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

NucPred

Fetching Q86UR5 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MSSAVGPRGPRPPTVPPPMQELPDLSHLTEEERNIIMAVMDRQKEEEEKE    50
  51  EAMLKCVVRDMAKPAACKTPRNAENQPHQPSPRLHQQFESYKEQVRKIGE   100
 101  EARRYQGEHKDDAPTCGICHKTKFADGCGHLCSYCRTKFCARCGGRVSLR   150
 151  SNNEDKVVMWVCNLCRKQQEILTKSGAWFFGSGPQQTSQDGTLSDTATGA   200
 201  GSEVPREKKARLQERSRSQTPLSTAAASSQDAAPPSAPPDRSKGAEPSQQ   250
 251  ALGPEQKQASSRSRSEPPRERKKTPGLSEQNGKGALKSERKRVPKTSAQP   300
 301  VEGAVEERERKERRESRRLEKGRSQDYPDTPEKRDEGKAADEEKQRKEED   350
 351  YQTRYRSDPNLARYPVKPPPEEQQMRMHARVSRARHERRHSDVALPRTEA   400
 401  GAALPEGKAGKRAPAAARASPPDSPRAYSAERTAETRAPGAKQLTNHSPP   450
 451  APRHGPVPAEAPELKAQEPLRKQSRLDPSSAVLMRKAKREKVETMLRNDS   500
 501  LSSDQSESVRPSPPKPHRSKRGGKKRQMSVSSSEEEGVSTPEYTSCEDVE   550
 551  LESESVSEKGDLDYYWLDPATWHSRETSPISSHPVTWQPSKEGDRLIGRV   600
 601  ILNKRTTMPKDSGALLGLKVVGGKMTDLGRLGAFITKVKKGSLADVVGHL   650
 651  RAGDEVLEWNGKPLPGATNEEVYNIILESKSEPQVEIIVSRPIGDIPRIP   700
 701  ESSHPPLESSSSSFESQKMERPSISVISPTSPGALKDAPQVLPGQLSVKL   750
 751  WYDKVGHQLIVNVLQATDLPARVDGRPRNPYVKMYFLPDRSDKSKRRTKT   800
 801  VKKILEPKWNQTFVYSHVHRRDFRERMLEITVWDQPRVQEEESEFLGEIL   850
 851  IELETALLDDEPHWYKLQTHDESSLPLPQPSPFMPRRHIHGESSSKKLQR   900
 901  SQRISDSDISDYEVDDGIGVVPPVGYRSSARESKSTTLTVPEQQRTTHHR   950
 951  SRSVSPHRGNDQGKPRSRLPNVPLQRSLDEIHPTRRSRSPTRHHDASRSP  1000
1001  VDHRTRDVDSQYLSEQDSELLMLPRAKRGRSAECLHTTRHLVRHYKTLPP  1050
1051  KMPLLQSSSHWNIYSSILPAHTKTKSVTRQDISLHHECFNSTVLRFTDEI  1100
1101  LVSELQPFLDRARSASTNCLRPDTSLHSPERERGRWSPSLDRRRPPSPRI  1150
1151  QIQHASPENDRHSRKSERSSIQKQTRKGTASDAERVLPTCLSRRGHAAPR  1200
1201  ATDQPVIRGKHPARSRSSEHSSIRTLCSMHHLVPGGSAPPSPLLTRMHRQ  1250
1251  RSPTQSPPADTSFSSRRGRQLPQVPVRSGSIEQASLVVEERTRQMKMKVH  1300
1301  RFKQTTGSGSSQELDREQYSKYNIHKDQYRSCDNVSAKSSDSDVSDVSAI  1350
1351  SRTSSASRLSSTSFMSEQSERPRGRISSFTPKMQGRRMGTSGRSIMKSTS  1400
1401  VSGEMYTLEHNDGSQSDTAVGTVGAGGKKRRSSLSAKVVAIVSRRSRSTS  1450
1451  QLSQTESGHKKLKSTIQRSTETGMAAEMRKMVRQPSRESTDGSINSYSSE  1500
1501  GNLIFPGVRLGADSQFSDFLDGLGPAQLVGRQTLATPAMGDIQIGMEDKK  1550
1551  GQLEVEVIRARSLTQKPGSKSTPAPYVKVYLLENGACIAKKKTRIARKTL  1600
1601  DPLYQQSLVFDESPQGKVLQVIVWGDYGRMDHKCFMGVAQILLEELDLSS  1650
1651  MVIGWYKLFPPSSLVDPTLTPLTRRASQSSLESSTGPPCIRS          1692

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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