGKEAAP  1350
1351  SQVRPREPMSVLMMANREVVNTELGSYRDSAENEECGQPMDDIQVNMMTL  1400
1401  AEHIIEATPDRIKQENFVPMESSGLERTDPATISSTMSWLASYLADADCL  1450
1451  PSAAQIRSAYNEPLTPSSNTSLSPVGSPVSEIAFEKPNLPSAADWSEFLS  1500
1501  ASTSEKVENEFAQLTLSDHEQRELYEAARLVQTAFRKYKGRPLREQQEVA  1550
1551  AAVIQRCYRKYKQYALYKKMTQAAILIQSKFRSYYEQKKFQQSRRAAVLI  1600
1601  QKYYRSYKKCGKRRQARRTAVIVQQKLRSSLLTKKQDQAARKIMRFLRRC  1650
1651  RHSPLVDHRLYKRSERIEKGQGT                             1673

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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