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

NucPred

Fetching Q9QYP0 from www.uniprot.org...

The NucPred score for your sequence is 0.51 (see score help below)

   1  MALGGALAAALALAFAVLGPLSHKVLAGDCKGQRQVLREAPGFVTDGAGN    50
  51  YSVNGNCEWLIEAPSPQHRILLDFLFLDTECTYDYLFVYDGDSPQGPLLA   100
 101  SLSGSTRPPPIEASSGKMLLHLFSDANYNLLGFNASFRFSLCPGGCQNHG   150
 151  QCKSPGVCVCEPGWGGPDCGLQECSAYCGSHGTCASTLGPCRCEPGFLGR   200
 201  ACDLHLWENQGAGWWHSVSAGDPAFSARVGAAGAFLSPPGLLAVFGGQDL   250
 251  NKALGDLVLYNFSTNTWESWDLTPAPAARHSHVAVAWAGFLVLMGGELAN   300
 301  GLLTNDVWAFSPLGGGHWELLAPPASSSSGPPGLAGHAAALVDDIWLYVS   350
 351  GGRTQHDLFSSGLFRFRLDHTSRGYWEQVIPAGGRPPAATGHSMVFHAPS   400
 401  RTLLVHGGHRPSTARFSVRVNSTELFHVDRRVWTTLKGRDGLQGPRERAF   450
 451  HTASVLGNYMVVYGGNVHTHYQEEKCYEDGIFFYHLGCHQWVSGAELAPP   500
 501  GTPEGRAAPPSGRYSHVAAVLGGSVLLVAGGYSGRPRGDLMAYKVPPFVF   550
 551  QAPALDYHLDYCSMYTDHSVCSRDPECSWCQGACQSAPPPGTPSGACPAA   600
 601  SCLGLGRLLSDCQACLAFSSPTAPPRGPGTLGWCVHNESCLPRPEQARCR   650
 651  GEQISGTVGWWGPAPVFVTSLEACVTQSFLPGLHLLTFQQPPNASQPDKV   700
 701  SIVRSTTITLTPSAETDVSLVYRGFIYPMLPGGPGGPGAEDVAVWARAQR   750
 751  LHVLARMARGPDTENMEEVGRWVAQQEKETRRLQRPGSSRLFPLPGRGNK   800
 801  YAVEIRGQLNGSAGPGHSELTLLWDRTGVPGGSEISFFFLEPYRSLACSS   850
 851  YSSCLGCLADQGCGWCLNSATCHLRQGRAHCEDDGNGESLLVLVPALCPL   900
 901  CEEHRDCHACTQDPFCEWHQSTNRKGDAACSRRGRGRGALKNPEECPPLC   950
 951  SQRLTCEDCLANSSQCAWCQSTHTCFLFAAYLARYPHGGCRGWDDSVHSE  1000
1001  PRCRSCHGFLTCHECLQSHECGWCGNEDNPTLGRCLQGDFSGPLGGGNCS  1050
1051  LWVGEGLGLPVALPARWAYARCPDVDECRLGLARCHPRATCLNTPLSYEC  1100
1101  HCQRGYQGDGITHCNRTCLEDCGHGVCSGPPDFTCVCDLGWTSDLPPPTP  1150
1151  APGPPAPRCSRDCGCNFHSHCRRRGPGYCDECQDWTWGEHCERCRPGSFG  1200
1201  NATGSGGCRPCQCNGHGDPRRGHCDNLSGLCFCQDHTEGAHCQICSPGYY  1250
1251  GDPRAGGSCFRECGGRALLTNVSSVALGSRRFGGLLPPGGGTARAGPGLS  1300
1301  YCVWVVSATEALQPCAPGTLCPPLTLTFSPDSSTPCTLSYVLAFDGFPRF  1350
1351  LDTGVVQSDRSLIAAFCGQRRDRPLTVQALSGLLVLHWEANGSSSWGFNA  1400
1401  SVGSARCGSGGPGSCPVPQECVPQDGAAGAGLCRCPQGWAGPHCRMALCP  1450
1451  ENCNAHTGAGICNQSLGVCICAEGFGGPDCATKLDGGQLVWETLMDSRLS  1500
1501  ADTASRFLHRLGHTMVEGPDATLWMFGGLGLPQGLLGNLYRYSVSERRWT  1550
1551  QMLAGAEDGGPGPSPRSFHAAAYVPAGRGAMYLLGGLTAGGITCDFWVLN  1600
1601  LTTLQWRQEKAPQSIELPAVAGHTLTARRGLSLLLVGGYSPENGFNQQLL  1650
1651  EYQLATTWVSGAQSGTPPTGLYGHSAVYHEATDSLYVFGGFRFHVELAAP  1700
1701  SPELYSLHCPDRTWSLLAPSQGAKPRPRLFHASALLGDTMVVLGGRSDPD  1750
1751  EFSSDVLLYQVNCNTWLLPDLTRPAFVGSPMEESVAHAVAAVGSRLYISG  1800
1801  GFGGVALGRLLALTLPPDPCRLLPSPEACNQSGACTWCHGACLSGDQAHR  1850
1851  LGCGVPPCSPMPRSPEECRRLRTCSECLARHPRTLQPGDGEASVPRCKWC  1900
1901  TNCPEGACIGRNGSCTSENDCRINQREVFWAGNCSEAACGAADCEQCTRE  1950
1951  GKCMWTRQFKRTGETRRILSVQPTYDWTCFSHSLLNVSPMPVESSPPLPC  2000
2001  PTPCHLLPNCTSCLASKGADGGWQHCVWSSSLQQCLSPSYLPLRCMAGGC  2050
2051  GRLLRGPESCSLGCAQATQCALCLRRPHCGWCAWGGQDGGGHCMEGGLSG  2100
2101  PRDGLTCGRPGASWAFLSCPPEDECANGHHDCNETQNCHDQPHGYECSCK  2150
2151  TGYTMDNVTGVCRPVCAQGCVNGSCVEPDHCRCHFGFVGRNCSTECRCNR  2200
2201  HSECAGVGARDHCLLCRNHTKGSHCEQCLPLFVGSALGGGTCRPCHAFCR  2250
2251  GNSHVCVSRKELEMARREPEKYSLDPEEIEAWVAEGPSEDEAVCVNCQNN  2300
2301  SYGDRCESCLHGYFLLDGKCTKCQCNGHADTCNEQDGTGCPCQNNTETGV  2350
2351  CQGSSPSDRRDCYKYQCAKCRESFHGSPLGGQQCYRLISVEQECCLDPTS  2400
2401  QTNCFHEPKRRALGPGRTVLFGVQPKFTNVDIRLTLDVTFGAVDLYVSTS  2450
2451  YDTFVVRVAPDTGVHTVHIQPPPPPPPPPPPADGVPRVASDLGGLGTGSG  2500
2501  SGSPVEPRVREVWPRGLITYVTVTEPSAVLVVRSVRDRLVITYPHEHHAL  2550
2551  KSSRFYLLLLGVGDPNGPGANGSADSQGLLFFRQDQAHIDLFVFFSVFFS  2600
2601  CFFLFLSLCVLLWKAKQALDQRQEQRRHLQEMTKMASRPFAKVTVCFPPD  2650
2651  PAGPAPAWKPAGLPPPAFRRSEPFLAPLLLTGAGGPWGPMGGGCCPPALP  2700
2701  ATTAGLRAGPITLEPTEDGMAGVATLLLQLPGGPHAPNGACLGSALVTLR  2750
2751  HRLHEYCGGSGGAGGSGHGGGGGRKGLLSQDNLTSMSL              2788

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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