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

NucPred

Fetching O08562 from www.uniprot.org...

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

   1  MAMLPPPGPQSFVHFTKQSLALIEQRISEEKAKEHKDEKKDDEEEGPKPS    50
  51  SDLEAGKQLPFIYGDIPPGMVSEPLEDLDPYYADKKTFIVLNKGKAIFRF   100
 101  NATPALYMLSPFSPLRRISIKILVHSLFSMLIMCTILTNCIFMTLSNPPE   150
 151  WTKNVEYTFTGIYTFESLIKILARGFCVGEFTFLRDPWNWLDFVVIVFAY   200
 201  LTEFVNLGNVSALRTFRVLRALKTISVIPGLKTIVGALIQSVKKLSDVMI   250
 251  LTVFCLSVFALIGLQLFMGNLKHKCFRKELEENETLESIMNTAESEEELK   300
 301  KYFYYLEGSKDALLCGFSTDSGQCPEGYICVKAGRNPDYGYTSFDTFSWA   350
 351  FLALFRLMTQDYWENLYQQTLRAAGKTYMIFFVVVIFLGSFYLINLILAV   400
 401  VAMAYEEQNQANIEEAKQKELEFQQMLDRLKKEQEEAEAIAAAAAEFTSI   450
 451  GRSRIMGLSESSSETSRLSSKSAKERRNRRKKKKQKMSSGEEKGDDEKLS   500
 501  KSGSEESIRKKSFHLGVEGHHRTREKRLSTPNQSPLSIRGSLFSARRSSR   550
 551  TSLFSFKGRGRDLGSETEFADDEHSIFGDNESRRGSLFVPHRPRERRSSN   600
 601  ISQASRSPPVLPVNGKMHSAVDCNGVVSLVDGPSALMLPNGQLLPEVIID   650
 651  KATSDDSGTTNQMRKKRLSSSYFLSEDMLNDPHLRQRAMSRASILTNTVE   700
 701  ELEESRQKCPPWWYRFAHTFLIWNCSPYWIKFKKLIYFIVMDPFVDLAIT   750
 751  ICIVLNTLFMAMEHHPMTEEFKNVLAVGNLIFTGIFAAEMVLKLIAMDPY   800
 801  EYFQVGWNIFDSLIVTLSLIELFLADVEGLSVLRSFRLLRVFKLAKSWPT   850
 851  LNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVGMQLFGKSYKECVCKINV   900
 901  DCKLPRWHMNDFFHSFLIVFRVLCGEWIETMWDCMEVAGQTMCLIVYMMV   950
 951  MVIGNLVVLNLFLALLLSSFSSDNLTAIEEDTDANNLQIAVARIKRGINY  1000
1001  VKQTLREFILKSFSKKPKGSKDTKRTADPNNKKENYISNRTLAEMSKDHN  1050
1051  FLKEKDRISGYGSSLDKSFMDENDYQSFIHNPSLTVTVPIAPGESDLEIM  1100
1101  NTEELSSDSDSDYSKEKRNRSSSSECSTVDNPLPGEEEAEAEPVNADEPE  1150
1151  ACFTDGCVRRFPCCQVNVDSGKGKVWWTIRKTCYRIVEHSWFESFIVLMI  1200
1201  LLSSGALAFEDIYIEKKKTIKIILEYADKIFTYIFILEMLLKWVAYGYKT  1250
1251  YFTNAWCWLDFLIVDVSLVTLVANTLGYSDLGPIKSLRTLRALRPLRALS  1300
1301  RFEGMRVVVNALIGAIPSIMNVLLVCLIFWLIFSIMGVNLFAGKFYECVN  1350
1351  TTDGSRFPTSQVANRSECFALMNVSGNVRWKNLKVNFDNVGLGYLSLLQV  1400
1401  ATFKGWMDIMYAAVDSVNVNEQPKYEYSLYMYIYFVIFIIFGSFFTLNLF  1450
1451  IGVIIDNFNQQKKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQKPIPRPGN  1500
1501  KFQGCIFDLVTNQAFDITIMVLICLNMVTMMVEKEGQTEYMDYVLHWINM  1550
1551  VFIILFTGECVLKLISLRHYYFTVGWNIFDFVVVILSIVGMFLAEMIEKY  1600
1601  FVSPTLFRVIRLARIGRILRLIKGAKGIRTLLFALMMSLPALFNIGLLLF  1650
1651  LVMFIYAIFGMSNFAYVKKEAGINDMFNFETFGNSMICLFQITTSAGWDG  1700
1701  LLAPILNSAPPDCDPKKVHPGSSVEGDCGNPSVGIFYFVSYIIISFLVVV  1750
1751  NMYIAVILENFSVATEESTEPLSEDDFEMFYEVWEKFDPDATQFIEFCKL  1800
1801  SDFAAALDPPLLIAKPNKVQLIAMDLPMVSGDRIHCLDILFAFTKRVLGE  1850
1851  GGEMDSLRSQMEERFMSANPSKVSYEPITTTLKRKQEEVSATIIQRAYRR  1900
1901  YRLRQHVKNISSIYIKDGDRDDDLPNKEDTVFDNVNENSSPEKTDVTAST  1950
1951  ISPPSYDSVTKPDQEKYETDKTEKEDKEKDESRK                  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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