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

NucPred

Fetching Q28644 from www.uniprot.org...

The NucPred score for your sequence is 0.60 (see score help below)

   1  MAMLPPPGPQSFVRFTKQSLALIEQRIAEGKTKEPKEEKKDDHDEGPKPS    50
  51  SDLEAGKQLPFIYGDIPAGMVSEPLEDLDPYYADKKTFIVLNKGKAIFRF   100
 101  NATPALYILSPFSPLRRISIKILVHSLFSMLIMCTILTNCIFMTMNNPAE   150
 151  WTKNVEYTFTGIYTFESLVKIFARGFCVGEFTFLRDPWNWLDFIVIVFAY   200
 201  LTEFVNLGNVSALRTFRVLRALKTISVIPGLKTIVGALIQSVKKLSDVII   250
 251  LTVFCLSVFALIGLQLFMGHLKHKCLRKIENETLESIMSSIESEEDYKKY   300
 301  FYYLEGSKDALLCGFSTDSGQCPEGYYCVKAGRNPDYGYTSFDTFSWAFL   350
 351  ALFRLMTQDYWENLYQQTLRAAGKTYMIFFVVVIFLGSFYLINLILAVVA   400
 401  MAYEEQNQANIEEAKQKELEFQQMLDRLKKEQEEAEAIAAAAAEYTSIGR   450
 451  SRIMGLSESSSETSKLSSKSAKERRNRRKKKNQKKLSSGEEKGDDEKLSK   500
 501  SESEESISRKQFHLGVEGHRLAREKRLSAPNQSPLSIRGSLFSARRSSRT   550
 551  SLFSFKGRGKDIGSETEFADDEHSIFGDNESRRGSLFVPQRPQERRSSNL   600
 601  SQASRSPPMLQMNGKMHSAVDCNGVVSLVDGPSALMLPNGQLLPEVIIDK   650
 651  ATSDDSGTTQIRKKRRSSSYLLSEDMLNDPHLRQRAMSRASILTNTVEEL   700
 701  EESRQKCPSWWYRFAHTFLIWNCSPFWIKFKKFIYIIVMDPFVDLAITIC   750
 751  IVLNTLFMAMEHHPMTEEFKNVLVVGNLVFTGIFAAEMVLKLIAMDPYEY   800
 801  FQVGWNVFDSLIVTLSLVELFLADVEGLSVLRSFRLLRVFKLAKSWPTLN   850
 851  MLIKIIGNSVGPLGNLTLVLAIIVFIFAVVGMQLFGKSYKECVCKINDDC   900
 901  SLPRWHMNDFFHSFLIVFRVLCGEWIETMWDCMEVAGQAMCLIVYMMVMV   950
 951  IGNLVVLNLFLALLLSSFSSDNLSAIEEDTDANNLQIAVTRIKKGINYVK  1000
1001  QTLRELILKAFSKKPKISKEIRQAEDLNSKKENYISNRTLAEMSKDYNFH  1050
1051  KEKDKISGFGSSMDKYLMEESDHQSFIHNPSLTVTVPIAPGESDLENMNT  1100
1101  EELSSDSESEYSKERLNRSSSSECSTVDNALPGEGEEAEAEPVNSDEPEA  1150
1151  CFTDGCVRRFPCCQVSIESGKGKIWWNIRKTCYRIVEHSWFESFIVLMIL  1200
1201  LSSGALAFEDIYIEKKKTIKIILEYADKIFTYIFILEMLLKWVAYGYKTY  1250
1251  FTNAWCWLDFLIVDVSLVTLVANTLGYSDLGPIKSLRTLRALRPLRALSR  1300
1301  FEGMRVVVNALIGAIPSIMNVLLVCLIFWLIFSIMGVNLFAGKFYQCVNT  1350
1351  TDDSRFPTKQVSNRSECFALMNGSQNVRWKNLKVNFDNVGLRYLSLLQVA  1400
1401  TFKGWMDIMYAAVDSVNVDQQPSYEHNLYMYIYFVIFIIFGSFFTLNLFI  1450
1451  GVIIDNFNQQKKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQKPIPRPGNK  1500
1501  FQGCIFDLVTNQAFDITIMILICLNMVTMMVEKEGQSDYMTDVLYWINVV  1550
1551  FIILFTGECVLKLISLRHYYFTIGWNIFDFVVVILSIVGMFLAELIETYF  1600
1601  VSPTLFRVIRLARIGRILRLIKGAKGIRTLLFALMMSLPALFNIGLLLFL  1650
1651  VMFIYAIFGMSNFAYVKKEAGINDMFNFETFGNSMICLFQITTSAGWDGL  1700
1701  LAPILNSAPPDCDPKKVHPGSSTEGDCGSPSVGIFYFVSYIIISFLVVVN  1750
1751  MYIAVILENFSVATEESTEPLSEDDFEMFYEVWEKFDPDATQFIEYSKLS  1800
1801  DFAAALDPPLLIAKPNKVQLIAMDLPMVSGDRIHCLDILFAFTKRVLGES  1850
1851  GEMDSLRSQMEERFMSANPSKVSYEPITTTLKRKQEDVSATVIQRAYRRY  1900
1901  RLRQNVKNISSIYIKEGDKDDDLPNKGDIVFDNVNSSSPEKTDATASTIS  1950
1951  PPSYDSVTKPDKEKYEKDKTEKEDKGKDGKETKK                  1984

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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