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

NucPred

Fetching Q8WN96 from www.uniprot.org...

The NucPred score for your sequence is 0.73 (see score help below)

   1  MSDKMSSFLYIGDIVSLYAEGSVNGFINTLGLVDDRCVVHPEAGDLANPP    50
  51  KKFRDCLFKVCPMNRYSAQKQYWKAKQAKQGNHTEAALLKKLQHAAELEQ   100
 101  KQNESENKKLLGEIVKYSNVIQLLHIKSNKYLTVNKRLPALLEKNAMRVS   150
 151  LDAAGNEGSWFYIHPFWKLRSEGDNIVVGGKVVLMPVNAGQPLHASNIEL   200
 201  LDNPGCKEVNAVNCNTSWKITLFMKYSSYREDVLKGGDVVRLFHAEQEKF   250
 251  LTCDEYEKKQHIFLRTTLRQSATSATSSKALWEIEVVHHDPCRGGAGQWN   300
 301  SLFRFKHLATGNYLAAELNPDYRDAQNEGKNVRDGDLPASKKKRQAGEKI   350
 351  MYTLVSVPHGNDIASLFELDATTLQRADCLVPRNSYVRLRHLCTNTWVTS   400
 401  TSIPIDTDEERPVMLKIGTCQTKEDKEAFAIVSVPPSEVRDLDFANDANK   450
 451  VLATTVKKLENGTITQNERRFVTKLLEDLIFFVADVPNNGQDVLDVLITK   500
 501  PNRERQKLMREQNILAQVFGILKAPFKEKAGEGSMLRLEDLGDQRYAPYK   550
 551  YMLRLCYRVLGHSQQDYRKNQEYIAKNFCVMQSQIGYDILAEDTITALLH   600
 601  NNRKLLEKHITAKEIETFVSLLRRNREPRFLDYLSDLCVSNTTAIPVTQE   650
 651  LICKFMLSPGNADILIQTKLVSMQGDNPMESAILSDDIDEEEVWLYWIDS   700
 701  NKEPHGKAIRHLAQEAKEGTKADLEVLTYYRYQLNLFARMCLDRQYLAIN   750
 751  QISTQLSVDLILRCMSDESLPFDLRASFCRLMLHMHVDRDPQESVVPVRY   800
 801  ARLWTEIPTKITIHEYDSITDSSRNDMKRKFALTMEFVEEYLKEVVNQPF   850
 851  PFGDKEKNKLTFEVVHLARNLIYFGFYSFSELLRLTRTLLAILDIVQAPM   900
 901  SSYFERLSKFQDGGNNVMRTIHGVGEMMTQMVLSRGSIFPMSVPDIQPSL   950
 951  HPSKQGSPTDHEDVTVMDTKLKIIEILQFILSVRLDYGISYMLSIYKKEF  1000
1001  GENNGNAEMSTNGSPDTLLPSAIVPDIDEIAAQAETMFAGRKEKNPVQLD  1050
1051  DEGGRTFLRVLIHLIMHDYPPLLSGALQLLFKHFSQRAEVLQAFKQVQLL  1100
1101  VSNQDVDNYKQIKADLDQLRLTVEKSELWVEKSSSYENGEMGENQVKGGE  1150
1151  EPIEDSNILSPVQDGTKKPQIDSNKSNNYRIVKEILIRLSKLCVQNKKCR  1200
1201  NQHQRLLKNMGAHSVVLDLLQIPYEKNDEKMNEVMNLAHTFLQNFCRGNP  1250
1251  QNQVLLHKHLNLFLTPGLLEAETMRHIFMNNYHLCNEISERVVQHFVHCI  1300
1301  ETHGRHVEYLRFLQTIVKADGKYVKKCQDMVMTELINGGEDVLIFYNDRA  1350
1351  SFPILLHMMCSERDRGDESGPLAYHITLVELLAACTEGKNVYTEIKCNSL  1400
1401  LPLDDIVRVVTHDDCIPEVKIAYVNFVNHCYVDTEVEMKEIYTSNHIWKL  1450
1451  FENFLVDMARVCNTTTDRKHADTFLEKCVTESIMNIVSGFFNSPFSDNST  1500
1501  SLQTHQPVFIQLLQSAFRIYNCTWPNPAQKASVESCIRTLAEVAKNRGIA  1550
1551  IPVDLDSQVNTLFLKSHSNMVQRAAMGWRLSARSGPRFKEALGGPSWDYR  1600
1601  NIIEKLQDVVASLEQQFSPMMQAEFSVLVDVLYSPELLFPEGSDARIRCG  1650
1651  AFMSKLINHTKKLMEKEEKLCIKILQTLREMLEKKDSFVEEGNTLRKILL  1700
1701  NRYFKGDYGVSINGHLSGTYCKTAQVGGSFSGQDSDKMGISMSDIQCLLD  1750
1751  KEGASELVIDVIVNTKNDRIFSEGILLGIALLEGGNTQTQYSFYQQLHEQ  1800
1801  KKSEKFFKVLYDRMKAAQKEIRSTVTVNTIDLGNKKRDDDTELMTSGPRM  1850
1851  RVRDSSLHLKEGMKGQLTEASSATSKAYCVYRREMDPEIDIMCAGPEAGN  1900
1901  AEDRSTEEVTMSPAIAIMQPISRFLQLLCENHNRELQHFLRNQNNKTNYN  1950
1951  LVCETLQFLDCICGSTTGGLGLLGLYINEKNVVLVNQTLESLTEYCQGPC  2000
2001  HENQTCIATHESNGIDIIIALILNDINPLGKYRMDLVLQLKNNAPKLLLA  2050
2051  IMESRHDSENAERILFNMRPRELVDVMKNAYNQGLECDHGDDEGGDDDVS  2100
2101  PKDVGHNIYILAHQLARHNKLLQQMLKPGSDPDDGDEALKYYANHTAQIE  2150
2151  IVRHDRTMEQIVFPVPNICEYLTRESKCRVFNTTERDEQGSKVNDFFQQT  2200
2201  EDLYNEMKWQKKIRSNPALFWFSRHISLWGSISFNLAVFINLAVALFYPF  2250
2251  GDDGDEGTLSPMFSILLWIAVAICTSMLFFFSKPVGIRPFLVSVMLRSIY  2300
2301  TIGLGPTLILLGAANLCNKIVFLVSFVGNRGTFTRGYRAVILDMAFLYHV  2350
2351  AYVLVCMLGLFVHEFFYSFLLFDLVYREETLLNVIKSVTRNGRSIILTAV  2400
2401  LALILVYLFSIIGFLFLKDDFTMEVDRLKNRTPITGSNAVPTMTLTSILS  2450
2451  TCEKDNCSPTIPASNTADEEYEDGIERTCDTLLMCIVTVLNQGLRNGGGV  2500
2501  GDVLRRPSKDEPLFAARVVYDLLFYFIVIIIVLNLIFGVIIDTFADLRSE  2550
2551  KQKKEEILKTTCFICGLERDKFDNKTVSFEEHIKSEHNMWHYLYFLVLVK  2600
2601  VKDPTEYTGPESYVAQMIVEKNLDWFPRMRAMSLVSSEGDSEQNEVRNLQ  2650
2651  EKLESTMSLVKQLSSQLAELKEQMTEQRKNKQRLGFLGSNTPHVNHHMPP  2700
2701  H                                                   2701

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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