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

NucPred

Fetching O08710 from www.uniprot.org...

The NucPred score for your sequence is 0.69 (see score help below)

   1  MTALVLWVSTLLSSVCLVAANIFEYQVDAQPLRPCELQREKAFLKQAEYV    50
  51  PQCSEDGSFQTVQCQNDGQSCWCVDSDGREVPGSRQLGRPTVCLSFCQLH   100
 101  KQRILLGSYINSTDALYLPQCQDSGNYAPVQCDLQRVQCWCVDTEGMEVY   150
 151  GTRQQGRPTRCPRSCEIRNRRLLHGVGDRSPPQCTADGEFMPVQCKFVNT   200
 201  TDMMIFDLIHNYNRFPDAFVTFSSFRGRFPEVSGYCYCADSQGRELAETG   250
 251  LELLLDEIYDTIFAGLDQASTFTQSTMYRILQRRFLAIQLVISGRFRCPT   300
 301  KCEVEQFAATRFGHSYIPRCHRDGHYQTVQCQTEGMCWCVDAQGREVPGT   350
 351  RQQGQPPSCAADQSCALERQQALSRFYFETPDYFSPQDLLSSEDRLAPVS   400
 401  GVRSDTSCPPRIKELFVDSGLLRSIAVEHYQRLSESRSLLREAIRAVFPS   450
 451  RELAGLALQFTTNPKRLQQNLFGGTFLANAAQFNLSGALGTRSTFNFSQF   500
 501  FQQFGLPGFLNRDRVTTLAKLLPVRLDSSSTPETLRVSEKTVAMNKRVVG   550
 551  NFGFKVNLQENQDALKFLVSLLELPEFLVFLQRAVSVPEDIARDLGDVME   600
 601  MVFSAQACKQMPGKFFVPSCTAGGSYEDIQCYAGECWCVDSRGKELDGSR   650
 651  VRGGRPRCPTKCEKQRAQMQSLASAQPAGSSFFVPTCTREGYFLPVQCFN   700
 701  SECYCVDTEGQVIPGTQSTVGEAKQCPSVCQLQAEQAFLGVVGVLLSNSS   750
 751  MVPSISNVYIPQCSASGQWRHVQCDGPHEQVFEWYERWKTQNGDGQELTP   800
 801  AALLMKIVSYREVASRNFSLFLQSLYDAGQQRIFPVLAQYPSLQDVPQVV   850
 851  LEGATTPPGENIFLDPYIFWQILNGQLSQYPGPYSDFNMPLEHFNLRSCW   900
 901  CVDEAGQKLDGTQTKPGEIPACPGPCEEVKLRVLKFIKETEEIVSASNAS   950
 951  SFPLGESFLVAKGIQLTSEELDLPPQFPSRDAFSEKFLRGGEYAIRLAAQ  1000
1001  STLTFYQSLRASLGKSDGAASLLWSGPYMPQCNMIGGWEPVQCHAGTGQC  1050
1051  WCVDGRGEFIPGSLMSRSSQMPQCPTNCELSRASGLISAWKQAGPQRNPG  1100
1101  PGDLFIPVCLQTGEYVRKQTSGTGTWCVDPASGEGMPVNTNGSAQCPGLC  1150
1151  DVLKSRALSRKVGLGYSPVCEALDGAFSPVQCDLAQGSCWCVLGSGEEVP  1200
1201  GTRVVGTQPACESPQCPLPFSGSDVADGVIFCETASSSGVTTVQQCQLLC  1250
1251  RQGLRSAFSPGPLICSLESQHWVTLPPPRACQRPQLWQTMQTQAHFQLLL  1300
1301  PPGKMCSVDYSGLLQAFQVFILDELIARGFCQIQVKTFGTLVSSTVCDNS  1350
1351  SIQVGCLTAERLGVNVTWKLQLEDISVGSLPDLYSIERAVTGQDLLGRFA  1400
1401  DLIQSGRFQLHLDSKTFSADTTLYFLNGDSFVTSPRTQLGCMEGFYRVPT  1450
1451  TRQDALGCVKCPEGSFSQDGRCTPCPAGTYQEQAGSSACIPCPRGRTTIT  1500
1501  TGAFSKTHCVTDCQKNEAGLQCDQNGQYQASQKNRDSGEVFCVDSEGRKL  1550
1551  QWLQTEAGLSESQCLMIRKFDKAPESKVIFDANSPVIVKSSVPSADSPLV  1600
1601  QCLTDCANDEACSFLTVSTMESEVSCDFYSWTRDNFACVTSDQEQDAMGS  1650
1651  LKATSFGSLRCQVKVRNSGKDSLAVYVKKGYESTAAGQKSFEPTGFQNVL  1700
1701  SGLYSPVVFSASGANLTDTHTYCLLACDNDSCCDGFIITQVKGGPTICGL  1750
1751  LSSPDILLCHINDWRDTSATQANATCAGVTYDQGSRQMTLSLGGQEFLQG  1800
1801  LALLEGTQDSFTSFQQVYLWKDSDMGSRPESMGCERGMVPRSDFPGDMAT  1850
1851  ELFSPVDITQVIVNTSHSLPSQQYWLFTHLFSAEQANLWCLSRCAQEPIF  1900
1901  CQLADITKSSSLYFTCFLYPEAQVCDNVMESNAKNCSQILPHQPTALFRR  1950
1951  KVVLNDRVKNFYTRLPFQKLTGISIRDKVPMSGKLISNGFFECERLCDRD  2000
2001  PCCTGFGFLNVSQLQGGEVTCLTLNSMGIQTCNEESGATWRILDCGSEDT  2050
2051  EVHTYPFGWYQKPAVWSDTPSFCPSAALQSLTEEKVTSDSWQTLALSSVI  2100
2101  VDPSIKHFDVAHISTAATSNFSMAQDFCLQQCSRHQDCLVTTLQIQPGVV  2150
2151  RCVFYPDIQNCIHSLRSHTCWLLLHEEATYIYRKSGIPLVQSDVTSTPSV  2200
2201  RIDSFGQLQGGSQVIKVGTAWKQVYRFLGVPYAAPPLADNRFRAPEVLNW  2250
2251  TGSWDATKPRASCWQPGTRTPTPPQINEDCLYLNVFVPENLVSNASVLVF  2300
2301  FHNTMEMEGSGGQLTIDGSILAAVGNFIVVTANYRLGVFGFLSSGSDEVA  2350
2351  GNWGLLDQVAALTWVQSHIGAFGGDPQRVTLAADRSGADVASIHLLISRP  2400
2401  TRLQLFRKALLMGGSALSPAAIISPERAQQQAAALAKEVGCPTSSIQEVV  2450
2451  SCLRQKPANILNDAQTKLLAVSGPFHYWGPVVDGQYLRELPSRRLKRPLP  2500
2501  VKVDLLIGGSQDDGLINRAKAVKQFEESQGRTNSKTAFYQALQNSLGGED  2550
2551  SDARILAAAVWYYSLEHSTDDYASFSRALENATRDYFIICPMVNMASLWA  2600
2601  RRTRGNVFMYHVPESYGHGSLELLADVQYAFGLPFYSAYQGQFSTEEQSL  2650
2651  SLKVMQYFSNFIRSGNPNYPHEFSRKAAEFATPWPDFIPGAGGESYKELS  2700
2701  AQLPNRQGLKQADCSFWSKYIQTLKDADGAKDAQLTKSEEEDLEVGPGLE  2750
2751  EDLSGSLEPVPKSYSK                                    2766

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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