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

NucPred

Fetching Q8K4L3 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MKRKERIARRLEGIENDSQPILLQSCTGLVTHRLLEEDTPRYMRATDPAS    50
  51  PHIGRSKEEEDTPGSSLEKQTPSKYCIETSGIHSSGSMDTHSLESKAERI   100
 101  ARYKAERRRQLAEKYGLTLDPEADSEYLSRYAKSRKDPDVTERRGKSDKQ   150
 151  EEQSKDANSRHSRTESGPRTSLVASQDCTPLGSNMSDQEQLLNVENQRRV   200
 201  QDPPLGEDGSSAFFSERSISFPEVPRSPKQIPSSPLQQPASPNHPGDSPL   250
 251  PTEARASTGKPTHEWFLQRDSEGDTPSLINWPSRVKVREKLVKEESARSS   300
 301  PELTSESLTQRRQQPAPAHFLPIQSESSTFDRVTSKAVSSLQPSQSGVLP   350
 351  TDPVHAIKLVTMDTPESTSEFSWVGSATPKVIKSTTLKILEGGSRDAPVL   400
 401  HICESKAEDWLSPEPLERSPKSLLTSEDDRLVRGHKDPSGNKDLDKAIIC   450
 451  SIDVESERERQVQHLPTQRTGRSEMLLYVQSGPVSQDATLTSHTKEASPK   500
 501  KRKVLARSLSDYTGPPQLQVPRHKDEAPSQELELQSSRAEGPGAEASVLD   550
 551  TRVSVAQLRNIFMESTRASKKPELQSRVERSAEGIGLPMERERGSRKPRR   600
 601  YLSPGESRKTSERFRTQPITSAERKESDRYPSGSEIPVVEDEEKVDERAK   650
 651  LSVAAKRLLFREMEKSFDEHTVPKRHSRNAAVEQRLRRLQDRSHTQPITT   700
 701  EEVVIAATEPIPASCSGVTHPVTARLPSPTVARSSVQPARLQASAHQKAL   750
 751  ARDQANEGRESAEPGEPDSSTLSLAEKLALFNKLSQPVSKAISTRNRIDV   800
 801  RQRRMNARYQTQPVTLGEVEQVQSGKLISFSPTVNTSVSIMASAVAPTYA   850
 851  GDLRKLSVDNNTSATDYKSPPAENSDSPVRSILKPQAWRPLVEHSGSKGM   900
 901  PGESGKTESKNALTVAAEDSGVQTRGAFEEEEEPSYPILGRVREGDGQKE   950
 951  PKHVVLRRGSLELGNPSAAHLGDELKEVSTAKSSLQENLDLKDKQASEEN  1000
1001  TDVETVMRKFSLKEFGETTSEQTEVAARKASVQMATPGAWKQQESSEQLA  1050
1051  EKLFKNPCAMFASGEVKVPVGDSFLDSPSKTMSIKERLALLKKSGEEDWK  1100
1101  NRLIRKQEYGKATGGLHTQEVEQSLKKKRVTESRESQMTIEERKHLITVR  1150
1151  EEAWKTKGRGAANDSTQFTVAGRMVKKGLASPTSITPISSPLCSKSRGTT  1200
1201  PVSKPLEDIEARPDMQLESDLKLDRLETFLRRLNNKVAGIQETVLTVTGK  1250
1251  SVKEVMKLDDDETFAKFYRSVDHSIPRSPVELEEDFDVIFDPYAPKLTSS  1300
1301  VAEHKRQVRPKRRVQASKNPLKLLAARDDLLQEYTEQRLNVAFMESKRMK  1350
1351  VEKMSSNSNFSEVTLAGLASRENFSNINLRSVNLMEQNSNNSAMPYKKLM  1400
1401  LLQIKGRRHVQTRLVEPRASSLNSGDCFLLLSPQYCFLWVGEFSNVIEKA  1450
1451  KASELATLIQTKRELGCRATYIQTIEEGINTHTHAAKDFWKLLGGQTSYQ  1500
1501  SAGDPKEDELYETAIIETNCVYRLTDDKLVPDDDYWGKIPKCSLLQSKEV  1550
1551  LVFDFGSEVYVWHGKEVTLAQRKIAFQLAKHLWNGTFDYENCDINPLDPG  1600
1601  ECNPLIPRKGQGRPDWAIFGRVTEHNETILFKEKFLDWTELKRPTEKNSG  1650
1651  EVVQQKDDPRADVKPYDVTRMVATPQITAGTILDGVNVGRGYGLVEGDDR  1700
1701  RQFEIATVSVDVWHILEFDYSRLPRQSIGQFHEGDAYVVKWKYMASTAVG  1750
1751  SRQKGEHLVRVAGKEKCVYFFWQGRHSTVSEKGTSALMTVELDEERGAQV  1800
1801  QVLQGKEPPCFLQCFQGGMVVHSGRREEEEENVQSEWRLYCVRGEVPMEG  1850
1851  NLLEVACHCSSLRSRTSMVVLNINKALIYLWHGCKAQGHTKEVGRTAANK  1900
1901  IKEECPLEAGLHSSSNVTIHECDEGSEPLGFWDALGRRDRKAYDCMLQDP  1950
1951  GSFNFAPRLFILSSSSGDFSATEFVYPAQAPSAVSSMPFLQEDLYSAPQP  2000
2001  ALFLVDNHHEVYLWQGWWPTENKITGSARIRWASDRKSAMETVLQYCRGK  2050
2051  NLKRPPPKSYLIHAGLEPLTFTNMFPSWEHREDIAEITEMDTEVSNQITL  2100
2101  VEDVLAKLCKTIYPLADLLARPLPEGVDPLKLEIYLTDEDFEFALDMSRD  2150
2151  EFNALPTWKQVNLKKSKGLF                                2170

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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