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

NucPred

Fetching Q09332 from www.uniprot.org...

The NucPred score for your sequence is 0.54 (see score help below)

   1  MLRAVALCVSVVLIALYTPTSGESSQSYPITTLINAKWTQTPLYLEIAEY    50
  51  LADEQAGLFWDYVSGVTKLDTVLNEYDTESQQYNAALELVKSHVSSPQLP   100
 101  LLRLVVSMHSLTPRIQTHFQLAEELRSSGSCQSFTFAQVGSELACSFNEL   150
 151  QKKLEVPLAKDSLDASVVTYSFDHIFPGSENNTRTVVLYGDLGSSQFRTY   200
 201  HKLLEKEANAGRIRYILRHQLAKKDKRPVRLSGYGVELHLKSTEYKSQDD   250
 251  APKPEAGSTSDEDLANESDVQGFDFKVLKQKHPTLKRALDQLRQRLLQGN   300
 301  DEIAQLKAWEFQDLGLQAAAAIAEIQGDETLQILQYTAHNFPMLARTLLA   350
 351  HKVTDGLRAEVKHNTEAFGRSLNVAPPDGALFINGLFFDADTMDLYSLIE   400
 401  TLRSEMRVLESLHSNNVRGSLASSLLALDLTASSKKEFAIDIRDTAVQWV   450
 451  NDIENDVQYRRWPSSVMDLLRPTFPGMLRNIRKNVFNLVLVVDALQPTAR   500
 501  SVIKLSESFVIHQAPIRLGLVFDARDANEDNLADYVAITCAYNYVSQKKD   550
 551  ARAALSFLTDIYAAVGETKVVTKKDIVKQLTKEFTSLSFAKAEEFLEEDS   600
 601  TYDYGRELAAEFIQRLGFGDKGQPQALLNGVPMPSNVVTADSDFEEAIFT   650
 651  EIMTHTSNLQKAVYKGELTDNDVAIDYLMNQPHVMPRLNQRILSQEDVKY   700
 701  LDINGVAYKNLGNVGVLNRLSNRDMTATLMDNLKYFGGKKSTELIGRASL   750
 751  QFLTIWVFADLETDQGRDLLTHALDYVQSGESVRVAFIPNTESSSASSRR   800
 801  NLNRLVWAAMQSLPPTQATEQVLKWLKKPKEKIEIPTQLEDILGSTELHL   850
 851  KMLRVYSQRVLGLNKSQRLVIGNGRLYGPLSSDESFDSADFALLARFSSL   900
 901  QYSDKVRQVLKESAQDVNEEFNSDTLLKLYASLLPRQTKTRFKLPTDLKT   950
 951  DHSVVKLPPKQENLPHFDVAAVLDPASRAAQKLTPILILLRQVLNCQLNL  1000
1001  YLIPVPQHSDMPVKNFYRYVVEPEVQFEANGGRSDGPLAKFSGLPANPLL  1050
1051  TQQLQVPENWLVEAVRAVYDLDNIKLTDIGGPVHSEFDLEYLLLEGHCFD  1100
1101  AASGAPPRGLQLVLGTQSQPTLVDTIVMANLGYFQLKANPGAWSLRLREG  1150
1151  KSADIYAISHIEGTNTHHSAGSSEVQVLITSLRSHVVKLRVSKKPGMQQA  1200
1201  ELLSDDNEQAAQSGMWNSIASSFGGGSANQAATDEDTETINIFSVASGHL  1250
1251  YERLLRIMMVSLLKHTKSPVKFWFLKNYLSPQFTDFLPHMASEYNFQYEL  1300
1301  VQYKWPRWLHQQTEKQRTIWGYKILFLDVLFPLNVRKIIFVDADAIVRTD  1350
1351  IKELYDMDLGGAPYAYTPFCDSRKEMEGFRFWKQGYWRSHLMGRRYHISA  1400
1401  LYVVDLKRFRKIAAGDRLRGQYQALSQDPNSLSNLDQDLPNNMIHQVAIK  1450
1451  SLPDDWLWCQTWCSDSNFKTAKVIDLCNNPQTKEAKLTAAQRIVPEWKDY  1500
1501  DAELKTLMSRIEDHENSHSRDSAVDDSVDDSVEVTTVTPSHEPKHGEL    1548

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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