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

NucPred

Fetching Q14571 from www.uniprot.org...

The NucPred score for your sequence is 0.69 (see score help below)

   1  MTEKMSSFLYIGDIVSLYAEGSVNGFISTLGLVDDRCVVHPEAGDLANPP    50
  51  KKFRDCLFKVCPMNRYSAQKQYWKAKQAKQGNHTEAALLKKLQHAAELEQ   100
 101  KQNESENKKLLGEIVKYSNVIQLLHIKSNKYLTVNKRLPALLEKNAMRVS   150
 151  LDAAGNEGSWFYIHPFWKLRSEGDNIVVGDKVVLMPVNAGQPLHASNIEL   200
 201  LDNPGCKEVNAVNCNTSWKITLFMKYSSYREDVLKGGDVVRLFHAEQEKF   250
 251  LTCDEYEKKQHIFLRTTLRQSATSATSSKALWEIEVVHHDPCRGGAGQWN   300
 301  SLFRFKHLATGNYLAAELNPDYRDAQNEGKNVRDGVPPTSKKKRQAGEKI   350
 351  MYTLVSVPHGNDIASLFELDATTLQRADCLVPRNSYVRLRHLCTNTWVTS   400
 401  TSIPIDTDEERPVMLKIGTCQTKEDKEAFAIVSVPLSEVRDLDFANDANK   450
 451  VLATTVKKLENGTITQNERRFVTKLLEDLIFFVADVPNNGQEVLDVVITK   500
 501  PNRERQKLMREQNILAQVFGILKAPFKEKAGEGSMLRLEDLGDQRYAPYK   550
 551  YMLRLCYRVLRHSQQDYRKNQEYIAKNFCVMQSQIGYDILAEDTITALLH   600
 601  NNRKLLEKHITAKEIETFVSLLRRNREPRFLDYLSDLCVSNTTAIPVTQE   650
 651  LICKFMLSPGNADILIQTKVVSMQADNPMESSILSDDIDDEEVWLYWIDS   700
 701  NKEPHGKAIRHLAQEAKEGTKADLEVLTYYRYQLNLFARMCLDRQYLAIN   750
 751  QISTQLSVDLILRCVSDESLPFDLRASFCRLMLHMHVDRDPQESVVPVRY   800
 801  ARLWTEIPTKITIHEYDSITDSSRNDMKRKFALTMEFVEEYLKEVVNQPF   850
 851  PFGDKEKNKLTFEVVHLARNLIYFGFYSFSELLRLTRTLLAILDIVQAPM   900
 901  SSYFERLSKFQDGGNNVMRTIHGVGEMMTQMVLSRGSIFPMSVPDVPPSI   950
 951  HPSKQGSPTEHEDVTVMDTKLKIIEILQFILSVRLDYRISYMLSIYKKEF  1000
1001  GEDNDNAETSASGSPDTLLPSAIVPDIDEIAAQAETMFAGRKEKNPVQLD  1050
1051  DEGGRTFLRVLIHLIMHDYPPLLSGALQLLFKHFSQRAEVLQAFKQVQLL  1100
1101  VSNQDVDNYKQIKADLDQLRLTVEKSELWVEKSSNYENGEIGESQVKGGE  1150
1151  EPIEESNILSPVQDGTKKPQIDSNKSNNYRIVKEILIRLSKLCVQNKKCR  1200
1201  NQHQRLLKNMGAHSVVLDLLQIPYEKNDEKMNEVMNLAHTFLQNFCRGNP  1250
1251  QNQVLLHKHLNLFLTPGLLEAETMRHIFMNNYHLCNEISERVVQHFVHCI  1300
1301  ETHGRHVEYLRFLQTIVKADGKYVKKCQDMVMTELINGGEDVLIFYNDRA  1350
1351  SFPILLHMMCSERDRGDESGPLAYHITLVELLAACTEGKNVYTEIKCNSL  1400
1401  LPLDDIVRVVTHDDCIPEVKIAYVNFVNHCYVDTEVEMKEIYTSNHIWKL  1450
1451  FENFLVDMARVCNTTTDRKHADIFLEKCVTESIMNIVSGFFNSPFSDNST  1500
1501  SLQTHQPVFIQLLQSAFRIYNCTWPNPAQKASVESCIRTLAEVAKNRGIA  1550
1551  IPVDLDSQVNTLFMKSHSNMVQRAAMGWRLSARSGPRFKEALGGPAWDYR  1600
1601  NIIEKLQDVVASLEHQFSPMMQAEFSVLVDVLYSPELLFPEGSDARIRCG  1650
1651  AFMSKLINHTKKLMEKEEKLCIKILQTLREMLEKKDSFVEEGNTLRKILL  1700
1701  NRYFKGDYSIGVNGHLSGAYSKTAQVGGSFSGQDSDKMGISMSDIQCLLD  1750
1751  KEGASELVIDVIVNTKNDRIFSEGIFLGIALLEGGNTQTQYSFYQQLHEQ  1800
1801  KKSEKFFKVLYDRMKAAQKEIRSTVTVNTIDLGNKKRDDDNELMTSGPRM  1850
1851  RVRDSTLHLKEGMKGQLTEASSATSKAYCVYRREMDPEIDIMCTGPEAGN  1900
1901  TEEKSAEEVTMSPAIAIMQPILRFLQLLCENHNRELQNFLRNQNNKTNYN  1950
1951  LVCETLQFLDCICGSTTGGLGLLGLYINEKNVALVNQNLESLTEYCQGPC  2000
2001  HENQTCIATHESNGIDIIIALILNDINPLGKYRMDLVLQLKNNASKLLLA  2050
2051  IMESRHDSENAERILFNMRPRELVDVMKNAYNQGLECDHGDDEGGDDGVS  2100
2101  PKDVGHNIYILAHQLARHNKLLQQMLKPGSDPDEGDEALKYYANHTAQIE  2150
2151  IVRHDRTMEQIVFPVPNICEYLTRESKCRVFNTTERDEQGSKVNDFFQQT  2200
2201  EDLYNEMKWQKKIRNNPALFWFSRHISLWGSISFNLAVFINLAVALFYPF  2250
2251  GDDGDEGTLSPLFSVLLWIAVAICTSMLFFFSKPVGIRPFLVSIMLRSIY  2300
2301  TIGLGPTLILLGAANLCNKIVFLVSFVGNRGTFTRGYRAVILDMAFLYHV  2350
2351  AYVLVCMLGLFVHEFFYSFLLFDLVYREETLLNVIKSVTRNGRSIILTAV  2400
2401  LALILVYLFSIIGFLFLKDDFTMEVDRLKNRTPVTGSHQVPTMTLTTMME  2450
2451  ACAKENCSPTIPASNTADEEYEDGIERTCDTLLMCIVTVLNQGLRNGGGV  2500
2501  GDVLRRPSKDEPLFAARVVYDLLFYFIVIIIVLNLIFGVIIDTFADLRSE  2550
2551  KQKKEEILKTTCFICGLERDKFDNKTVSFEEHIKSEHNMWHYLYFIVLVK  2600
2601  VKDPTEYTGPESYVAQMIVEKNLDWFPRMRAMSLVSNEGDSEQNEIRSLQ  2650
2651  EKLESTMSLVKQLSGQLAELKEQMTEQRKNKQRLGFLGSNTPHVNHHMPP  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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