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

NucPred

Fetching Q92349 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MDFRITEGSSPTSLSVSEKIAKLESCNDSRITCRPVRESKPTYTSGQKHS    50
  51  ALLSKLKRSKVTTDFCKLEESKGIICQENLHTEGAKSKTENISGEDKSSQ   100
 101  RRTRLKQIQEFISHRRSFLNSNANSVESEKILAENNHMFNVKSKLSNKES   150
 151  FIKTRRPRTNGELSDLSLQPKRIFSEPVNSHPSQSMFGNGVRASSGSYSL   200
 201  KRDLKDYEEELPSSKKRQRTPPPIVVTNFPQEIFPSKKISLSAKRRIQGK   250
 251  YSGENVRARIELARERNRKRDYVSNLSKGHTTNALEENPFNLGPNYRAST   300
 301  RKCNRIKEAINLFAAKNGSMEVPPKVSVGDSVLTTSQKFLQVIREKTALL   350
 351  MNQDSNSVQPQALAAAESPTTKAPTTKAPTSEAPPKGHVKQLAKQLGNIY   400
 401  MPQSINNVEPTSHSSISKVVNPSEKVISKIERACLAGNGNVHPSIKMEKN   450
 451  LELNPHPRTLNATEHKINSRIQVSKLNTKNELANADPKMYLLENLSDRLY   500
 501  FCKLAKLLLRKYPLDIAEHQFALVYSRFQRIPLKQISCLKQSLVAYYSVL   550
 551  SEVGITNEIMLRENRFSSPKTPEGLVSISKLLLDDREHLSHDERSYIQQL   600
 601  QSQIKSQSVHHENAAEEIRKMRNLRNSRINSQQVGEKVFVNPDVKTMDIQ   650
 651  ETFLQDYEDETFANEGLSASKFKEEFLLISDSKSDLNSEEIATPNSLEFK   700
 701  NNPRIKVPRSLLTILNLHDRSQLKLFEVCHNSEFKDPINLSNCLRNLLEK   750
 751  QLLSYNFTDWFASLGSEYENVYVKFISHYDFSSLNVYASFQKLCCDLYYG   800
 801  SDDYIHSPILQVFASCWLKQNSNYGFLNEDIIVKIVLILIDLHKSTYSKK   850
 851  LNSYVVPMETFVKYALEKLRPLISPDSVCILSKEDKKHWLKYKKNRSTFA   900
 901  KLLFSTWSNLPSDIGFILECMLKEYYDTFLKSPFAVPNAVQAQLHNQVRG   950
 951  DLTPKRNRSSLISELMKSSKLLKQESSGNKNSTSLESDAFKESSFVLNEE  1000
1001  NGGIYAGKEIDLPEPSVIDGRPHFSVFNYTHHMQEEKTHNRLPWHRRGMI  1050
1051  SYKKMVLSKNNRWVAGYWKKKYCIVDSGKLIFYKSDHLDPNACSNVSPIH  1100
1101  REFGLQSCLASPNLPPSINSNRNNVFYLNIPGNECYLFEAPSVLAMNEWI  1150
1151  HSLNFNAAMITCPPLPENITNTEYGWGYILTRAEKKAYYTAADGTKTFVG  1200
1201  DLAQLTRWSPMDIQGLQDIPRPLRDKVHILRDCVPSLLETCLLFQSLPEK  1250
1251  MEKCFAAGSKNYLKAMDNWNRKMKFLYERSMMYKEYQRVLECEYEYRKSH  1300
1301  DFYPTLSPVRYPYDFKGL                                  1318

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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