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

NucPred

Fetching Q9UQD0 from www.uniprot.org...

The NucPred score for your sequence is 0.53 (see score help below)

   1  MAARLLAPPGPDSFKPFTPESLANIERRIAESKLKKPPKADGSHREDDED    50
  51  SKPKPNSDLEAGKSLPFIYGDIPQGLVAVPLEDFDPYYLTQKTFVVLNRG   100
 101  KTLFRFSATPALYILSPFNLIRRIAIKILIHSVFSMIIMCTILTNCVFMT   150
 151  FSNPPDWSKNVEYTFTGIYTFESLVKIIARGFCIDGFTFLRDPWNWLDFS   200
 201  VIMMAYITEFVNLGNVSALRTFRVLRALKTISVIPGLKTIVGALIQSVKK   250
 251  LSDVMILTVFCLSVFALIGLQLFMGNLRNKCVVWPINFNESYLENGTKGF   300
 301  DWEEYINNKTNFYTVPGMLEPLLCGNSSDAGQCPEGYQCMKAGRNPNYGY   350
 351  TSFDTFSWAFLALFRLMTQDYWENLYQLTLRAAGKTYMIFFVLVIFVGSF   400
 401  YLVNLILAVVAMAYEEQNQATLEEAEQKEAEFKAMLEQLKKQQEEAQAAA   450
 451  MATSAGTVSEDAIEEEGEEGGGSPRSSSEISKLSSKSAKERRNRRKKRKQ   500
 501  KELSEGEEKGDPEKVFKSESEDGMRRKAFRLPDNRIGRKFSIMNQSLLSI   550
 551  PGSPFLSRHNSKSSIFSFRGPGRFRDPGSENEFADDEHSTVEESEGRRDS   600
 601  LFIPIRARERRSSYSGYSGYSQGSRSSRIFPSLRRSVKRNSTVDCNGVVS   650
 651  LIGGPGSHIGGRLLPEATTEVEIKKKGPGSLLVSMDQLASYGRKDRINSI   700
 701  MSVVTNTLVEELEESQRKCPPCWYKFANTFLIWECHPYWIKLKEIVNLIV   750
 751  MDPFVDLAITICIVLNTLFMAMEHHPMTPQFEHVLAVGNLVFTGIFTAEM   800
 801  FLKLIAMDPYYYFQEGWNIFDGFIVSLSLMELSLADVEGLSVLRSFRLLR   850
 851  VFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVGMQLFGKS   900
 901  YKECVCKINQDCELPRWHMHDFFHSFLIVFRVLCGEWIETMWDCMEVAGQ   950
 951  AMCLIVFMMVMVIGNLVVLNLFLALLLSSFSADNLAATDDDGEMNNLQIS  1000
1001  VIRIKKGVAWTKLKVHAFMQAHFKQREADEVKPLDELYEKKANCIANHTG  1050
1051  ADIHRNGDFQKNGNGTTSGIGSSVEKYIIDEDHMSFINNPNLTVRVPIAV  1100
1101  GESDFENLNTEDVSSESDPEGSKDKLDDTSSSEGSTIDIKPEVEEVPVEQ  1150
1151  PEEYLDPDACFTEGCVQRFKCCQVNIEEGLGKSWWILRKTCFLIVEHNWF  1200
1201  ETFIIFMILLSSGALAFEDIYIEQRKTIRTILEYADKVFTYIFILEMLLK  1250
1251  WTAYGFVKFFTNAWCWLDFLIVAVSLVSLIANALGYSELGAIKSLRTLRA  1300
1301  LRPLRALSRFEGMRVVVNALVGAIPSIMNVLLVCLIFWLIFSIMGVNLFA  1350
1351  GKYHYCFNETSEIRFEIEDVNNKTECEKLMEGNNTEIRWKNVKINFDNVG  1400
1401  AGYLALLQVATFKGWMDIMYAAVDSRKPDEQPKYEDNIYMYIYFVIFIIF  1450
1451  GSFFTLNLFIGVIIDNFNQQKKKFGGQDIFMTEEQKKYYNAMKKLGSKKP  1500
1501  QKPIPRPLNKIQGIVFDFVTQQAFDIVIMMLICLNMVTMMVETDTQSKQM  1550
1551  ENILYWINLVFVIFFTCECVLKMFALRHYYFTIGWNIFDFVVVILSIVGM  1600
1601  FLADIIEKYFVSPTLFRVIRLARIGRILRLIKGAKGIRTLLFALMMSLPA  1650
1651  LFNIGLLLFLVMFIFSIFGMSNFAYVKHEAGIDDMFNFETFGNSMICLFQ  1700
1701  ITTSAGWDGLLLPILNRPPDCSLDKEHPGSGFKGDCGNPSVGIFFFVSYI  1750
1751  IISFLIVVNMYIAIILENFSVATEESADPLSEDDFETFYEIWEKFDPDAT  1800
1801  QFIEYCKLADFADALEHPLRVPKPNTIELIAMDLPMVSGDRIHCLDILFA  1850
1851  FTKRVLGDSGELDILRQQMEERFVASNPSKVSYEPITTTLRRKQEEVSAV  1900
1901  VLQRAYRGHLARRGFICKKTTSNKLENGGTHREKKESTPSTASLPSYDSV  1950
1951  TKPEKEKQQRAEEGRRERAKRQKEVRESKC                      1980

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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