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

NucPred

Fetching Q9MEF2 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MGNQRNRVNLNPFRFWVFELREILREIKNSRYPFNSVGSFIHIFVHQERF    50
  51  LKLLDPRIWSVLRSQGSTGVVLFLVAVLIYRINNRNMIERKNIYLTGLLP   100
 101  IPTNFAGPRNETLEESFLSSNINRLIVSLLHLPKGKRLSESCFLDPKEST   150
 151  RVLPITKWRNWIGKRRDSSQLKGSSDQSRDHFDSIGTEDSEYHTLINQRE   200
 201  IQQRKERSSLLDPSFLQTERTEIESDRFSKGLSGSSSKSRLFTEGEKEMN   250
 251  NHLPPEEIEEFLGNPTRSILSFFSDEWSELHLGSNPTERSTVDQKLLKKE   300
 301  QEVSFAPFRRSETKEIVNLFKTMAYLQKTVSIHPISSDPGCDMVPKDELD   350
 351  SEERFQEMADLFTLSITEPDLVYHKGFAFSIDSSVLDQKQFLAEARDESK   400
 401  KKSLLVLPPVFYQENESFYRRIRKRGVQISCGNDLEDPKPKIVVFASNNI   450
 451  VEAVNQYRWIRNLIQIQYSTHGYIRNVLNRFFLMNRSDRNFEYGIQRDQI   500
 501  GNDTLNHRTFMKYTINQHLSNLKKSQKKGSDPLILISRTERSVNRDPNAY   550
 551  RYKWSKGSKNFQEHLEHFVSEQKSRFQVVFDRYRSIRNRYRSIRNRYRSR   600
 601  INQYSSDRSEVSDKKDNRYRSRINQYSSDRSEVSDQKNLAKFRSFVFSKL   650
 651  LLFLSNSLPFFFVSFGNTPPIQRSEIRVSELKGPNDRLCNQFLESIGLQL   700
 701  VYLKKLKPFLLDDHETSQKSKLLFNKKPEGMIDSFHTRNNRGKSLDSYFS   750
 751  MISHDQDNWLNPVKPFHRSSLISSFYKANRLRFLNNPHDFGFFCNKRFPF   800
 801  YVDIKNLDFTYGQFLNILFIRNTKFSLCGDKKKHAFLERDTISSIESQVS   850
 851  NLFKDFPQSGDERYNFYKYFHLAMRSDPLVRRAIYSIADISGTPLTEGQR   900
 901  VNFERTYCQPLSDMNLSDSEGKNLYQYLNFNSNMGLIYSEKCFSSEKRKK   950
 951  KKPEKRKEKKPEKRKEKKPEKRKEKKPEKRKEKKPEKRKEKKPEKRKEKK  1000
1001  PEKRKEKKQSLYLKQWVEKVQMDRALQGERVSLILSNWNLFKTYVMPFSL  1050
1051  TSTGYNLLKLMFLDTLGSYVMPLLRSSPKFVSICYAISDPCGISWRILQK  1100
1101  KLCLLQWNWISAISNKCFHKLLLSEESIHRNNESPSMTDLRWPNLGAFLY  1150
1151  SILFLLFVAGHLVFSHLLFLSQDFSELQRDFARAQSLMIPSYIVELRELL  1200
1201  DMYPAPRSFKKLFLAAREKLVNYLRWGGGRKSFLIHLFELLNITPNPIDR  1250
1251  IAFLKNTRHLSHTSKELYSLITELGDFSSLCSGQRYRYDQIIENVNGPCC  1300
1301  LIDDKIESWISNCDAIEDKEREFLVPFCNFTRETRIDQILLSLTHSDHLS  1350
1351  NNDSASQMSEEPGAFYLRHLVDIHKKGLMNYECNTSCLAERRIFLAHYQT  1400
1401  ITYSPCGDNRSHFPSHGKTFSLRLPLHPSRATLVIGSIGSGRSYLVKSLA  1450
1451  TNSYVPLITVVLNKFLKNWTPQGFDIHESGVYDEYGDDAEEANDYGASFF  1500
1501  DFLDNDSDDYEDRDSDDYDEPGASDDYEDRDMEDFVDSEMTEWLTKTNVP  1550
1551  LVYQLLDDEIDEFYITLQFELAKAMSPCILWIPNIHDLDAKESDYLSLGL  1600
1601  LVNHLSRDCGRRSTKNEILVIASTHIPQKVDPSLIGPDGLSTCIKTRRLL  1650
1651  VPQQQQCLFTLSYTRGFHLENKMFHTHTNEFESTILGPSVPDLVALTNEA  1700
1701  LSISITQKKSIIDTTTIRYALHRKTWDLEADRNLSPAKEHGTLFYQVGRA  1750
1751  FAHTVLLRNCPIDPISIYIKKNLCEAGDSSLYKWYFELGTSMKKLTILLY  1800
1801  LLTCSAGSIAQDLLSPPGPDEQNLITSYGLVENDSDLVHGLSDIVHGLLE  1850
1851  LEGALVGSSPTEEEVEGTEEEVEGTEEEVEGTEEEVEGTEEEVEGTEEEV  1900
1901  EGTEEEVEGTEDEEGEGTEEEVEGTEDEEGEGTEEEVEGTEDEEGEGTEE  1950
1951  EVEGTEDEEGEGTEDEEGEGTEEEVEGTEEEVEGTEDEEGEGTEKDSSQF  2000
2001  DNDRVTLLLRPKPRNPLDIQRLIYQHQKYESELEEDDDDDEDVFAPQKML  2050
2051  EDLFSELVWSPRIWHPWDFILDCEAEIPAEEIPEEEDPLPEEALETEVAV  2100
2101  WGEEEEGEADDEEDERLEAQQEDELLEEEDEELKEEEDELHEEEEEEEEE  2150
2151  EEEEEEDELHEEEEEEEEEDELQENDSEFFRSETQQPQARDGFSEEEGCF  2200
2201  RISQFMWVPGDPLSFLYKDTPFVEVLSYPEEATEISKELLRLLNPKTKRD  2250
2251  APKRARQRWWTKKKQDKHYELVLDRQRWLITKSSLSKSNGFFRSNTPSES  2300
2301  YQYLSNLFLSNRRLLDQITKTFFRKKWLFPDEMKIGFMEQ            2340

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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