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

NucPred

Fetching Q9ULL5 from www.uniprot.org...

The NucPred score for your sequence is 0.86 (see score help below)

   1  MDRNYPSAGFGDPLGAGAGWSYERSAKASLVYGSSRTSHPETDILHRQAY    50
  51  AAPHPLQSYATNHHPAGLSGLFDTGLHHAGSAGPDASVMNLISALESRGP   100
 101  QPGPSASSLLSQFRSPSWQTAMHTPGPTELFISGALPGSSTFPSSSALSA   150
 151  YQHPASFGSRPFPVPSSLSLQDPPFSPPANGLLSPHDVLHLKPSQAPTVP   200
 201  SSLGFERLAGGGVLGPAGLGPAQTPPYRPGPPDPPPPPRHLPTQFNLLAS   250
 251  SSAAAAAAEQSSPQLYNFSGAAPGPPPPERALPRQDTVIKHYQRPASAQP   300
 301  PPPPPPAHALQHYLSCGGSYPSMGHRANLACSPLGGGEPSPGAGEPSKAG   350
 351  PSGATAGASGRATGPEAAGGGGAGGGGGGYRPIIQSPGYKTGKGGYGAAA   400
 401  GGATRPPPPRSTATPKCQSLGGPAAAYATGKASGAGGAGGQAYSPGQPQG   450
 451  LLGPQAYGQGFGGGQAQDLSKAPSYSGGPPQPPSGPPPPGLATCQSYSPD   500
 501  QLQGQLYGVQGEPYPGPAAHSQGLPTASPSLSYSTGHSPALSGHGGGWGP   550
 551  SSLGGGGEASPSHIIRPLQSPPATGRPPGVGSPGAPGKYLSSVLASAPFL   600
 601  APPGAGSYAAGAGGYKGKGDGSELLAGPGGPPAERTEDEEFLIQHLLQAP   650
 651  SPPRTSGADGLVGEDGAADASKGLGGSGGAGGPPGTPYELAKEDPQRYHL   700
 701  QSVIRTSASLDEGATAALELGLGRLKEKKKGPERGGETPEGLATSVVHYG   750
 751  AGAKELGAFLQKSPPPPPPTAQSTQPTPHGLLLEAGGPDLPLVLPPPPPQ   800
 801  LLPSVLSHAPSPSPSASKVGVHLLEPATRDGAPQPPPPPPPPPPPMPLQL   850
 851  EAHLRSHGLEPAAPSPRLRPEESLDPPGAMQELLGALEPLPPAPGDTGVG   900
 901  PPNSEGKDPAGAYRSPSPQGTKAPRFVPLTSICFPDSLLQDEERSFFPTM   950
 951  EEMFGGGAADDYGKAGPPEDEGDPKAGAGPPPGPPAYDPYGPYCPGRASG  1000
1001  AGPETPGLGLDPNKPPELPSTVNAEPLGLIQSGPHQAAPPPPPPPPPPPA  1050
1051  PASEPKGGLTSPIFCSTKPKKLLKTSSFHLLRRRDPPFQTPKKLYAQEYE  1100
1101  FEADEDKADVPADIRLNPRRLPDLVSSCRSRPALSPLGDIDFCPPNPGPD  1150
1151  GPRRRGRKPTKAKRDGPPRPRGRPRIRPLEVPTTAGPASASTPTDGAKKP  1200
1201  RGRGRGRGRKAEEAGGTRLEPLKPLKIKLSVPKAGEGLGTSSGDAISGTD  1250
1251  HNSLDSSLTREKIEAKIKEVEEKQPEMKSGFMASFLDFLKSGKRHPPLYQ  1300
1301  AGLTPPLSPPKSVPPSVPARGLQPQPPATPAVPHPPPSGAFGLGGALEAA  1350
1351  ESEGLGLGCPSPCKRLDEELKRNLETLPSFSSDEEDSVAKNRDLQESISS  1400
1401  AISALDDPPLAGPKDTSTPDGPPLAPAAAVPGPPPLPGLPSANSNGTPEP  1450
1451  PLLEEKPPPTPPPAPTPQPQPPPPPPPPQPALPSPPPLVAPTPSSPPPPP  1500
1501  LPPPPPPAMPSPPPPPPPAAAPLAAPPEEPAAPSPEDPELPDTRPLHLAK  1550
1551  KQETAAVCGETDEEAGESGGEGIFRERDEFVIRAEDIPSLKLALQTGREP  1600
1601  PPIWRVQKALLQKFTPEIKDGQRQFCATSNYLGYFGDAKNRYQRLYVKFL  1650
1651  ENVNKKDYVRVCARKPWHRPPVPVRRSGQAKNPVSAGGSSAPPPKAPAPP  1700
1701  PKPETPEKTTSEKPPEQTPETAMPEPPAPEKPSLLRPVEKEKEKEKVTRG  1750
1751  ERPLRGERATSGRQTRPERSLATGQPATSRLPKARPTKVKAEPPPKKRKK  1800
1801  WLKEAGGNATAGGGPPGSSSDSESSPGAPSEDERAVPGRLLKTRAMREMY  1850
1851  RSYVEMLVSTALDPDMIQALEDTHDELYLPPMRKIDGLLNEHKKKVLKRL  1900
1901  SLSPALQDALHTFPQLQVEQSGEGSPEEGAVRLRPAGEPYNRKTLSKLKR  1950
1951  SVVRAQEFKVELEKSGYYTLYHSLHHYKYHTFLRCRDQTLAIEGGAEDLG  2000
2001  QEEVVQQCMRNQPWLEQLFDSFSDLLAQAQAHSRCG                2036

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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