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

NucPred

Fetching Q8R4U0 from www.uniprot.org...

The NucPred score for your sequence is 0.52 (see score help below)

   1  MARSKLLLGKLLPLILIFLGLLVQNACSPTEAPELTKRCDKKSTLTIKTE    50
  51  CQSCSVNIAVKCPDGYIKITNGTVGVRDCRYSLKIQSYVLDIPGCRHICR   100
 101  KDYLQPQCCPGHWGPDCMECPGGARAPCGGRGVCDEGMEGTGSCSCRAGF   150
 151  RGTACENCAAEDVFGPNCSAVCSCVHGVCNSGISGDGTCECLSAYRGPRC   200
 201  DKPIPECAALLCPENSRCSPSSKDETKLQCKCLPSYKGDGQTCKPINPCL   250
 251  KNVCHPHASCSYLGPNRHSCVCQKGYQGDGQVCLPVDPCQTSYGNCPTKS   300
 301  TVCRYDGPGQSHCECKEHYRNFVPGVGCSMTDICESKNPCHKNANCSTVS   350
 351  PGQTQCTCQKGYVGDGLNCYGNIMQRLRELNTEPRGMWQGQLTSFISILD   400
 401  RTYAWPLSNLGPFTVLLPSDKGLKGVDVKELLMDKEAARYFVKLHIIAGQ   450
 451  MSTEQMYNLDTFYTLTGKSGEIINKDKDNQLKLKLYGSKIVQIIQGNIVA   500
 501  SNGLVHILDRAMDKIEPTLESNPQQTIMTMLQPRYGKFRSLLEKTNVGQA   550
 551  LEKGGIDEPYTIFVPSNEALSNMTAGVLDYLLSPEGSRKLLELVRYHIVA   600
 601  FTQLEVATLVSTLHIRSMANQIITFNISSKGQILANNVAVDETEVAAKNG   650
 651  RIYTLTGVLIPPSILPILPHRCNETKREMKLGTCVRCFMKNWSKCPTNSE   700
 701  PTAIFTNKCFYGSRAWNLKIGCARYCDVTVEIPRCCKGFFGPDCNPCPGG   750
 751  FMNPCSGNGQCIDGLGGNGTCICEDGFQGSRCQFCSKPNRYGPQCNRTCQ   800
 801  CVHGICDNRLDSDGSCLPGTCREGTAGRFCDKQTSACGPYMQFCHIHATC   850
 851  EYSNETASCVCNDGYEGDGTLCSKKDPCLGSTSRGGCSPNAECIQASTGT   900
 901  YSCVCQRGWTGNGRDCVEINSCLLPSSGGCHDNATCLYVGPGQNECECKK   950
 951  GFRGNGIDCEPIISCLEQIEKCHPLATCQYTLSGVWSCVCQEGYEGNGVL  1000
1001  CYGNVLMELSFLSEAAVFYQWINNASLQSMLSATSNLTVLVPSLQAIKDM  1050
1051  DQNEKSFWLSRNNIPALIKYHTLLGTYRVADLQTLPSSHMLATSLQGSFL  1100
1101  RLDKADGNITIEGASFVDGDNAATNGVVHIINKVLIPQRGLTGSLPSLLT  1150
1151  RLEQMPDYSIFRGYIIHYNLASAIEAADAYTVFVPNNEAIESYIREKKAT  1200
1201  SLKEDILQYHVVLGEKLLRNDLHNGMHRETMLGFSYLLAFFLHNDQLYVN  1250
1251  EAPINYTNVATDKGVIHGLEKVLEIKKNRCDNNDTIIVRGKCGKCSQQTL  1300
1301  CPLETKPLSETRKCIYSVYFMGKRSIFIGCQLQCVRTIITSACCAGFFGP  1350
1351  QCQACPGKGQNVCSGNGFCLDGVNGTGTCECEQGFNGTACETCTEGKYGI  1400
1401  HCDQACSCVHGRCNQGPSGDGSCDCDVGWRGVKCDSEITTDNCNGTCHTS  1450
1451  ANCLLDPDGKASCKCAAGFQGNGTVCTAINACEISNGGCSAKADCKRTIP  1500
1501  GSRVCVCKAGYTGDGIVCLEINPCLENHGGCDRHAECTQTGPNQAVCNCL  1550
1551  PKYTGDGKVCTLINVCLTNNGGCSPFAFCNHTEQDQRTCTCKPDYTGDGI  1600
1601  VCRGSIHSELPKNPSTSQYFFQLQEHAVQELAGPGPFTVFVPSSDSFNSE  1650
1651  SKLKVWDKQGLMSQILRYHVVACQQLLLENLKVITSATTLQGEPISISVS  1700
1701  QDTVLINKKAKVLSSDIISTNGVIHVIDTLLSPQNLLITPKGASGRVLLN  1750
1751  LTTVAANHGYTKFSKLIQDSGLLKVITDPMHTPVTLFWPTDKALQALPQE  1800
1801  QQDFLFNEDNKDKLKAYLKFHVIRDTMALASDLPRSASWKTLQGSELSVR  1850
1851  CGTGSDVGELFLNGQMCRIIQRRLLFDGGVAYGIDCLLMDPTEGGRCDTF  1900
1901  TTFNIPGECGSCFSTPRCPLQSKPKGVRKKCIYNPLPFRRDVEGCQNLCT  1950
1951  LVVHVPRCCSGYFMPDCQACPGGPDTPCNNRGMCYDQYKPTGQCQCHTGF  2000
2001  NGTACELCLPGRFGPDCQPCGCSEHGQCDEGITGSGQCLCEAGWTGRFCD  2050
2051  APTVVIPVCIPACSMHATCMENNTCVCNLNYEGDGITCTVVDFCKQNNGG  2100
2101  CAKVAKCSQKGTQVSCSCQKGYKGDGHSCTEIDPCANGVNGGCHEHATCR  2150
2151  MTGPGKQKCECKSHYVGDGRDCEPEQLPLDRCLQDNGQCHPDANCVDLHF  2200
2201  QDTTVGVFHLRSPLGQYKLTFDKAKEACAKEAASIATYNQLSYAQKAKYH  2250
2251  LCSAGWLESGRVAYPTIYASKKCANIVGIVDYGTRTNKSEMWDVFCYRMK  2300
2301  DVNCTCKAGYVGDGFSCNGNLLQVLMSFPSLTNFLTEVLVFSRSSAQGRA  2350
2351  FLKHLTDLSISGTLFVPQNSGLPKNKSLSGRDIEHHLTNVNVSFYDDLVN  2400
2401  GTVLKTRLGSQLLITSSQDQLHQEARFVDGRAILQWDIIASNGVLHIISE  2450
2451  PLKAPPTAATAAHSGLGTGIFCAVVLVTGAIALAAYSYFRLNQRTTGFRR  2500
2501  FESEDDIDALAFGKQQPESITNPLYETSTPAAPEPSCDPFTDSGERELEN  2550
2551  SDPLGALRS                                           2559

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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