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

NucPred

Fetching P16621 from www.uniprot.org...

The NucPred score for your sequence is 0.63 (see score help below)

   1  MGLQMTAARPIAALSLLVLSLLTWTHPTIVDAAHPPEIIRKPQNQGVRVG    50
  51  GVASFYCAARGDPPPSIVWRKNGKKVSGTQSRYTVLEQPGGISILRIEPV   100
 101  RAGRDDAPYECVAENGVGDAVSADATLTIYEGDKTPAGFPVITQGPGTRV   150
 151  IEVGHTVLMTCKAIGNPTPNIYWIKNQTKVDMSNPRYSLKDGFLQIENSR   200
 201  EEDQGKYECVAENSMGTEHSKATNLYVKVRRVPPTFSRPPETISEVMLGS   250
 251  NLNLSCIAVGSPMPHVKWMKGSEDLTPENEMPIGRNVLQLINIQESANYT   300
 301  CIAASTLGQIDSVSVVKVQSLPTAPTDVQISEVTATSVRLEWSYKGPEDL   350
 351  QYYVIQYKPKNANQAFSEISGIITMYYVVRALSPYTEYEFYVIAVNNIGR   400
 401  GPPSAPATCTTGETKMESAPRNVQVRTLSSSTMVITWEPPETPNGQVTGY   450
 451  KVYYTTNSNQPEASWNSQMVDNSELTTVSELTPHAIYTVRVQAYTSMGAG   500
 501  PMSTPVQVKAQQGVPSQPSNFRATDIGETAVTLQWTKPTHSSENIVHYEL   550
 551  YWNDTYANQAHHKRISNSEAYTLDGLYPDTLYYIWLAARSQRGEGATTPP   600
 601  IPVRTKQYVPGAPPRNITAIATSSTTISLSWLPPPVERSNGRIIYYKVFF   650
 651  VEVGREDDEATTMTLNMTSIVLDELKRWTEYKIWVLAGTSVGDGPRSHPI   700
 701  ILRTQEDVPGDPQDVKATPLNSTSIHVSWKPPLEKDRNGIIRGYHIHAQE   750
 751  LRDEGKGFLNEPFKFDVVDTLEFNVTGLQPDTKYSIQVAALTRKGDGDRS   800
 801  AAIVVKTPGGVPVRPTVSLKIMEREPIVSIELEWERPAQTYGELRGYRLR   850
 851  WGVKDQALKEEMLSGPQMTKKRFDNLERGVEYEFRVAGSNHIGIGQETVK   900
 901  IFQTPEGTPGGPPSNITIRFQTPDVLCVTWDPPTREHRNGIITRYDVQFH   950
 951  KKIDHGLGSERNMTLRKAVFTNLEENTEYIFRVRAYTKQGAGPFSDKLIV  1000
1001  ETERDMGRAPMSLQAEATSEQTAEIWWEPVTSRGKLLGYKIFYTMTAVED  1050
1051  LDDWQTKTVGLTESADLVNLEKFAQYAVAIAARFKNGLGRLSEKVTVRIK  1100
1101  PEDVPLNLRAHDVSTHSMTLSWSPPIRLTPVNYKISFDAMKVFVDSQGFS  1150
1151  QTQIVPKREIILKHYVKTHTINELSPFTTYNVNVSAIPSDYSYRPPTKIT  1200
1201  VTTQMAAPQPMVKPDFYGVVNGEEILVILPQASEEYGPISHYYLVVVPED  1250
1251  KSNLHKIPDQFLTDDLLPGRNKPERPNAPYIAAKFPQRSIPFTFHLGSGD  1300
1301  DYHNFTNRKLEREKRYRIFVRAVVDTPQKHLYTSSPFSEFLSLDMREAPP  1350
1351  GERPHRPDPNWPAEPEVSVNRNKDEPEILWVVLPLMVSTFIVSTALIVLC  1400
1401  VVKRRRQPCKTPDQAAVTRPLMAADLGAGPTPSDPVDMRRLNFQTPGMIS  1450
1451  HPPIPISEFANHIERLKSNDNQKFSQEYESIEPGQQFTWDNSNLEHNKSK  1500
1501  NRYANVTAYDHSRVQLPAVEGVVGSDYINANYCDGYRKHNAYVATQGPLQ  1550
1551  ETFVDFWRMCWELKTATIVMMTRLEERTRIKCDQYWPTRGTETYGQIFVT  1600
1601  ITETQELATYSIRTFQLCRQGFNDRREIKQLQFTAWPDHGVPDHPAPFLQ  1650
1651  FLRRCRALTPPESGPVIVHCSAGVGRTGCYIVIDSMLERMKHEKIIDIYG  1700
1701  HVTCLRAQRNYMVQTEDQYIFIHDAILEAIICGVTEVPARNLHTHLQKLL  1750
1751  ITEPGETISGMEVEFKKLSNVKMDSSKFVTANLPCNKHKNRLVHILPYES  1800
1801  SRVYLTPIHGIEGSDYVNASFIDGYRYRSAYIAAQGPVQDAAEDFWRMLW  1850
1851  EHNSTIVVMLTKLKEMGREKCFQYWPHERSVRYQYYVVDPIAEYNMPQYK  1900
1901  LREFKVTDARDGSSRTVRQFQFIDWPEQGVPKSGEGFIDFIGQVHKTKEQ  1950
1951  FGQDGPITVHCSAGVGRSGVFITLSIVLERMQYEGVLDVFQTVRILRSQR  2000
2001  PAMVQTEDQYHFCYRAALEYLGSFDNYTN                       2029

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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