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

NucPred

Fetching Q8CD54 from www.uniprot.org...

The NucPred score for your sequence is 0.72 (see score help below)

   1  MASEVVCGLIFRLLLPICLAVACAFRYNGLSFVYLIYLLLIPLFSEPTKA    50
  51  TMQGHTGRLLQSLCITSLSFLLLHIIFHITLASLEAQHRITPAYNCSTWE   100
 101  KTFRQIGFESLKGADAGNGIRVFVPDIGMFIASLTIWLVCRTIVKKPDTE   150
 151  EIAQLNSECENEELAGGEKMDSEEALIYEEDLDGEEGMEGELEESTKLKI   200
 201  LRRFASVASKLKEFIGNMITTAGKVVVTILLGSSGMMLPSLTSAVYFFVF   250
 251  LGLCTWWSWCRTFDPLLFGCLCVLLAIFTAGHLIGLYLYQFQFFQEAVPP   300
 301  NDYYARLFGIKSVIQTDCASTWKIIVNPDLSWYHHANPILLLVMYYTLAT   350
 351  LIRIWLQEPLVQEEMAKEDEGALDCSSNQNTAERRRSLWYATQYPTDERK   400
 401  LLSMTQDDYKPSDGLLVTVNGNPVDYHTIHPSLPIENGPAKTDLYTTPQY   450
 451  RWEPSEESSEKKEEEEDKREDSEGEGSQEEKRSVRMHAMVAVFQFIMKQS   500
 501  YICALIAMMAWSITYHSWLTFVLLIWSCTLWMIRNRRKYAMISSPFMVVY   550
 551  ANLLLVLQYIWSFELPEIKKVPGFLEKKEPGELASKILFTITFWLLLRQH   600
 601  LTEQKALREKEALLSEVKIGSQELEEKEDEELQDVQVEGEPTEKEEEEEE   650
 651  EIKEERHEVKKEEEEEVEEDDDQDIMKVLGNLVVALFIKYWIYVCGGMFF   700
 701  FVSFEGKIVMYKIIYMVLFLFCVALYQVHYEWWRKILKYFWMSVVIYTML   750
 751  VLIFIYTYQFENFPGLWQNMTGLKKEKLEDLGLKQFTVAELFTRIFIPTS   800
 801  FLLVCILHLHYFHDRFLELTDLKSIPSKEDNTIYSHAKVNGRVYLIINRL   850
 851  AHPEGSLPDLAIMNMTASLDKPEVQKLAESGEERPEECVKKTEKGEAGKD   900
 901  SDESEEEEDEEEESEEEESSDLRNKWHLVIDRLTVLFLKFLEYFHKLQVF   950
 951  MWWILELHIIKIVSSYIIWVTVKEVSLFNYVFLISWAFALPYAKLRRAAS  1000
1001  SVCTVWTCVIIVCKMLYQLQTIKPENFSVNCSLPNENQTNIPLHELNKSL  1050
1051  LYSAPVDPTEWVGLRKSSPLLVYLRNNLLMLAILAFEVTVYRHQEYYRGR  1100
1101  NNLTAPVSKTIFHDITRLHLDDGLINCAKYFVNYFFYKFGLETCFLMSVN  1150
1151  VIGQRMDFYAMIHACWLIGVLYRRRRKAIAEVWPKYCCFLACIITFQYFV  1200
1201  CIGIPPAPCRDYPWRFKGAYFNDNIIKWLYFPDFIVRPNPVFLVYDFMLL  1250
1251  LCASLQRQIFEDENKAAVRIMAGDNVEICMNLDAASFSQHNPVPDFIHCR  1300
1301  SYLDMSKVIIFSYLFWFVLTIIFITGTTRISIFCMGYLVACFYFLLFGGD  1350
1351  LLLKPIKSILRYWDWLIAYNVFVITMKNILSIGACGYIGALVRNSCWLIQ  1400
1401  AFSLACTVKGYQMPEDDSRCKLPSGEAGIIWDSICFAFLLLQRRVFMSYY  1450
1451  FLHVVADIKASQILASRGAELFQATIVKAVKARIEEEKKSMDQLKRQMDR  1500
1501  IKARQQKYKKGKERMLSLTQESGEGQDIQKVSEEDDEREADKQKAKGKKK  1550
1551  QWWRPWVDHASMVRSGDYYLFETDSEEEEEEELKKEDEEPPRKSAFQFVY  1600
1601  QAWITDPKTALRQRRKEKKKLAREEQKERRKGSGDGPVEWEDREDEPVKK  1650
1651  KSDGPDNIIKRIFNILKFTWVLFLATVDSFTTWLNSISREHIDISTVLRI  1700
1701  ERCMLTREIKKGNVPTRESIHMYYQNHIMNLSRESGLDTIDEHSGAGSRA  1750
1751  QAAHRMDSLDSRDSISSCYTEATLLISRQSTLDDLDGQDPVPKTSERARP  1800
1801  RLRKMFSLDMSSSSADSGSVASSEPTQCTMLYSRQGTTETIEEVEAEAEE  1850
1851  EVVEGLEPELHDAEEKEYAAEYEAGVEEISLTPDEELPQFSTDDCEAPPS  1900
1901  YSKAVSFEHLSFASQDDSGAKNHMVVSPDDSRTDKLESSILPPLTHELTA  1950
1951  SDLLMSKMFHDDELEESEKFYVDQPRFLLLFYAMYNTLVARSEMVCYFVI  2000
2001  ILNHMTSASIITLLLPILIFLWAMLSVPRPSRRFWMMAIVYTEVAIVVKY  2050
2051  FFQFGFFPWNKDLEIYKERPYFPPNIIGVEKKEGYVLYDLIQLLALFFHR  2100
2101  SILKCHGLWDEDDIVDSNTDKEGSDDELSLDQGRRGSSDSLKSINLAASV  2150
2151  ESVHVTFPEQPAAIRRKRSCSSSQISPRSSFSSNRSKRGSTSTRNSSQKG  2200
2201  SSVLSLKQKSKRELYMEKLQEHLIKAKAFTIKKTLQIYVPIRQFFYDLIH  2250
2251  PDYSAVTDVYVLMFLADTVDFIIIVFGFWAFGKHSAAADITSSLSEDQVP  2300
2301  GPFLVMVLIQFGTMVVDRALYLRKTVLGKVIFQVILVFGIHFWMFFILPG  2350
2351  VTERKFSQNLVAQLWYFVKCVYFGLSAYQIRCGYPTRVLGNFLTKSYNYV  2400
2401  NLFLFQGFRLVPFLTELRAVMDWVWTDTTLSLSSWICVEDIYAHIFILKC  2450
2451  WRESEKRYPQPRGQKKKKAVKYGMGGMIIVLLICIVWFPLLFMSLIKSVA  2500
2501  GVINQPLDVSVTITLGGYQPIFTMSAQQSQLKVMDNSKYNEFLKSFGPNS  2550
2551  GAMQFLENYEREDVTVAELEGNSNSLWTISPPSKQKMIQELTDPNSCFSV  2600
2601  VFSWSIQRNMTLGAKAEIATDKLSFPLAVATRNSIAKMIAGNDTESSNTP  2650
2651  VTIEKIYPYYVKAPSDSNSKPIKQLLSENNFMNITIILFRDNVTKSNSEW  2700
2701  WVLNLTGSRIFNQGSQALELVVFNDKVSPPSLGFLAGYGIMGLYASVVLV  2750
2751  IGKFVREFFSGISHSIMFEELPNVDRILKLCTDIFLVRETGELELEEDLY  2800
2801  AKLIFLYRSPETMIKWTREKTN                              2822

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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