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

NucPred

Fetching Q14643 from www.uniprot.org...

The NucPred score for your sequence is 0.76 (see score help below)

   1  MSDKMSSFLHIGDICSLYAEGSTNGFISTLGLVDDRCVVQPETGDLNNPP    50
  51  KKFRDCLFKLCPMNRYSAQKQFWKAAKPGANSTTDAVLLNKLHHAADLEK   100
 101  KQNETENRKLLGTVIQYGNVIQLLHLKSNKYLTVNKRLPALLEKNAMRVT   150
 151  LDEAGNEGSWFYIQPFYKLRSIGDSVVIGDKVVLNPVNAGQPLHASSHQL   200
 201  VDNPGCNEVNSVNCNTSWKIVLFMKWSDNKDDILKGGDVVRLFHAEQEKF   250
 251  LTCDEHRKKQHVFLRTTGRQSATSATSSKALWEVEVVQHDPCRGGAGYWN   300
 301  SLFRFKHLATGHYLAAEVDPDFEEECLEFQPSVDPDQDASRSRLRNAQEK   350
 351  MVYSLVSVPEGNDISSIFELDPTTLRGGDSLVPRNSYVRLRHLCTNTWVH   400
 401  STNIPIDKEEEKPVMLKIGTSPVKEDKEAFAIVPVSPAEVRDLDFANDAS   450
 451  KVLGSIAGKLEKGTITQNERRSVTKLLEDLVYFVTGGTNSGQDVLEVVFS   500
 501  KPNRERQKLMREQNILKQIFKLLQAPFTDCGDGPMLRLEELGDQRHAPFR   550
 551  HICRLCYRVLRHSQQDYRKNQEYIAKQFGFMQKQIGYDVLAEDTITALLH   600
 601  NNRKLLEKHITAAEIDTFVSLVRKNREPRFLDYLSDLCVSMNKSIPVTQE   650
 651  LICKAVLNPTNADILIETKLVLSRFEFEGVSSTGENALEAGEDEEEVWLF   700
 701  WRDSNKEIRSKSVRELAQDAKEGQKEDRDVLSYYRYQLNLFARMCLDRQY   750
 751  LAINEISGQLDVDLILRCMSDENLPYDLRASFCRLMLHMHVDRDPQEQVT   800
 801  PVKYARLWSEIPSEIAIDDYDSSGASKDEIKERFAQTMEFVEEYLRDVVC   850
 851  QRFPFSDKEKNKLTFEVVNLARNLIYFGFYNFSDLLRLTKILLAILDCVH   900
 901  VTTIFPISKMAKGEENKGNNDVEKLKSSNVMRSIHGVGELMTQVVLRGGG   950
 951  FLPMTPMAAAPEGNVKQAEPEKEDIMVMDTKLKIIEILQFILNVRLDYRI  1000
1001  SCLLCIFKREFDESNSQTSETSSGNSSQEGPSNVPGALDFEHIEEQAEGI  1050
1051  FGGSEENTPLDLDDHGGRTFLRVLLHLTMHDYPPLVSGALQLLFRHFSQR  1100
1101  QEVLQAFKQVQLLVTSQDVDNYKQIKQDLDQLRSIVEKSELWVYKGQGPD  1150
1151  ETMDGASGENEHKKTEEGNNKPQKHESTSSYNYRVVKEILIRLSKLCVQE  1200
1201  SASVRKSRKQQQRLLRNMGAHAVVLELLQIPYEKAEDTKMQEIMRLAHEF  1250
1251  LQNFCAGNQQNQALLHKHINLFLNPGILEAVTMQHIFMNNFQLCSEINER  1300
1301  VVQHFVHCIETHGRNVQYIKFLQTIVKAEGKFIKKCQDMVMAELVNSGED  1350
1351  VLVFYNDRASFQTLIQMMRSERDRMDENSPLMYHIHLVELLAVCTEGKNV  1400
1401  YTEIKCNSLLPLDDIVRVVTHEDCIPEVKIAYINFLNHCYVDTEVEMKEI  1450
1451  YTSNHMWKLFENFLVDICRACNNTSDRKHADSILEKYVTEIVMSIVTTFF  1500
1501  SSPFSDQSTTLQTRQPVFVQLLQGVFRVYHCNWLMPSQKASVESCIRVLS  1550
1551  DVAKSRAIAIPVDLDSQVNNLFLKSHSIVQKTAMNWRLSARNAARRDSVL  1600
1601  AASRDYRNIIERLQDIVSALEDRLRPLVQAELSVLVDVLHRPELLFPENT  1650
1651  DARRKCESGGFICKLIKHTKQLLEENEEKLCIKVLQTLREMMTKDRGYGE  1700
1701  KLISIDELDNAELPPAPDSENATEELEPSPPLRQLEDHKRGEALRQVLVN  1750
1751  RYYGNVRPSGRRESLTSFGNGPLSAGGPGKPGGGGGGSGSSSMSRGEMSL  1800
1801  AEVQCHLDKEGASNLVIDLIMNASSDRVFHESILLAIALLEGGNTTIQHS  1850
1851  FFCRLTEDKKSEKFFKVFYDRMKVAQQEIKATVTVNTSDLGNKKKDDEVD  1900
1901  RDAPSRKKAKEPTTQITEEVRDQLLEASAATRKAFTTFRREADPDDHYQP  1950
1951  GEGTQATADKAKDDLEMSAVITIMQPILRFLQLLCENHNRDLQNFLRCQN  2000
2001  NKTNYNLVCETLQFLDCICGSTTGGLGLLGLYINEKNVALINQTLESLTE  2050
2051  YCQGPCHENQNCIATHESNGIDIITALILNDINPLGKKRMDLVLELKNNA  2100
2101  SKLLLAIMESRHDSENAERILYNMRPKELVEVIKKAYMQGEVEFEDGENG  2150
2151  EDGAASPRNVGHNIYILAHQLARHNKELQSMLKPGGQVDGDEALEFYAKH  2200
2201  TAQIEIVRLDRTMEQIVFPVPSICEFLTKESKLRIYYTTERDEQGSKIND  2250
2251  FFLRSEDLFNEMNWQKKLRAQPVLYWCARNMSFWSSISFNLAVLMNLLVA  2300
2301  FFYPFKGVRGGTLEPHWSGLLWTAMLISLAIVIALPKPHGIRALIASTIL  2350
2351  RLIFSVGLQPTLFLLGAFNVCNKIIFLMSFVGNCGTFTRGYRAMVLDVEF  2400
2401  LYHLLYLVICAMGLFVHEFFYSLLLFDLVYREETLLNVIKSVTRNGRSII  2450
2451  LTAVLALILVYLFSIVGYLFFKDDFILEVDRLPNETAVPETGESLASEFL  2500
2501  FSDVCRVESGENCSSPAPREELVPAEETEQDKEHTCETLLMCIVTVLSHG  2550
2551  LRSGGGVGDVLRKPSKEEPLFAARVIYDLLFFFMVIIIVLNLIFGVIIDT  2600
2601  FADLRSEKQKKEEILKTTCFICGLERDKFDNKTVTFEEHIKEEHNMWHYL  2650
2651  CFIVLVKVKDSTEYTGPESYVAEMIKERNLDWFPRMRAMSLVSSDSEGEQ  2700
2701  NELRNLQEKLESTMKLVTNLSGQLSELKDQMTEQRKQKQRIGLLGHPPHM  2750
2751  NVNPQQPA                                            2758

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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