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

NucPred

Fetching P04775 from www.uniprot.org...

The NucPred score for your sequence is 0.58 (see score help below)

   1  MARSVLVPPGPDSFRFFTRESLAAIEQRIAEEKAKRPKQERKDEDDENGP    50
  51  KPNSDLEAGKSLPFIYGDIPPEMVSEPLEDLDPYYINKKTFIVLNKGKAI   100
 101  SRFSATSALYILTPFNPIRKLAIKILVHSLFNVLIMCTILTNCVFMTMSN   150
 151  PPDWTKNVEYTFTGIYTFESLIKILARGFCLEDFTFLRNPWNWLDFTVIT   200
 201  FAYVTEFVNLGNVSALRTFRVLRALKTISVIPGLKTIVGALIQSVKKLSD   250
 251  VMILTVFCLSVFALIGLQLFMGNLRNKCLQWPPDNSTFEINITSFFNNSL   300
 301  DWNGTAFNRTVNMFNWDEYIEDKSHFYFLEGQNDALLCGNSSDAGQCPEG   350
 351  YICVKAGRNPNYGYTSFDTFSWAFLSLFRLMTQDFWENLYQLTLRAAGKT   400
 401  YMIFFVLVIFLGSFYLINLILAVVAMAYEEQNQATLEEAEQKEAEFQQML   450
 451  EQLKKQQEEAQAAAAAASAESRDFSGAGGIGVFSESSSVASKLSSKSEKE   500
 501  LKNRRKKKKQKEQAGEEEKEDAVRKSASEDSIRKKGFQFSLEGSRLTYEK   550
 551  RFSSPHQSLLSIRGSLFSPRRNSRASLFNFKGRVKDIGSENDFADDEHST   600
 601  FEDNDSRRDSLFVPHRHGERRPSNVSQASRASRGIPTLPMNGKMHSAVDC   650
 651  NGVVSLVGGPSALTSPVGQLLPEGTTTETEIRKRRSSSYHVSMDLLEDPS   700
 701  RQRAMSMASILTNTMEELEESRQKCPPCWYKFANMCLIWDCCKPWLKVKH   750
 751  VVNLVVMDPFVDLAITICIVLNTLFMAMEHYPMTEQFSSVLSVGNLVFTG   800
 801  IFTAEMFLKIIAMDPYYYFQEGWNIFDGFIVSLSLMELGLANVEGLSVLR   850
 851  SFRLLRVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVGM   900
 901  QLFGKSYKECVCKISNDCELPRWHMHHFFHSFLIVFRVLCGEWIETMWDC   950
 951  MEVAGQTMCLTVFMMVMVIGNLVVLNLFLALLLSSFSSDNLAATDDDNEM  1000
1001  NNLQIAVGRMQKGIDFVKRKIREFIQKAFVRKQKALDEIKPLEDLNNKKD  1050
1051  SCISNHTTIEIGKDLNYLKDGNGTTSGIGSSVEKYVVDESDYMSFINNPS  1100
1101  LTVTVPIALGESDFENLNTEEFSSESDMEESKEKLNATSSSEGSTVDIGA  1150
1151  PAEGEQPEAEPEESLEPEACFTEDCVRKFKCCQISIEEGKGKLWWNLRKT  1200
1201  CYKIVEHNWFETFIVFMILLSSGALAFEDIYIEQRKTIKTMLEYADKVFT  1250
1251  YIFILEMLLKWVAYGFQMYFTNAWCWLDFLIVDVSLVSLTANALGYSELG  1300
1301  AIKSLRTLRALRPLRALSRFEGMRVVVNALLGAIPSIMNVLLVCLIFWLI  1350
1351  FSIMGVNLFAGKFYHCINYTTGEMFDVSVVNNYSECQALIESNQTARWKN  1400
1401  VKVNFDNVGLGYLSLLQVATFKGWMDIMYAAVDSRNVELQPKYEDNLYMY  1450
1451  LYFVIFIIFGSFFTLNLFIGVIIDNFNQQKKKFGGQDIFMTEEQKKYYNA  1500
1501  MKKLGSKKPQKPIPRPANKFQGMVFDFVTKQVFDISIMILICLNMVTMMV  1550
1551  ETDDQSQEMTNILYWINLVFIVLFTGECVLKLISLRHYYFTIGWNIFDFV  1600
1601  VVILSIVGMFLAELIEKYFVSPTLFRVIRLARIGRILRLIKGAKGIRTLL  1650
1651  FALMMSLPALFNIGLLLFLVMFIYAIFGMSNFAYVKREVGIDDMFNFETF  1700
1701  GNSMICLFQITTSAGWDGLLAPILNSGPPDCDPEKDHPGSSVKGDCGNPS  1750
1751  VGIFFFVSYIIISFLVVVNMYIAVILENFSVATEESAEPLSEDDFEMFYE  1800
1801  VWEKFDPDATQFIEFCKLSDFAAALDPPLLIAKPNKVQLIAMDLPMVSGD  1850
1851  RIHCLDILFAFTKRVLGESGEMDALRIQMEERFMASNPSKVSYEPITTTL  1900
1901  KRKQEEVSAIVIQRAYRRYLLKQKVKKVSSIYKKDKGKEDEGTPIKEDII  1950
1951  TDKLNENSTPEKTDVTPSTTSPPSYDSVTKPEKEKFEKDKSEKEDKGKDI  2000
2001  RESKK                                               2005

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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