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

NucPred

Fetching O95477 from www.uniprot.org...

The NucPred score for your sequence is 0.48 (see score help below)

   1  MACWPQLRLLLWKNLTFRRRQTCQLLLEVAWPLFIFLILISVRLSYPPYE    50
  51  QHECHFPNKAMPSAGTLPWVQGIICNANNPCFRYPTPGEAPGVVGNFNKS   100
 101  IVARLFSDARRLLLYSQKDTSMKDMRKVLRTLQQIKKSSSNLKLQDFLVD   150
 151  NETFSGFLYHNLSLPKSTVDKMLRADVILHKVFLQGYQLHLTSLCNGSKS   200
 201  EEMIQLGDQEVSELCGLPREKLAAAERVLRSNMDILKPILRTLNSTSPFP   250
 251  SKELAEATKTLLHSLGTLAQELFSMRSWSDMRQEVMFLTNVNSSSSSTQI   300
 301  YQAVSRIVCGHPEGGGLKIKSLNWYEDNNYKALFGGNGTEEDAETFYDNS   350
 351  TTPYCNDLMKNLESSPLSRIIWKALKPLLVGKILYTPDTPATRQVMAEVN   400
 401  KTFQELAVFHDLEGMWEELSPKIWTFMENSQEMDLVRMLLDSRDNDHFWE   450
 451  QQLDGLDWTAQDIVAFLAKHPEDVQSSNGSVYTWREAFNETNQAIRTISR   500
 501  FMECVNLNKLEPIATEVWLINKSMELLDERKFWAGIVFTGITPGSIELPH   550
 551  HVKYKIRMDIDNVERTNKIKDGYWDPGPRADPFEDMRYVWGGFAYLQDVV   600
 601  EQAIIRVLTGTEKKTGVYMQQMPYPCYVDDIFLRVMSRSMPLFMTLAWIY   650
 651  SVAVIIKGIVYEKEARLKETMRIMGLDNSILWFSWFISSLIPLLVSAGLL   700
 701  VVILKLGNLLPYSDPSVVFVFLSVFAVVTILQCFLISTLFSRANLAAACG   750
 751  GIIYFTLYLPYVLCVAWQDYVGFTLKIFASLLSPVAFGFGCEYFALFEEQ   800
 801  GIGVQWDNLFESPVEEDGFNLTTSVSMMLFDTFLYGVMTWYIEAVFPGQY   850
 851  GIPRPWYFPCTKSYWFGEESDEKSHPGSNQKRISEICMEEEPTHLKLGVS   900
 901  IQNLVKVYRDGMKVAVDGLALNFYEGQITSFLGHNGAGKTTTMSILTGLF   950
 951  PPTSGTAYILGKDIRSEMSTIRQNLGVCPQHNVLFDMLTVEEHIWFYARL  1000
1001  KGLSEKHVKAEMEQMALDVGLPSSKLKSKTSQLSGGMQRKLSVALAFVGG  1050
1051  SKVVILDEPTAGVDPYSRRGIWELLLKYRQGRTIILSTHHMDEADVLGDR  1100
1101  IAIISHGKLCCVGSSLFLKNQLGTGYYLTLVKKDVESSLSSCRNSSSTVS  1150
1151  YLKKEDSVSQSSSDAGLGSDHESDTLTIDVSAISNLIRKHVSEARLVEDI  1200
1201  GHELTYVLPYEAAKEGAFVELFHEIDDRLSDLGISSYGISETTLEEIFLK  1250
1251  VAEESGVDAETSDGTLPARRNRRAFGDKQSCLRPFTEDDAADPNDSDIDP  1300
1301  ESRETDLLSGMDGKGSYQVKGWKLTQQQFVALLWKRLLIARRSRKGFFAQ  1350
1351  IVLPAVFVCIALVFSLIVPPFGKYPSLELQPWMYNEQYTFVSNDAPEDTG  1400
1401  TLELLNALTKDPGFGTRCMEGNPIPDTPCQAGEEEWTTAPVPQTIMDLFQ  1450
1451  NGNWTMQNPSPACQCSSDKIKKMLPVCPPGAGGLPPPQRKQNTADILQDL  1500
1501  TGRNISDYLVKTYVQIIAKSLKNKIWVNEFRYGGFSLGVSNTQALPPSQE  1550
1551  VNDAIKQMKKHLKLAKDSSADRFLNSLGRFMTGLDTKNNVKVWFNNKGWH  1600
1601  AISSFLNVINNAILRANLQKGENPSHYGITAFNHPLNLTKQQLSEVALMT  1650
1651  TSVDVLVSICVIFAMSFVPASFVVFLIQERVSKAKHLQFISGVKPVIYWL  1700
1701  SNFVWDMCNYVVPATLVIIIFICFQQKSYVSSTNLPVLALLLLLYGWSIT  1750
1751  PLMYPASFVFKIPSTAYVVLTSVNLFIGINGSVATFVLELFTDNKLNNIN  1800
1801  DILKSVFLIFPHFCLGRGLIDMVKNQAMADALERFGENRFVSPLSWDLVG  1850
1851  RNLFAMAVEGVVFFLITVLIQYRFFIRPRPVNAKLSPLNDEDEDVRRERQ  1900
1901  RILDGGGQNDILEIKELTKIYRRKRKPAVDRICVGIPPGECFGLLGVNGA  1950
1951  GKSSTFKMLTGDTTVTRGDAFLNKNSILSNIHEVHQNMGYCPQFDAITEL  2000
2001  LTGREHVEFFALLRGVPEKEVGKVGEWAIRKLGLVKYGEKYAGNYSGGNK  2050
2051  RKLSTAMALIGGPPVVFLDEPTTGMDPKARRFLWNCALSVVKEGRSVVLT  2100
2101  SHSMEECEALCTRMAIMVNGRFRCLGSVQHLKNRFGDGYTIVVRIAGSNP  2150
2151  DLKPVQDFFGLAFPGSVLKEKHRNMLQYQLPSSLSSLARIFSILSQSKKR  2200
2201  LHIEDYSVSQTTLDQVFVNFAKDQSDDDHLKDLSLHKNQTVVDVAVLTSF  2250
2251  LQDEKVKESYV                                         2261

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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