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

NucPred

Fetching Q60ZN5 from www.uniprot.org...

The NucPred score for your sequence is 0.77 (see score help below)

   1  MNYRIFLLFCTTTVLWSVVSTQLVLGKPPIFQNTGPVEQKVAVEGEIVRL    50
  51  KCDDAELAEQYEWRVGDASGDLIAASRFAQVTVSRTNDNQKYRCVARNTV   100
 101  GAAISPPSVVRSKYLDDFDASDESAQYDVLAGIGRHFVLRTPRLLSSRNL   150
 151  DISYSWIKDDSNQVTPDATHFVTANGDLVVTSVKRDDFGTYKLMASSDDL   200
 201  KEIVSKEYIVKDNGMAPSLQNTLSIIYFSPERTIVESSMPHDEKFDCVTS   250
 251  FEAKDDVRIRWFLNGQPITGSEVGIKTTMNNRRLIISNPSGFTRGEHKLE   300
 301  CRADAAMGRTSDQNSAYLTFISRPVLKDLPNEIHKKVGSSLTLKCGVKKK   350
 351  SSMDIKWYRNGLMMNTQRGKLTIDRIRQEDFGLYQCEAVNEAGADMSSVW   400
 401  VKEGDINNDTMVMGMSEDGRSLEEEISMETPPPRKLKFFDSSKSQEQLFP   450
 451  FTSDIESSQRLTKTPKDLTAASGTDKITLECAAAGSPPPHIVWFLNGNGI   500
 501  QTDSVKYDFSNGDLTIHDIRKSDEGEYTCEISGTDVKASANVQVNGDSLI   550
 551  EYGPADQKSLIGTNVEFSCEVAKEYARKATVEWYLNDALLPVNGNSGLRI   600
 601  SRNRKGSLIIRQVGPDNTGEYRCRVTVDGREENASAMLQIIEKPAMPERV   650
 651  RAELHNETMPAKVRVRWNEGFDGNEPIIKHAIEIRTMGPTGLWSDWTTAI   700
 701  DNIPKDDGKPCCWADIEDLRPSSTAEFRVVASNKHGPGKPSLPSSSVTMP   750
 751  QQPPSAAPRNVAASARSPHSVMVQWQQPKEEQDSGDFLGYVVRYRLAGYS   800
 801  SLTWNEKNLTTKDARNTLVDELITWREYEIQVAAYNKRGLGVFSESIEVT   850
 851  TAEGRPTQAPKNVRVKVLNSTAVSLEFTAPEQQRIPGVNLGYKVQFWKGE   900
 901  PEKGELYKQVILDPDRRQLSTVVNELEKFGHYNLTVLCFTTPGDGPKSNI   950
 951  LRVVTEEDTPEAVDELSIAEVMYNGAVLTWNPPMKENGIVTKYTIRHWAS  1000
1001  SSPDVKTKHEVDGSTTNITIDGLQPSTRYGVDVMASTKKGDGPVEETKFE  1050
1051  SGVPPELPGRPSMLSIGDISATTVQLHFTPGFDGHTAIRQWIVEGKMADS  1100
1101  SVFAHIFNVSSPKARSIIVTGLRPFTQYQLRLIAENVKGRGAPSEPSRTF  1150
1151  ETLQTNPETPSQRLFTEPVSATSISVSWTPLLATHWNGQPKGYLIVYREV  1200
1201  DEDNWKEVRTPALRSSEHTVTDLRPFTTYEVNVFSENVFGRSLPTDAVKA  1250
1251  RTYESVPSGSPRNIVVTAEGSKSAIVKWDPVAELSTNGDVIGYKLRVVPE  1300
1301  RESLMADETREIDVPGQSTLMTKVSNLRPFTSYYVYMSAYTIVGNGPENS  1350
1351  TPLSFETLEDVPAPPESFQCSQISEQDVRMKWLPPGSPNGKITNYVISYW  1400
1401  KSHEPRSMAIDAQVAGNLLMFSAMSLSPNTQYTFAIKAKNSKGESEEAVA  1450
1451  EVMTSSVRLPVRNAPAPVRDTTSQHLATEITIRWDESLPRKLTEDAESPV  1500
1501  RAVQVSYQKTNEDEWLTLEKKFEYSKRRAVIKHLSPNSMFRFRIRFIGDF  1550
1551  LESSWSPESEWMRTLPSAPFAQPISLKATPYERNSVQLEWVVPHKSTWNS  1600
1601  DAIGYRIHYREYPSNETWQMEEIAVHDPHEDREEKVLAKLSTFRHYIIRM  1650
1651  RLFNSEGEGPFSAPVFVYVGYSIPKRNLTNIITEPLSSSSIRVKWDAWPK  1700
1701  EDSETVTSFKVRYVPVASVLSSVSSEEEVMIVDTNECILSDLRKFAEYQI  1750
1751  SVSPYNRAGEGKMSQVREKTLEDKPGPVGVLRFSDVLMDSVKVSWDEPAQ  1800
1801  PNGMVIGYIVNYKGYRMQEEFKNEDQQRTSRNYFDSHGLAEGVTYFFSVW  1850
1851  AETSAGKGELRSANVTIGPSKDGPLPPSKPQITSGQSYVTLSWNDVANSD  1900
1901  EIVGHLLQAKRVSVAEETENGYVSQRPRRNEIRGAKSAAQTSASSNSNRP  1950
1951  THPIGEWITLRPTDGKSEKEQVSYRELQPSSFYVFRVFTRNVRGIGRASP  2000
2001  ETEQLFVPESIPDDPFYTTWWFMALVAMAAFVLIVIIIAILCVTGSSAKY  2050
2051  RREKRSRSIDSLQLADGNFASFQLKGTSAANMTRSRELPTRPGTTQSWLS  2100
2101  DQSREPPAYGSVLGDGRNNGGVMNMYGLATDVIPPLPNSGPPHASLEAMQ  2150
2151  KLSALVGRDIRSQNTAYVVSSSARGSDNERNEYMPTRSDLYGTRSEYGRV  2200
2201  EYRGHIPSSSGGSQPQGSPQQQQEPYDSFDEEDDVDDDTVIRGDRTMTDG  2250
2251  ADDIARHYGSTDQYRDTWRKVRDTDMVRAPILTNQQPSSAAGRSSTTDST  2300
2301  SEGPWANIPATPNLTAGFSSFV                              2322

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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