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

NucPred

Fetching Q9WTU3 from www.uniprot.org...

The NucPred score for your sequence is 0.50 (see score help below)

   1  MAARVLAPPGPDSFKPFTPESLANIERRIAESKLKKPPKADGSHREDDED    50
  51  SKPKPNSDLEAGKSLPFIYGDIPQGLVAVPLEDFDPYYLTQKTFVVLNRG   100
 101  KTLFRFSATPALYILSPFNLIRRIAIKILIHSVFSMIIMCTILTNCVFMT   150
 151  FSNPPEWSKNVEYTFTGIYTFESLVKIIARGFCIDGFTFLRDPWNWLDFS   200
 201  VIMMAYVTEFVDLGNVSALRTFRVLRALKTISVIPGLKTIVGALIQSVKK   250
 251  LSDVMILTVFCLSVFALIGLQLFMGNLRNKCVVWPINFNESYLENGTRGF   300
 301  DWEEYINNKTNFYMVPGMLEPLLCGNSSDAGQCPEGFQCMKAGRNPNYGY   350
 351  TSFDTFSWAFLALFRLMTQDYWENLYQLTLRAAGKTYMIFFVLVIFVGSF   400
 401  YLVNLILAVVAMAYEEQNQATLEEAEQKEAEFKAMLEQLKKQQEEAQAAA   450
 451  MATSAGTVSEDAIEEEGEDGVGSPRSSSELSKLSSKSAKERRNRRKKRKQ   500
 501  KELSEGEEKGDPEKVFKSESEDGMRRKAFRLPDNRIGRKFSIMNQSLLSI   550
 551  PGSPFLSRHNSKSSIFSFRGPGRFRDPGSENEFADDEHSTVEESEGRRDS   600
 601  LFIPIRARERRSSYSGYSGYSQCSRSSRIFPSLRRSVKRNSTVDCNGVVS   650
 651  LIGPGSHIGRLLPEATTEVEIKKKGPGSLLVSMEQLASYGRKDRINSIMS   700
 701  VVTNTLVEELEESQRKCPPCWYKFANTFLIWECHPYWIKLKEIVNLIVMD   750
 751  PFVDLAITICIVLNTLFMAMEHHPMTPQFEHVLAVGNLVFTGIFTAEMFL   800
 801  KLIAMDPYYYFQEGWNIFDGFIVSLSLMELGLADVEGLSVLRSFRLLRVF   850
 851  KLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVGMQLFGKSYK   900
 901  ECVCKISQECKLPRWHMNDFFHSFLIVFRVLCGEWIETMWDCMEVAGQAM   950
 951  CLIVFMMVMVIGNLVVLNLFLALLLSSFSADNLAATDDDGEMNNLQISVI  1000
1001  RIKKGVAWAKVKVHAFMQAHFKQREADEVKPLDELYEKKANCIANHTGVD  1050
1051  IHRNGDFQKNGNGTTSGIGSSVEKYIIDEDHMSFINNPNLTVRVPIAVGE  1100
1101  SDFENLNTEDVSSESDPEGSKDKLDDTSSSEGSTIDIKPEVEEVPVEQPE  1150
1151  EYLDPDACFTEGCVQRFKCCQVNIEEGLGKSWWILRKTCFLIVEHNWFET  1200
1201  FIIFMILLSSGALAFEDIYIEQRKTIRTILEYADKVFTYIFILEMLLKWT  1250
1251  AYGFVKFFTNAWCWLDFLIVAVSLVSLIANALGYSELGAIKSLRTLRALR  1300
1301  PLRALSRFEGMRVVVNALVGAIPSIMNVLLVCLIFWLIFSIMGVNLFAGK  1350
1351  YHYCFNETSEIRFEIDEVNNKTDCEKLMEGNNTEIRWKNVKINFDNVGAG  1400
1401  YLALLQVATFKGWMDIMYAAVDSRKPDEQPDYEGNIYMYIYFVIFIIFGS  1450
1451  FFTLNLFIGVIIDNFNQQKKKFGGQDIFMTEEQKKYYNAMKKLGSKKPQK  1500
1501  PIPRPLNKIQGIVFDFVTQQAFDIVIMMLICLNMVTMMVETDTQSKQMEN  1550
1551  ILYWINLVFVIFFTCECVLKMFALRHYYFTIGWNIFDFVVVILSIVGMFL  1600
1601  ADIIEKYFVSPTLFRVIRLARIGRILRLIKGAKGIRTLLFALMMSLPALF  1650
1651  NIGLLLFLVMFIFSIFGMSNFAYVKHEAGIDDMFNFETFGNSMICLFQIT  1700
1701  TSAGWDGLLLPILNRPPDCSLDKEHPGSGFKGDCGNPSVGIFFFVSYIII  1750
1751  SFLIVVNMYIAIILENFSVATEESADPLSEDDFETFYEIWEKFDPDATQF  1800
1801  IEYCKLADFADALEHPLRVPKPNTIELIAMDLPMVSGDRIHCLDILFAFT  1850
1851  KRVLGDSGELDILRQQMEERFVASNPSKVSYEPITTTLRRKQEEVSAVVL  1900
1901  QRAYRGHLARRGFICRKITSNKLENGGTHREKKESTPSTASLPSYDSVTK  1950
1951  PDKEKQQRAEEGRRERAKRQKEVRESKC                        1978

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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