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

NucPred

Fetching Q9Z329 from www.uniprot.org...

The NucPred score for your sequence is 0.68 (see score help below)

   1  MSDKMSSFLYIGDIVSLYAEGSVNGFISTLGLVDDRCVVHPEAGDLANPP    50
  51  KKFRDCLFKVCPMNRYSAQKQYWKAKQAKQGNHTEAALLKKLQHAAELEQ   100
 101  KQNESENRKLLGEIVKYSNVIQLLHIKSNKYLTVNKRLPALLEKNAMRVS   150
 151  LDAAGNEGSWFYIHPFWKLRSEGDNIVVGDKVVLMPVNAGQPLHASNVEL   200
 201  LDNPGCKEVNAVNCNTSWKITLFMKFSSYREDVLKGGDVVRLFHAEQEKF   250
 251  LTCDDYEKKQHIFLRTTLRQSATSATSSKALWEIEVVHHDPCRGGAGQWN   300
 301  SLFRFKHLATGNYLAAELNPDYRDAQNEGKNVKDGEIPTPKKKRQAGEKI   350
 351  MYTLVSVPHGNDIASLFELDATTLQRADCLVPRNSYVRLRHLCTNTWVTS   400
 401  TTIPIDTEEERPVMLKIGTCQTKEDKEAFAIVCVPLSEVRDLDFANDANK   450
 451  VLATTVKKLENGSITQNERRFVTKLLEDLIFFVADVTNNGQDVLDVVITK   500
 501  PNRERQKLMREQNILAQVFGILKAPFKEKAGEGSMLRLEDLGDQRYAPYK   550
 551  YVLRLCYRVLRHSQQDYRKNQEYIAKNFCVMQSQIGYDILAEDTITALLH   600
 601  NNRKLLEKHITAKEIETFVSLLRRNREPRFLDYLSDLCVSNSTAIPVTQE   650
 651  LICKFMLSPGNADILIQTKLVSMQVENPMESSILPDDIDDEEVWLYWIDS   700
 701  NKEPHGKAIRHLAQEAREGTKADLEVLTYYRYQLNLFARMCLDRQYLAIN   750
 751  QISTQLSVDLILRCVSDESLPFDLRASFCRLMLHMHVDRDPQESVVPVRY   800
 801  ARLWTEIPTKITIHEYDSITDSSRNDMKRKFALTMEFVEEYLKEVVNQPF   850
 851  PFGDKEKNKLTFEVVHLARNLIYFGFYSFSELLRLTRTLLAILDIVQAPM   900
 901  SSYFERLSKFQDGSNNVMRTIHGVGEMMTQMVLSRGSIFPVSVPDAQPIV   950
 951  HPSKQASPGEQEDVTVMDTKLKVIEILQFILSVRLDYRISYMLSIYKKEF  1000
1001  GDNNDNGDPSASGTPDTLLPSALVPDIDEIAAQAETMFAGRKEKTPVQLD  1050
1051  DEGGRTFLRVLIHLIMHDYAPLLSGALQLLFKHFSQRAEVLQAFKQVQLL  1100
1101  VSNQDVDNYKQIKADLDQLRLTVEKSELWVEKSGSYENGDVGEGQAKGGE  1150
1151  EANEESNLLSPVQDGAKTPQIDSNKGNNYRIVKEILIRLSKLCVQNKKCR  1200
1201  NQHQRLLKNMGAHSVVLDLLQIPYEKTDEKMNEVMDLAHTFLQNFCRGNP  1250
1251  QNQVLLHKHLNLFLTPGLLEAETMRHIFMNNYHLCNEISERVVQHFVHCI  1300
1301  ETHGRHVEYLRFLQTIVKADGKYVKKCQDMVMTELINGGEDVLIFYNDRA  1350
1351  SFPILLNMMCSERARGDESGPLAYHITLVELLAACTEGKNVYTEIKCNSL  1400
1401  LPLDDIVRVVTHDDCIPEVKIAYVNFVNHCYVDTEVEMKEIYTSNHIWKL  1450
1451  FENFLVDMARVCNTTTDRKHADTFLERCVTESVMNIVSGFFNSPFSDNST  1500
1501  SLQTHQPVFIQLLQSAFRIYNCTWPNPAQKASVESCIRALAEVAKNRGIA  1550
1551  IPVDLDSQVNTLFMKNHSSTVQRAAMGWRLSARSGPRFKEALGGPAWDYR  1600
1601  NIIEKLQDVVASLEQQFSPMMQAEFSVLVDVLYSPELLFPEGSDARIRCG  1650
1651  AFMSKLINHTKKLMEKEEKLCIKILQTLREMLEKKDSFMEEGSTLRRILL  1700
1701  NRYFKGDHSISVNGPLSGAYAKTAQVGGSFSGQDSDKKGISMSDIQCLLD  1750
1751  KEGASELVIDVIVNTKNDRIFSEGILLGIALLEGGNTQTQYSFYQQLHEQ  1800
1801  KKSEKFFKVLYDRMKAAQKEIRSTVTVNTIDLGSKKREEDSDVMALGPRM  1850
1851  RVRDSSLHLREGMKGQLTEASSATSKAYCVYRREMDPEIDTMCPGQEAGS  1900
1901  AEEKSAEEVTMSPAITIMRPILRFLQLLCENHNRELQNFLRNQNNKTNYN  1950
1951  LVCETLQFLDCICGSTTGGLGLLGLYINERNVALVNQTLESLTEYCQGPC  2000
2001  HENQTCIATHESNGIDIIIALILNDINPLGKYRMDLVLQLKNNASKLLLA  2050
2051  IMESRHDSENAERILFNMRPRELVDVMKNAYNQGLECDHGDEEGGDDGVS  2100
2101  PKDVGHNIYILAHQLARHNKLLQQMLKPGSDPEEGDEALKYYANHTAQIE  2150
2151  IVRHDRTMEQIVFPVPNICEFLTRESKYRVFNTTERDEQGSKVNDFFQQT  2200
2201  EDLYNEMKWQKKIRNNPALFWFSRHISLWGSISFNLAVFINLAVALFYPF  2250
2251  GDDGDEGTLSPMFSVLLWVAVAICTSMLFFFSKPVGIRPFLVSVMLRSIY  2300
2301  TIGLGPTLILLGAANLCNKIVFLVSFVGNRGTFTRGYRAVILDMAFLYHV  2350
2351  AYVLVCMLGLFVHEFFYSFLLFDLVYREETLLNVIKSVTRNGRSIILTAV  2400
2401  LALILVYLFSIIGFLFLKDDFTMEVDRLKNRTPVTGNHGVPTMTLSSMME  2450
2451  TCQKENCSPTIPSSNTAGEEGEDGIERTCDTLLMCIVTVLNQGLRNGGGV  2500
2501  GDVLRRPSKDEPLFAARVVYDLLFFFIVIIIVLNLIFGVIIDTFADLRSE  2550
2551  KQKKEEILKTTCFICGLERDKFDNKTVSFEEHIKSEHNMWHYLYFIVLVK  2600
2601  VKDPTEYTGPESYVAQMITEKNLDWFPRMRAMSLVSNEGDSEQNEIRNLQ  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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